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  • Articles  (149)
  • Models, Molecular  (149)
  • 1990-1994  (149)
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  • 1994  (56)
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  • Articles  (149)
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  • 1990-1994  (149)
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  • 1
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    Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-24
    Description: Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets the reverse transcriptase of human immunodeficiency virus (HIV) and is at present used to treat AIDS. Although crystals of the two complexes belong to different space groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces. In the pol beta active site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are present in the amino acid sequences of all polymerases so far studied and are also spatially similar in the four polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal structures are now known. A two-metal ion mechanism is described for the nucleotidyl transfer reaction and may apply to all polymerases. In the ternary complex structures analyzed, pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, H -- Sawaya, M R -- Kumar, A -- Wilson, S H -- Kraut, J -- CA17374/CA/NCI NIH HHS/ -- ES06839/ES/NIEHS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jun 24;264(5167):1891-903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego 92093-0317.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7516580" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA Polymerase I/*chemistry/metabolism ; DNA Primers/*chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Deoxycytosine Nucleotides/*chemistry/metabolism ; Dideoxynucleotides ; HIV Reverse Transcriptase ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; RNA-Directed DNA Polymerase/chemistry/metabolism ; Rats ; Recombinant Proteins ; Templates, Genetic ; Thymine Nucleotides/chemistry/metabolism ; Viral Proteins ; Zidovudine/analogs & derivatives/chemistry/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Structure of an electron transfer complex: methylamine dehydrogenase, amicyanin, and cytochrome c551i (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-04-01
    Description: The crystal structure of a ternary protein complex has been determined at 2.4 angstrom resolution. The complex is composed of three electron transfer proteins from Paracoccus denitrificans, the quinoprotein methylamine dehydrogenase, the blue copper protein amicyanin, and the cytochrome c551i. The central region of the c551i is folded similarly to several small bacterial c-type cytochromes; there is a 45-residue extension at the amino terminus and a 25-residue extension at the carboxyl terminus. The methylamine dehydrogenase-amicyanin interface is largely hydrophobic, whereas the amicyanin-cytochrome interface is more polar, with several charged groups present on each surface. Analysis of the simplest electron transfer pathways between the redox partners points out the importance of other factors such as energetics in determining the electron transfer rates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, L -- Durley, R C -- Mathews, F S -- Davidson, V L -- GM41574/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Apr 1;264(5155):86-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8140419" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Computer Graphics ; Cytochrome c Group/*chemistry/metabolism ; Electron Transport ; Hydrogen Bonding ; *Indolequinones ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/metabolism ; Paracoccus denitrificans/*chemistry/enzymology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Quinones/chemistry/metabolism ; Software ; Tryptophan/analogs & derivatives/chemistry/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Routes to catalysis: structure of a catalytic antibody and comparison with its natural counterpart (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-02-04
    Description: The three-dimensional structure of a catalytic antibody (1F7) with chorismate mutase activity has been determined to 3.0 A resolution as a complex with a transition state analog. The structural data suggest that the antibody stabilizes the same conformationally restricted pericyclic transition state as occurs in the uncatalyzed reaction. Overall shape and charge complementarity between the combining site and the transition state analog dictate preferential binding of the correct substrate enantiomer in a conformation appropriate for reaction. Comparison with the structure of a chorismate mutase enzyme indicates an overall similarity between the catalytic mechanism employed by the two proteins. Differences in the number of specific interactions available for restricting the rotational degrees of freedom in the transition state, and the lack of multiple electrostatic interactions that might stabilize charge separation in this highly polarized metastable species, are likely to account for the observed 10(4) times lower activity of the antibody relative to that of the natural enzymes that catalyze this reaction. The structure of the 1F7 Fab'-hapten complex provides confirmation that the properties of an antibody catalyst faithfully reflect the design of the transition state analog.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haynes, M R -- Stura, E A -- Hilvert, D -- Wilson, I A -- AI-23498/AI/NIAID NIH HHS/ -- GM-38273/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Feb 4;263(5147):646-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8303271" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Catalytic/*chemistry/metabolism ; Bacillus subtilis/enzymology ; Binding Sites ; Binding Sites, Antibody ; Catalysis ; Chorismate Mutase/*chemistry/metabolism ; Chorismic Acid/metabolism ; Crystallization ; Haptens ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/metabolism ; Models, Molecular ; Thermodynamics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Identification of the target of a transcription activator protein by protein-protein photocrosslinking (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-07-01
    Description: Here it is shown, with the use of protein-protein photocrosslinking, that the carboxyl-terminal region of the alpha subunit of RNA polymerase (RNAP) is in direct physical proximity to the activating region of the catabolite gene activator protein (CAP) in the ternary complex of the lac promoter, RNAP, and CAP. These results strongly support the proposal that transcription activation by CAP involves protein-protein contact between the carboxyl-terminal region of the alpha subunit and the activating region of CAP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Y -- Ebright, Y W -- Ebright, R H -- GM41376/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jul 1;265(5168):90-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Rutgers University, New Brunswick, NJ 08855.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8016656" target="_blank"〉PubMed〈/a〉
    Keywords: Azides/metabolism ; Cross-Linking Reagents ; Crystallography, X-Ray ; Cyclic AMP Receptor Protein/chemistry/*metabolism ; DNA-Directed RNA Polymerases/chemistry/*metabolism ; Lac Operon ; Models, Molecular ; *Promoter Regions, Genetic ; Pyridines/metabolism ; *Transcriptional Activation
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-21
    Description: The structure of the heterodimeric flavocytochrome c sulfide dehydrogenase from Chromatium vinosum was determined at a resolution of 2.53 angstroms. It contains a glutathione reductase-like flavin-binding subunit and a diheme cytochrome subunit. The diheme cytochrome folds as two domains, each resembling mitochondrial cytochrome c, and has an unusual interpropionic acid linkage joining the two heme groups in the interior of the subunit. The active site of the flavoprotein subunit contains a catalytically important disulfide bridge located above the pyrimidine portion of the flavin ring. A tryptophan, threonine, or tyrosine side chain may provide a partial conduit for electron transfer to one of the heme groups located 10 angstroms from the flavin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Z W -- Koh, M -- Van Driessche, G -- Van Beeumen, J J -- Bartsch, R G -- Meyer, T E -- Cusanovich, M A -- Mathews, F S -- GM-20530/GM/NIGMS NIH HHS/ -- GM-21277/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 21;266(5184):430-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939681" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromatium/*enzymology ; Computer Graphics ; Crystallography, X-Ray ; Cytochrome c Group/*chemistry ; Electron Transport ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Models, Molecular ; Oxidoreductases/*chemistry ; Protein Conformation ; Protein Structure, Secondary
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  • 6
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    Rules for alpha-helix termination by glycine (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-05-20
    Description: A predictive rule for protein folding is presented that involves two recurrent glycine-based motifs that cap the carboxyl termini of alpha helices. In proteins, helices that terminated in glycine residues were found predominantly in one of these two motifs. These glycine structures had a characteristic pattern of polar and apolar residues. Visual inspection of known helical sequences was sufficient to distinguish the two motifs from each other and from internal glycines that fail to terminate helices. These glycine motifs--in which the local sequence selects between available structures--represent an example of a stereochemical rule for protein folding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aurora, R -- Srinivasan, R -- Rose, G D -- GM 29458/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 May 20;264(5162):1126-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8178170" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Glycine/*chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Oligopeptides/chemistry ; *Protein Folding ; *Protein Structure, Secondary
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  • 7
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    Structure of the allosteric regulatory enzyme of purine biosynthesis (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-03
    Description: Multi-wavelength anomalous diffraction (MAD) has been used to determine the structure of the regulatory enzyme of de novo synthesis of purine nucleotides, glutamine 5-phosphoribosyl-1-pyrophosphate (PRPP) amidotransferase, from Bacillus subtilis. This allosteric enzyme, a 200-kilodalton tetramer, is subject to end product regulation by purine nucleotides. The metalloenzyme from B. subtilis is a paradigm for the higher eukaryotic enzymes, which have been refractory to isolation in stable form. The two folding domains of the polypeptide are correlated with functional domains for glutamine binding and for transfer of ammonia to the substrate PRPP. Eight molecules of the feedback inhibitor adenosine monophosphate (AMP) are bound to the tetrameric enzyme in two types of binding sites: the PRPP catalytic site of each subunit and an unusual regulatory site that is immediately adjacent to each active site but is between subunits. An oxygen-sensitive [4Fe-4S] cluster in each subunit is proposed to regulate protein turnover in vivo and is distant from the catalytic site. Oxygen sensitivity of the cluster is diminished by AMP, which blocks a channel through the protein to the cluster. The structure is representative of both glutamine amidotransferases and phosphoribosyltransferases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, J L -- Zaluzec, E J -- Wery, J P -- Niu, L -- Switzer, R L -- Zalkin, H -- Satow, Y -- DK-42303/DK/NIDDK NIH HHS/ -- GM-24658/GM/NIGMS NIH HHS/ -- R37 DK042303/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1994 Jun 3;264(5164):1427-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8197456" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Allosteric Regulation ; Amidophosphoribosyltransferase/*chemistry/metabolism ; Amino Acid Sequence ; Animals ; Bacillus subtilis/*enzymology ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; Oxygen/pharmacology ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae
    Print ISSN: 0036-8075
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  • 8
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    Crystal structure of human protein tyrosine phosphatase 1B (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-11
    Description: Protein tyrosine phosphatases (PTPs) constitute a family of receptor-like and cytoplasmic signal transducing enzymes that catalyze the dephosphorylation of phosphotyrosine residues and are characterized by homologous catalytic domains. The crystal structure of a representative member of this family, the 37-kilodalton form (residues 1 to 321) of PTP1B, has been determined at 2.8 A resolution. The enzyme consists of a single domain with the catalytic site located at the base of a shallow cleft. The phosphate recognition site is created from a loop that is located at the amino-terminus of an alpha helix. This site is formed from an 11-residue sequence motif that is diagnostic of PTPs and the dual specificity phosphatases, and that contains the catalytically essential cysteine and arginine residues. The position of the invariant cysteine residue within the phosphate binding site is consistent with its role as a nucleophile in the catalytic reaction. The structure of PTP1B should serve as a model for other members of the PTP family and as a framework for understanding the mechanism of tyrosine dephosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barford, D -- Flint, A J -- Tonks, N K -- CA53840/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1397-404.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, NY 11724.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128219" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Tyrosine Phosphatases/*chemistry/isolation & purification/metabolism ; Substrate Specificity ; Tungsten Compounds/metabolism
    Print ISSN: 0036-8075
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  • 9
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    Open "back door" in a molecular dynamics simulation of acetylcholinesterase (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-04
    Description: The enzyme acetylcholinesterase generates a strong electrostatic field that can attract the cationic substrate acetylcholine to the active site. However, the long and narrow active site gorge seems inconsistent with the enzyme's high catalytic rate. A molecular dynamics simulation of acetylcholinesterase in water reveals the transient opening of a short channel, large enough to pass a water molecule, through a thin wall of the active site near tryptophan-84. This simulation suggests that substrate, products, or solvent could move through this "back door," in addition to the entrance revealed by the crystallographic structure. Electrostatic calculations show a strong field at the back door, oriented to attract the substrate and the reaction product choline and to repel the other reaction product, acetate. Analysis of the open back door conformation suggests a mutation that could seal the back door and thus test the hypothesis that thermal motion of this enzyme may open multiple routes of access to its active site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gilson, M K -- Straatsma, T P -- McCammon, J A -- Ripoll, D R -- Faerman, C H -- Axelsen, P H -- Silman, I -- Sussman, J L -- New York, N.Y. -- Science. 1994 Mar 4;263(5151):1276-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Houston, TX 77204-5641.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8122110" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcholine/metabolism ; Acetylcholinesterase/*chemistry/metabolism ; Binding Sites ; Catalysis ; Choline/metabolism ; Computer Simulation ; Crystallography, X-Ray ; Electrochemistry ; Models, Molecular ; *Protein Conformation
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  • 10
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    The structural basis of sequence-independent peptide binding by OppA protein (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-10
    Description: Specific protein-ligand interactions are critical for cellular function, and most proteins select their partners with sharp discrimination. However, the oligopeptide-binding protein of Salmonella typhimurium (OppA) binds peptides of two to five amino acid residues without regard to sequence. The crystal structure of OppA reveals a three-domain organization, unlike other periplasmic binding proteins. In OppA-peptide complexes, the ligands are completely enclosed in the protein interior, a mode of binding that normally imposes tight specificity. The protein fulfills the hydrogen bonding and electrostatic potential of the ligand main chain and accommodates the peptide side chains in voluminous hydrated cavities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tame, J R -- Murshudov, G N -- Dodson, E J -- Neil, T K -- Dodson, G G -- Higgins, C F -- Wilkinson, A J -- New York, N.Y. -- Science. 1994 Jun 10;264(5165):1578-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of York, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8202710" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; Carrier Proteins/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Lipoproteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Oligopeptides/chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary
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  • 11
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    Padlock probes: circularizing oligonucleotides for localized DNA detection (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-09-30
    Description: Nucleotide sequence information derived from DNA segments of the human and other genomes is accumulating rapidly. However, it frequently proves difficult to use such short DNA segments to identify clones in genomic libraries or fragments in blots of the whole genome or for in situ analysis of chromosomes. Oligonucleotide probes, consisting of two target-complementary segments, connected by a linker sequence, were designed. Upon recognition of the specific nucleic acid molecule the ends of the probes were joined through the action of a ligase, creating circular DNA molecules catenated to the target sequence. These probes thus provide highly specific detection with minimal background.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nilsson, M -- Malmgren, H -- Samiotaki, M -- Kwiatkowski, M -- Chowdhary, B P -- Landegren, U -- New York, N.Y. -- Science. 1994 Sep 30;265(5181):2085-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beijer Laboratory, Department of Medical Genetics, Biomedical Center, Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7522346" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cells, Cultured ; Chromosomes, Human, Pair 12 ; Cystic Fibrosis Transmembrane Conductance Regulator ; DNA/*analysis ; DNA, Circular/*analysis ; Genetic Vectors ; Humans ; In Situ Hybridization ; Lymphocytes ; Membrane Proteins/genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Oligonucleotide Probes/chemistry ; Repetitive Sequences, Nucleic Acid ; Templates, Genetic
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  • 12
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    Encapsulation of methane and other small molecules in a self-assembling superstructure (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-04
