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  • Protein Conformation  (136)
  • American Association for the Advancement of Science (AAAS)  (136)
  • American Association of Petroleum Geologists (AAPG)
  • 1985-1989  (136)
Collection
Publisher
  • American Association for the Advancement of Science (AAAS)  (136)
  • American Association of Petroleum Geologists (AAPG)
Years
Year
  • 1
    Publication Date: 1989-01-13
    Description: The chemical synthesis of biologically active peptides and polypeptides can be achieved by using a convergent strategy of condensing protected peptide segments to form the desired molecule. An oxime support increases the ease with which intermediate protected peptides can be synthesized and makes this approach useful for the synthesis of peptides in which secondary structural elements have been redesigned. The extension of these methods to large peptides and proteins, for which folding of secondary structures into functional tertiary structures is critical, is discussed. Models of apolipoproteins, the homeo domain from the developmental protein encoded by the Antennapedia gene of Drosophila, a part of the Cro repressor, and the enzyme ribonuclease T1 and a structural analog have been synthesized with this method.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaiser, E T -- Mihara, H -- Laforet, G A -- Kelly, J W -- Walters, L -- Findeis, M A -- Sasaki, T -- DK07825/DK/NIDDK NIH HHS/ -- GM12054/GM/NIGMS NIH HHS/ -- HL-186577/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1989 Jan 13;243(4888):187-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Bioorganic Chemistry and Biochemistry, Rockefeller University, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2492114" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Apolipoprotein A-I ; Apolipoproteins A/chemical synthesis ; Humans ; Indicators and Reagents ; Lipoproteins, HDL/chemical synthesis ; Peptides/*chemical synthesis ; Protein Conformation ; Proteins/*chemical synthesis
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  • 2
    Publication Date: 1989-06-30
    Description: Complementary DNA's that encode an adenylyl cyclase were isolated from a bovine brain library. Most of the deduced amino acid sequence of 1134 residues is divisible into two alternating sets of hydrophobic and hydrophilic domains. Each of the two large hydrophobic domains appears to contain six transmembrane spans. Each of the two large hydrophilic domains contains a sequence that is homologous to a single cytoplasmic domain of several guanylyl cyclases; these sequences may represent nucleotide binding sites. An unexpected topographical resemblance between adenylyl cyclase and various plasma membrane channels and transporters was observed. This structural complexity suggests possible, unappreciated functions for this important enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krupinski, J -- Coussen, F -- Bakalyar, H A -- Tang, W J -- Feinstein, P G -- Orth, K -- Slaughter, C -- Reed, R R -- Gilman, A G -- CA16519/CA/NCI NIH HHS/ -- GM12230/GM/NIGMS NIH HHS/ -- GM34497/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1989 Jun 30;244(4912):1558-64.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75235.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2472670" target="_blank"〉PubMed〈/a〉
    Keywords: *Adenylyl Cyclases/genetics/isolation & purification ; Amino Acid Sequence ; Animals ; Base Sequence ; Brain/enzymology ; *Carrier Proteins ; Cattle ; Cell Line ; Cloning, Molecular ; DNA/genetics ; Electrophoresis, Polyacrylamide Gel ; *Ion Channels ; Membrane Proteins ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Protein Conformation ; Transfection
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-03-31
    Description: C/EBP is a rat liver nuclear protein capable of sequence-specific interaction with DNA. The DNA sequences to which C/EBP binds in vitro have been implicated in the control of messenger RNA synthesis. It has therefore been predicted that C/EBP will play a role in regulating gene expression in mammalian cells. The region of the C/EBP polypeptide required for direct interaction with DNA has been identified and shown to bear amino acid sequence relatedness with the product of the myc, fos, and jun proto-oncogenes. The arrangement of these related amino acid sequences led to the prediction of a new structural motif, termed the "leucine zipper," that plays a role in facilitating sequence-specific interaction between protein and DNA. Experimental tests now provide support for the leucine zipper hypothesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Landschulz, W H -- Johnson, P F -- McKnight, S L -- New York, N.Y. -- Science. 1989 Mar 31;243(4899):1681-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Carnegie Institution of Washington, Department of Embryology, Baltimore, MD 21210.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2494700" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; CCAAT-Enhancer-Binding Proteins ; Cross-Linking Reagents ; DNA/*metabolism ; Glutaral ; Leucine ; Liver/*analysis ; Macromolecular Substances ; Molecular Weight ; Mutation ; Nuclear Proteins/genetics/*metabolism ; Protein Conformation ; Rats ; Repetitive Sequences, Nucleic Acid ; Structure-Activity Relationship
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  • 4
    Publication Date: 1989-08-11
    Description: The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, M S -- Gippert, G P -- Soman, K V -- Case, D A -- Wright, P E -- GM 36643/GM/NIGMS NIH HHS/ -- GM38794/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 11;245(4918):635-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2503871" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cysteine/metabolism ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Histidine/metabolism ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Metalloproteins/*metabolism ; Molecular Sequence Data ; Molecular Structure ; Protein Conformation ; Solutions ; Thermodynamics ; Xenopus ; Zinc/metabolism
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-11-17
    Description: Rana esculenta tropomyosin assembles in vivo into a coiled-coil alpha helix from two different subunits, alpha and beta, which are present in about equal concentrations. Although the native composition is alpha beta, a mixture of equal amounts of alpha alpha and beta beta is produced by refolding dissociated alpha and beta at low temperature in vitro. Refolding kinetics showed that alpha alpha formed first and was relatively stable with regard to chain exchange below approximately 20 degrees C. Equilibration of the homodimer mixture at 30 degrees and 34 degrees C for long times, however, resulted in the formation of the native alpha beta molecule by chain exchange. Biosynthesis of alpha beta from separate alpha and beta genes is, therefore, favored thermodynamically over the formation of homodimers, and biological factors need not be invoked to explain the preferred native alpha beta composition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lehrer, S S -- Qian, Y D -- Hvidt, S -- HL22461/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1989 Nov 17;246(4932):926-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Muscle Research, Boston Biomedical Research Institute, MA 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2814515" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Kinetics ; Macromolecular Substances ; Muscle, Smooth/metabolism ; Muscles/metabolism ; Myocardium/metabolism ; Protein Conformation ; Protein Denaturation ; Protein Processing, Post-Translational ; Rana esculenta ; Thermodynamics ; Tropomyosin/genetics/*metabolism
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  • 6
    Publication Date: 1989-08-11
    Description: The products of the nuclear oncogenes fos and jun are known to form heterodimers that bind to DNA and modulate transcription. Both proteins contain a leucine zipper that is important for heterodimer formation. Peptides corresponding to these leucine zippers were synthesized. When mixed, these peptides preferentially form heterodimers over homodimers by at least 1000-fold. Both homodimers and the heterodimer are parallel alpha helices. The leucine zipper regions from Fos and Jun therefore correspond to autonomous helical dimerization sites that are likely to be short coiled coils, and these regions are sufficient to determine the specificity of interaction between Fos and Jun. The Fos leucine zipper forms a relatively unstable homodimer. Instability of homodimers provides a thermodynamic driving force for preferential heterodimer formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Shea, E K -- Rutkowski, R -- Stafford, W F 3rd -- Kim, P S -- RR05711/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 11;245(4918):646-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2503872" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Circular Dichroism ; *DNA-Binding Proteins ; Disulfides ; *Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Peptide Fragments/chemical synthesis ; Protein Conformation ; *Proto-Oncogene Proteins ; Proto-Oncogene Proteins c-fos ; Proto-Oncogene Proteins c-jun ; *Transcription Factors
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  • 7
    Publication Date: 1989-01-06
    Description: The temperature dependences of the reduction potentials (E degrees') of wild-type human myoglobin (Mb) and three site-directed mutants have been measured by the use of thin-layer spectroelectrochemistry. Residue Val68, which is in van der Waals contact with the heme in Mb, has been replaced by Glu, Asp, and Asn. The changes in E degrees' and the standard entropy (delta S degrees') and enthalpy (delta H degrees') of reduction in the mutant proteins were determined relative to values for wild type; the change in E degrees' at 25 degrees C was about -200 millivolts for the Glu and Asp mutants, and about -80 millivolts for the Asn mutant. At pH 7.0, reduction of Fe(III) to Fe(II) in the Glu and Asp mutants is accompanied by uptake of a proton by the protein. These studies demonstrate that Mb can tolerate substitution of a buried hydrophobic group by potentially charged and polar residues and that such amino acid replacements can lead to substantial changes in the redox thermodynamics of the protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Varadarajan, R -- Zewert, T E -- Gray, H B -- Boxer, S G -- DK 19038/DK/NIDDK NIH HHS/ -- GM 27738/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Jan 6;243(4887):69-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2563171" target="_blank"〉PubMed〈/a〉
    Keywords: Asparagine ; Aspartic Acid ; Glutamates ; Glutamic Acid ; Heme/metabolism ; Humans ; Mutation ; Myoglobin/*metabolism ; Oxidation-Reduction ; Protein Conformation ; Recombinant Proteins/*metabolism ; Thermodynamics ; Valine
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  • 8
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-07-21
    Description: In the Table of Contents of the 24 March 1989 issue, the title of the report "Histamine is an intracellular messenger mediating platelet aggregation" by S. P. Saxena et al. appearing on page 1596 was incorrectly printed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tong, L -- Milburn, M V -- de Vos, A M -- Kim, S H -- New York, N.Y. -- Science. 1989 Jul 21;245(4915):244.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2665078" target="_blank"〉PubMed〈/a〉
    Keywords: Humans ; Molecular Structure ; Protein Conformation ; *Proto-Oncogene Proteins ; Proto-Oncogene Proteins p21(ras)
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  • 9
    Publication Date: 1989-01-06
    Description: The high affinity of the noncovalent interaction between biotin and streptavidin forms the basis for many diagnostic assays that require the formation of an irreversible and specific linkage between biological macromolecules. Comparison of the refined crystal structures of apo and a streptavidin:biotin complex shows that the high affinity results from several factors. These factors include the formation of multiple hydrogen bonds and van der Waals interactions between biotin and the protein, together with the ordering of surface polypeptide loops that bury the biotin in the protein interior. Structural alterations at the biotin binding site produce quaternary changes in the streptavidin tetramer. These changes apparently propagate through cooperative deformations in the twisted beta sheets that link tetramer subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weber, P C -- Ohlendorf, D H -- Wendoloski, J J -- Salemme, F R -- New York, N.Y. -- Science. 1989 Jan 6;243(4887):85-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Central Research & Development Department, E. I. du Pont de Neumours and Company, Inc., Wilmington, DE 19880-0228.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2911722" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*metabolism ; Binding Sites ; Biotin/*metabolism ; Macromolecular Substances ; Models, Molecular ; Protein Conformation ; Streptavidin ; X-Ray Diffraction
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  • 10
    Publication Date: 1989-07-28
    Description: Two members of the hsp70 family, termed hsc70 and BiP, have been implicated in promoting protein folding and assembly processes in the cytoplasm and the lumen of the endoplasmic reticulum, respectively. Short hydrophilic (8 to 25 residues) synthetic peptides have now been tested as possible mimics of polypeptide chain substrates to help define an enzymatic basis for these activities. Both BiP and hsc70 have specific peptide binding sites. Peptide binding elicits hydrolysis of adenosine triphosphate, with the subsequent release of bound peptide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flynn, G C -- Chappell, T G -- Rothman, J E -- GM-25662/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Jul 28;245(4916):385-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Lewis Thomas Laboratory, Princeton University, NJ 08544.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2756425" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Carrier Proteins/*metabolism ; Cattle ; Endoplasmic Reticulum/metabolism ; Heat-Shock Proteins/*metabolism ; Hydrolysis ; Microsomes, Liver/metabolism ; *Molecular Chaperones ; Molecular Sequence Data ; Peptides/*metabolism ; Protein Binding ; Protein Conformation
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  • 11
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-01-06