    Description: Physical inclusion of small molecules in larger structural lattices is well known in the crystalline state and is a common feature of the chemistry of zeolites. In the liquid state, a variety of synthetic macrocyclic molecules are available to complex and contain smaller guest species. An alternative strategy for binding is explored: assembly of cavity-forming structures from small subunits. Encapsulation of small guest molecules such as methane can be achieved with a synthetic structure that assembles reversibly through hydrogen bonding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Branda, N -- Wyler, R -- Rebek, J Jr -- New York, N.Y. -- Science. 1994 Mar 4;263(5151):1267-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8122107" target="_blank"〉PubMed〈/a〉
    Keywords: Benzyl Compounds/chemistry ; Chemistry, Physical ; Chloroform ; Hydrogen Bonding ; Imidazoles/chemistry ; Magnetic Resonance Spectroscopy ; Methane/*chemistry ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Physicochemical Phenomena ; Polymers/*chemistry ; Temperature ; Thermodynamics
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  • 13
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    Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-11-04
    Description: The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schumacher, M A -- Choi, K Y -- Zalkin, H -- Brennan, R G -- GM 24658/GM/NIGMS NIH HHS/ -- GM 49244/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Nov 4;266(5186):763-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland 97201-3098.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7973627" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Base Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; *Escherichia coli Proteins ; Hydrogen Bonding ; Hypoxanthine ; Hypoxanthines/metabolism ; Lac Repressors ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Operator Regions, Genetic ; Protein Conformation ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/genetics/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 14
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    The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reesei (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-07-22
    Description: Cellulose is the major polysaccharide of plants where it plays a predominantly structural role. A variety of highly specialized microorganisms have evolved to produce enzymes that either synergistically or in complexes can carry out the complete hydrolysis of cellulose. The structure of the major cellobiohydrolase, CBHI, of the potent cellulolytic fungus Trichoderma reesei has been determined and refined to 1.8 angstrom resolution. The molecule contains a 40 angstrom long active site tunnel that may account for many of the previously poorly understood macroscopic properties of the enzyme and its interaction with solid cellulose. The active site residues were identified by solving the structure of the enzyme complexed with an oligosaccharide, o-iodobenzyl-1-thio-beta-cellobioside. The three-dimensional structure is very similar to a family of bacterial beta-glucanases with the main-chain topology of the plant legume lectins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Divne, C -- Stahlberg, J -- Reinikainen, T -- Ruohonen, L -- Pettersson, G -- Knowles, J K -- Teeri, T T -- Jones, T A -- New York, N.Y. -- Science. 1994 Jul 22;265(5171):524-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Uppsala University, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8036495" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Cellobiose/analogs & derivatives/chemistry/metabolism ; Cellulose/metabolism ; Cellulose 1,4-beta-Cellobiosidase ; Computer Graphics ; Crystallography, X-Ray ; Glycoside Hydrolases/*chemistry/metabolism ; Hydrogen Bonding ; Iodobenzenes/chemistry/metabolism ; Models, Molecular ; Protein Structure, Secondary ; Trichoderma/*enzymology
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    NMR solution structure of a peptide nucleic acid complexed with RNA (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-08-05
    Description: Peptide nucleic acids (PNA) incorporating nucleic acid bases into an achiral polyamide backbone bind to DNA in a sequence-dependent manner. The structure of a PNA-ribonucleic acid (RNA) complex was determined with nuclear magnetic resonance methods. A hexameric PNA formed a 1:1 complex with a complementary RNA that is an antiparallel, right-handed double helix with Watson-Crick base pairing similar to the "A" form structure of RNA duplexes. The achiral PNA backbone assumed a distinct conformation upon binding that differed from previously proposed models and provides a basis for further structure-based design of antisense agents.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, S C -- Thomson, S A -- Veal, J M -- Davis, D G -- New York, N.Y. -- Science. 1994 Aug 5;265(5173):777-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Glaxo Research Institute, Research Triangle Park, NC 27709.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7519361" target="_blank"〉PubMed〈/a〉
    Keywords: Magnetic Resonance Spectroscopy ; Models, Molecular ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry ; Peptides/*chemistry ; RNA/*chemistry
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  • 16
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    Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-23
    Description: HIV integrase is the enzyme responsible for inserting the viral DNA into the host chromosome; it is essential for HIV replication. The crystal structure of the catalytically active core domain (residues 50 to 212) of HIV-1 integrase was determined at 2.5 A resolution. The central feature of the structure is a five-stranded beta sheet flanked by helical regions. The overall topology reveals that this domain of integrase belongs to a superfamily of polynucleotidyl transferases that includes ribonuclease H and the Holliday junction resolvase RuvC. The active site region is identified by the position of two of the conserved carboxylate residues essential for catalysis, which are located at similar positions in ribonuclease H. In the crystal, two molecules form a dimer with a extensive solvent-inaccessible interface of 1300 A2 per monomer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dyda, F -- Hickman, A B -- Jenkins, T M -- Engelman, A -- Craigie, R -- Davies, D R -- New York, N.Y. -- Science. 1994 Dec 23;266(5193):1981-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892-0560.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7801124" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA Nucleotidyltransferases/*chemistry ; HIV-1/*enzymology ; Hydrogen Bonding ; Integrases ; Models, Molecular ; Molecular Sequence Data ; Protein Folding ; Protein Structure, Secondary ; Ribonuclease H/chemistry ; Solubility ; Virus Integration
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  • 17
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    Molecular basis of mammalian sexual determination: activation of Mullerian inhibiting substance gene expression by SRY (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-02
    Description: The pathway of male sexual development in mammals is initiated by SRY, a gene on the short arm of the Y chromosome. Its expression in the differentiating gonadal ridge directs testicular morphogenesis, characterized by elaboration of Mullerian inhibiting substance (MIS) and testosterone. SRY and MIS each belong to conserved gene families that function in the control of growth and differentiation. Structural and biochemical studies of the DNA binding domain of SRY (the HMG box) revealed a protein-DNA interaction consisting of partial side chain intercalation into a widened minor groove. Functional studies of SRY in a cell line from embryonic gonadal ridge demonstrated activation of a gene-regulatory pathway leading to expression of MIS. SRY molecules containing mutations associated with human sex reversal have altered structural interactions with DNA and failed to induce transcription of MIS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haqq, C M -- King, C Y -- Ukiyama, E -- Falsafi, S -- Haqq, T N -- Donahoe, P K -- Weiss, M A -- GM51558/GM/NIGMS NIH HHS/ -- HD30812/HD/NICHD NIH HHS/ -- P30HD28138/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 1994 Dec 2;266(5190):1494-500.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pediatric Surgical Research Laboratory, Massachusetts General Hospital, Boston 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7985018" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anti-Mullerian Hormone ; Base Sequence ; Cell Line ; DNA/metabolism ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Female ; *Gene Expression Regulation, Developmental ; Genitalia, Male/*embryology ; *Glycoproteins ; Growth Inhibitors/biosynthesis/*genetics ; Humans ; Male ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mullerian Ducts ; *Nuclear Proteins ; Sex Differentiation/*genetics ; Sex-Determining Region Y Protein ; Testicular Hormones/biosynthesis/*genetics ; Transcription Factors/chemistry/*genetics/metabolism
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  • 18
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    Flu virus invasion: halfway there (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carr, C M -- Kim, P S -- New York, N.Y. -- Science. 1994 Oct 14;266(5183):234-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Cambridge, MA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939658" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/metabolism/virology ; Endocytosis ; Endosomes/virology ; Hemagglutinin Glycoproteins, Influenza Virus ; Hemagglutinins, Viral/chemistry/*physiology ; Hydrogen-Ion Concentration ; *Membrane Fusion ; Models, Biological ; Models, Molecular ; Orthomyxoviridae/immunology/*physiology ; Protein Conformation ; Viral Envelope Proteins/chemistry/*physiology
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  • 19
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    Protein-DNA recognition: new perspectives and underlying themes (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-02-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Hippel, P H -- GM-15792/GM/NIGMS NIH HHS/ -- GM-29158/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Feb 11;263(5148):769-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8303292" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Thermodynamics
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  • 20
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    Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-04-15
    Description: The most frequently occurring resistance of Gram-negative bacteria against tetracyclines is triggered by drug recognition of the Tet repressor. This causes dissociation of the repressor-operator DNA complex and enables expression of the resistance protein TetA, which is responsible for active efflux of tetracycline. The 2.5 angstrom resolution crystal structure of the homodimeric Tet repressor complexed with tetracycline-magnesium reveals detailed drug recognition. The orientation of the operator-binding helix-turn-helix motifs of the repressor is inverted in comparison with other DNA binding proteins. The repressor-drug complex is unable to interact with DNA because the separation of the DNA binding motifs is 5 angstroms wider than usually observed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hinrichs, W -- Kisker, C -- Duvel, M -- Muller, A -- Tovar, K -- Hillen, W -- Saenger, W -- New York, N.Y. -- Science. 1994 Apr 15;264(5157):418-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Kristallographie, Freie Universitat Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8153629" target="_blank"〉PubMed〈/a〉
    Keywords: Antiporters/*chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; Crystallography, X-Ray ; DNA, Bacterial/metabolism ; Helix-Loop-Helix Motifs ; Hydrogen Bonding ; Magnesium/chemistry ; Models, Molecular ; Mutation ; Operator Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Repressor Proteins/*chemistry/genetics/metabolism ; Tetracycline/*chemistry/metabolism ; *Tetracycline Resistance/genetics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 21
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    Molecule makers learn the rules of a crooked game (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flam, F -- New York, N.Y. -- Science. 1994 Mar 18;263(5153):1563-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128241" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Models, Molecular ; Protein Conformation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary
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  • 22
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    High-resolution structure of the oligomerization domain of p53 by multidimensional NMR (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-07-15
    Description: The three-dimensional structure of the oligomerization domain (residues 319 to 360) of the tumor suppressor p53 has been solved by multidimensional heteronuclear magnetic resonance (NMR) spectroscopy. The domain forms a 20-kilodalton symmetric tetramer with a topology made up from a dimer of dimers. The two primary dimers each comprise two antiparallel helices linked by an antiparallel beta sheet. One beta strand and one helix are contributed from each monomer. The interface between the two dimers forming the tetramer is mediated solely by helix-helix contacts. The overall result is a symmetric, four-helix bundle with adjacent helices oriented antiparallel to each other and with the two antiparallel beta sheets located on opposing faces of the molecule. The tetramer is stabilized not only by hydrophobic interactions within the protein core but also by a number of electrostatic interactions. The implications of the structure of the tetramer for the biological function of p53 are discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clore, G M -- Omichinski, J G -- Sakaguchi, K -- Zambrano, N -- Sakamoto, H -- Appella, E -- Gronenborn, A M -- New York, N.Y. -- Science. 1994 Jul 15;265(5170):386-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8023159" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Computer Graphics ; DNA/chemistry/metabolism ; Genes, p53 ; Macromolecular Substances ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Protein Conformation ; Protein Structure, Secondary ; Tumor Suppressor Protein p53/*chemistry/genetics/metabolism
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  • 23
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    Vibrationally coherent photochemistry in the femtosecond primary event of vision (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-10-21
    Description: Femtosecond pump-probe experiments reveal the impulsive production of photoproduct in the primary event in vision. The retinal chromophore of rhodopsin was excited with a 35-femtosecond pulse at 500 nanometers, and transient changes in absorption were measured with 10-femtosecond probe pulses. At probe wavelengths within the photo-product absorption band, oscillatory features with a period of 550 femtoseconds (60 wavenumbers) were observed whose phase and amplitude demonstrate that they are the result of nonstationary vibrational motion in the ground state of the photoproduct. The observation of coherent vibrational motion of the photoproduct supports the idea that the primary step in vision is a vibrationally coherent process and that the high quantum yield of the cis--〉trans isomerization in rhodopsin is a consequence of the extreme speed of the excited-state torsional motion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Q -- Schoenlein, R W -- Peteanu, L A -- Mathies, R A -- Shank, C V -- EY-02051/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 21;266(5184):422-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Materials Sciences Division, Lawrence Berkeley Laboratory, University of California, 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939680" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle ; Fourier Analysis ; Isomerism ; *Light ; Models, Molecular ; Photic Stimulation ; Photochemistry ; Rhodopsin/analogs & derivatives/*chemistry ; Spectrum Analysis ; Vision, Ocular/*physiology
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  • 24
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    Coupling of local folding to site-specific binding of proteins to DNA (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-02-11
    Description: Thermodynamic studies have demonstrated the central importance of a large negative heat capacity change (delta C degree assoc) in site-specific protein-DNA recognition. Dissection of the large negative delta C degree assoc and the entropy change of protein-ligand and protein-DNA complexation provide a thermodynamic signature identifying processes in which local folding is coupled to binding. Estimates of the number of residues that fold on binding obtained from this analysis agree with structural data. Structural comparisons indicate that these local folding transitions create key parts of the protein-DNA interface. The energetic implications of this "induced fit" model for DNA site recognition are considered.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spolar, R S -- Record, M T Jr -- GM23467/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Feb 11;263(5148):777-84.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Wisconsin-Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8303294" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; *Protein Folding ; Thermodynamics
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  • 25
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    Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-07-15
    Description: The tailspike protein (TSP) of Salmonella typhimurium phage P22 is a part of the apparatus by which the phage attaches to the bacterial host and hydrolyzes the O antigen. It has served as a model system for genetic and biochemical analysis of protein folding. The x-ray structure of a shortened TSP (residues 109 to 666) was determined to a 2.0 angstrom resolution. Each subunit of the homotrimer contains a large parallel beta helix. The interdigitation of the polypeptide chains at the carboxyl termini is important to protrimer formation in the folding pathway and to thermostability of the mature protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Steinbacher, S -- Seckler, R -- Miller, S -- Steipe, B -- Huber, R -- Reinemer, P -- New York, N.Y. -- Science. 1994 Jul 15;265(5170):383-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biochemie, Abteilung Strukturforschung, Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8023158" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacteriophage P22 ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Glycoside Hydrolases/*chemistry/genetics ; Models, Molecular ; Point Mutation ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Viral Proteins/*chemistry/genetics ; *Viral Tail Proteins
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  • 26
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    Design of a G.C-specific DNA minor groove-binding peptide (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-10-28
    Description: A four-ring tripeptide containing alternating imidazole and pyrrole carboxamides specifically binds six-base pair 5'-(A,T)GCGC(A,T)-3' sites in the minor groove of DNA. The designed peptide has a specificity completely reversed from that of the tripyrrole distamycin, which binds A,T sequences. Structural studies with nuclear magnetic resonance revealed that two peptides bound side-by-side and in an antiparallel orientation in the minor groove. Each of the four imidazoles in the 2:1 ligand-DNA complex recognized a specific guanine amino group in the GCGC core through a hydrogen bond. Targeting a designated four-base pair G.C tract by this synthetic ligand supports the generality of the 2:1 peptide-DNA motif for sequence-specific minor groove recognition of DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geierstanger, B H -- Mrksich, M -- Dervan, P B -- Wemmer, D E -- GM-27681/GM/NIGMS NIH HHS/ -- GM-43129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 28;266(5185):646-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Group in Biophysics, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939719" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Computer Graphics ; DNA/chemistry/*metabolism ; Drug Design ; Hydrogen Bonding ; Imidazoles/chemical synthesis/*chemistry/metabolism ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligopeptides/chemical synthesis/*chemistry/metabolism ; Protein Conformation ; Pyrroles/chemical synthesis/*chemistry/metabolism
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  • 27
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    Crystal structure of the principal neutralization site of HIV-1 (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-04-01
    Description: The crystal structure of a complex between a 24-amino acid peptide from the third variable (V3) loop of human immunodeficiency virus-type 1 (HIV-1) gp 120 and the Fab fragment of a broadly neutralizing antibody (59.1) was determined to 3 angstrom resolution. The tip of the V3 loop containing the Gly-Pro-Gly-Arg-Ala-Phe sequence adopts a double-turn conformation, which may be the basis of its conservation in many HIV-1 isolates. A complete map of the HIV-1 principal neutralizing determinant was constructed by stitching together structures of V3 loop peptides bound to 59.1 and to an isolate-specific (MN) neutralizing antibody (50.1). Structural conservation of the overlapping epitopes suggests that this biologically relevant conformation could be of use in the design of synthetic vaccines and drugs to inhibit HIV-1 entry and virus-related cellular fusion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghiara, J B -- Stura, E A -- Stanfield, R L -- Profy, A T -- Wilson, I A -- GM-46192/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Apr 1;264(5155):82-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7511253" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/immunology ; Antigen-Antibody Complex/*chemistry/immunology ; Antigen-Antibody Reactions ; Computer Graphics ; Crystallography, X-Ray ; Epitopes/chemistry/immunology ; HIV Antibodies/*chemistry/immunology ; HIV Envelope Protein gp120/*chemistry/immunology ; HIV-1/*chemistry/immunology ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/*chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Neutralization Tests ; Peptide Fragments/*chemistry/immunology ; Protein Conformation ; Protein Structure, Secondary
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  • 28
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    DNA bending by asymmetric phosphate neutralization (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-16
    Description: DNA is often bent when complexed with proteins. Understanding the forces responsible for DNA bending would be of fundamental value in exploring the interplay of these macromolecules. A series of experiments was devised to test the hypothesis that proteins with cationic surfaces can induce substantial DNA bending by neutralizing phosphates on one DNA face. Repulsions between phosphates in the remaining anionic helix are predicted to result in an unbalanced compression force acting to deform the DNA toward the protein. This hypothesis is supported by the results of electrophoretic experiments in which DNA spontaneously bends when one helical face is partially modified by incorporation of neutral phosphate analogs. Phasing with respect to a site of intrinsic DNA curvature (hexadeoxyadenylate tract) permits estimation of the electrostatic bend angle, and demonstrates that such modified DNAs are deformed toward the neutralized surface, as predicted. Similar model systems may be useful in exploring the extent to which phosphate neutralization can account for DNA bending by particular proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strauss, J K -- Maher, L J 3rd -- GM47814/GM/NIGMS NIH HHS/ -- P30 CA36727-08/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1994 Dec 16;266(5192):1829-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha 68198-6805.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7997878" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cations/chemistry ; DNA/*chemistry ; DNA-Binding Proteins/chemistry ; Electrochemistry ; Electrophoresis, Polyacrylamide Gel ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Nucleosomes/chemistry ; Oligodeoxyribonucleotides ; Organophosphorus Compounds/chemistry ; Phosphates/*chemistry ; Thermodynamics
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  • 29
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    Crystal structure of a catalytic antibody with a serine protease active site (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-08-19
    Description: The three-dimensional structure of an unusually active hydrolytic antibody with a phosphonate transition state analog (hapten) bound to the active site has been solved to 2.5 A resolution. The antibody (17E8) catalyzes the hydrolysis of norleucine and methionine phenyl esters and is selective for amino acid esters that have the natural alpha-carbon L configuration. A plot of the pH-dependence of the antibody-catalyzed reaction is bell-shaped with an activity maximum at pH 9.5; experiments on mechanism lend support to the formation of a covalent acyl-antibody intermediate. The structural and kinetic data are complementary and support a hydrolytic mechanism for the antibody that is remarkably similar to that of the serine proteases. The antibody active site contains a Ser-His dyad structure proximal to the phosphorous atom of the bound hapten that resembles two of the three components of the Ser-His-Asp catalytic triad of serine proteases. The antibody active site also contains a Lys residue to stabilize oxyanion formation, and a hydrophobic binding pocket for specific substrate recognition of norleucine and methionine side chains. The structure identifies active site residues that mediate catalysis and suggests specific mutations that may improve the catalytic efficiency of the antibody. This high resolution structure of a catalytic antibody-hapten complex shows that antibodies can converge on active site structures that have arisen through natural enzyme evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, G W -- Guo, J -- Huang, W -- Fletterick, R J -- Scanlan, T S -- DK39304/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1994 Aug 19;265(5175):1059-64.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8066444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Catalytic/*chemistry/immunology/metabolism ; Binding Sites ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Haptens/metabolism ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrolysis ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Serine Endopeptidases/*chemistry/metabolism
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  • 30
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    Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-01-21
    Description: Collagenase is a zinc-dependent endoproteinase and is a member of the matrix metalloproteinase (MMP) family of enzymes. The MMPs participate in connective tissue remodeling events and aberrant regulation has been associated with several pathologies. The 2.4 angstrom resolution structure of the inhibited enzyme revealed that, in addition to the catalytic zinc, there is a second zinc ion and a calcium ion which play a major role in stabilizing the tertiary structure of collagenase. Despite scant sequence homology, collagenase shares structural homology with two other endoproteinases, bacterial thermolysin and crayfish astacin. The detailed description of protein-inhibitor interactions present in the structure will aid in the design of compounds that selectively inhibit individual members of the MMP family. Such inhibitors will be useful in examining the function of MMPs in pathological processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lovejoy, B -- Cleasby, A -- Hassell, A M -- Longley, K -- Luther, M A -- Weigl, D -- McGeehan, G -- McElroy, A B -- Drewry, D -- Lambert, M H -- New York, N.Y. -- Science. 1994 Jan 21;263(5145):375-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Glaxo Research Institute, Research Triangle Park, NC 27709.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8278810" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Calcium/metabolism ; Collagenases/*chemistry/metabolism ; Computer Graphics ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Matrix Metalloproteinase 8 ; Matrix Metalloproteinase Inhibitors ; Metalloendopeptidases/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thermolysin/chemistry ; Zinc/metabolism
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    Taking the data in hand--literally--with virtual reality (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-08-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taubes, G -- New York, N.Y. -- Science. 1994 Aug 12;265(5174):884-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8052844" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Graphics ; *Computer Simulation ; Drug Design ; Models, Molecular ; User-Computer Interface
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  • 32
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    An all D-amino acid opioid peptide with central analgesic activity from a combinatorial library (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-23
    Description: A synthetic combinatorial library containing 52,128,400 D-amino acid hexapeptides was used to identify a ligand for the mu opioid receptor. The peptide, Ac-rfwink-NH2, bears no resemblance to any known opioid peptide. Simulations using molecular dynamics, however, showed that three amino acid moieties have the same spatial orientation as the corresponding pharmacophoric groups of the opioid peptide PLO17. Ac-rfwink-NH2 was shown to be a potent agonist at the mu receptor and induced long-lasting analgesia in mice. Analgesia produced by intraperitoneally administered Ac-rfwink-NH2 was blocked by intracerebroventricular administration of naloxone, demonstrating that this peptide may cross the blood-brain barrier.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dooley, C T -- Chung, N N -- Wilkes, B C -- Schiller, P W -- Bidlack, J M -- Pasternak, G W -- Houghten, R A -- DA-000138/DA/NIDA NIH HHS/ -- DA-02615/DA/NIDA NIH HHS/ -- DA-03742/DA/NIDA NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1994 Dec 23;266(5193):2019-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Torrey Pines Institute for Molecular Studies, San Diego, CA 92121.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7801131" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Analgesics/chemistry/metabolism/*pharmacology ; Animals ; Brain/metabolism ; Dose-Response Relationship, Drug ; Endorphins/pharmacology ; Enkephalin, Ala(2)-MePhe(4)-Gly(5)- ; Enkephalin, D-Penicillamine (2,5)- ; Enkephalins/metabolism ; Guinea Pigs ; Injections, Intraventricular ; Male ; Mice ; Models, Molecular ; Molecular Sequence Data ; Naloxone/administration & dosage/pharmacology ; Opioid Peptides/chemistry/metabolism/*pharmacology ; Pain Measurement ; Protein Conformation ; Rats ; Receptors, Opioid, mu/agonists/metabolism ; Stereoisomerism
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  • 33
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    How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-09
    Description: The crystal structure of a 27-kilodalton methylcobalamin-containing fragment of methionine synthase from Escherichia coli was determined at 3.0 A resolution. This structure depicts cobalamin-protein interactions and reveals that the corrin macrocycle lies between a helical amino-terminal domain and an alpha/beta carboxyl-terminal domain that is a variant of the Rossmann fold. Methylcobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in the adenosylcobalamin-dependent enzymes methylmalonyl-coenzyme A mutase and glutamate mutase, suggesting that displacement of the dimethylbenzimidazole will be a feature common to many cobalamin-binding proteins. Thus the cobalt ligand, His759, and the neighboring residues Asp757 and Ser810, may form a catalytic quartet, Co-His-Asp-Ser, that modulates the reactivity of the B12 prosthetic group in methionine synthase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Drennan, C L -- Huang, S -- Drummond, J T -- Matthews, R G -- Lidwig, M L -- GM08570/GM/NIGMS NIH HHS/ -- GM16429/GM/NIGMS NIH HHS/ -- GM24908/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1994 Dec 9;266(5191):1669-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Research Division, University of Michigan, Ann Arbor 48109-1055.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7992050" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase/*chemistry/metabolism ; Amino Acid Isomerases/chemistry ; Amino Acid Sequence ; Benzimidazoles ; Catalysis ; Computer Graphics ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli/*enzymology ; Histidine/metabolism ; *Intramolecular Transferases ; Ligands ; Methylation ; Methylmalonyl-CoA Mutase/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Vitamin B 12/*analogs & derivatives/chemistry/metabolism
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    HIV integrase structure catalyzes drug search (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Brien, C -- New York, N.Y. -- Science. 1994 Dec 23;266(5193):1946.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7801119" target="_blank"〉PubMed〈/a〉
    Keywords: Antiviral Agents/pharmacology ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA Nucleotidyltransferases/antagonists & inhibitors/*chemistry/metabolism ; DNA-Binding Proteins/metabolism ; Drug Design ; HIV-1/drug effects/*enzymology ; Integrases ; Models, Molecular ; Virus Integration
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  • 35
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    Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-21
    Description: The molecular structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli, co-crystallized with an S,R-methylphosphinate and adenosine triphosphate, was determined by x-ray diffraction to a resolution of 2.3 angstroms. A catalytic mechanism for the ligation of two D-alanine substrates is proposed in which a helix dipole and a hydrogen-bonded triad of tyrosine, serine, and glutamic acid assist binding and deprotonation steps. From sequence comparison, it is proposed that a different triad exists in a recently discovered D-alanine:D-lactate ligase (VanA) present in vancomycin-resistant enterococci. A molecular mechanism for the altered specificity of VanA is suggested.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fan, C -- Moews, P C -- Walsh, C T -- Knox, J R -- 1RO1-AI-34330/AI/NIAID NIH HHS/ -- GM-49338/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 21;266(5184):439-43.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269-3125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939684" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/metabolism ; Amino Acid Sequence ; Bacterial Proteins/chemistry ; Binding Sites ; *Carbon-Oxygen Ligases ; Computer Graphics ; Crystallography, X-Ray ; Dipeptides/biosynthesis ; Drug Resistance, Microbial ; Escherichia coli/drug effects/*enzymology ; Hydrogen Bonding ; Ligases/chemistry ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Peptide Synthases/*chemistry/genetics/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Substrate Specificity ; Vancomycin/*pharmacology
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  • 36
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    Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-01-21
    Description: The structure of the 52-amino acid DNA-binding domain of the prokaryotic Hin recombinase, complexed with a DNA recombination half-site, has been solved by x-ray crystallography at 2.3 angstrom resolution. The Hin domain consists of a three-alpha-helix bundle, with the carboxyl-terminal helix inserted into the major groove of DNA, and two flanking extended polypeptide chains that contact bases in the minor groove. The overall structure displays features resembling both a prototypical bacterial helix-turn-helix and the eukaryotic homeodomain, and in many respects is an intermediate between these two DNA-binding motifs. In addition, a new structural motif is seen: the six-amino acid carboxyl-terminal peptide of the Hin domain runs along the minor groove at the edge of the recombination site, with the peptide backbone facing the floor of the groove and side chains extending away toward the exterior. The x-ray structure provides an almost complete explanation for DNA mutant binding studies in the Hin system and for DNA specificity observed in the Hin-related family of DNA invertases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, J A -- Johnson, R C -- Dickerson, R E -- GM-31299/GM/NIGMS NIH HHS/ -- GM-38509/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jan 21;263(5145):348-55.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Institute, University of California, Los Angeles 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8278807" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Composition ; Base Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Nucleotidyltransferases/chemistry/*metabolism ; Helix-Loop-Helix Motifs ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; *Recombination, Genetic
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  • 37
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    Toxic shock syndrome toxin-1 complexed with a class II major histocompatibility molecule HLA-DR1 (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-16
    Description: The three-dimensional structure of a Staphylococcus aureus superantigen, toxic shock syndrome toxin-1 (TSST-1), complexed with a human class II major histocompatibility molecule (DR1), was determined by x-ray crystallography. The TSST-1 binding site on DR1 overlaps that of the superantigen S. aureus enterotoxin B (SEB), but the two binding modes differ. Whereas SEB binds primarily off one edge of the peptide binding site of DR1, TSST-1 extends over almost one-half of the binding site and contacts both the flanking alpha helices of the histocompatibility antigen and the bound peptide. This difference suggests that the T cell receptor (TCR) would bind to TSST-1:DR1 very differently than to DR1:peptide or SEB:DR1. It also suggests that TSST-1 binding may be dependent on the peptide, though less so than TCR binding, providing a possible explanation for the inability of TSST-1 to competitively block SEB binding to all DR1 molecules on cells (even though the binding sites of TSST-1 and SEB on DR1 overlap almost completely) and suggesting the possibility that T cell activation by superantigen could be directed by peptide antigen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, J -- Urban, R G -- Strominger, J L -- Wiley, D C -- New York, N.Y. -- Science. 1994 Dec 16;266(5192):1870-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Children's Hospital, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7997880" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Toxins ; Binding Sites ; Crystallography, X-Ray ; Enterotoxins/*chemistry/metabolism ; HLA-DR1 Antigen/*chemistry/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell/metabolism ; *Staphylococcus aureus ; Superantigens/*chemistry/metabolism
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  • 38