    Description: Plasminogen activator therapy for acute myocardial infarction has become standard medical practice. Bleeding complications, however, limit the utility of the currently available agents. This article reviews how the tools of molecular biology and protein engineering are being used to develop safer and more effective plasminogen activators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haber, E -- Quertermous, T -- Matsueda, G R -- Runge, M S -- HL-19259/HL/NHLBI NIH HHS/ -- HL-28015/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1989 Jan 6;243(4887):51-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cardiac Unit, Massachusetts General Hospital, Boston 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2492113" target="_blank"〉PubMed〈/a〉
    Keywords: Humans ; Myocardial Infarction/*drug therapy ; Plasminogen Activators/*therapeutic use ; Protein Conformation ; Recombinant Proteins/therapeutic use ; Streptokinase/therapeutic use ; Tissue Plasminogen Activator/therapeutic use ; Urokinase-Type Plasminogen Activator/therapeutic use
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  • 12
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-01-27
    Description: Recently, a hypothetical structure called a leucine zipper was proposed that defines a new class of DNA binding proteins. The common feature of these proteins is a region spanning approximately 30 amino acids that contains a periodic repeat of leucines every seven residues. A peptide corresponding to the leucine zipper region of the yeast transcriptional activator GCN4 was synthesized and characterized. This peptide associates in the micromolar concentration range to form a very stable dimer of alpha helices with a parallel orientation. Although some features of the leucine zipper model are supported by our experimental data, the peptide has the characteristics of a coiled coil.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Shea, E K -- Rutkowski, R -- Kim, P S -- New York, N.Y. -- Science. 1989 Jan 27;243(4890):538-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2911757" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chromatography, High Pressure Liquid ; Circular Dichroism ; DNA/metabolism ; *DNA-Binding Proteins ; Disulfides ; *Fungal Proteins ; *Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Peptide Fragments ; Protein Conformation ; *Protein Kinases ; Repetitive Sequences, Nucleic Acid ; *Saccharomyces cerevisiae Proteins ; *Transcription Factors
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  • 13
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-08-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J L -- New York, N.Y. -- Science. 1989 Aug 11;245(4918):598.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2669127" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Endopeptidases ; HIV/*enzymology ; HIV Protease ; Molecular Structure ; *Protease Inhibitors ; Protein Conformation ; X-Ray Diffraction
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  • 14
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-03-03
    Description: Passage of proteins across membranes during export from their site of synthesis to their final destination is mediated by leader peptides that paradoxically exhibit a unity of function in spite of a diversity of sequence. These leader peptides act in at least two stages of the export process: at entry into the pathway and subsequently during translocation across the membrane. How selectivity is imposed on the system in the absence of a consensus among the sequences of leader peptides is the main issue discussed here.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Randall, L L -- Hardy, S J -- GM29798/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Mar 3;243(4895):1156-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry/Biophysics Program, Washington State University, Pullman 99164.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2646712" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biological Transport ; Cell Membrane/*metabolism ; Escherichia coli/metabolism ; *Models, Biological ; Protein Conformation ; Protein Precursors/metabolism ; Protein Sorting Signals/*physiology ; Proteins/*metabolism ; Structure-Activity Relationship
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  • 15
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-08-04
    Description: Membrane-exposed residues are more hydrophobic than buried interior residues in the transmembrane regions of the photosynthetic reaction center from Rhodobacter sphaeroides. This hydrophobic organization is opposite to that of water-soluble proteins. The relative polarities of interior and surface residues of membrane and water soluble proteins are not simply reversed, however. The hydrophobicities of interior residues of both membrane and water-soluble proteins are comparable, whereas the bilayer-exposed residues of membrane proteins are more hydrophobic than the interior residues, and the aqueous-exposed residues of water-soluble proteins are more hydrophilic than the interior residues. A method of sequence analysis is described, based on the periodicity of residue replacement in homologous sequences, that extends conclusions derived from the known atomic structure of the reaction center to the more extensive database of putative transmembrane helical sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rees, D C -- DeAntonio, L -- Eisenberg, D -- GM31299/GM/NIGMS NIH HHS/ -- GM39558/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 4;245(4917):510-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2667138" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Proteins ; Cell Membrane/analysis ; Chemistry, Physical ; Fourier Analysis ; *Membrane Proteins ; Photosynthetic Reaction Center Complex Proteins ; Physicochemical Phenomena ; Protein Conformation ; Rhodobacter sphaeroides/*ultrastructure ; Solubility ; Water
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  • 16
    Publication Date: 1989-09-08
    Description: Complementary DNAs for the beta subunit of the dihydropyridine-sensitive calcium channel of rabbit skeletal muscle were isolated on the basis of peptide sequences derived from the purified protein. The deduced primary structure is without homology to other known protein sequences and is consistent with the beta subunit being a peripheral membrane protein associated with the cytoplasmic aspect of the sarcolemma. The protein contains sites that might be expected to be preferentially phosphorylated by protein kinase C and guanosine 3',5'-monophosphate-dependent protein kinase. A messenger RNA for this protein appears to be expressed in brain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ruth, P -- Rohrkasten, A -- Biel, M -- Bosse, E -- Regulla, S -- Meyer, H E -- Flockerzi, V -- Hofmann, F -- New York, N.Y. -- Science. 1989 Sep 8;245(4922):1115-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Physiologische Chemie, Medizinische Fakultat, Homburg/Saar, Federal Republic of Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2549640" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcium Channel Blockers/*metabolism/pharmacology ; Calcium Channels/drug effects/*metabolism ; Dihydropyridines/*metabolism/pharmacology ; Molecular Sequence Data ; Muscles/*analysis ; Phosphorylation ; Protein Conformation ; RNA, Messenger/isolation & purification ; Rabbits ; Receptors, Nicotinic/drug effects/*isolation & purification/metabolism
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  • 17
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-11-17
    Description: The proposal that the absorption maximum of the visual pigments is governed by interaction of the 11-cis-retinal chromophore with charged carboxylic acid side chains in the membrane-embedded regions of the proteins has been tested by mutating five Asp and Glu residues thought to be buried in rhodopsin. Changing Glu113 to Gln causes a dramatic shift in the absorption maximum from 500 nanometers to 380 nanometers, a decrease in the pKa (acidity constant) of the protonated Schiff base of the chromophore to about 6, and a greatly increased reactivity with hydroxylamine. Thus Glu113 appears to be the counterion to the protonated Schiff base. Wavelength modulation in visual pigments apparently is not governed by electrostatic interaction with carboxylate residues, other than the counterion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhukovsky, E A -- Oprian, D D -- 5T32 GM07596-11/GM/NIGMS NIH HHS/ -- EY07965/EY/NEI NIH HHS/ -- R01 EY007965/EY/NEI NIH HHS/ -- S07 RR07044/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1989 Nov 17;246(4932):928-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Brandeis University, Waltham, MA 02254.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2573154" target="_blank"〉PubMed〈/a〉
    Keywords: *Aspartic Acid ; Glutamates ; Glutamic Acid ; Hydrogen-Ion Concentration ; Hydroxylamine ; Hydroxylamines/pharmacology ; Models, Molecular ; Mutation ; Protein Conformation ; Retinal Pigments/*metabolism ; Retinaldehyde/*metabolism ; Retinoids/*metabolism ; Rhodopsin/genetics/*metabolism ; Schiff Bases ; Spectrophotometry
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  • 18
    Publication Date: 1989-11-17
    Description: The zona pellucida surrounding mouse oocytes is an extracellular matrix composed of three sulfated glycoproteins, ZP1, ZP2, and ZP3. It has been demonstrated that a monoclonal antibody to ZP3 injected into female mice inhibits fertilization by binding to the zona pellucida and blocking sperm penetration. A complementary DNA encoding ZP3 was randomly cleaved and 200- to 1000-base pair fragments were cloned into the expression vector lambda gt11. This epitope library was screened with the aforementioned contraceptive antibody, and the positive clones were used to map the seven-amino acid epitope recognized by the antibody. Female mice were immunized with a synthetic peptide containing this B cell epitope coupled to a carrier protein to provide helper T cell epitopes. The resultant circulating antibodies to ZP3 bound to the zona pellucida of immunized animals and produced long-lasting contraception. The lack of ovarian histopathology or cellular cytotoxicity among the immunized animals may be because of the absence of zona pellucida T cell epitopes in this vaccine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Millar, S E -- Chamow, S M -- Baur, A W -- Oliver, C -- Robey, F -- Dean, J -- New York, N.Y. -- Science. 1989 Nov 17;246(4932):935-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2479101" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens/immunology ; Base Sequence ; Cloning, Molecular ; *Contraception ; *Contraception, Immunologic ; DNA/genetics ; *Egg Proteins ; Epitopes/analysis ; Female ; Glycoproteins/genetics/*immunology ; Male ; *Membrane Glycoproteins ; Mice ; Molecular Sequence Data ; Ovum/*physiology ; Protein Conformation ; RNA, Messenger/genetics ; *Receptors, Cell Surface ; *Vaccination ; Zona Pellucida/*physiology
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  • 19
    Publication Date: 1989-12-01
    Description: The structure of a complex between a peptide inhibitor with the sequence N-acetyl-Thr-Ile-Nle-psi[CH2-NH]-Nle-Gln-Arg.amide (Nle, norleucine) with chemically synthesized HIV-1 (human immunodeficiency virus 1) protease was determined at 2.3 A resolution (R factor of 0.176). Despite the symmetric nature of the unliganded enzyme, the asymmetric inhibitor lies in a single orientation and makes extensive interactions at the interface between the two subunits of the homodimeric protein. Compared with the unliganded enzyme, the protein molecule underwent substantial changes, particularly in an extended region corresponding to the "flaps" (residues 35 to 57 in each chain), where backbone movements as large as 7 A are observed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, M -- Schneider, J -- Sathyanarayana, B K -- Toth, M V -- Marshall, G R -- Clawson, L -- Selk, L -- Kent, S B -- Wlodawer, A -- A-127302/PHS HHS/ -- N01-C0-74101/PHS HHS/ -- SM-24483/SM/CMHS SAMHSA HHS/ -- New York, N.Y. -- Science. 1989 Dec 1;246(4934):1149-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NCI-Frederick Cancer Research Facility, BRI-Basic Research Program, MD 21701.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2686029" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chemistry, Physical ; Crystallization ; Endopeptidases/*metabolism ; Gene Products, gag/metabolism ; HIV Protease ; HIV-1/*enzymology ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; Oligopeptides/*metabolism ; Physicochemical Phenomena ; Protease Inhibitors/*metabolism ; Protein Conformation
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  • 20
    Publication Date: 1989-08-04
    Description: The crystal structure of glycogen phosphorylase a complexed with its substrates, orthophosphate and maltopentaose, has been determined and refined at a resolution of 2.8 angstroms. With oligosaccaride bound at the glycogen storage site, the phosphate ion binds at the catalytic site and causes the regulatory and catalytic domains to separate with the loss of stabilizing interactions between them. Homotropic cooperativity between the active sites of the allosteric dimer results from rearrangements in isologous contacts between symmetry-related helices in the subunit interface. The conformational changes in the core of the interface are correlated with those observed on covalent activation by phosphorylation at Ser14 (phosphorylase b----a).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldsmith, E J -- Sprang, S R -- Hamlin, R -- Xuong, N H -- Fletterick, R J -- DK31507-05/DK/NIDDK NIH HHS/ -- GM00085-05/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 4;245(4917):528-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2756432" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Amino Acid Sequence ; Binding Sites ; Catalysis ; Crystallization ; Crystallography ; Enzyme Activation ; Glucosephosphates/metabolism ; Glycogen/metabolism ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Structure ; Oligosaccharides ; Phosphates/metabolism ; Phosphorylase a/*metabolism ; Phosphorylases/*metabolism ; Protein Conformation ; X-Ray Diffraction
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  • 21
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-02-03
    Description: The dynamic character of phospholipid aggregates limits conventional structural studies to the determination of average molecular features. In order to develop more detailed descriptions of phospholipid structure for comparison with experiment, the molecular dynamics of a hydrated lysophosphatidylethanolamine (LPE) micelle, incorporating 85 LPE and 1591 water molecules, have been simulated. Comparison of the initial and equilibrated micelles shows substantial differences both in LPE hydrocarbon chain conformation and polar head-group-solvent interactions. Although these changes produce only subtle effects on the averaged structural properties of the system, the alterations in hydrocarbon chain packing and head-group solvation appear to mimic a polymorphic pretransition from a spherical toward a cylindrical micelle structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wendoloski, J J -- Kimatian, S J -- Schutt, C E -- Salemme, F R -- New York, N.Y. -- Science. 1989 Feb 3;243(4891):636-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉E. I. du Pont de Nemours & Company, Central Research and Development Department, Wilmington, DE 19880.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2916118" target="_blank"〉PubMed〈/a〉
    Keywords: *Colloids ; *Computer Simulation ; Crystallization ; Fatty Acids ; Glycerol ; Hydrogen Bonding ; Lipid Bilayers ; *Lysophospholipids ; *Micelles ; Molecular Structure ; Protein Conformation ; Solutions ; Solvents
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  • 22
    Publication Date: 1989-03-10
    Description: The x-ray crystal structure of recombinant human renin has been determined. Molecular dynamics techniques that included crystallographic data as a restraint were used to improve an initial model based on porcine pepsinogen. The present agreement factor for data from 8.0 to 2.5 angstroms (A) is 0.236. Some of the surface loops are poorly determined, and these disordered regions border a 30 A wide solvent channel. Comparison of renin with other aspartyl proteinases shows that, although the structural cores and active sites are highly conserved, surface residues, some of which are critical for specificity, vary greatly (up to 10A). Knowledge of the actual structure, as opposed to the use of models based on related enzymes, should facilitate the design of renin inhibitors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sielecki, A R -- Hayakawa, K -- Fujinaga, M -- Murphy, M E -- Fraser, M -- Muir, A K -- Carilli, C T -- Lewicki, J A -- Baxter, J D -- James, M N -- New York, N.Y. -- Science. 1989 Mar 10;243(4896):1346-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Alberta, Edmonton, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2493678" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid Endopeptidases ; Cardiovascular Agents/pharmacology ; Endopeptidases/metabolism ; Humans ; Models, Molecular ; Pepsin A/metabolism ; Protein Conformation ; *Recombinant Proteins/metabolism ; *Renin/metabolism
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  • 23
    Publication Date: 1989-05-19
    Description: The gramicidin A transmembrane channel is believed to consist of two head-to-head beta helices. Computer-generated models were used to formulate the structure of new single-chain channel molecules based on the gramicidin motif. The chemical synthesis of two tartaric acid-gramicidin A hybrids and single-channel analyses of their conducting properties are reported. These studies illustrate the rational design and synthesis of long-lived channels with tunable conductance properties and provide support for current molecular models of the natural (dimeric) gramicidin channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stankovic, C J -- Heinemann, S H -- Delfino, J M -- Sigworth, F J -- Schreiber, S L -- NS-21501/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1989 May 19;244(4906):813-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2471263" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computer Simulation ; Electric Conductivity ; Gramicidin/*metabolism ; Ion Channels/*metabolism ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Structure ; Protein Conformation ; Protein Multimerization ; Tartrates/*metabolism ; Thermodynamics
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  • 24
    Publication Date: 1989-03-31
    Description: The protein products of the fos and jun proto-oncogenes form a heterodimeric complex that participates in a stable high affinity interaction with DNA elements containing AP-1 binding sites. The effects of deletions and point mutations in Fos and Jun on protein complex formation and DNA binding have been examined. The data suggest that Fos and Jun dimerize via a parallel interaction of helical domains containing a heptad repeat of leucine residues (the leucine zipper). Dimerization is required for DNA binding and results in the appropriate juxtaposition of basic amino acid regions from Fos and Jun, both of which are required for association with DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gentz, R -- Rauscher, F J 3rd -- Abate, C -- Curran, T -- New York, N.Y. -- Science. 1989 Mar 31;243(4899):1695-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Oncology, Roche Institute of Molecular Biology, Nutley, NJ 07110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2494702" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cross-Linking Reagents ; DNA/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Glutaral ; Immunosorbent Techniques ; *Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Proto-Oncogene Proteins/genetics/*metabolism ; Proto-Oncogene Proteins c-fos ; Proto-Oncogene Proteins c-jun ; Rats ; Repetitive Sequences, Nucleic Acid ; Structure-Activity Relationship ; Transcription Factors/genetics/*metabolism
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  • 25
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-11-17
    Description: C/EBP is a sequence-specific DNA binding protein that regulates gene expression in certain mammalian cells. The region of the C/EBP polypeptide required for specific recognition of DNA is related in amino acid sequence to other regulatory proteins, including the Fos and Jun transforming proteins. It has been proposed that these proteins bind DNA via a bipartite structural motif, consisting of a dimerization interface termed the "leucine zipper" and a DNA contact surface termed the "basic region." An evaluation of the properties of conserved amino acids within the basic region of 11 deduced protein sequences, coupled with the observation that they are located at an invariant distance from the leucine zipper, has led to the formulation of a "scissors-grip" model for DNA binding. The architectural features of this model are well suited for interaction with directly abutted, dyadsymmetric DNA sequences. Data supportive of the model were obtained with chemical probes of protein: DNA complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vinson, C R -- Sigler, P B -- McKnight, S L -- New York, N.Y. -- Science. 1989 Nov 17;246(4932):911-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Research Laboratories, Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2683088" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; *Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides ; Protein Conformation ; Substrate Specificity
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  • 26
    Publication Date: 1989-02-17
    Description: The human immunodeficiency virus (HIV-1) encodes a protease that is essential for viral replication and is a member of the aspartic protease family. The recently determined three-dimensional structure of the related protease from Rous sarcoma virus has been used to model the smaller HIV-1 dimer. The active site has been analyzed by comparison to the structure of the aspartic protease, rhizopuspepsin, complexed with a peptide inhibitor. The HIV-1 protease is predicted to interact with seven residues of the protein substrate. This information can be used to design protease inhibitors and possible antiviral drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weber, I T -- Miller, M -- Jaskolski, M -- Leis, J -- Skalka, A M -- Wlodawer, A -- CA-06927/CA/NCI NIH HHS/ -- CA38046/CA/NCI NIH HHS/ -- N01-CO-74101/CO/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1989 Feb 17;243(4893):928-31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystallography Laboratory, NCI-Frederick Cancer Research Facility, MD 21701.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2537531" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Avian Sarcoma Viruses/enzymology ; Binding Sites ; HIV-1/*enzymology ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Peptide Hydrolases/*metabolism ; Protein Conformation
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  • 27
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-04-21
    Description: Sodium channels from diverse excitable membranes are very similar in their structure, yet surprisingly heterogeneous in their behavior. The processes that govern the opening and closing of sodium channels have appeared difficult to describe in terms of a single, unifying molecular scheme. Now cardiac sodium channels have been analyzed by high-resolution single-channel recordings over a broad range of potentials. Channels exhibited both complex and simple gating patterns at different voltages. Such behavioral diversity can be explained by the balance between two molecular transitions whereby channels can exit the open state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yue, D T -- Lawrence, J H -- Marban, E -- HL01874/HL/NHLBI NIH HHS/ -- HL36957/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1989 Apr 21;244(4902):349-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomedical Engineering, 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/2540529" target="_blank"〉PubMed〈/a〉
    Keywords: Electric Conductivity ; Heart/*physiology ; Membrane Potentials ; Neurons/physiology ; Probability ; Protein Conformation ; Sodium Channels/*physiology
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  • 28
    Publication Date: 1989-08-11
    Description: The rational design of drugs that can inhibit the action of viral proteases depends on obtaining accurate structures of these enzymes. The crystal structure of chemically synthesized HIV-1 protease has been determined at 2.8 angstrom resolution (R factor of 0.184) with the use of a model based on the Rous sarcoma virus protease structure. In this enzymatically active protein, the cysteines were replaced by alpha-amino-n-butyric acid, a nongenetically coded amino acid. This structure, in which all 99 amino acids were located, differs in several important details from that reported previously by others. The interface between the identical subunits forming the active protease dimer is composed of four well-ordered beta strands from both the amino and carboxyl termini and residues 86 to 94 have a helical conformation. The observed arrangement of the dimer interface suggests possible designs for dimerization inhibitors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wlodawer, A -- Miller, M -- Jaskolski, M -- Sathyanarayana, B K -- Baldwin, E -- Weber, I T -- Selk, L M -- Clawson, L -- Schneider, J -- Kent, S B -- N01-CO-74101/CO/NCI NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 11;245(4918):616-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystallography Laboratory, NCI-Frederick Cancer Research Facility, MD 21701.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2548279" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aspartic Acid Endopeptidases ; Avian Sarcoma Viruses/enzymology ; Binding Sites ; Crystallization ; *Endopeptidases/chemical synthesis ; HIV Protease ; HIV-1/*enzymology ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein Conformation ; Solutions ; X-Ray Diffraction
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  • 29
    Publication Date: 1989-07-14
    Description: Nearly 20 percent of the packaged RNA in bean-pod mottle virus (BPMV) binds to the capsid interior in a symmetric fashion and is clearly visible in the electron density map. The RNA displaying icosahedral symmetry is single-stranded with well-defined polarity and stereochemical properties. Interactions with protein are dominated by nonbonding forces with few specific contacts. The tertiary and quaternary structures of the BPMV capsid proteins are similar to those observed in animal picornaviruses, supporting the close relation between plant comoviruses and animal picornaviruses established by previous biological studies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Z G -- Stauffacher, C -- Li, Y -- Schmidt, T -- Bomu, W -- Kamer, G -- Shanks, M -- Lomonossoff, G -- Johnson, J E -- AI18764/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1989 Jul 14;245(4914):154-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2749253" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Capsid/*metabolism/ultrastructure ; Crystallography ; Electron Probe Microanalysis ; Electrophoresis, Polyacrylamide Gel ; Macromolecular Substances ; Molecular Sequence Data ; Mosaic Viruses/*analysis/genetics/ultrastructure ; Plant Viruses/*analysis/genetics/ultrastructure ; Protein Conformation ; RNA, Viral/*metabolism/ultrastructure
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  • 30
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-02-10
    Description: As the originator of the oxygen in our atmosphere, the photosynthetic water-splitting enzyme of chloroplasts is vital for aerobic life on the earth. It has a manganese cluster at its active site, but it is poorly understood at the molecular level. Polarized synchrotron radiation was used to examine the x-ray absorption of manganese in oriented chloroplasts. The manganese site, in the "resting" (S1) state, is an asymmetric cluster, which probably contains four manganese atoms, with interatomic separations of 2.7 and 3.3 angstroms; the vector formed by the 3.3-angstrom manganese pair is oriented perpendicular to the membrane plane. Comparisons with model compounds suggest that the cluster contains bridging oxide or hydroxide ligands connecting the manganese atoms, perhaps with carboxylate bridges connecting the 3.3-angstrom manganese pair.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉George, G N -- Prince, R C -- Cramer, S P -- New York, N.Y. -- Science. 1989 Feb 10;243(4892):789-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉EXXON Research and Engineering Company, Annandale, NJ 08801.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2916124" target="_blank"〉PubMed〈/a〉
    Keywords: Chloroplasts/*ultrastructure ; *Manganese ; Particle Accelerators ; *Photosynthesis ; Protein Conformation
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  • 31
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-02-03