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    Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-07-15
    Description: Mutations in the p53 tumor suppressor are the most frequently observed genetic alterations in human cancer. The majority of the mutations occur in the core domain which contains the sequence-specific DNA binding activity of the p53 protein (residues 102-292), and they result in loss of DNA binding. The crystal structure of a complex containing the core domain of human p53 and a DNA binding site has been determined at 2.2 angstroms resolution and refined to a crystallographic R factor of 20.5 percent. The core domain structure consists of a beta sandwich that serves as a scaffold for two large loops and a loop-sheet-helix motif. The two loops, which are held together in part by a tetrahedrally coordinated zinc atom, and the loop-sheet-helix motif form the DNA binding surface of p53. Residues from the loop-sheet-helix motif interact in the major groove of the DNA, while an arginine from one of the two large loops interacts in the minor groove. The loops and the loop-sheet-helix motif consist of the conserved regions of the core domain and contain the majority of the p53 mutations identified in tumors. The structure supports the hypothesis that DNA binding is critical for the biological activity of p53, and provides a framework for understanding how mutations inactivate it.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cho, Y -- Gorina, S -- Jeffrey, P D -- Pavletich, N P -- NCI CA08748-29/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1994 Jul 15;265(5170):346-55.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8023157" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; Genes, p53 ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; *Mutation ; Nucleic Acid Conformation ; *Protein Conformation ; Protein Structure, Secondary ; Tumor Suppressor Protein p53/*chemistry/genetics/metabolism
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  • 39
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    Chemical sequence control of beta-sheet assembly in macromolecular crystals of periodic polypeptides (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-09-02
    Description: A family of uniform periodic polypeptides has been prepared by bacterial expression of the corresponding artificial genes, with the objective of exploring the potential for control of supramolecular organization in genetically engineered protein-based polymeric materials. The repeating units of the polypeptides consist of oligomeric alanyl-glycine sequences interspersed with glutamic acid residues inserted at intervals of 8 to 14 amino acids. Crystallization of such materials from formic acid produces beta-sheet structures in the solid state, as shown by vibrational spectroscopy, nuclear magnetic resonance spectroscopy, and wide-angle x-ray diffraction. The diffraction results, together with observations from electron microscopy, are consistent with the formation of needle-shaped lamellar crystals whose thickness is controlled by the periodicity of the primary sequence. These results can be used to control solid-state structure in macromolecular materials.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krejchi, M T -- Atkins, E D -- Waddon, A J -- Fournier, M J -- Mason, T L -- Tirrell, D A -- New York, N.Y. -- Science. 1994 Sep 2;265(5177):1427-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Polymer Science and Engineering, University of Massachusetts, Amherst 01003.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8073284" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Computer Simulation ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Microscopy, Electron ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemistry ; *Protein Engineering ; *Protein Structure, Secondary ; Recombinant Proteins/*chemistry/ultrastructure ; Spectrum Analysis, Raman
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    Alpha-helical coiled coils: more facts and better predictions (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-01-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, C -- Parry, D A -- AR17346/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jan 28;263(5146):488-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02254-9110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8290957" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; *DNA-Binding Proteins ; Fungal Proteins/chemistry ; Hemagglutinin Glycoproteins, Influenza Virus ; Hemagglutinins, Viral/chemistry ; Leucine Zippers ; Models, Molecular ; Protein Kinases/chemistry ; *Protein Structure, Secondary ; *Protein Structure, Tertiary ; *Saccharomyces cerevisiae Proteins ; Spectrin/chemistry
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  • 41
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    Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-01-21
    Description: Mechanistic information and structure-based design methods have been used to design a series of nonpeptide cyclic ureas that are potent inhibitors of human immunodeficiency virus (HIV) protease and HIV replication. A fundamental feature of these inhibitors is the cyclic urea carbonyl oxygen that mimics the hydrogen-bonding features of a key structural water molecule. The success of the design in both displacing and mimicking the structural water molecule was confirmed by x-ray crystallographic studies. Highly selective, preorganized inhibitors with relatively low molecular weight and high oral bioavailability were synthesized.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lam, P Y -- Jadhav, P K -- Eyermann, C J -- Hodge, C N -- Ru, Y -- Bacheler, L T -- Meek, J L -- Otto, M J -- Rayner, M M -- Wong, Y N -- New York, N.Y. -- Science. 1994 Jan 21;263(5145):380-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Virology Research, DuPont Merck Pharmaceutical Company, Wilmington, DE 19880.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8278812" target="_blank"〉PubMed〈/a〉
    Keywords: Administration, Oral ; Animals ; Azepines/*chemistry/metabolism/pharmacokinetics/pharmacology ; Binding Sites ; Biological Availability ; Cell Line ; Crystallography, X-Ray ; Dogs ; *Drug Design ; Drug Evaluation, Preclinical ; HIV Protease/chemistry/metabolism ; HIV Protease Inhibitors/*chemistry/metabolism/pharmacokinetics/pharmacology ; HIV-1/drug effects/physiology ; Hydrogen Bonding ; Models, Molecular ; Molecular Conformation ; Molecular Weight ; Rats ; Recombinant Proteins/chemistry/metabolism ; Urea ; Virus Replication/drug effects
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  • 42
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    Time-resolved detection of structural changes during the photocycle of spin-labeled bacteriorhodopsin (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-10-07
    Description: Bacteriorhodopsin was selectively spin labeled at residues 72, 101, or 105 after replacement of the native amino acids by cysteine. Only the electron paramagnetic resonance spectrum of the label at 101 was time-dependent during the photocycle. The spectral change rose with the decay of the M intermediate and fell with recovery of the ground state. The transient signal is interpreted as the result of movement in the C-D or E-F interhelical loop, or in both, coincident with protonation changes at the key aspartate 96 residue. These results link the optically characterized intermediates with localized conformational changes in bacteriorhodopsin during the photocycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Steinhoff, H J -- Mollaaghababa, R -- Altenbach, C -- Hideg, K -- Krebs, M -- Khorana, H G -- Hubbell, W L -- EY05216/EY/NEI NIH HHS/ -- GM28289/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 7;266(5182):105-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Biophysik, Ruhr-Universitat Bochum, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939627" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry/genetics ; Electron Spin Resonance Spectroscopy ; Light ; Models, Molecular ; Mutagenesis, Site-Directed ; *Protein Conformation ; Protein Structure, Secondary ; Spin Labels
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    A unified polymerase mechanism for nonhomologous DNA and RNA polymerases (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Steitz, T A -- Smerdon, S J -- Jager, J -- Joyce, C M -- GM28550/GM/NIGMS NIH HHS/ -- GM39546/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Dec 23;266(5193):2022-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7528445" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA Polymerase I/*chemistry/metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; HIV Reverse Transcriptase ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; RNA-Directed DNA Polymerase/*chemistry/metabolism ; Viral Proteins
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  • 44
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    Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-09-02
    Description: Mechanisms of guanosine triphosphate (GTP) hydrolysis by members of the G protein alpha subunit-p21ras superfamily of guanosine triphosphatases have been studied extensively but have not been well understood. High-resolution x-ray structures of the GTP gamma S and GDP.AlF4- complexes formed by the G protein Gi alpha 1 demonstrate specific roles in transition-state stabilization for two highly conserved residues. Glutamine204 (Gln61 in p21ras) stabilizes and orients the hydrolytic water in the trigonal-bipyramidal transition state. Arginine 178 stabilizes the negative charge at the equatorial oxygen atoms of the pentacoordinate phosphate intermediate. Conserved only in the G alpha family, this residue may account for the higher hydrolytic rate of G alpha proteins relative to those of the p21ras family members. The fold of Gi alpha 1 differs from that of the homologous Gt alpha subunit in the conformation of a helix-loop sequence located in the alpha-helical domain that is characteristic of these proteins; this site may participate in effector binding. The amino-terminal 33 residues are disordered in GTP gamma S-Gi alpha 1, suggesting a mechanism that may promote release of the beta gamma subunit complex when the alpha subunit is activated by GTP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coleman, D E -- Berghuis, A M -- Lee, E -- Linder, M E -- Gilman, A G -- Sprang, S R -- DK 46371/DK/NIDDK NIH HHS/ -- GM34497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Sep 2;265(5177):1405-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Dallas, TX.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8073283" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Compounds/metabolism ; Arginine/chemistry ; Binding Sites ; Catalysis ; Computer Graphics ; Crystallography, X-Ray ; Fluorides/metabolism ; GTP-Binding Proteins/*chemistry/metabolism ; Glutamine/chemistry ; Guanosine 5'-O-(3-Thiotriphosphate)/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/*metabolism ; Helix-Loop-Helix Motifs ; Hydrogen Bonding ; Hydrolysis ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary
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  • 45
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    Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-07
    Description: The structure of a protein triple helix has been determined at 1.9 angstrom resolution by x-ray crystallographic studies of a collagen-like peptide containing a single substitution of the consensus sequence. This peptide adopts a triple-helical structure that confirms the basic features determined from fiber diffraction studies on collagen: supercoiling of polyproline II helices and interchain hydrogen bonding that follows the model II of Rich and Crick. In addition, the structure provides new information concerning the nature of this protein fold. Each triple helix is surrounded by a cylinder of hydration, with an extensive hydrogen bonding network between water molecules and peptide acceptor groups. Hydroxyproline residues have a critical role in this water network. The interaxial spacing of triple helices in the crystal is similar to that in collagen fibrils, and the water networks linking adjacent triple helices in the crystal structure are likely to be present in connective tissues. The breaking of the repeating (X-Y-Gly)n pattern by a Gly--〉Ala substitution results in a subtle alteration of the conformation, with a local untwisting of the triple helix. At the substitution site, direct interchain hydrogen bonds are replaced with interstitial water bridges between the peptide groups. Similar conformational changes may occur in Gly--〉X mutated collagens responsible for the diseases osteogenesis imperfecta, chondrodysplasias, and Ehlers-Danlos syndrome IV.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bella, J -- Eaton, M -- Brodsky, B -- Berman, H M -- AR 19626/AR/NIAMS NIH HHS/ -- GM 21589/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 7;266(5182):75-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Rutgers University, New Brunswick, NJ 08855.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7695699" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/chemistry ; Amino Acid Sequence ; Collagen/*chemistry ; Computer Graphics ; Crystallography, X-Ray ; Glycine/chemistry ; Hydrogen Bonding ; Hydroxyproline/chemistry ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Peptides/*chemistry ; *Protein Conformation ; Protein Structure, Secondary
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    The mobile flavin of 4-OH benzoate hydroxylase (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-07
    Description: Para-hydroxybenzoate hydroxylase inserts oxygen into substrates by means of the labile intermediate, flavin C(4a)-hydroperoxide. This reaction requires transient isolation of the flavin and substrate from the bulk solvent. Previous crystal structures have revealed the position of the substrate para-hydroxybenzoate during oxygenation but not how it enters the active site. In this study, enzyme structures with the flavin ring displaced relative to the protein were determined, and it was established that these or similar flavin conformations also occur in solution. Movement of the flavin appears to be essential for the translocation of substrates and products into the solvent-shielded active site during catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gatti, D L -- Palfey, B A -- Lah, M S -- Entsch, B -- Massey, V -- Ballou, D P -- Ludwig, M L -- GM 11106/GM/NIGMS NIH HHS/ -- GM 16429/GM/NIGMS NIH HHS/ -- GM 20877/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1994 Oct 7;266(5182):110-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, University of Michigan, Ann Arbor 48109.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939628" target="_blank"〉PubMed〈/a〉
    Keywords: Benzoate 4-Monooxygenase ; Binding Sites ; Catalysis ; Computer Graphics ; Flavin-Adenine Dinucleotide/chemistry/metabolism ; Flavins/*chemistry/metabolism ; Hydrogen Bonding ; Mixed Function Oxygenases/*chemistry/metabolism ; Models, Molecular ; Molecular Conformation ; Oxidation-Reduction ; Parabens/metabolism ; Protein Conformation
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    Folding pattern diversity of integral membrane proteins (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-05-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cowan, S W -- Rosenbusch, J P -- New York, N.Y. -- Science. 1994 May 13;264(5161):914-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biozentrum, University of Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8178151" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Bacteriorhodopsins/chemistry ; Cell Membrane/chemistry ; Hydrogen Bonding ; Membrane Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Porins/chemistry ; *Protein Folding ; Protein Structure, Secondary
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  • 48
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    Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-03-11
    Description: Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 A resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically in the crystal from adenosine triphosphate (ATP) and serine hydroxamate, and the second is with a synthetic analog of seryl adenylate (5'-O-[N-(L-seryl)-sulfamoyl]adenosine), which is a strong inhibitor of the enzyme. Both molecules are bound in a similar fashion by a network of hydrogen bond interactions in a deep hydrophilic cleft formed by the antiparallel beta sheet and surrounding loops of the synthetase catalytic domain. Four regions in the primary sequence are involved in the interactions, including the motif 2 and 3 regions of class 2 synthetases. Apart from the specific recognition of the serine side chain, the interactions are likely to be similar in all class 2 synthetases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Belrhali, H -- Yaremchuk, A -- Tukalo, M -- Larsen, K -- Berthet-Colominas, C -- Leberman, R -- Beijer, B -- Sproat, B -- Als-Nielsen, J -- Grubel, G -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1432-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉EMBL Grenoble Outstation, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128224" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/*analogs & derivatives/chemical synthesis/metabolism ; Adenosine Monophosphate/*analogs & derivatives/chemical synthesis/metabolism ; Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment ; Serine/*analogs & derivatives/chemical synthesis/metabolism ; Serine-tRNA Ligase/*chemistry/metabolism ; Thermus thermophilus/*enzymology
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    Pf1 virus structure: helical coat protein and DNA with paraxial phosphates (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-07-29
    Description: The helical path of the DNA in filamentous bacteriophage Pf1 was deduced from different kinds of existing structural information, including results from x-ray fiber diffraction. The DNA has the same pitch, 16 angstroms, as the surrounding helix of protein subunits; the rise and rotation per nucleotides are 6.1 angstroms and 132 degrees, respectively; and the phosphates are 2.5 angstroms from the axis. The DNA in Pf1 is, therefore, the most extended and twisted DNA structure known. On the basis of the DNA structure and extensive additional information about the protein, a model of the virion is proposed. In the model, the DNA bases reach out, into the protein, and the lysine and arginine side chains reach in, between the DNA bases, to stabilize the paraxial phosphate charges; the conformation of the protein subunit is a combination of alpha and 3(10) helices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, D J -- Day, L A -- GM42286/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jul 29;265(5172):671-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, New York, NY 10016.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8036516" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Capsid/*chemistry ; *Capsid Proteins ; DNA, Viral/*chemistry ; Inovirus/chemistry/genetics/*ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phosphates/analysis ; Protein Structure, Secondary ; X-Ray Diffraction
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  • 50
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    The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser) (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-11