    Description: The question of how the amino acid sequence of a protein specifies its three-dimensional structure remains to be answered. Proteins are so large and complex that it is difficult to discern the features in their sequences that contribute to their structural stability and function. One approach to this problem is de novo design of model proteins, much simpler than their natural counterparts, yet containing sufficient information in their sequences to specify a given function (for example, folding in aqueous solution, folding in membranes, or formation of ion channels). Designed proteins provide simple model systems for understanding protein structure and function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeGrado, W F -- Wasserman, Z R -- Lear, J D -- New York, N.Y. -- Science. 1989 Feb 3;243(4891):622-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉E. I. du Pont de Nemours & Company, Central Research and Development Department, Wilmington, DE 19898.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2464850" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ion Channels ; Macromolecular Substances ; Models, Molecular ; Protein Conformation ; *Proteins ; Solubility ; Structure-Activity Relationship ; Tropomyosin ; Water
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  • 32
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-03-31
    Description: Uncoated recA-DNA complexes were imaged with the scanning tunneling microscope (STM). The images, which reveal the right-handed helical structure of the complexes with subunits clearly resolved, are comparable in quality to STM images of metal-coated specimens. Possible conduction mechanisms that allow STM imaging of biological macromolecules are discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amrein, M -- Durr, R -- Stasiak, A -- Gross, H -- Travaglini, G -- New York, N.Y. -- Science. 1989 Mar 31;243(4899):1708-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Cell Biology, Swiss Federal Institute of Technology, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2928803" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates ; Acetic Acid ; Adsorption ; Aluminum Silicates ; DNA/*metabolism ; Electrochemistry ; Macromolecular Substances ; Magnesium ; Magnesium Chloride ; *Microscopy, Electron ; Molecular Structure ; Protein Conformation ; Rec A Recombinases/*metabolism
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  • 33
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1989-02-17
    Description: Mutant flies in which the gene coding for the Shaker potassium channel is deleted still have potassium currents similar to those coded by the Shaker gene. This suggests the presence of a family of Shaker-like genes in Drosophila. By using a Shaker complementary DNA probe and low-stringency hybridization, three additional family members have now been isolated, Shab, Shaw, and Shal. The Shaker family genes are not clustered in the genome. The deduced proteins of Shab, Shaw, and Shal have high homology to the Shaker protein; the sequence identity of the integral membrane portions is greater than 50 percent. These genes are organized similarly to Shaker in that only a single homology domain containing six presumed membrane-spanning segments common to all voltage-gated ion channels is coded by each messenger RNA. Thus, potassium channel diversity could result from an extended gene family, as well as from alternate splicing of the Shaker primary transcript.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, A -- Wei, A G -- Baker, K -- Salkoff, L -- 1 RO1 NS24785-01/NS/NINDS NIH HHS/ -- GMO 7200/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Feb 17;243(4893):943-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy and Neurobiology, 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/2493160" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Blotting, Northern ; Carrier Proteins/*genetics ; Drosophila Proteins ; Drosophila melanogaster/*genetics ; *Genes ; Molecular Sequence Data ; *Multigene Family ; Potassium Channels/*physiology ; Protein Conformation ; RNA, Messenger/genetics ; Shab Potassium Channels
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  • 34
    Publication Date: 1989-06-09
    Description: The three-dimensional structure of human serum albumin has been solved at 6.0 angstrom (A) resolution by the method of multiple isomorphous replacement. Crystals were grown from solutions of polyethylene glycol in the infrequently observed space group P42(1)2 (unit cell constants a = b = 186.5 +/- 0.5 A and c = 81.0 +/- 0.5 A) and diffracted x-rays to lattice d-spacings of less than 2.9 A. The electron density maps are of high quality and revealed the structure as a predominantly alpha-helical globin protein in which the course of the polypeptide can be traced. The binding loci of several organic compounds have been determined.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, D C -- He, X M -- Munson, S H -- Twigg, P D -- Gernert, K M -- Broom, M B -- Miller, T Y -- New York, N.Y. -- Science. 1989 Jun 9;244(4909):1195-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Aeronautics and Space Administration, Space Sciences Laboratory, Marshall Space Flight Center, AL 35812.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2727704" target="_blank"〉PubMed〈/a〉
    Keywords: Humans ; *Models, Molecular ; Polyethylene Glycols ; Protein Conformation ; *Serum Albumin ; X-Ray Diffraction
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  • 35
    Publication Date: 1989-03-10
    Description: A strategy, termed homolog-scanning mutagenesis, was used to identify the epitopes on human growth hormone (hGH) for binding to its cloned liver receptor and eight different monoclonal antibodies (Mab's). Segments of sequences (7 to 30 residues long) that were derived from homologous hormones known not to bind to the hGH receptor or Mab's, were systematically substituted throughout the hGH gene to produce a set of 17 chimeric hormones. Each Mab or receptor was categorized by a particular subset of mutant hormones was categorized by a particular subset of mutant hormones that disrupted binding. Each subset of the disruptive mutations mapped within close proximity on a three-dimensional model of hGH, even though the residues changed within each subset were usually distant in the primary sequence. The mapping analysis correctly predicted those Mab's which could or could not block binding of the receptor to hGH and further suggested (along with other data) that the folding of these chimeric hormones is like that of HGH. By this analysis, three discontinuous polypeptide determinants in hGH--the loop between residues 54 and 74, the central portion of helix 4 to the carboxyl terminus, and to a lesser extent the amino-terminal region of helix 1--modulate binding to the liver receptor. Homolog-scanning mutagenesis should be of general use in identifying sequences that cause functional variation among homologous proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cunningham, B C -- Jhurani, P -- Ng, P -- Wells, J A -- New York, N.Y. -- Science. 1989 Mar 10;243(4896):1330-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Chemistry, Genentech, Inc., South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2466339" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal ; Chimera ; Cloning, Molecular ; Epitopes/*analysis ; Genes ; Growth Hormone/*genetics/immunology/metabolism ; Humans ; Liver/metabolism ; Molecular Sequence Data ; *Mutation ; Protein Conformation ; Receptors, Somatotropin/*genetics/metabolism ; Sequence Homology, Nucleic Acid
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  • 36
    Publication Date: 1989-06-02
    Description: A strategy, called alanine-scanning mutagenesis, was used to identify specific side chains in human growth hormone (hGH) that strongly modulate binding to the hGH receptor cloned from human liver. Single alanine mutations (62 in total) were introduced at every residue contained within the three discontinuous segments of hGH (residues 2 to 19, 54 to 74, and 167 to 191) that have been implicated in receptor recognition. The alanine scan revealed a cluster of a dozen large side chains that when mutated to alanine each showed more than a four times lower binding affinity to the hGH receptor. Many of these residues that promote binding to the hGH receptor are altered in homologs of hGH (such as placental lactogens and prolactins) that do not bind tightly to the hGH receptor. The overall folding of these mutant proteins was indistinguishable from that of the wild-type hGH, as determined by strong cross-reactivities with seven different conformationally sensitive monoclonal antibodies. The alanine scan also identified at least one side chain, Glu174, that hindered binding because when it was mutated to alanine the receptor affinity increased by more than a factor of four.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cunningham, B C -- Wells, J A -- New York, N.Y. -- Science. 1989 Jun 2;244(4908):1081-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Chemistry, Genentech, South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2471267" target="_blank"〉PubMed〈/a〉
    Keywords: *Alanine ; Amino Acid Sequence ; Antibodies, Monoclonal ; Disulfides ; Epitopes/immunology ; Growth Hormone/genetics/immunology/*metabolism ; Humans ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; *Mutation ; Placental Lactogen ; Prolactin ; Protein Conformation ; Receptors, Somatotropin/*metabolism ; Structure-Activity Relationship
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  • 37
    Publication Date: 1988-09-16
    Description: In the proposed "zinc finger" DNA-binding motif, each repeat unit binds a zinc metal ion through invariant Cys and His residues and this drives the folding of each 30-residue unit into an independent nucleic acid-binding domain. To obtain structural information, we synthesized single and double zinc finger peptides from the yeast transcription activator ADR1, and assessed the metal-binding and DNA-binding properties of these peptides, as well as the solution structure of the metal-stabilized domains, with the use of a variety of spectroscopic techniques. A single zinc finger can exist as an independent structure sufficient for zinc-dependent DNA binding. An experimentally determined model of the single finger is proposed that is consistent with circular dichroism, one- and two-dimensional nuclear magnetic resonance, and visual spectroscopy of the single-finger peptide reconstituted in the presence of zinc.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parraga, G -- Horvath, S J -- Eisen, A -- Taylor, W E -- Hood, L -- Young, E T -- Klevit, R E -- New York, N.Y. -- Science. 1988 Sep 16;241(4872):1489-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle 98195.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3047872" target="_blank"〉PubMed〈/a〉
    Keywords: Circular Dichroism ; DNA Mutational Analysis ; *DNA-Binding Proteins ; Magnetic Resonance Spectroscopy ; Metalloproteins ; Protein Conformation ; Saccharomyces cerevisiae ; Structure-Activity Relationship ; *Transcription Factors ; Zinc/*physiology
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  • 38
    Publication Date: 1988-07-01
    Description: A method of combinatorial cassette mutagenesis was designed to readily determine the informational content of individual residues in protein sequences. The technique consists of simultaneously randomizing two or three positions by oligonucleotide cassette mutagenesis, selecting for functional protein, and then sequencing to determine the spectrum of allowable substitutions at each position. Repeated application of this method to the dimer interface of the DNA-binding domain of lambda repressor reveals that the number and type of substitutions allowed at each position are extremely variable. At some positions only one or two residues are functionally acceptable; at other positions a wide range of residues and residue types are tolerated. The number of substitutions allowed at each position roughly correlates with the solvent accessibility of the wild-type side chain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reidhaar-Olson, J F -- Sauer, R T -- AI-15706/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1988 Jul 1;241(4861):53-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3388019" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Codon ; DNA/genetics/metabolism ; *DNA-Binding Proteins ; Macromolecular Substances ; Molecular Sequence Data ; Mutation ; Plasmids ; Protein Conformation ; Repressor Proteins/*genetics ; Structure-Activity Relationship ; Transcription Factors/*genetics ; Viral Proteins ; Viral Regulatory and Accessory Proteins
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  • 39
    Publication Date: 1988-04-15
    Description: The solution conformation of plastocyanin from the green alga Scenedesmus obliquus has been determined from distance and dihedral angle constraints derived by nuclear magnetic resonance (NMR) spectroscopy. Structures were generated with distance geometry and restrained molecular dynamics calculations. A novel molecular replacement method was also used with the same NMR constraints to generate solution structures of S. obliquus plastocyanin from the x-ray structure of the homologous poplar protein. Scenedesmus obliquus plastocyanin in solution adopts a beta-barrel structure. The backbone conformation is well defined and is similar overall to that of poplar plastocyanin in the crystalline state. The distinctive acidic region of the higher plant plastocyanins, which functions as a binding site for electron transfer proteins and inorganic complexes, differs in both shape and charge in S. obliquus plastocyanin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, J M -- Case, D A -- Chazin, W J -- Gippert, G P -- Havel, T F -- Powls, R -- Wright, P E -- GM36643/GM/NIGMS NIH HHS/ -- GM38221/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Apr 15;240(4850):314-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3353725" target="_blank"〉PubMed〈/a〉
    Keywords: Calorimetry ; Chlorophyta/*metabolism ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; *Plant Proteins ; *Plastocyanin ; Protein Conformation
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  • 40
    Publication Date: 1988-12-02
    Description: D-galactose-binding (or chemoreceptor) protein of Escherichia coli serves as an initial component for both chemotaxis towards galactose and glucose and high-affinity active transport of the two sugars. Well-refined x-ray structures of the liganded forms of the wild-type and a mutant protein isolated from a strain defective in chemotaxis but fully competent in transport have provided a molecular view of the sugar-binding site and of a site for interacting with the Trg transmembrane signal transducer. The geometry of the sugar-binding site, located in the cleft between the two lobes of the bilobate protein, is novel in that it is designed for tight binding and sequestering of either the alpha or beta anomer of the D-stereoisomer of the 4-epimers galactose and glucose. Binding specificity and affinity are conferred primarily by polar planar side-chain residues that form intricate networks of cooperative and bidentate hydrogen bonds with the sugar substrates, and secondarily by aromatic residues that sandwich the pyranose ring. Each of the pairs of anomeric hydroxyls and epimeric hydroxyls is recognized by a distinct Asp residue. The site for interaction with the transducer is about 18 A from the sugar-binding site. Mutation of Gly74 to Asp at this site, concomitant with considerable changes in the local ordered water structures, contributes to the lack of productive interaction with the transmembrane signal transducer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vyas, N K -- Vyas, M N -- Quiocho, F A -- New York, N.Y. -- Science. 1988 Dec 2;242(4883):1290-5.〈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/3057628" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*ultrastructure ; Binding Sites ; *Calcium-Binding Proteins ; Carrier Proteins/*ultrastructure ; *Chemotaxis ; Computer Simulation ; DNA Mutational Analysis ; Escherichia coli ; Galactose/metabolism ; Glucose/metabolism ; Hydrogen Bonding ; Models, Molecular ; *Monosaccharide Transport Proteins ; *Periplasmic Binding Proteins ; Protein Conformation ; Structure-Activity Relationship ; X-Ray Diffraction
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  • 41
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-07-08
    Description: Gramicidin, a linear polypeptide composed of hydrophobic amino acids with alternating L- and D- configurations, forms transmembrane ion channels. The crystal structure of a gramicidin-cesium complex has been determined at 2.0 angstrom resolution. In this structure, gramicidin forms a 26 angstrom long tube comprised of two polypeptide chains arranged as antiparallel beta strands that are wrapped into a left-handed helical coil with 6.4 residues per turn. The polypeptide backbone forms the interior of the hydrophilic, solvent-filled pore and the side chains form a hydrophobic and relatively regular surface on the outside of the pore. This example of a crystal structure of a solvent-filled ion pore provides a basis for understanding the physical nature of ion translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wallace, B A -- Ravikumar, K -- New York, N.Y. -- Science. 1988 Jul 8;241(4862):182-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Center for Biophysics, Rensselaer Polytechnic Institute, Troy, NY 12180.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2455344" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cesium ; Computer Simulation ; Crystallography ; *Gramicidin ; *Ion Channels ; Ligands ; Macromolecular Substances ; *Membrane Proteins ; Models, Molecular ; Protein Conformation
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  • 42
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-09-02
    Description: Study of proteins that recognize specific DNA sequences has yielded much information, but the field is still in its infancy. Already two major structural motifs have been discovered, the helix-turn-helix and zinc finger, and numerous examples of DNA-binding proteins containing either of them are known. The restriction enzyme Eco RI uses yet a different motif. Additional motifs are likely to be found as well. There is a growing understanding of some of the physical chemistry involved in protein-DNA binding, but much remains to be learned before it becomes possible to engineer a protein that binds to a specific DNA sequence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schleif, R -- New York, N.Y. -- Science. 1988 Sep 2;241(4870):1182-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Department of Biochemistry, Brandeis University, Waltham, MA 02254.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2842864" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Binding Sites ; Chemical Phenomena ; Chemistry ; DNA/metabolism ; DNA Restriction Enzymes/metabolism ; DNA-Binding Proteins/*metabolism ; Deoxyribonuclease EcoRI ; Electrochemistry ; Nucleic Acids/metabolism ; Protein Conformation ; Zinc
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  • 43
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-11-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J L -- New York, N.Y. -- Science. 1988 Nov 11;242(4880):863-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2460921" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/prevention & control ; Amino Acid Sequence ; Antigens/*immunology ; Epitopes/immunology ; Major Histocompatibility Complex ; Protein Conformation ; T-Lymphocytes/*immunology ; Viral Vaccines
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  • 44
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J L -- New York, N.Y. -- Science. 1988 Feb 19;239(4842):863.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3124269" target="_blank"〉PubMed〈/a〉
    Keywords: GTP-Binding Proteins/metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Neoplasms/genetics ; Protein Conformation ; *Proto-Oncogene Proteins/genetics/metabolism ; Proto-Oncogene Proteins p21(ras)
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  • 45
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-11-11
    Description: A peptide 60 residues in length that corresponds to the homeo domain of Antennapedia (Antp), a protein governing development in Drosophila, was synthesized by segment condensation with protected peptide segments prepared on an oxime resin. A footprinting assay showed that the homeo domain binds specifically to a TAA repeat DNA sequence in the Antp gene. Thus the Antp homeo domain has a sequence-specific DNA binding property. The circular dichroism spectra of the homeo domain peptide showed the presence of a significant amount of alpha-helical structure in aqueous solution and in 50 percent trifluoroethanol. The alpha helicity measured in water appears to depend on the peptide concentration, which suggests that the peptide aggregates. These results support the hypothesis that the homeo domain binds to DNA through a helix-turn-helix motif.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mihara, H -- Kaiser, E T -- RR 862/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1988 Nov 11;242(4880):925-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Bioorganic Chemistry and Biochemistry, Rockefeller University, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2903553" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Chromatography, High Pressure Liquid ; Circular Dichroism ; DNA/*metabolism ; Drosophila/*growth & development ; Electrophoresis, Polyacrylamide Gel ; *Genes, Homeobox ; Insect Hormones/*chemical synthesis/genetics/metabolism ; Molecular Sequence Data ; Peptide Fragments/*chemical synthesis/genetics ; Protein Conformation ; Repetitive Sequences, Nucleic Acid
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  • 46
    Publication Date: 1988-06-17
    Description: The specificity of complex formation between cytochrome b5 (cyt b5) and cytochrome c (cyt c) is believed to involve the formation of salt linkages between specific carboxylic acid residues of cyt b5 with lysine residues on cyt c. Site-directed mutagenesis was used to alter the specified acidic residues of cyt b5 to the corresponding amide analogues, which resulted in a lower affinity for complex formation with cyt c. The dissociation of the complex under high pressure resulted in specific volume changes, the magnitude of which reflected the degree of solvation of the acidic residues in the proposed protein-protein interface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rodgers, K K -- Pochapsky, T C -- Sligar, S G -- GM 31756/GM/NIGMS NIH HHS/ -- GM 33775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Jun 17;240(4859):1657-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Illinois, Urbana 61801.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2837825" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cytochrome b Group/genetics/*metabolism ; Cytochrome c Group/*metabolism ; Cytochromes b5 ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrostatic Pressure ; Macromolecular Substances ; Mutation ; Protein Conformation ; Rats ; Solubility ; Thermodynamics
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  • 47
    Publication Date: 1988-12-16
    Description: Three variations to the structure of the nicotinamide adenine dinucleotide (NAD)-dependent L-lactate dehydrogenase from Bacillus stearothermophilus were made to try to change the substrate specificity from lactate to malate: Asp197----Asn, Thr246----Gly, and Gln102----Arg). Each modification shifts the specificity from lactate to malate, although only the last (Gln102----Arg) provides an effective and highly specific catalyst for the new substrate. This synthetic enzyme has a ratio of catalytic rate (kcat) to Michaelis constant (Km) for oxaloacetate of 4.2 x 10(6)M-1 s-1, equal to that of native lactate dehydrogenase for its natural substrate, pyruvate, and a maximum velocity (250 s-1), which is double that reported for a natural malate dehydrogenase from B. stearothermophilus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilks, H M -- Hart, K W -- Feeney, R -- Dunn, C R -- Muirhead, H -- Chia, W N -- Barstow, D A -- Atkinson, T -- Clarke, A R -- Holbrook, J J -- New York, N.Y. -- Science. 1988 Dec 16;242(4885):1541-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Bristol, United Kingdom.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3201242" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Geobacillus stearothermophilus/*enzymology/genetics ; Kinetics ; L-Lactate Dehydrogenase/*genetics/metabolism ; Malate Dehydrogenase/*metabolism ; Models, Molecular ; Protein Conformation ; Substrate Specificity
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  • 48
    Publication Date: 1988-03-11
    Description: Two-dimensional crystals of cholera toxin bound to receptors in a lipid membrane give diffraction extending to 15 A resolution. Three-dimensional structure determination reveals a ring of five B subunits on the membrane surface, with one-third of the A subunit occupying the center of the ring. The remaining mass of the A subunit appears to penetrate the hydrophobic interior of the membrane. Cleavage of a disulfide bond in the A subunit, which activates the toxin, causes a major conformational change, with the A subunit mostly exiting from the B ring.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ribi, H O -- Ludwig, D S -- Mercer, K L -- Schoolnik, G K -- Kornberg, R D -- AI21144/AI/NIAID NIH HHS/ -- GM07276-12/GM/NIGMS NIH HHS/ -- GM07365/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1988 Mar 11;239(4845):1272-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3344432" target="_blank"〉PubMed〈/a〉
    Keywords: *Cholera Toxin ; G(M1) Ganglioside ; *Liposomes ; Macromolecular Substances ; Microscopy, Electron ; Models, Molecular ; Phosphatidylethanolamines ; Protein Conformation
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  • 49
    Publication Date: 1988-08-26
    Description: Several complementary DNAs (cDNAs) coding for sphingolipid activator protein-2 (SAP-2) were isolated from a lambda gt-11 human hepatoma library by means of polyclonal antibodies. The nucleotide sequence of the largest cDNA was colinear with the derived amino acid sequence of SAP-2 and with the nucleotide sequence of the cDNA coding for the 70-kilodalton precursor of SAP-1 (SAP precursor cDNA). The coding sequence for mature SAP-2 was located 3' to that coding for SAP-1 in the SAP precursor cDNA. Both SAP-1 and SAP-2 appeared to be derived by proteolytic processing from a common precursor that is coded by a genetic locus on human chromosome 10. Two other domains similar to SAP-1 and SAP-2 were also identified in SAP precursor protein. Each of the four domains was approximately 80 amino acid residues long, had nearly identical placement of cysteine residues, potential glycosylation sites, and proline residues. Each domain also contained internal amino acid sequences capable of forming amphipathic helices separated by helix breakers to give a cylindrical hydrophobic domain that is probably stabilized by disulfide bridges. Protein immunoblotting experiments indicated that SAP precursor protein (70 kilodaltons) as well as immunoreactive SAP-like proteins of intermediate sizes (65, 50, and 31 kilodaltons) are present in most human tissues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Brien, J S -- Kretz, K A -- Dewji, N -- Wenger, D A -- Esch, F -- Fluharty, A L -- DK 38795/DK/NIDDK NIH HHS/ -- HD 18983/HD/NICHD NIH HHS/ -- NS 08682/NS/NINDS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1988 Aug 26;241(4869):1098-101.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurosciences, University of California, San Diego, La Jolla 92093.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2842863" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Carcinoma, Hepatocellular/analysis ; Chromosome Mapping ; Chromosomes, Human, Pair 10 ; DNA/genetics/isolation & purification ; Glycoproteins/analysis/*genetics ; Humans ; Liver Neoplasms/analysis ; Male ; Mice ; Mice, Nude ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Protein Conformation ; Protein Precursors/analysis/genetics ; Protein Processing, Post-Translational ; Rats ; Saposins ; Sphingolipid Activator Proteins ; Tissue Distribution
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  • 50
    Publication Date: 1988-02-05
    Description: To investigate the relation between protein stability and the predicted stabilities of individual secondary structural elements, residue Pro86 in an alpha-helix in phage T4 lysozyme was replaced by ten different amino acids. The x-ray crystal structures of seven of the mutant lysozymes were determined at high resolution. In each case, replacement of the proline resulted in the formation of an extended alpha-helix. This involves a large conformational change in residues 81 to 83 and smaller shifts that extend 20 angstroms across the protein surface. Unexpectedly, all ten amino acid substitutions marginally reduce protein thermostability. This insensitivity of stability to the amino acid at position 86 is not simply explained by statistical and thermodynamic criteria for helical propensity. The observed conformational changes illustrate a general mechanism by which proteins can tolerate mutations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alber, T -- Bell, J A -- Sun, D P -- Nicholson, H -- Wozniak, J A -- Cook, S -- Matthews, B W -- GM 20066/GM/NIGMS NIH HHS/ -- GM 21967/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Feb 5;239(4840):631-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3277275" target="_blank"〉PubMed〈/a〉