    Description: The crystal structure of Thermus thermophilus seryl-transfer RNA synthetase, a class 2 aminoacyl-tRNA synthetase, complexed with a single tRNA(Ser) molecule was solved at 2.9 A resolution. The structure revealed how insertion of conserved base G20b from the D loop into the core of the tRNA determines the orientation of the long variable arm, which is a characteristic feature of most serine specific tRNAs. On tRNA binding, the antiparallel coiled-coil domain of one subunit of the synthetase makes contacts with the variable arm and T psi C loop of the tRNA and directs the acceptor stem of the tRNA into the active site of the other subunit. Specificity depends principally on recognition of the shape of tRNA(Ser) through backbone contacts and secondarily on sequence specific interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Biou, V -- Yaremchuk, A -- Tukalo, M -- Cusack, S -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1404-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Grenoble Outstation, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128220" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Base Composition ; Base Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Transfer, Amino Acyl/*chemistry/metabolism ; Serine-tRNA Ligase/*chemistry/metabolism ; Substrate Specificity ; Thermus thermophilus/*enzymology
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    High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-03-25
    Description: The three-dimensional structure of a member of the beta subfamily of chemokines, human macrophage inflammatory protein-1 beta (hMIP-1 beta), has been determined with the use of solution multidimensional heteronuclear magnetic resonance spectroscopy. Human MIP-1 beta is a symmetric homodimer with a relative molecular mass of approximately 16 kilodaltons. The structure of the hMIP-1 beta monomer is similar to that of the related alpha chemokine interleukin-8 (IL-8). However, the quaternary structures of the two proteins are entirely distinct, and the dimer interface is formed by a completely different set of residues. Whereas the IL-8 dimer is globular, the hMIP-1 beta dimer is elongated and cylindrical. This provides a rational explanation for the absence of cross-binding and reactivity between the alpha and beta chemokine subfamilies. Calculation of the solvation free energies of dimerization suggests that the formation and stabilization of the two different types of dimers arise from the burial of hydrophobic residues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lodi, P J -- Garrett, D S -- Kuszewski, J -- Tsang, M L -- Weatherbee, J A -- Leonard, W J -- Gronenborn, A M -- Clore, G M -- New York, N.Y. -- Science. 1994 Mar 25;263(5154):1762-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8134838" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chemokine CCL4 ; Computer Graphics ; Cytokines/*chemistry ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Interleukin-8/chemistry ; Macrophage Inflammatory Proteins ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Monokines/*chemistry ; Protein Conformation ; Protein Structure, Secondary ; Sequence Alignment
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  • 52
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    Experimental support for the "hydrophobic zipper" hypothesis (1994)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1994-01-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gronenborn, A M -- Clore, G M -- New York, N.Y. -- Science. 1994 Jan 28;263(5146):536.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8290964" target="_blank"〉PubMed〈/a〉
    Keywords: Hydrogen Bonding ; Interleukin-1/*chemistry ; Models, Molecular ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary
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    New enzyme structure reveals cell's rotary engine (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-08-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Brien, C -- New York, N.Y. -- Science. 1994 Aug 26;265(5176):1176-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8066459" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/biosynthesis ; Crystallization ; Crystallography, X-Ray ; Intracellular Membranes/enzymology ; Mitochondria/enzymology ; Models, Molecular ; Protein Conformation ; Proton-Translocating ATPases/*chemistry/metabolism ; Protons
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Taking a first look at a tyrosine phosphatase (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1373.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128216" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Phosphates/metabolism ; Protein Conformation ; Protein Folding ; Protein Tyrosine Phosphatases/*chemistry/metabolism ; Tungsten Compounds/metabolism
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    Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-11-18
    Description: Solution structures of two Src homology 3 (SH3) domain-ligand complexes have been determined by nuclear magnetic resonance. Each complex consists of the SH3 domain and a nine-residue proline-rich peptide selected from a large library of ligands prepared by combinatorial synthesis. The bound ligands adopt a left-handed polyproline type II (PPII) helix, although the amino to carboxyl directionalities of their helices are opposite. The peptide orientation is determined by a salt bridge formed by the terminal arginine residues of the ligands and the conserved aspartate-99 of the SH3 domain. Residues at positions 3, 4, 6, and 7 of both peptides also intercalate into the ligand-binding site; however, the respective proline and nonproline residues show exchanged binding positions in the two complexes. These structural results led to a model for the interactions of SH3 domains with proline-rich peptides that can be used to predict critical residues in complexes of unknown structure. The model was used to identify correctly both the binding orientation and the contact and noncontact residues of a peptide derived from the nucleotide exchange factor Sos in association with the amino-terminal SH3 domain of the adaptor protein Grb2.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, S -- Chen, J K -- Yu, H -- Simon, J A -- Schreiber, S L -- GM44993/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Nov 18;266(5188):1241-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7526465" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Proteins, Signal Transducing ; Alanine/chemistry ; Amino Acid Sequence ; Arginine/chemistry ; Binding Sites ; GRB2 Adaptor Protein ; Glycine/chemistry ; Guanine Nucleotide Exchange Factors ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Oligopeptides/chemistry/*metabolism ; Peptides/chemistry/metabolism ; Proline/chemistry ; Proline-Rich Protein Domains ; Protein Conformation ; Protein Structure, Secondary ; Protein-Tyrosine Kinases/chemistry/*metabolism ; Proteins/chemistry/metabolism ; Proto-Oncogene Proteins pp60(c-src)/chemistry/*metabolism ; src-Family Kinases
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    Crystal structure of the DNA binding domain of the heat shock transcription factor (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-01-14
    Description: The structure of the DNA binding domain, determined at 1.8 angstrom resolution, contains a three-helix bundle that is capped by a four-stranded antiparallel beta sheet. This structure is a variant of the helix-turn-helix motif, typified by catabolite activator protein. In the heat shock transcription factor, the first helix of the motif (alpha 2) has an alpha-helical bulge and a proline-induced kink. The angle between the two helices of the motif (alpha 2 and alpha 3) is about 20 degrees smaller than the average for canonical helix-turn-helix proteins. Nevertheless, the relative positions of the first and third helices of the bundle (alpha 1 and alpha 3) are conserved. It is proposed here that the first helix of the three-helix bundle be considered a component of the helix-turn-helix motif.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harrison, C J -- Bohm, A A -- Nelson, H C -- GM08295/GM/NIGMS NIH HHS/ -- GM44086/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jan 14;263(5144):224-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8284672" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; DNA/*metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; *Heat-Shock Proteins ; *Helix-Loop-Helix Motifs ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Transcription Factors/*chemistry
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    Cooperativity induced by a single mutation at the subunit interface of a dimeric enzyme: glutathione reductase (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-11-13
    Description: When glycine418 of Escherichia coli glutathione reductase, which is in a closely packed region of the dimer interface, is replaced with a bulky tryptophan residue, the enzyme becomes highly cooperative (Hill coefficient 1.76) for glutathione binding. The cooperativity is lost when the mutant subunit is hybridized with a wild-type subunit to create a heterodimer. The mutation appears to disrupt atomic packing at the dimer interface, which induces a change of kinetic mechanism. A single mutation in a region of the protein remote from the active site can thus act as a molecular switch to confer cooperativity on an enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scrutton, N S -- Deonarain, M P -- Berry, A -- Perham, R N -- New York, N.Y. -- Science. 1992 Nov 13;258(5085):1140-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, United Kingdom.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1439821" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Escherichia coli/*enzymology/genetics ; Genes, Bacterial ; Glutathione/metabolism ; Glutathione Reductase/*chemistry/genetics/metabolism ; Glycine/chemistry ; Kinetics ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; *Mutagenesis, Site-Directed ; NADP/metabolism ; Plasmids ; Protein Multimerization ; Tryptophan/chemistry
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    Actin constitution: guaranteeing the right to assemble (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wertman, K F -- Drubin, D G -- GM42759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Oct 30;258(5083):759-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1439782" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/genetics/metabolism ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Models, Molecular ; Molecular Structure ; Mutation ; Rabbits ; Tetrahymena/chemistry
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    Three-dimensional structure of dimeric human recombinant macrophage colony-stimulating factor (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-11-20
    Description: Macrophage colony-stimulating factor (M-CSF) triggers the development of cells of the monocyte-macrophage lineage and has a variety of stimulatory effects on mature cells of this class. The biologically active form of M-CSF is a disulfide-linked dimer that activates an intrinsic tyrosine kinase activity on the M-CSF receptor by inducing dimerization of the receptor molecules. The structure of a recombinant human M-CSF dimer, determined at 2.5 angstroms by x-ray crystallography, contains two bundles of four alpha helices laid end-to-end, with an interchain disulfide bond. Individual monomers of M-CSF show a close structural similarity to the cytokines granulocyte-macrophage colony-stimulating factor and human growth hormone. Both of these cytokines are monomeric in their active form, and their specific receptors lack intrinsic tyrosine kinase activity. The similarity of these structures suggests that the receptor binding determinants for all three cytokines may be similar.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pandit, J -- Bohm, A -- Jancarik, J -- Halenbeck, R -- Koths, K -- Kim, S H -- New York, N.Y. -- Science. 1992 Nov 20;258(5086):1358-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1455231" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography ; Disulfides ; Granulocyte-Macrophage Colony-Stimulating Factor/ultrastructure ; Growth Hormone/chemistry ; Macrophage Colony-Stimulating Factor/*ultrastructure ; Models, Molecular ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/ultrastructure ; Sequence Homology, Amino Acid ; X-Ray Diffraction
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    Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease Eco RI (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-01-24
    Description: The c-Myc oncoprotein belongs to a family of proteins whose DNA binding domains contain a basic region-helix-loop-helix (bHLH) motif. Systematic mutagenesis of c-Myc revealed that dimerized bHLH motifs formed a parallel four-helix bundle with the amino termini of helices 1 and 2 directed toward the inner and outer nucleotides of the DNA binding site, respectively. Both the basic region and the carboxyl-terminal end of the loop contributed to DNA binding specificity. The DNA binding domain of c-Myc may therefore be structurally similar to that of restriction endonuclease Eco RI.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halazonetis, T D -- Kandil, A N -- New York, N.Y. -- Science. 1992 Jan 24;255(5043):464-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cancer Research, Merck Sharp and Dohme Research Laboratories, West Point, PA 19486.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1734524" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*chemistry ; Deoxyribonuclease EcoRI/*chemistry ; Humans ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Proto-Oncogene Proteins c-myc/*chemistry ; Sequence Alignment ; Transcription Factors/chemistry
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    Converting trypsin to chymotrypsin: the role of surface loops (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-03-06
    Description: Trypsin (Tr) and chymotrypsin (Ch) have similar tertiary structures, yet Tr cleaves peptides at arginine and lysine residues and Ch prefers large hydrophobic residues. Although replacement of the S1 binding site of Tr with the analogous residues of Ch is sufficient to transfer Ch specificity for ester hydrolysis, specificity for amide hydrolysis is not transferred. Trypsin is converted to a Ch-like protease when the binding pocket alterations are further modified by exchange of the Ch surface loops 185 through 188 and 221 through 225 for the analogous Tr loops. These loops are not structural components of either the S1 binding site or the extended substrate binding sites. This mutant enzyme is equivalent to Ch in its catalytic rate, but its substrate binding is impaired. Like Ch, this mutant utilizes extended substrate binding to accelerate catalysis, and substrate discrimination occurs during the acylation step rather than in substrate binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hedstrom, L -- Szilagyi, L -- Rutter, W J -- DK21344/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Mar 6;255(5049):1249-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hormone Research Institute, University of California, San Francisco 94143-0534.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1546324" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chymotrypsin/*chemistry/metabolism ; Hydrolysis ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Mutagenesis, Site-Directed ; Protein Conformation ; Substrate Specificity ; Trypsin/*chemistry/genetics/metabolism
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    Crystal structure of transforming growth factor-beta 2: an unusual fold for the superfamily (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-17
    Description: The transforming growth factors-beta (TGF-beta 1 through -beta 5) are a family of homodimeric cytokines that regulate proliferation and function in many cell types. Family members have 66 to 80% sequence identity and nine strictly conserved cysteines. A crystal structure of a member of this family, TGF-beta 2, has been determined at 2.1 angstrom (A) resolution and refined to an R factor of 0.172. The monomer lacks a well-defined hydrophobic core and displays an unusual elongated nonglobular fold with dimensions of approximately 60 A by 20 A by 15 A. Eight cysteines form four intrachain disulfide bonds, which are clustered in a core region forming a network complementary to the network of hydrogen bonds. The dimer is stabilized by the ninth cysteine, which forms an interchain disulfide bond, and by two identical hydrophobic interfaces. Sequence profile analysis of other members of the TGF-beta superfamily, including the activins, inhibins, and several developmental factors, imply that they also adopt the TGF-beta fold.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Daopin, S -- Piez, K A -- Ogawa, Y -- Davies, D R -- New York, N.Y. -- Science. 1992 Jul 17;257(5068):369-73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1631557" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography ; Drosophila ; Humans ; Mice ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Transforming Growth Factor beta/*chemistry ; Xenopus laevis
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    Tertiary structure around the guanosine-binding site of the Tetrahymena ribozyme (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-24
    Description: A cleavage reagent directed to the active site of the Tetrahymena catalytic RNA was synthesized by derivatization of the guanosine substrate with a metal chelator. When complexed with iron(II), this reagent cleaved the RNA in five regions. Cleavage at adenosine 207, which is far from the guanosine-binding site in the primary and secondary structure, provides a constraint for the higher order folding of the RNA. This cleavage site constitutes physical evidence for a key feature of the Michel-Westhof model. Targeting a reactive entity to a specific site should be generally useful for determining proximity within folded RNA molecules or ribonucleoprotein complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, J F -- Cech, T R -- New York, N.Y. -- Science. 1992 Apr 24;256(5056):526-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1315076" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Edetic Acid/metabolism ; Free Radicals ; Guanosine/*metabolism ; Guanosine Monophosphate/metabolism ; Iron/metabolism ; Iron Chelating Agents/metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Nucleic Acid Conformation ; Pentetic Acid/metabolism ; RNA, Catalytic/*chemistry/metabolism ; Tetrahymena/*chemistry
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    Electron-tunneling pathways in proteins (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-12-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beratan, D N -- Onuchic, J N -- Winkler, J R -- Gray, H B -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1740-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Pittsburgh, PA 15260.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1334572" target="_blank"〉PubMed〈/a〉
    Keywords: Cytochrome c Group/*chemistry/metabolism ; Cytochrome-c Peroxidase/*chemistry/metabolism ; *Electron Transport ; Models, Molecular ; Photosynthesis ; Protein Conformation ; Proteins/*chemistry ; Saccharomyces cerevisiae/metabolism ; X-Ray Diffraction
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    Human growth hormone and extracellular domain of its receptor: crystal structure of the complex (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-17