    Keywords: Enzyme Stability ; Escherichia coli/enzymology ; Models, Molecular ; Muramidase/*genetics/metabolism ; Mutation ; *Proline ; Protein Conformation ; T-Phages/*enzymology/genetics ; X-Ray Diffraction
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  • 51
    Publication Date: 1988-12-23
    Description: Homozygous inheritance of the Z-type mutant form of the alpha 1-antitrypsin (alpha 1AT) gene results in the most common form of alpha 1AT deficiency, a human hereditary disease associated with a high risk for the development of emphysema and an increased incidence of neonatal hepatitis. The alpha 1AT-synthesizing cells of individuals with the Z gene have normal alpha 1AT messenger RNA levels, but alpha 1AT secretion is markedly reduced secondary to accumulation of newly synthesized alpha 1AT in the rough endoplasmic reticulum. Crystallographic analysis of alpha 1AT predicts that in normal alpha 1AT, a negatively charged Glu342 is adjacent to positively charged Lys290. Thus the Glu342----Lys342 Z mutation caused the loss of a normal salt bridge, resulting in the intracellular aggregation of the Z molecule. The prediction was made that a second mutation in the alpha 1AT genet that changed the positively charged Lys290 to a negatively charged Glu290 would correct the secretion defect. When the second mutation was added to the Z-type complementary DNA, the resulting gene directed the synthesis and secretion of amounts of alpha 1AT similar to that directed by the normal alpha 1AT complementary DNA in an in vitro eukaryotic expression system. This suggests the possibility that a human hereditary disease can be corrected by inserting an additional mutation in the same gene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brantly, M -- Courtney, M -- Crystal, R G -- New York, N.Y. -- Science. 1988 Dec 23;242(4886):1700-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pulmonary Branch, National Heart, Lung, and Blood Institute, Bethesda, MD.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2904702" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Codon ; DNA/genetics ; Electrochemistry ; Endoplasmic Reticulum/metabolism ; Glutamates ; Glutamic Acid ; Humans ; Lysine ; *Mutation ; Protein Conformation ; RNA, Messenger/metabolism ; Structure-Activity Relationship ; Transfection ; alpha 1-Antitrypsin/*genetics/secretion ; alpha 1-Antitrypsin Deficiency
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  • 52
    Publication Date: 1988-08-12
    Description: The interaction between receptors and guanine nucleotide binding (G) proteins leads to G protein activation and subsequent regulation of effector enzymes. The molecular basis of receptor-G protein interaction has been examined by using the ability of the G protein from rods (transducin) to cause a conformational change in rhodopsin as an assay. Synthetic peptides corresponding to two regions near the carboxyl terminus of the G protein alpha subunit, Glu311-Val328 and Ile340-Phe350, compete with G protein for interaction with rhodopsin. Amino acid substitution studies show that Cys321 is required for this effect. Ile340-Phe350 and a modified peptide, acetyl-Glu311-Lys329-amide, mimic G protein effects on rhodopsin conformation, showing that these peptides bind to and stabilize the activated conformation of rhodopsin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamm, H E -- Deretic, D -- Arendt, A -- Hargrave, P A -- Koenig, B -- Hofmann, K P -- EY06062/EY/NEI NIH HHS/ -- EY06225/EY/NEI NIH HHS/ -- RP05369/PHS HHS/ -- etc. -- New York, N.Y. -- Science. 1988 Aug 12;241(4867):832-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Biophysics, University of Illinois College of Medicine, Chicago 60680.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3136547" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal ; Antigen-Antibody Complex ; Binding Sites ; GTP-Binding Proteins/*metabolism ; Kinetics ; Macromolecular Substances ; Membrane Proteins/*metabolism ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Retinal Pigments/*metabolism ; Rhodopsin/analogs & derivatives/*metabolism ; Transducin
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  • 53
    Publication Date: 1988-06-03
    Description: The human immunodeficiency virus type 1 (HIV-1) uses the CD4 protein as a receptor for infection of susceptible cells. A candidate structure for the HIV-1 binding site on the CD4 protein was identified by epitope mapping with a family of eight functionally distinct CD4-specific monoclonal antibodies in conjunction with a panel of large CD4-derived synthetic peptides. All of the seven epitopes that were located reside within two immunoglobulin-like disulfide loops situated between residues 1 and 168 of the CD4 protein. The CD4-specific monoclonal antibody OKT4A, a potent inhibitor of HIV-1 binding, recognized a site between residues 32 and 47 on the CD4 protein. By analogy to other members of the immunoglobulin superfamily of proteins, this particular region has been predicted to exist as a protruding loop. A synthetic analog of this loop (residues 25 to 58) showed a concentration-dependent inhibition of HIV-1-induced cell fusion. It is proposed that a loop extending from residues 37 to 53 of the CD4 protein is a binding site for the AIDS virus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jameson, B A -- Rao, P E -- Kong, L I -- Hahn, B H -- Shaw, G M -- Hood, L E -- Kent, S B -- AI25784/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1988 Jun 3;240(4857):1335-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2453925" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Monoclonal/immunology ; Binding, Competitive ; Cell Fusion ; Disulfides/metabolism ; Epitopes/immunology ; Fluorescent Antibody Technique ; HIV/immunology/*metabolism ; HIV Envelope Protein gp120 ; Humans ; Immunoglobulins ; Peptide Fragments/chemical synthesis/immunology ; Protein Conformation ; Radioimmunoassay ; Receptors, HIV ; Receptors, Virus/*immunology ; Retroviridae Proteins/immunology ; T-Lymphocytes, Helper-Inducer/immunology/*microbiology
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  • 54
    Publication Date: 1988-09-16
    Description: During the early stages of its developmental program, Dictyostelium discoideum expresses cell surface cyclic adenosine monophosphate (cyclic AMP) receptors. It has been suggested that these receptors coordinate the aggregation of individual cells into a multicellular organism and regulate the expression of a large number of developmentally regulated genes. The complementary DNA (cDNA) for the cyclic AMP receptor has now been cloned from lambda gt-11 libraries by screening with specific antiserum. The 2-kilobase messenger RNA (mRNA) that encodes the receptor is undetectable in growing cells, rises to a maximum at 3 to 4 hours of development, and then declines. In vitro transcribed complementary RNA, when hybridized to cellular mRNA, specifically arrests in vitro translation of the receptor polypeptide. When the cDNA is expressed in Dictyostelium cells, the undifferentiated cells specifically bind cyclic AMP. Cell lines transformed with a vector that expresses complementary mRNA (antisense) do not express the cyclic AMP receptor protein. These cells fail to enter the aggregation stage of development during starvation, whereas control and wild-type cells aggregate and complete the developmental program within 24 hours. The phenotype of the antisense transformants suggests that the cyclic AMP receptor is essential for development. The deduced amino acid sequence of the receptor reveals a high percentage of hydrophobic residues grouped in seven domains, similar to the rhodopsins and other receptors believed to interact with G proteins. It shares amino acid sequence identity and is immunologically cross-reactive with bovine rhodopsin. A model is proposed in which the cyclic AMP receptor crosses the bilayer seven times with a serine-rich cytoplasmic carboxyl terminus, the proposed site of ligand-induced receptor phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klein, P S -- Sun, T J -- Saxe, C L 3rd -- Kimmel, A R -- Johnson, R L -- Devreotes, P N -- GM 34933/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Sep 16;241(4872):1467-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological 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/3047871" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Dictyostelium/*growth & development/physiology ; Membrane Proteins/physiology ; Molecular Sequence Data ; Protein Conformation ; Receptors, Cyclic AMP/*physiology ; Solubility
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  • 55
    Publication Date: 1988-06-24
    Description: A 30-amino-acid segment of C/EBP, a newly discovered enhancer binding protein, shares notable sequence similarity with a segment of the cellular Myc transforming protein. Display of these respective amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The periodic array of at least four leucines was also noted in the sequences of the Fos and Jun transforming proteins, as well as that of the yeast gene regulatory protein, GCN4. The polypeptide segments containing these periodic arrays of leucine residues are proposed to exist in an alpha-helical conformation, and the leucine side chains extending from one alpha helix interdigitate with those displayed from a similar alpha helix of a second polypeptide, facilitating dimerization. This hypothetical structure is referred to as the "leucine zipper," and it may represent a characteristic property of a new category of DNA binding proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Landschulz, W H -- Johnson, P F -- McKnight, S L -- New York, N.Y. -- Science. 1988 Jun 24;240(4860):1759-64.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3289117" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Computer Simulation ; *DNA-Binding Proteins ; *Enhancer Elements, Genetic ; *Leucine ; Models, Molecular ; Protein Conformation ; Proto-Oncogene Proteins ; Structure-Activity Relationship
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  • 56
    Publication Date: 1988-07-08
    Description: The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 120 K and at 0.86 angstrom resolution. The pentadecapeptide crystallizes as a left-handed antiparallel double-stranded helical dimer with 5.6 amino acid residues per turn. The helix has an overall length of 31 angstroms and an average inner channel diameter of 4.80 angstroms. The channel of this crystalline form is void of ions or solvent molecules. The channel diameter varies from a minimum of 3.85 angstroms to a maximum of 5.47 angstroms and contains three pockets where the cross-channel contacts are 5.25 angstroms or greater. The range of variation seen for the phi and psi torsion angles of the backbone of the helix suggests that these potential ion binding sites can be induced to travel the length of the channel in a peristaltic manner by cooperatively varying these angles. The indole rings of the eight tryptophan residues of the dimer are overlapped in three separate regions on the outer surface of the helix when viewed down the barrel of the channel. This arrangement would permit long-chained lipid molecules to nest parallel to the outer channel surface between these protruding tryptophan regions and act like molecular splines to constrain helical twist deformations of the channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Langs, D A -- GM32812/GM/NIGMS NIH HHS/ -- HL32303/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1988 Jul 8;241(4862):188-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Foundation of Buffalo, NY 14203.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2455345" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography ; *Gramicidin ; *Ion Channels ; *Membrane Proteins ; Models, Molecular ; Protein Conformation
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  • 57
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-01-15
    Description: Tau protein is a family of microtubule binding proteins, heterogeneous in molecular weight, that are induced during neurite outgrowth and are found prominently in neurofibrillary tangles in Alzheimer's disease. The predicted amino acid sequences of two forms of tau protein from mouse brain were determined from complementary DNA clones. These forms are identical in their amino-terminal sequences but differ in their carboxyl-terminal domains. Both proteins contain repeated sequences that may be tubulin binding sites. The sequence suggests that tau is an elongated molecule with no extensive alpha-helical or beta-sheet domains. These complementary DNAs should enable the study of various functional domains of tau and the study of tau expression in normal and pathological states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, G -- Cowan, N -- Kirschner, M -- GM32099/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Jan 15;239(4837):285-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3122323" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; *Brain Chemistry ; Codon ; DNA/genetics ; DNA, Recombinant ; Mice ; Microtubule-Associated Proteins/*genetics ; Molecular Sequence Data ; Molecular Weight ; Nerve Tissue Proteins/genetics ; Protein Conformation ; RNA, Messenger/genetics ; Repetitive Sequences, Nucleic Acid ; tau Proteins
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  • 58
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-04-29
    Description: Apolipoprotein E is a plasma protein that serves as a ligand for low density lipoprotein receptors and, through its interaction with these receptors, participates in the transport of cholesterol and other lipids among various cells of the body. A mutant form of apolipoprotein E that is defective in binding to low density lipoprotein receptors is associated with familial type III hyperlipoproteinemia, a genetic disorder characterized by elevated plasma cholesterol levels and accelerated coronary artery disease. Apolipoprotein E is synthesized in various organs, including liver, brain, spleen, and kidney, and is present in high concentrations in interstitial fluid, where it appears to participate in cholesterol redistribution from cells with excess cholesterol to those requiring cholesterol. Apolipo-protein E also appears to be involved in the repair response to tissue injury; for example, markedly increased amounts of apolipoprotein E are found at sites of peripheral nerve injury and regeneration. Other functions of apolipoprotein E, unrelated to lipid transport, are becoming known, including immunoregulation and modulation of cell growth and differentiation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mahley, R W -- New York, N.Y. -- Science. 1988 Apr 29;240(4852):622-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gladstone Foundation Laboratories for Cardiovascular Disease, University of California, San Francisco 94140-0608.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3283935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Apolipoproteins E/genetics/*physiology ; Biological Transport ; Cholesterol/*metabolism ; Gene Expression Regulation ; Humans ; Hyperlipoproteinemia Type III/genetics/metabolism ; Immunity ; Lipid Metabolism ; Molecular Sequence Data ; Polymorphism, Genetic ; Protein Conformation ; Receptors, LDL/metabolism
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  • 59
    Publication Date: 1988-11-11
    Description: The repressors of temperate bacteriophages such as 434 and lambda control transcription by binding to a set of DNA operator sites. The different affinity of repressor for each of these sites ensures efficient regulation. High-resolution x-ray crystallography was used to study the DNA-binding domain of phage 434 repressor in complex with a synthetic DNA operator. The structure shows recognition of the operator by direct interactions with base pairs in the major groove, combined with the sequence-dependent ability of DNA to adopt the required conformation on binding repressor. In particular, a network of three-centered bifurcated hydrogen bonds among base pairs in the operator helps explain why 434 repressor prefers certain sites over others. These bonds, which stabilize the conformation of the bound DNA, can form only with certain sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aggarwal, A K -- Rodgers, D W -- Drottar, M -- Ptashne, M -- Harrison, S C -- GMS-29109/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Nov 11;242(4880):899-907.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3187531" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Binding Sites ; DNA/*metabolism ; *DNA-Binding Proteins ; Hydrogen Bonding ; Molecular Structure ; Nucleic Acid Conformation ; *Operator Regions, Genetic ; Protein Binding ; Protein Conformation ; Repressor Proteins/*metabolism ; Software ; Transcription Factors/*metabolism ; Viral Proteins/*metabolism ; Viral Regulatory and Accessory Proteins ; X-Ray Diffraction
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  • 60
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-10-14
    Description: Oligonucleotide-directed mutagenesis of the codons for glutamine-68 (Gln68), lysine-72 (Lys72), isoleucine-79 (Ile79), alanine-80 (Ala80), and threonine-81 (Thr81) of the Escherichia coli trpR (tryptophan aporepressor) gene was used to make mutant repressors with each of 36 different amino acid changes. Mutant repressors were tested for binding to each member of a set of 28 different operators closely related to the consensus trp operator. Of the 36 mutant repressors, 11 bind a subset of the 28 operators; 5 of these have new binding specificities. These new specificities indicate that the hydroxyl group of Thr81 makes a specific contact with one of the four critical base pairs in a trp operator half-site, and the methyl group of Thr81 determines specificity at a second, critical base pair. The Trp repressor does not use the first two amino acids of its "recognition alpha-helix," Ile79 and Ala80, to make sequence-specific DNA contacts, and interacts with its operator in vivo in a way fundamentally different from the way that phage lambda repressor, lambda Cro protein, and coliphage 434 repressor contact their respective binding sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bass, S -- Sorrells, V -- Youderian, P -- GM34150/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Oct 14;242(4876):240-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of Southern California, Los Angeles 90089-1481.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3140377" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/genetics ; Amino Acid Sequence ; Apoproteins/*genetics/metabolism ; Bacterial Proteins ; Base Sequence ; Binding Sites ; Codon ; DNA, Bacterial/*metabolism ; Escherichia coli/*genetics ; *Escherichia coli Proteins ; Glutamine/genetics ; Isoleucine/genetics ; Lysine/genetics ; Mutation ; Operator Regions, Genetic ; Protein Conformation ; Repressor Proteins/*genetics/metabolism ; Threonine/genetics ; Transcription Factors/*genetics
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  • 61
    Publication Date: 1988-08-12
    Description: A novel x-ray diffraction technique, multiple-wavelength anomalous dispersion (MAD) phasing, has been applied to the de novo determination of an unknown protein structure, that of the "blue" copper protein isolated from cucumber seedlings. This method makes use of crystallographic phases determined from measurements made at several wavelengths and has recently been made technically feasible through the use of intense, polychromatic synchrotron radiation together with accurate data collection from multiwire electronic area detectors. In contrast with all of the conventional methods of solving protein structures, which require either multiple isomorphous derivatives or coordinates of a similar structure for molecular replacement, this technique allows direct solution of the classical "phase problem" in x-ray crystallography. MAD phase assignment should be particularly useful for determining structures of small to medium-sized metalloproteins for which isomorphous derivatives are difficult or impossible to make. The structure of this particular protein provides new insights into the spectroscopic and redox properties of blue copper proteins, an important class of metalloproteins widely distributed in nature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guss, J M -- Merritt, E A -- Phizackerley, R P -- Hedman, B -- Murata, M -- Hodgson, K O -- Freeman, H C -- New York, N.Y. -- Science. 1988 Aug 12;241(4867):806-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Inorganic Chemistry, University of Sydney, New South Wales, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3406739" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Bacterial Proteins ; *Metalloproteins/metabolism ; Models, Molecular ; Plants/*metabolism ; Protein Conformation ; X-Ray Diffraction/methods
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  • 62
    Publication Date: 1988-10-21
    Description: Single-chain antigen-binding proteins are novel recombinant polypeptides, composed of an antibody variable light-chain amino acid sequence (VL) tethered to a variable heavy-chain sequence (VH) by a designed peptide that links the carboxyl terminus of the VL sequence to the amino terminus of the VH sequence. These proteins have the same specificities and affinities for their antigens as the monoclonal antibodies whose VL and VH sequences were used to construct the recombinant genes that were expressed in Escherichia coli. Three of these proteins, one derived from the sequence for a monoclonal antibody to growth hormone and two derived from the sequences of two different monoclonal antibodies to fluorescein, were designed, constructed, synthesized, purified, and assayed. These proteins are expected to have significant advantages over monoclonal antibodies in a number of applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bird, R E -- Hardman, K D -- Jacobson, J W -- Johnson, S -- Kaufman, B M -- Lee, S M -- Lee, T -- Pope, S H -- Riordan, G S -- Whitlow, M -- 1-R43-GM39646-01/GM/NIGMS NIH HHS/ -- 1-R43-GM39662-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Oct 21;242(4877):423-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genex Corporation, Gaithersburg, MD 20877.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3140379" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Escherichia coli/genetics ; Genes ; Genetic Vectors ; Humans ; *Immunoglobulin Heavy Chains/genetics ; *Immunoglobulin Light Chains/genetics ; *Immunoglobulin Variable Region/genetics ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; *Recombinant Proteins ; X-Ray Diffraction
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  • 63
    Publication Date: 1988-02-19
    Description: The crystal structure at 2.7 A resolution of the normal human c-H-ras oncogene protein lacking a flexible carboxyl-terminal 18 residue reveals that the protein consists of a six-stranded beta sheet, four alpha helices, and nine connecting loops. Four loops are involved in interactions with bound guanosine diphosphate: one with the phosphates, another with the ribose, and two with the guanine base. Most of the transforming proteins (in vivo and in vitro) have single amino acid substitutions at one of a few key positions in three of these four loops plus one additional loop. The biological functions of the remaining five loops and other exposed regions are at present unknown. However, one loop corresponds to the binding site for a neutralizing monoclonal antibody and another to a putative "effector region"; mutations in the latter region do not alter guanine nucleotide binding or guanosine triphosphatase activity but they do reduce the transforming activity of activated proteins. The data provide a structural basis for understanding the known biochemical properties of normal as well as activated ras oncogene proteins and indicate additional regions in the molecule that may possibly participate in other cellular functions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Vos, A M -- Tong, L -- Milburn, M V -- Matias, P M -- Jancarik, J -- Noguchi, S -- Nishimura, S -- Miura, K -- Ohtsuka, E -- Kim, S H -- CA 45593/CA/NCI NIH HHS/ -- GM 29287/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Feb 19;239(4842):888-93.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkely 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2448879" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/immunology ; Binding Sites ; Catalysis ; Crystallization ; Epitopes/immunology ; Escherichia coli/genetics ; GTP Phosphohydrolases ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Neoplasms/genetics ; Phosphates/metabolism ; Protein Conformation ; Proto-Oncogene Proteins/genetics/immunology/*metabolism ; Proto-Oncogene Proteins p21(ras) ; Recombinant Proteins/metabolism ; X-Ray Diffraction
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  • 64
    Publication Date: 1988-04-22
    Description: The three-dimensional structure of most enzymes is unknown; however, many enzymes may have structural motifs similar to those in the known structures of functionally related enzymes. Evidence is presented that an enzyme of unknown structure [Ile-transfer RNA (tRNA) synthetase] may share a functionally important structural motif with an enzyme of related function (Tyr-tRNA synthetase). This approach involves (i) identifying segments of Ile-tRNA synthetase that have been unusually conserved during evolution, (ii) predicting the function of one such segment by assuming a structural relation between Ile-tRNA synthetase and Tyr-tRNA synthetase, and (iii) testing the predicted function by mutagenesis and subsequent biochemical analysis. Random mutations were introduced by cassette mutagenesis into a ten-amino-acid segment of Ile-tRNA synthetase that was predicted to be involved in the formation of the binding site for isoleucine. Few amino acid substitutions appear to be tolerated in this region. However, one substitution (independently isolated twice) increased the Michaelis constant Km for isoleucine in the adenylate synthesis reaction by greater than 6000-fold, but had little effect on the Km for adenosine triphosphate, the apparent Km for tRNA, or the rate constant kcat.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clarke, N D -- Lien, D C -- Schimmel, P -- GM15539/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Apr 22;240(4851):521-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3282306" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acyl-tRNA Synthetases ; Binding Sites ; DNA Mutational Analysis ; Escherichia coli/enzymology ; *Isoleucine-tRNA Ligase ; Kinetics ; Protein Conformation ; Saccharomyces cerevisiae/enzymology ; Structure-Activity Relationship
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  • 65
    Publication Date: 1988-04-08
    Description: Site-directed mutagenesis of the large fragment of DNA polymerase I (Klenow fragment) yielded two mutant proteins lacking 3',5'-exonuclease activity but having normal polymerase activity. Crystallographic analysis of the mutant proteins showed that neither had any alteration in protein structure other than the expected changes at the mutation sites. These results confirmed the presumed location of the exonuclease active site on the small domain of Klenow fragment and its physical separation from the polymerase active site. An anomalous scattering difference Fourier of a complex of the wild-type enzyme with divalent manganese ion and deoxythymidine monophosphate showed that the exonuclease active site has binding sites for two divalent metal ions. The properties of the mutant proteins suggest that one metal ion plays a role in substrate binding while the other is involved in catalysis of the exonuclease reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Derbyshire, V -- Freemont, P S -- Sanderson, M R -- Beese, L -- Friedman, J M -- Joyce, C M -- Steitz, T A -- GM-22778/GM/NIGMS NIH HHS/ -- GM-28550/GM/NIGMS NIH HHS/ -- RR-01644/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1988 Apr 8;240(4849):199-201.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University Medical School, New Haven, CT 06510.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2832946" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Computer Graphics ; Crystallography ; DNA Mutational Analysis ; *DNA Polymerase I/genetics ; Escherichia coli/enzymology ; Exonucleases ; Metals ; Models, Molecular ; Protein Conformation ; Structure-Activity Relationship
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  • 66
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-05-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jasny, B -- New York, N.Y. -- Science. 1988 May 6;240(4853):722-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3363357" target="_blank"〉PubMed〈/a〉
    Keywords: *Information Systems ; Magnetic Resonance Spectroscopy ; Protein Conformation ; *Proteins ; X-Ray Diffraction
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  • 67
    Publication Date: 1988-08-05