    Description: Binding of human growth hormone (hGH) to its receptor is required for regulation of normal human growth and development. Examination of the 2.8 angstrom crystal structure of the complex between the hormone and the extracellular domain of its receptor (hGHbp) showed that the complex consists of one molecule of growth hormone per two molecules of receptor. The hormone is a four-helix bundle with an unusual topology. The binding protein contains two distinct domains, similar in some respects to immunoglobulin domains. The relative orientation of these domains differs from that found between constant and variable domains in immunoglobulin Fab fragments. Both hGHbp domains contribute residues that participate in hGH binding. In the complex both receptors donate essentially the same residues to interact with the hormone, even though the two binding sites on hGH have no structural similarity. Generally, the hormone-receptor interfaces match those identified by previous mutational analyses. In addition to the hormone-receptor interfaces, there is also a substantial contact surface between the carboxyl-terminal domains of the receptors. The relative extents of the contact areas support a sequential mechanism for dimerization that may be crucial for signal transduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Vos, A M -- Ultsch, M -- Kossiakoff, A A -- New York, N.Y. -- Science. 1992 Jan 17;255(5042):306-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1549776" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography ; Growth Hormone/*chemistry/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Structure ; Mutation ; Receptors, Somatotropin/*chemistry/metabolism ; Signal Transduction
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    Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-10
    Description: Six "cavity-creating" mutants, Leu46----Ala (L46A), L99A, L118A, L121A, L133A, and Phe153----Ala (F153A), were constructed within the hydrophobic core of phage T4 lysozyme. The substitutions decreased the stability of the protein at pH 3.0 by different amounts, ranging from 2.7 kilocalories per mole (kcal mol-1) for L46A and L121A to 5.0 kcal mol-1 for L99A. The double mutant L99A/F153A was also constructed and decreased in stability by 8.3 kcal mol-1. The x-ray structures of all of the variants were determined at high resolution. In every case, removal of the wild-type side chain allowed some of the surrounding atoms to move toward the vacated space but a cavity always remained, which ranged in volume from 24 cubic angstroms (A3) for L46A to 150 A3 for L99A. No solvent molecules were observed in any of these cavities. The destabilization of the mutant Leu----Ala proteins relative to wild type can be approximated by a constant term (approximately 2.0 kcal mol-1) plus a term that increases in proportion to the size of the cavity. The constant term is approximately equal to the transfer free energy of leucine relative to alanine as determined from partitioning between aqueous and organic solvents. The energy term that increases with the size of the cavity can be expressed either in terms of the cavity volume (24 to 33 cal mol-1 A-3) or in terms of the cavity surface area (20 cal mol-1 A-2). The results suggest how to reconcile a number of conflicting reports concerning the strength of the hydrophobic effect in proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eriksson, A E -- Baase, W A -- Zhang, X J -- Heinz, D W -- Blaber, M -- Baldwin, E P -- Matthews, B W -- GM12989/GM/NIGMS NIH HHS/ -- GM13709/GM/NIGMS NIH HHS/ -- GM21967/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jan 10;255(5041):178-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, OR.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1553543" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calorimetry ; Models, Molecular ; Molecular Sequence Data ; Muramidase/*chemistry/*genetics ; Mutagenesis, Site-Directed ; Protein Conformation ; Structure-Activity Relationship ; T-Phages/enzymology/genetics ; Thermodynamics ; X-Ray Diffraction
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    An unlikely sugar substrate site in the 1.65 A structure of the human aldose reductase holoenzyme implicated in diabetic complications (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-03
    Description: Aldose reductase, which catalyzes the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a wide variety of aromatic and aliphatic carbonyl compounds, is implicated in the development of diabetic and galactosemic complications involving the lens, retina, nerves, and kidney. A 1.65 angstrom refined structure of a recombinant human placenta aldose reductase reveals that the enzyme contains a parallel beta 8/alpha 8-barrel motif and establishes a new motif for NADP-binding oxidoreductases. The substrate-binding site is located in a large, deep elliptical pocket at the COOH-terminal end of the beta barrel with a bound NADPH in an extended conformation. The highly hydrophobic nature of the active site pocket greatly favors aromatic and apolar substrates over highly polar monosaccharides. The structure should allow for the rational design of specific inhibitors that might provide molecular understanding of the catalytic mechanism, as well as possible therapeutic agents.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, D K -- Bohren, K M -- Gabbay, K H -- Quiocho, F A -- DK-39,044/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 3;257(5066):81-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1621098" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Reductase/*chemistry/metabolism ; Amino Acid Sequence ; Binding Sites ; *Diabetes Complications ; Diabetes Mellitus/*enzymology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; X-Ray Diffraction/methods
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    Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-12-11
    Description: The crystal structure of a 1:1 complex between yeast cytochrome c peroxidase and yeast iso-1-cytochrome c was determined at 2.3 A resolution. This structure reveals a possible electron transfer pathway unlike any previously proposed for this extensively studied redox pair. The shortest straight line between the two hemes closely follows the peroxidase backbone chain of residues Ala194, Ala193, Gly192, and finally Trp191, the indole ring of which is perpendicular to, and in van der Waals contact with, the peroxidase heme. The crystal structure at 2.8 A of a complex between yeast cytochrome c peroxidase and horse heart cytochrome c was also determined. Although crystals of the two complexes (one with cytochrome c from yeast and the other with cytochrome c from horse) grew under very different conditions and belong to different space groups, the two complex structures are closely similar, suggesting that cytochrome c interacts with its redox partners in a highly specific manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, H -- Kraut, J -- DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1748-55.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego, La Jolla 92093-0317.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1334573" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cytochrome c Group/*chemistry/metabolism ; Cytochrome-c Peroxidase/*chemistry/metabolism ; *Electron Transport ; Heme/metabolism ; Horses ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Saccharomyces cerevisiae/metabolism ; X-Ray Diffraction/methods
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    Toward a dynamical structure of DNA: comparison of theoretical and experimental NOE intensities (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-31
    Description: Comparisons of experimental and calculated interproton nuclear Overhauser effect (NOE) buildup curves for duplex d(CGCGAATTCGCG)2 have been made. The calculated NOEs are based on molecular dynamics simulations including counterions and water and on the single-structure canonical A, B, and crystal forms. The calculated NOE effects include consideration of the motions of individual interproton vectors and the anisotropic tumbling of the DNA. The effects due to inclusion of anisotropic tumbling are much larger than those due to the local motion, and both improve the agreement between calculated and experimental results. The predictions based on the dynamical models agree significantly better with experiment than those based on either of the canonical forms or the crystal structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Withka, J M -- Swaminathan, S -- Srinivasan, J -- Beveridge, D L -- Bolton, P H -- 1T32 GM-08271/GM/NIGMS NIH HHS/ -- GM-37909/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jan 31;255(5044):597-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemistry Department, Wesleyan University, Middletown, CT 06459.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1736362" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA/*chemistry ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry ; Time Factors
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    Emerging principles for the recognition of peptide antigens by MHC class I molecules (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-14
    Description: Class I major histocompatibility complex (MHC) molecules interact with self and foreign peptides of diverse amino acid sequences yet exhibit distinct allele-specific selectivity for peptide binding. The structures of the peptide-binding specificity pockets (subsites) in the groove of murine H-2Kb as well as human histocompatibility antigen class I molecules have been analyzed. Deep but highly conserved pockets at each end of the groove bind the amino and carboxyl termini of peptide through extensive hydrogen bonding and, hence, dictate the orientation of peptide binding. A deep polymorphic pocket in the middle of the groove provides the chemical and structural complementarity for one of the peptide's anchor residues, thereby playing a major role in allele-specific peptide binding. Although one or two shallow pockets in the groove may also interact with specific peptide side chains, their role in the selection of peptide is minor. Thus, usage of a limited number of both deep and shallow pockets in multiple combinations appears to allow the binding of a broad range of peptides. This binding occurs with high affinity, primarily because of extensive interactions with the peptide backbone and the conserved hydrogen bonding network at both termini of the peptide. Interactions between the anchor residue (or residues) and the corresponding allele-specific pocket provide sufficient extra binding affinity not only to enhance specificity but also to endure the presentation of the peptide at the cell surface for recognition by T cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsumura, M -- Fremont, D H -- Peterson, P A -- Wilson, I A -- CA-09523/CA/NCI NIH HHS/ -- CA-97489/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):927-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1323878" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens/chemistry/*metabolism ; Binding Sites ; H-2 Antigens/chemistry/*metabolism ; HLA-A2 Antigen/chemistry ; Histocompatibility Antigens Class I/chemistry/*metabolism ; Hydrogen Bonding ; Mice ; Models, Molecular ; Molecular Sequence Data ; Ovalbumin/chemistry/metabolism ; Peptide Fragments/chemistry/metabolism ; Peptides/chemistry/*metabolism ; Protein Conformation ; Solvents ; Vesicular stomatitis Indiana virus/metabolism ; Viral Proteins/chemistry/*metabolism
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    Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-03-20
    Description: The highly symmetric pyruvate dehydrogenase multienzyme complexes have molecular masses ranging from 5 to 10 million daltons. They consist of numerous copies of three different enzymes: pyruvate dehydrogenase, dihydrolipoyl transacetylase, and lipoamide dehydrogenase. The three-dimensional crystal structure of the catalytic domain of Azotobacter vinelandii dihydrolipoyl transacetylase has been determined at 2.6 angstrom (A) resolution. Eight trimers assemble as a hollow truncated cube with an edge of 125 A, forming the core of the multienzyme complex. Coenzyme A must enter the 29 A long active site channel from the inside of the cube, and lipoamide must enter from the outside. The trimer of the catalytic domain of dihydrolipoyl transacetylase has a topology identical to chloramphenicol acetyl transferase. The atomic structure of the 24-subunit cube core provides a framework for understanding all pyruvate dehydrogenase and related multienzyme complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mattevi, A -- Obmolova, G -- Schulze, E -- Kalk, K H -- Westphal, A H -- de Kok, A -- Hol, W G -- New York, N.Y. -- Science. 1992 Mar 20;255(5051):1544-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Groningen, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1549782" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Azotobacter vinelandii/enzymology ; Chloramphenicol O-Acetyltransferase/genetics ; Humans ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Pyruvate Dehydrogenase Complex/*chemistry/genetics ; Sequence Homology, Nucleic Acid
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    A conformation of cyclosporin A in aqueous environment revealed by the X-ray structure of a cyclosporin-Fab complex (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-03
    Description: The conformation of the immunosuppressive drug cyclosporin A (CsA) in a complex with a Fab molecule has been established by crystallographic analysis to 2.65 angstrom resolution. This conformation of CsA is similar to that recently observed in the complex with the rotamase cyclophilin, its binding protein in vivo, and totally different from its conformation in an isolated form as determined from x-ray and nuclear magnetic resonance analysis. Because the surfaces of CsA interacting with cyclophilin or with the Fab are not identical, these results suggest that the conformation of CsA observed in the bound form preexists in aqueous solution and is not produced by interaction with the proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Altschuh, D -- Vix, O -- Rees, B -- Thierry, J C -- New York, N.Y. -- Science. 1992 Apr 3;256(5053):92-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1566062" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Isomerases/chemistry/metabolism ; Amino Acid Sequence ; Carrier Proteins/chemistry/metabolism ; Cyclosporine/*chemistry/immunology/metabolism ; Immunoglobulin Fab Fragments/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Peptidylprolyl Isomerase ; Protein Binding ; Protein Conformation ; Solutions ; X-Ray Diffraction/methods
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    Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-06-26
    Description: A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of AIDS, reveals an asymmetric dimer. The polymerase (pol) domain of the 66-kilodalton subunit has a large cleft analogous to that of the Klenow fragment of Escherichia coli DNA polymerase I. However, the 51-kilodalton subunit of identical sequence has no such cleft because the four subdomains of the pol domain occupy completely different relative positions. Two of the four pol subdomains appear to be structurally related to subdomains of the Klenow fragment, including one containing the catalytic site. The subdomain that appears likely to bind the template strand at the pol active site has a different structure in the two polymerases. Duplex A-form RNA-DNA hybrid can be model-built into the cleft that runs between the ribonuclease H and pol active sites. Nevirapine is almost completely buried in a pocket near but not overlapping with the pol active site. Residues whose mutation results in drug resistance have been approximately located.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kohlstaedt, L A -- Wang, J -- Friedman, J M -- Rice, P A -- Steitz, T A -- GM 39546/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jun 26;256(5065):1783-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1377403" target="_blank"〉PubMed〈/a〉
    Keywords: Azepines/pharmacology ; Binding Sites ; Crystallography ; DNA Polymerase I/chemistry ; Escherichia coli/genetics ; HIV-1/*enzymology ; Models, Molecular ; Molecular Structure ; Nevirapine ; Protein Conformation ; Pyridines/pharmacology ; RNA-Directed DNA Polymerase/*chemistry
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    Beta ribbon: a new DNA recognition motif (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-03-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, S H -- New York, N.Y. -- Science. 1992 Mar 6;255(5049):1217-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1546321" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; DNA/*chemistry/metabolism ; Models, Molecular ; Molecular Structure ; *Nucleic Acid Conformation
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  • 75
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    Internal stark effect measurement of the electric field at the amino terminus of an alpha helix (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-14
    Description: The strengths of electrostatic interactions in biological molecules are difficult to calculate or predict because they occur in complicated, inhomogeneous environments. The electric field at the amino terminus of an alpha helix in water has been determined by measuring the shift in the absorption band for a covalently attached, neutral probe molecule with an electric dipole moment difference between the ground and excited electronic states (an internal Stark effect). The field at the interface between the helix and the solvent is found to be an order of magnitude stronger than expected from the dielectric properties of bulk water. Furthermore, although the total electric dipole moment of the helix increases with length, the electric field at the amino terminus does not.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lockhart, D J -- Kim, P S -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):947-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1502559" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/*chemistry ; Electrochemistry ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemistry ; *Protein Conformation ; Proteins/*chemistry ; Spectrophotometry, Ultraviolet ; Water
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    Constructing proteins by dovetailing unprotected synthetic peptides: backbone-engineered HIV protease (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-10
    Description: Backbone-engineered HIV-1 protease was prepared by a total chemical synthesis approach that combines the act of joining two peptides with the generation of an analog structure. Unprotected synthetic peptide segments corresponding to the two halves of the HIV-1 protease monomer polypeptide chain were joined cleanly and in high yield through unique mutually reactive functional groups, one on each segment. Ligation was performed in 6 molar guanidine hydrochloride, thus circumventing limited solubility of protected peptide segments, the principal problem of the classical approach to the chemical synthesis of proteins. The resulting fully active HIV-1 protease analog contained a thioester replacement for the natural peptide bond between Gly51-Gly52 in each of the two active site flaps, a region known to be highly sensitive to mutational changes of amino acid side chains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schnolzer, M -- Kent, S B -- New York, N.Y. -- Science. 1992 Apr 10;256(5054):221-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1566069" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Guanidine ; Guanidines ; HIV Protease/*chemical synthesis/metabolism ; HIV-1/*enzymology ; Indicators and Reagents ; Mass Spectrometry ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemical synthesis ; Protein Conformation
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    Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-14
    Description: Joint refinement of macromolecules against crystallographic and nuclear magnetic resonance (NMR) observations is presented as a way of combining experimental information from the two methods. The model of interleukin-1 beta derived by the joint x-ray and NMR refinement is shown to be consistent with the experimental observations of both methods and to have crystallographic R value and geometrical parameters that are of the same quality as or better than those of models obtained by conventional crystallographic studies. The few NMR observations that are violated by the model serve as an indicator for genuine differences between the crystal and solution structures. The joint x-ray-NMR refinement can resolve structural ambiguities encountered in studies of multidomain proteins, in which low- to medium-resolution diffraction data can be complemented by higher resolution NMR data obtained for the individual domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaanan, B -- Gronenborn, A M -- Cohen, G H -- Gilliland, G L -- Veerapandian, B -- Davies, D R -- Clore, G M -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laborator of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1502561" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Interleukin-1/*chemistry ; Magnetic Resonance Spectroscopy/*methods ; Models, Molecular ; *Protein Conformation ; Proteins/*chemistry ; X-Ray Diffraction/*methods
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    Molecular code for cooperativity in hemoglobin (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-01-03
    Description: Although tetrameric hemoglobin has been studied extensively as a prototype for understanding mechanisms of allosteric regulation, the functional and structural properties of its eight intermediate ligation forms have remained elusive. Recent experiments on the energetics of cooperativity of these intermediates, along with assignments of their quaternary structures, have revealed that the allosteric mechanism is controlled by a previously unrecognized symmetry feature: quaternary switching from form T to form R occurs whenever heme-site binding creates a tetramer with at least one ligated subunit on each dimeric half-molecule. This "symmetry rule" translates the configurational isomers of heme-site ligation into six observed switchpoints of quaternary transition. Cooperativity arises from both "concerted" quaternary switching and "sequential" modulation of binding within each quaternary form, T and R. Binding affinity is regulated through a hierarchical code of tertiary-quaternary coupling that includes the classical allosteric models as limiting cases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ackers, G K -- Doyle, M L -- Myers, D -- Daugherty, M A -- P01-HL40453/HL/NHLBI NIH HHS/ -- R37-GM24486/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jan 3;255(5040):54-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1553532" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Calorimetry ; Circular Dichroism ; Hemoglobins/*chemistry/genetics/metabolism ; Kinetics ; Ligands ; Macromolecular Substances ; Models, Molecular ; Mutation ; Oxyhemoglobins/chemistry/metabolism ; Protein Conformation ; Thermodynamics
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    Structural basis of the intrasteric regulation of myosin light chain kinases (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-10-02
    Description: The smooth muscle myosin light chain kinase (smMLCK) catalytic core was modeled by using the crystallographic coordinates of the cyclic AMP-dependent protein kinase catalytic subunit (cAPK) and a bound pseudosubstrate inhibitor peptide, PKI(5-24). Despite only 30% identity in amino acid sequence, the MLCK sequence can be readily accommodated in this structure. With the exception of the short B-helix, all major elements of secondary structure in the core are very likely conserved. The active site of the modeled MLCK complements the known requirements for peptide substrate recognition. MLCK contains a pseudosubstrate sequence that overlaps the calmodulin binding domain and has been proposed to act as an intrasteric inhibitor and occupy the substrate binding site in the absence of Ca(2+)-calmodulin. The pseudosubstrate sequence can be modeled easily into the entire backbone of PKI(5-24). The results demonstrate that the intrasteric model for regulation of MLCK by intramolecular competitive inhibition is structurally plausible.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knighton, D R -- Pearson, R B -- Sowadski, J M -- Means, A R -- Ten Eyck, L F -- Taylor, S S -- Kemp, B E -- T32CA09523/CA/NCI NIH HHS/ -- T32DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Oct 2;258(5079):130-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California San Diego, La Jolla 92093-0654.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1439761" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chromosome Mapping ; Crystallography ; *Gene Expression Regulation, Enzymologic ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Myosin-Light-Chain Kinase/*chemistry ; Oligopeptides/genetics/metabolism ; Peptide Fragments ; Peptides/genetics/metabolism ; Protein Binding/physiology ; Protein Kinases/chemistry ; Sequence Alignment ; Sequence Homology
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  • 80
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    Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected] (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-06-05
    Description: The D and L forms of the enzyme HIV-1 protease have been prepared by total chemical synthesis. The two proteins had identical covalent structures. However, the folded protein-enzyme enantiomers showed reciprocal chiral specificity on peptide substrates. That is, each enzyme enantiomer cut only the corresponding substrate enantiomer. Reciprocal chiral specificity was also evident in the effect of enantiomeric inhibitors. These data imply that the folded forms of the chemically synthesized D- and L-enzyme molecules are mirror images of one another in all elements of the three-dimensional structure. Enantiomeric proteins are expected to display reciprocal chiral specificity in all aspects of their biochemical interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Milton, R C -- Milton, S C -- Kent, S B -- New York, N.Y. -- Science. 1992 Jun 5;256(5062):1445-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1604320" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Amino Acids ; HIV Protease/chemical synthesis/*chemistry/*metabolism ; Kinetics ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Oligopeptides/pharmacology ; Protein Conformation ; Stereoisomerism ; Substrate Specificity ; X-Ray Diffraction
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  • 81
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    Evidence that eukaryotes and eocyte prokaryotes are immediate relatives (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-03
    Description: The phylogenetic origin of eukaryotes has been unclear because eukaryotic nuclear genes have diverged substantially from prokaryotic ones. The genes coding for elongation factor EF-1 alpha were compared among various organisms. The EF-1 alpha sequences of eukaryotes contained an 11-amino acid segment that was also found in eocytes (extremely thermophilic, sulfur-metabolizing bacteria) but that was absent in all other bacteria. The related (paralogous) genes encoding elongation factor EF-2 and initiation factor IF-2 also lacked the 11-amino acid insert. These data imply that the eocytes are the closest surviving relatives (sister taxon) of the eukaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rivera, M C -- Lake, J A -- New York, N.Y. -- Science. 1992 Jul 3;257(5066):74-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biology Institute, University of California, Los Angeles 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1621096" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteria/*genetics ; Base Sequence ; *Biological Evolution ; DNA, Bacterial/genetics ; Humans ; Models, Molecular ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/chemistry/*genetics ; Peptide Elongation Factors/*genetics ; Peptide Initiation Factors/*genetics ; Phylogeny ; Plants/genetics ; Prokaryotic Initiation Factor-2 ; Protein Conformation ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Nucleic Acid
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  • 82
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    Biology approaches the teraflop era (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stone, R -- New York, N.Y. -- Science. 1992 Apr 24;256(5056):440-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1570506" target="_blank"〉PubMed〈/a〉
    Keywords: *Biology ; *Computers ; Drug Design ; Models, Molecular ; Proteins/chemistry ; Software ; Technology, Pharmaceutical
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  • 83
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    Conformation of the TAR RNA-arginine complex by NMR spectroscopy (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-03
    Description: The messenger RNAs of human immunodeficiency virus-1 (HIV-1) have an RNA hairpin structure, TAR, at their 5' ends that contains a six-nucleotide loop and a three-nucleotide bulge. The conformations of TAR RNA and of TAR with an arginine analog specifically bound at the binding site for the viral protein, Tat, were characterized by nuclear magnetic resonance (NMR) spectroscopy. Upon arginine binding, the bulge changes conformation, and essential nucleotides for binding, U23 and A27.U38, form a base-triple interaction that stabilizes arginine hydrogen bonding to G26 and phosphates. Specificity in the arginine-TAR interaction appears to be derived largely from the structure of the RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Puglisi, J D -- Tan, R -- Calnan, B J -- Frankel, A D -- Williamson, J R -- AI29135/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 3;257(5066):76-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1621097" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/*metabolism ; Base Sequence ; Binding Sites ; Gene Products, tat/metabolism ; HIV-1/*genetics ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Messenger/*chemistry/metabolism ; RNA, Viral/*chemistry/metabolism ; RNA-Binding Proteins/*chemistry/metabolism ; tat Gene Products, Human Immunodeficiency Virus
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  • 84
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    Molecular characterization of helix-loop-helix peptides (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-02-21
    Description: A class of regulators of eukaryotic gene expression contains a conserved amino acid sequence responsible for protein oligomerization and binding to DNA. This structure consists of an arginine- and lysine-rich basic region followed by a helix-loop-helix motif, which together mediate specific binding to DNA. Peptides were prepared that span this motif in the MyoD protein; in solution, they formed alpha-helical dimers and tetramers. They bound to DNA as dimers and their alpha-helical content increased on binding. Parallel and antiparallel four-helix models of the DNA-bound dimer were constructed. Peptides containing disulfide bonds were engineered to test the correctness of the two models. A disulfide that is compatible with the parallel model promotes specific interaction with DNA, whereas a disulfide compatible with the antiparallel model abolishes specific binding. Electron paramagnetic resonance (EPR) measurements of nitroxide-labeled peptides provided intersubunit distance measurements that also supported the parallel model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anthony-Cahill, S J -- Benfield, P A -- Fairman, R -- Wasserman, Z R -- Brenner, S L -- Stafford, W F 3rd -- Altenbach, C -- Hubbell, W L -- DeGrado, W F -- GM13731/GM/NIGMS NIH HHS/ -- GM14321/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Feb 21;255(5047):979-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnology Department, DuPont Merck Pharmaceutical Co., Wilmington, DE 19880-0328.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1312255" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Circular Dichroism ; DNA-Binding Proteins/*chemistry ; Disulfides ; Electron Spin Resonance Spectroscopy ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Regulatory Sequences, Nucleic Acid ; Sequence Alignment ; Transcription Factors/*chemistry
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  • 85
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    Structural evidence for induced fit as a mechanism for antibody-antigen recognition (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-02-21
    Description: The three-dimensional structure of a specific antibody (Fab 17/9) to a peptide immunogen from influenza virus hemagglutinin [HA1(75-110)] and two independent crystal complexes of this antibody with bound peptide (TyrP100-LeuP108) have been determined by x-ray crystallographic techniques at 2.0 A, 2.9 A, and 3.1 A resolution, respectively. The nonapeptide antigen assumes a type I beta turn in the antibody combining site and interacts primarily with the Fab hypervariable loops L3, H2, and H3. Comparison of the bound and unbound Fab structures shows that a major rearrangement in the H3 loop accompanies antigen binding. This conformational change results in the creation of a binding pocket for the beta turn of the peptide, allowing TyrP105 to be accommodated. The conformation of the peptide bound to the antibody shows similarity to its cognate sequence in the HA1, suggesting a possible mechanism for the cross-reactivity of this Fab with monomeric hemagglutinin. The structures of the free and antigen bound antibodies demonstrate the flexibility of the antibody combining site and provide an example of induced fit as a mechanism for antibody-antigen recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rini, J M -- Schulze-Gahmen, U -- Wilson, I A -- AI-23498/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1992 Feb 21;255(5047):959-65.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1546293" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/ultrastructure ; *Antigen-Antibody Reactions ; Hemagglutinins, Viral/*immunology ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/*ultrastructure ; Immunoglobulin G/ultrastructure ; In Vitro Techniques ; Influenza A virus/immunology ; Mice ; Models, Molecular ; Molecular Sequence Data ; Motion ; Peptides/chemistry/immunology ; Protein Binding ; Protein Conformation ; X-Ray Diffraction
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  • 86
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    Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-08-28
    Description: The crystal structure of calcium-bound calmodulin (Ca(2+)-CaM) bound to a peptide analog of the CaM-binding region of chicken smooth muscle myosin light chain kinase has been determined and refined to a resolution of 2.4 angstroms (A). The structure is compact and has the shape of an ellipsoid (axial ratio approximately 2:1). The bound CaM forms a tunnel diagonal to its long axis that engulfs the helical peptide, with the hydrophobic regions of CaM melded into a single area that closely covers the hydrophobic side of the peptide. There is a remarkably high pseudo-twofold symmetry between the closely associated domains. The central helix of the native CaM is unwound and expanded into a bend between residues 73 and 77. About 185 contacts (less than 4 A) are formed between CaM and the peptide, with van der Waals contacts comprising approximately 80% of this total.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meador, W E -- Means, A R -- Quiocho, F A -- New York, N.Y. -- Science. 1992 Aug 28;257(5074):1251-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1519061" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calmodulin/*chemistry ; Crystallography ; Models, Molecular ; Molecular Sequence Data ; Myosin-Light-Chain Kinase/*metabolism ; Protein Conformation
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  • 87
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    Three-dimensional structure of an angiotensin II-Fab complex at 3 A: hormone recognition by an anti-idiotypic antibody (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-07-24
    Description: The elucidation of bioactive conformations of small peptide hormones remains an elusive goal to structural chemists because of the inherent flexibility of these molecules. Angiotensin II (AII), the major effector of the renin-angiotensin system, is an octapeptide hormone for which no clear structural models exist. Peptide hormones such as AII share the property that they bind to their receptors with high affinities, in spite of the fact that they must overcome an extremely large conformational entropy barrier to bind in one conformation. A "surrogate system" that consists of a high-affinity monoclonal antibody (MAb) and AII has been used to study a bound conformation of AII. The crystallographic structure of the complex reveals a structure of AII that is compatible with predicted bioactive conformations of AII derived from structure-activity studies and theoretical calculations. In the complex, the deeply bound hormone is folded into a compact structure in which two turns bring the amino and carboxyl termini close together. The antibody of this complex (MAb 131) has the unusual property that it was not generated against AII, but rather against an anti-idiotypic antibody reactive with a MAb to AII, which renders this antibody an anti-anti-idiotypic antibody. The high affinity for AII of the original MAb to AII was passed on to MAb 131 through a structural determinant on the anti-idiotypic antibody. Strikingly, the conformation of AII in this complex is highly similar to complementarity determining region loops of antibodies, possibly indicating that a true molecular mimic of bound AII was present on the anti-idiotypic antibody against which MAb 131 was elicited.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Ronco, P M -- Verroust, P J -- Brunger, A T -- Amzel, L M -- GM44692/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Jul 24;257(5069):502-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1636085" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Angiotensin II/*chemistry/immunology/metabolism ; Animals ; Antibodies, Anti-Idiotypic/*chemistry/metabolism ; Antibodies, Monoclonal/*chemistry/metabolism ; Antigen-Antibody Complex ; Humans ; Immunoglobulin Fab Fragments/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; X-Ray Diffraction
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  • 88
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    Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: The x-ray structures of a murine MHC class I molecule (H-2Kb) were determined in complex with two different viral peptides, derived from the vesicular stomatitis virus nucleoprotein (52-59), VSV-8, and the Sendai virus nucleoprotein (324-332), SEV-9. The H-2Kb complexes were refined at 2.3 A for VSV-8 and 2.5 A for SEV-9. The structure of H-2Kb exhibits a high degree of similarity with human HLA class I, although the individual domains can have slightly altered dispositions. Both peptides bind in extended conformations with most of their surfaces buried in the H-2Kb binding groove. The nonamer peptide maintains the same amino- and carboxyl-terminal interactions as the octamer primarily by the insertion of a bulge in the center of an otherwise beta conformation. Most of the specific interactions are between side-chain atoms of H-2Kb and main-chain atoms of peptide. This binding scheme accounts in large part for the enormous diversity of peptide sequences that bind with high affinity to class I molecules. Small but significant conformational changes in H-2Kb are associated with peptide binding, and these synergistic movements may be an integral part of the T cell receptor recognition process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fremont, D H -- Matsumura, M -- Stura, E A -- Peterson, P A -- Wilson, I A -- CA-09523/CA/NCI NIH HHS/ -- CA-97489/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):919-27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1323877" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; H-2 Antigens/*chemistry/metabolism ; Mice ; Models, Molecular ; Molecular Sequence Data ; Parainfluenza Virus 1, Human/metabolism ; Protein Binding ; Protein Conformation ; Solvents ; Vesicular stomatitis Indiana virus/metabolism ; Viral Proteins/*chemistry/metabolism ; X-Ray Diffraction
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  • 89
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    Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III (1992)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1992-10-16
    Description: The crystal structure of the DNA repair enzyme endonuclease III, which recognizes and cleaves DNA at damaged bases, has been solved to 2.0 angstrom resolution with an R factor of 0.185. This iron-sulfur [4Fe-4S] enzyme is elongated and bilobal with a deep cleft separating two similarly sized domains: a novel, sequence-continuous, six-helix domain (residues 22 to 132) and a Greek-key, four-helix domain formed by the amino-terminal and three carboxyl-terminal helices (residues 1 to 21 and 133 to 211) together with the [4Fe-4S] cluster. The cluster is bound entirely within the carboxyl-terminal loop with a ligation pattern (Cys-X6-Cys-X2-Cys-X5-Cys) distinct from all other known [4Fe-4S] proteins. Sequence conservation and the positive electrostatic potential of conserved regions identify a surface suitable for binding duplex B-DNA across the long axis of the enzyme, matching a 46 angstrom length of protected DNA. The primary role of the [4Fe-4S] cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone. The crystallographically identified inhibitor binding region, which recognizes the damaged base thymine glycol, is a seven-residue beta-hairpin (residues 113 to 119). Location and side chain orientation at the base of the inhibitor binding site implicate Glu112 in the N-glycosylase mechanism and Lys120 in the beta-elimination mechanism. Overall, the structure reveals an unusual fold and a new biological function for [4Fe-4S] clusters and provides a structural basis for studying recognition of damaged DNA and the N-glycosylase and apurinic/apyrimidinic-lyase mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuo, C F -- McRee, D E -- Fisher, C L -- O'Handley, S F -- Cunningham, R P -- Tainer, J A -- GM 46312/GM/NIGMS NIH HHS/ -- HL07695/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1992 Oct 16;258(5081):434-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1411536" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/ultrastructure ; Base Sequence ; Crystallography ; Cysteine/chemistry ; *DNA Repair ; DNA-Binding Proteins/*ultrastructure ; Deoxyribonuclease (Pyrimidine Dimer) ; Endodeoxyribonucleases/*ultrastructure ; Iron-Sulfur Proteins/*ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Oligodeoxyribonucleotides/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; X-Ray Diffraction
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  • 90
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    A critical role for conserved residues in the cleft of HLA-A2 in presentation of a nonapeptide to T cells (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: The peptide binding cleft of the class I human histocompatibility antigen, HLA-A2, contains conserved amino acid residues clustered in the two ends of the cleft in pockets A and F as well as polymorphic residues. The function of two conserved tyrosines in the A pocket was investigated by mutating them to phenylalanines and of a conserved tyrosine and threonine in the F pocket by mutating them to phenylalanine and valine, respectively. Presentation of influenza virus peptides and of intact virus to cytolytic T lymphocytes (CTLs) was then examined. The magnitude of the reduction seen by the mutation of the two tyrosines in the A pocket suggests that hydrogen bonds involving them have a critical function in the binding of the NH2-terminal NH3+ of the peptide nonamer and possibly of all bound peptide nonamers. In contrast, the mutations in the F pocket had no effect on CTL recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Latron, F -- Pazmany, L -- Morrison, J -- Moots, R -- Saper, M A -- McMichael, A -- Strominger, J L -- AI 20182/AI/NIAID NIH HHS/ -- CA 47554/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):964-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1380181" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; B-Lymphocytes/immunology ; Binding Sites ; Cell Line ; Cloning, Molecular ; Epitopes/immunology/metabolism ; HLA-A2 Antigen/chemistry/genetics/*metabolism ; Influenza A virus ; Kinetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Oligopeptides/immunology/*metabolism ; Protein Conformation ; Recombinant Proteins/chemistry/metabolism ; T-Lymphocytes, Cytotoxic/*immunology ; Transfection ; Viral Proteins/metabolism
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  • 91
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    Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-11-06
    Description: Fibronectin type III domains are found in many different proteins including cell surface receptors and cell adhesion molecules. The crystal structure of one such domain from the extracellular matrix protein tenascin was determined. The structure was solved by multiwavelength anomalous diffraction (MAD) phasing of the selenomethionyl protein and has been refined to 1.8 angstrom resolution. The folding topology of this domain is identical to that of the extracellular domains of the human growth hormone receptor, the second domain of CD4, and PapD. Although distinct, this topology is similar to that of immunoglobulin constant domains. An Arg-Gly-Asp (RGD) sequence that can function for cell adhesion is found in a tight turn on an exposed loop.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leahy, D J -- Hendrickson, W A -- Aukhil, I -- Erickson, H P -- CA-47056/CA/NCI NIH HHS/ -- DE-07801/DE/NIDCR NIH HHS/ -- GM-34102/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Nov 6;258(5084):987-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1279805" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cell Adhesion Molecules, Neuronal/*chemistry ; Chickens ; Crystallization ; Escherichia coli/genetics ; Extracellular Matrix Proteins/*chemistry ; Fibronectins/*chemistry ; Humans ; Immunoglobulin Constant Regions/chemistry ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein Folding ; Protein Structure, Secondary ; Receptors, Somatotropin/chemistry ; Recombinant Proteins/chemistry ; Tenascin ; *X-Ray Diffraction
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  • 92
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    Rational design of potent antagonists to the human growth hormone receptor (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-06-19
    Description: A hybrid receptor was constructed that contained the extracellular binding domain of the human growth hormone (hGH) receptor linked to the transmembrane and intracellular domains of the murine granulocyte colony-stimulating factor receptor. Addition of hGH to a myeloid leukemia cell line (FDC-P1) that expressed the hybrid receptor caused proliferation of these cells. The mechanism for signal transduction of the hybrid receptor required dimerization because monoclonal antibodies to the hGH receptor were agonists whereas their monovalent fragments were not. Receptor dimerization occurs sequentially--a receptor binds to site 1 on hGH, and then a second receptor molecule binds to site 2 on hGH. On the basis of this sequential mechanism, which may occur in many other cytokine receptors, inactive hGH analogs were designed that were potent antagonists to hGH-induced cell proliferation. Such antagonists could be useful for treating clinical conditions of hGH excess, such as acromegaly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fuh, G -- Cunningham, B C -- Fukunaga, R -- Nagata, S -- Goeddel, D V -- Wells, J A -- New York, N.Y. -- Science. 1992 Jun 19;256(5064):1677-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1535167" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Monoclonal ; Cell Division/drug effects ; Cell Line ; DNA Replication/drug effects ; Dose-Response Relationship, Drug ; Growth Hormone/analysis/physiology ; Humans ; Models, Molecular ; Receptors, Granulocyte Colony-Stimulating Factor/physiology ; Receptors, Somatotropin/*physiology ; Signal Transduction/physiology ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 93
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    Recognition of angiotensin II: antibodies at different levels of an idiotypic network are superimposable (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-24
    Description: Genetic and sequence information are reported for an angiotensin II-reactive antibody (Ab1, MAb 110) and an anti--anti-idiotypic antibody (Ab3, MAb 131) that have identical antigen binding properties and that are related by an anti-idiotypic antibody (Ab2-beta) that satisfies accepted biochemical criteria for an internal image-bearing antibody. The sequences of the variable regions of the Ab3 and of the Ab1 are nearly identical, even though the Ab1 is an antibody to a peptide and the Ab3 is an antibody to a globular protein. Significantly, amino acid residues that make critical contacts with antigen in the crystal structure of the Ab3-antigen complex are highly conserved in Ab1, suggesting that the epitopes of the Ab2-beta recognized by the Ab3 do indeed resemble the bound structure of the antigen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Desiderio, S V -- Ronco, P M -- Verroust, P J -- Amzel, L M -- 6M 44692/PHS HHS/ -- New York, N.Y. -- Science. 1992 Jul 24;257(5069):528-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University Medical School, Baltimore, MD 21205.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1636087" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Angiotensin II/chemistry/*immunology ; Animals ; Antibodies, Anti-Idiotypic/chemistry/genetics/*immunology ; Antibodies, Monoclonal/chemistry/genetics/*immunology ; Antigen-Antibody Complex ; Base Sequence ; Cell Line ; Hybridomas/immunology ; Immunoglobulin Heavy Chains/genetics/immunology ; Immunoglobulin Light Chains/genetics/immunology ; Immunoglobulin Variable Region/chemistry/genetics/immunology ; Mice ; Mice, Inbred BALB C/immunology ; Models, Molecular ; Molecular Sequence Data ; Plasmacytoma ; Protein Conformation
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 94
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    Researchers get a first look at the versatile TGF-beta family (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hoffman, M -- New York, N.Y. -- Science. 1992 Jul 17;257(5068):332.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1631555" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography ; Humans ; Models, Molecular ; Molecular Structure ; Transforming Growth Factor beta/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 95
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    The role of crystal polarity in alpha-amino acid crystals for induced nucleation of ice (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-05-08
    Description: The hydrophobic faces of single crystals of a series of pairs of racemic and chiral-resolved hydrophobic alpha-amino acids were used as a substrate, onto which water vapor has been cooled to freezing. The morphologies and molecular packing arrangements within each crystal pair are similar but only one of each pair exhibits a polar axis, parallel to the hydrophobic face exposed to water. Those crystals that have a polar axis induce a freezing point higher by 4 degrees to 5 degrees C than the corresponding crystals that do not have a polar axis. The results are interpreted in terms of an electric field mechanism that helps align the water molecules into ice-like clusters en route to crystallization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gavish, M -- Wang, J L -- Eisenstein, M -- Lahav, M -- Leiserowitz, L -- New York, N.Y. -- Science. 1992 May 8;256(5058):815-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials and Inferfaces, Weizmann Institute of Science, Rehovot, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1589763" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/*chemistry ; Animals ; Crystallization ; *Ice ; Isomerism ; Models, Molecular
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
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    Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S] (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-12-04
    Description: Phthalate dioxygenase reductase (PDR) is a prototypical iron-sulfur flavoprotein (36 kilodaltons) that utilizes flavin mononucleotide (FMN) to mediate electron transfer from the two-electron donor, reduced nicotinamide adenine nucleotide (NADH), to the one-electron acceptor, [2Fe-2S]. The crystal structure of oxidized PDR from Pseudomonas cepacia has been analyzed at 2.0 angstrom resolution resolution; reduced PDR and pyridine nucleotide complexes have been analyzed at 2.7 angstrom resolution. NADH, FMN, and the [2Fe-2S] cluster, bound to distinct domains, are brought together near a central cleft in the molecule, with only 4.9 angstroms separating the flavin 8-methyl and a cysteine sulfur ligated to iron. The domains that bind FMN and [2Fe-2S] are packed so that the flavin ring and the plane of the [2Fe-2S] core are approximately perpendicular. The [2Fe-2S] group is bound by four cysteines in a site resembling that in plant ferredoxins, but its redox potential (-174 millivolts at pH 7.0) is much higher than the potentials of plant ferredoxins. Structural and sequence similarities assign PDR to a distinct family of flavoprotein reductases, all related to ferredoxin NADP(+)-reductase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Correll, C C -- Batie, C J -- Ballou, D P -- Ludwig, M L -- GM 16429/GM/NIGMS NIH HHS/ -- GM 20877/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Dec 4;258(5088):1604-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Biophysics, University of Michigan, Ann Arbor 48109.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1280857" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Burkholderia cepacia/enzymology ; Electron Transport ; Flavin Mononucleotide/*metabolism ; Iron-Sulfur Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; NAD/*metabolism ; Oxidoreductases/*chemistry/metabolism ; *Protein Conformation ; *Protein Structure, Secondary ; Sequence Homology, Amino Acid
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  • 97
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    Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-09-18
    Description: The nitrogenase enzyme system catalyzes the ATP (adenosine triphosphate)-dependent reduction of dinitrogen to ammonia during the process of nitrogen fixation. Nitrogenase consists of two proteins: the iron (Fe)-protein, which couples hydrolysis of ATP to electron transfer, and the molybdenum-iron (MoFe)-protein, which contains the dinitrogen binding site. In order to address the role of ATP in nitrogen fixation, the crystal structure of the nitrogenase Fe-protein from Azotobacter vinelandii has been determined at 2.9 angstrom (A) resolution. Fe-protein is a dimer of two identical subunits that coordinate a single 4Fe:4S cluster. Each subunit folds as a single alpha/beta type domain, which together symmetrically ligate the surface exposed 4Fe:4S cluster through two cysteines from each subunit. A single bound ADP (adenosine diphosphate) molecule is located in the interface region between the two subunits. Because the phosphate groups of this nucleotide are approximately 20 A from the 4Fe:4S cluster, it is unlikely that ATP hydrolysis and electron transfer are directly coupled. Instead, it appears that interactions between the nucleotide and cluster sites must be indirectly coupled by allosteric changes occurring at the subunit interface. The coupling between protein conformation and nucleotide hydrolysis in Fe-protein exhibits general similarities to the H-Ras p21 and recA proteins that have been recently characterized structurally. The Fe-protein structure may be relevant to the functioning of other biochemical energy-transducing systems containing two nucleotide-binding sites, including membrane transport proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Georgiadis, M M -- Komiya, H -- Chakrabarti, P -- Woo, D -- Kornuc, J J -- Rees, D C -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Sep 18;257(5077):1653-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Columbia University, New York, NY 10032.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1529353" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism/pharmacology ; Amino Acid Sequence ; Azotobacter vinelandii/*enzymology ; Binding Sites ; Chemistry, Physical ; Crystallization ; Electron Transport ; Hydrolysis ; Iron-Sulfur Proteins/*chemistry ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Molybdoferredoxin/chemistry ; Nitrogenase/*chemistry/metabolism ; Physicochemical Phenomena ; Protein Conformation ; X-Ray Diffraction
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
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    Getting some "backbone": how MHC binds peptides (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barinaga, M -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):880-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1502554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Histocompatibility Antigens Class I/*chemistry/metabolism ; Humans ; Hydrogen Bonding ; Major Histocompatibility Complex ; Models, Molecular ; Protein Binding ; Protein Conformation ; Proteins/chemistry/metabolism ; T-Lymphocytes/immunology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
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    The disulfide folding pathway of BPTI (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Creighton, T E -- New York, N.Y. -- Science. 1992 Apr 3;256(5053):111-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1373519" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Aprotinin/*chemistry ; Cattle ; *Cysteine ; *Disulfides ; Kinetics ; Models, Molecular ; Protein Conformation
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 100
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    NMR determination of residual structure in a urea-denatured protein, the 434-repressor (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-09-11
    Description: A nuclear magnetic resonance (NMR) structure determination is reported for the polypeptide chain of a globular protein in strongly denaturing solution. Nuclear Overhauser effect (NOE) measurements with a 7 molar urea solution of the amino-terminal 63-residue domain of the 434-repressor and distance geometry calculations showed that the polypeptide segment 54 to 59 forms a hydrophobic cluster containing the side chains of Val54, Val56, Trp58, and Leu59. This residual structure in the urea-unfolded protein is related to the corresponding region of the native, folded protein by simple rearrangements of the residues 58 to 60. Based on these observations a model for the early phase of refolding of the 434-repressor(1-63) is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neri, D -- Billeter, M -- Wider, G -- Wuthrich, K -- New York, N.Y. -- Science. 1992 Sep 11;257(5076):1559-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Molekularbiologie und Biophysik, ETH-Honggerberg, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1523410" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Denaturation ; Repressor Proteins/*chemistry/pharmacology ; Urea/*pharmacology ; Viral Proteins
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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