    Description: The x-ray structures of the allosteric enzyme aspartate transcarbamylase from Escherichia coli have been solved and refined for both allosteric forms. The T form was determined in the presence of the heterotropic inhibitor cytidine triphosphate, CTP, while the R form was determined in the presence of the bisubstrate analog N-phosphonacetyl-L-aspartate. These two x-ray structures provide the starting point for an understanding of how allosteric enzymes are able to control the rates of metabolic pathways. Insights into the mechanisms of both catalysis and homotropic cooperativity have been obtained by using site-directed mutagenesis to probe residues thought to be critical to the function of the enzyme based on these x-ray structures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kantrowitz, E R -- Lipscomb, W N -- GM 06920/GM/NIGMS NIH HHS/ -- GM26237/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Aug 5;241(4866):669-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Boston College, MA 02167.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3041592" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Aspartate Carbamoyltransferase/*physiology ; Binding Sites ; Chemical Phenomena ; Chemistry ; Escherichia coli/*enzymology ; Macromolecular Substances ; Protein Conformation ; Structure-Activity Relationship
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  • 68
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-10-07
    Description: Voltage-sensitive ion channels mediate action potentials in electrically excitable cells and play important roles in signal transduction in other cell types. In the past several years, their protein components have been identified, isolated, and restored to functional form in the purified state. Na+ and Ca2+ channels consist of a principal transmembrane subunit, which forms the ion-conducting pore and is expressed with a variable number of associated subunits in different cell types. The principal subunits of voltage-sensitive Na+, Ca2+, and K+ channels are homologous members of a gene family. Models relating the primary structures of these principal subunits to their functional properties have been proposed, and experimental results have begun to define a functional map of these proteins. Coordinated application of biochemical, biophysical, and molecular genetic methods should lead to a clear understanding of the molecular basis of electrical excitability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Catterall, W A -- New York, N.Y. -- Science. 1988 Oct 7;242(4875):50-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, School of Medicine, University of Washington, Seattle 98195.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2459775" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Electric Conductivity ; Ion Channels/*physiology ; Membrane Glycoproteins/*genetics ; Models, Molecular ; Neurotoxins/metabolism ; Protein Conformation ; Receptors, Cholinergic/physiology
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  • 69
    Publication Date: 1988-07-01
    Description: The three-dimensional structure of ribulose-1,5-biphosphate carboxylase-oxygenase (RuBisCO), has been determined at 2.6 A resolution. This enzyme initiates photosynthesis by combining carbon dioxide with ribulose bisphosphate to form two molecules of 3-phosphoglycerate. In plants, RuBisCO is built from eight large (L) and eight small (S) polypeptide chains, or subunits. Both S chains and the NH2-terminal domain (N) of L are antiparallel beta, "open-face-sandwich" domains with four-stranded beta sheets and flanking alpha helices. The main domain (B) of L is an alpha/beta barrel containing most of the catalytic residues. The active site is in a pocket at the opening of the barrel that is partly covered by the N domain of a neighboring L chain. The domain contacts of the molecule and its conserved residues are discussed in terms of this structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapman, M S -- Suh, S W -- Curmi, P M -- Cascio, D -- Smith, W W -- Eisenberg, D S -- New York, N.Y. -- Science. 1988 Jul 1;241(4861):71-4.〈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/3133767" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Macromolecular Substances ; Molecular Sequence Data ; Plants/*enzymology ; Protein Conformation ; Rhodospirillum rubrum/enzymology ; *Ribulose-Bisphosphate Carboxylase ; X-Ray Diffraction
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  • 70
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-04-01
    Description: Tat, the transactivating protein from HIV, forms a metal-linked dimer with metal ions bridging cysteine-rich regions from each monomer. This novel arrangement is distinct from the "zinc finger" domain observed in other eukaryotic regulatory proteins. Ultraviolet absorption spectra show that Tat binds two Zn2+ or two Cd2+ ions per monomer, and electrophoresis of the Tat-metal complexes demonstrates that the protein forms metal-linked dimers. Partial proteolysis and circular dichroism spectra suggest that metal binding has its primary effects in the cysteine-rich region and relatively little effect on the folding of other regions. These results suggest new directions for biological studies and new approaches to drug design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frankel, A D -- Bredt, D S -- Pabo, C O -- GM31471/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Apr 1;240(4848):70-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, 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/2832944" target="_blank"〉PubMed〈/a〉
    Keywords: Cadmium/*metabolism ; Circular Dichroism ; Cobalt/metabolism ; Cysteine ; Electrophoresis, Polyacrylamide Gel ; Gene Products, tat ; HIV/*analysis ; Macromolecular Substances ; Metals/metabolism ; Oncogene Proteins, Viral ; Oxidation-Reduction ; Peptide Fragments/metabolism ; Peptide Hydrolases/metabolism ; Protein Conformation ; Spectrophotometry ; Sulfhydryl Compounds/metabolism ; Transcription Factors/*metabolism ; Zinc/*metabolism ; tat Gene Products, Human Immunodeficiency Virus
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  • 71
    Publication Date: 1988-11-11
    Description: The crystal structure of a complex containing the DNA-binding domain of lambda repressor and a lambda operator site was determined at 2.5 A resolution and refined to a crystallographic R factor of 24.2 percent. The complex is stabilized by an extensive network of hydrogen bonds between the protein and the sugar-phosphate backbone. Several side chains form hydrogen bonds with sites in the major groove, and hydrophobic contacts also contribute to the specificity of binding. The overall arrangement of the complex is quite similar to that predicted from earlier modeling studies, which fit the protein dimer against linear B-form DNA. However, the cocrystal structure reveals important side chain-side chain interactions that were not predicted from the modeling or from previous genetic and biochemical studies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jordan, S R -- Pabo, C O -- GM-31471/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Nov 11;242(4880):893-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics, Howard Hughes Medical Institute, 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/3187530" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Binding Sites ; Chemical Phenomena ; Chemistry ; Crystallization ; DNA/*metabolism ; *DNA-Binding Proteins ; Glutamine/metabolism ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; Nucleic Acid Conformation ; *Operator Regions, Genetic ; Protein Binding ; Protein Conformation ; Repressor Proteins/genetics/*metabolism ; Sugar Phosphates/metabolism ; Transcription Factors/*metabolism ; Viral Proteins ; Viral Regulatory and Accessory Proteins
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  • 72
    Publication Date: 1988-06-03
    Description: The alpha 2 and beta 2 adrenergic receptors, both of which are activated by epinephrine, but which can be differentiated by selective drugs, have opposite effects (inhibitory and stimulatory) on the adenylyl cyclase system. The two receptors are homologous with each other, rhodopsin, and other receptors coupled to guanine nucleotide regulatory proteins and they contain seven hydrophobic domains, which may represent transmembrane spanning segments. The function of specific structural domains of these receptors was determined after construction and expression of a series of chimeric alpha 2-,beta 2-adrenergic receptor genes. The specificity for coupling to the stimulatory guanine nucleotide regulatory protein lies within a region extending from the amino terminus of the fifth hydrophobic domain to the carboxyl terminus of the sixth. Major determinants of alpha 2- and beta 2-adrenergic receptor agonist and antagonist ligand binding specificity are contained within the seventh membrane spanning domain. Chimeric receptors should prove useful for elucidating the structural basis of receptor function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kobilka, B K -- Kobilka, T S -- Daniel, K -- Regan, J W -- Caron, M G -- Lefkowitz, R J -- HL 16037/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1988 Jun 3;240(4857):1310-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Medicine, Duke University Medical Center, Durham, NC 27710.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2836950" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Chimera ; Cloning, Molecular ; GTP-Binding Proteins/metabolism ; Humans ; Molecular Sequence Data ; Pindolol/analogs & derivatives/metabolism ; Protein Conformation ; Receptors, Adrenergic, alpha/*genetics ; Receptors, Adrenergic, beta/*genetics ; Yohimbine/metabolism
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  • 73
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1988-10-28
    Description: The principle of transition-state stabilization asserts that the occurrence of enzymic catalysis is equivalent to saying that an enzyme binds the transition state much more strongly than it binds the ground-state reactants. An outline of the origin and gradual acceptance of this idea is presented, and elementary transition-state theory is reviewed. It is pointed out that a misconception about the theory has led to oversimplification of the accepted expression relating catalysis and binding, and an amended expression is given. Some implications of the transition-state binding principle are then explored. The amended expression suggests that internal molecular dynamics may also play a role in enzymic catalysis. Although such effects probably do not make a major contribution, their magnitude is completely unknown. Two examples of recent advances due to application of the transition-state binding principle are reviewed, one pertaining to the zinc protease mechanism and the other to the generation of catalytic antibodies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kraut, J -- New York, N.Y. -- Science. 1988 Oct 28;242(4878):533-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, San Diego, La Jolla 92093.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3051385" target="_blank"〉PubMed〈/a〉
    Keywords: *Catalysis ; Chemistry, Physical ; DNA Mutational Analysis ; Enzymes/*physiology ; Physicochemical Phenomena ; Protein Conformation ; Structure-Activity Relationship
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  • 74
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-12-04
    Description: The relatively nonspecific single-stranded deoxyribonuclease, staphylococcal nuclease, was selectively fused to an oligonucleotide binding site of defined sequence to generate a hybrid enzyme. A cysteine was substituted for Lys116 in the enzyme by oligonucleotide-directed mutagenesis and coupled to an oligonucleotide that contained a 3'-thiol. The resulting hybrid enzyme cleaved single-stranded DNA at sites adjacent to the oligonucleotide binding site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Corey, D R -- Schultz, P G -- New York, N.Y. -- Science. 1987 Dec 4;238(4832):1401-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3685986" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; DNA, Single-Stranded/metabolism ; Hydrolysis ; Micrococcal Nuclease/*genetics/metabolism ; Models, Molecular ; Mutation ; Protein Conformation ; Staphylococcus aureus/enzymology/genetics ; Substrate Specificity
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  • 75
    Publication Date: 1987-02-20
    Description: Four clones were isolated from an adult human brain complementary DNA library with an oligonucleotide probe corresponding to the first 20 amino acids of the beta peptide of brain amyloid from Alzheimer's disease. The open reading frame of the sequenced clone coded for 97 amino acids, including the known amino acid sequence of this polypeptide. The 3.5-kilobase messenger RNA was detected in mammalian brains and human thymus. The gene is highly conserved in evolution and has been mapped to human chromosome 21.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldgaber, D -- Lerman, M I -- McBride, O W -- Saffiotti, U -- Gajdusek, D C -- New York, N.Y. -- Science. 1987 Feb 20;235(4791):877-80.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3810169" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/*genetics ; Amino Acid Sequence ; Amyloid/*genetics ; *Chromosomes, Human, Pair 21 ; Cloning, Molecular ; DNA/genetics ; Humans ; Protein Conformation ; RNA, Messenger/genetics ; Solubility ; Transcription, Genetic
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  • 76
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J L -- New York, N.Y. -- Science. 1987 Oct 30;238(4827):613-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3313727" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens ; Binding Sites ; *HLA Antigens ; Humans ; Models, Molecular ; Protein Conformation
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  • 77
    Publication Date: 1987-06-12
    Description: A basic amphiphilic alpha-helix is a structural feature common to many calmodulin-binding peptides and proteins. A set of fluorescent analogues of a very tight binding inhibitor (dissociation constant of 200 picomolar) of calmodulin has been synthesized. The fluorescent amino acid tryptophan has been systematically moved throughout the sequence of this peptide. The fluorescence properties for the peptides repeat every three to four residues and are consistent with the periodicity observed for an alpha-helix.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Neil, K T -- Wolfe, H R Jr -- Erickson-Viitanen, S -- DeGrado, W F -- New York, N.Y. -- Science. 1987 Jun 12;236(4807):1454-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3589665" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Calmodulin/metabolism ; Calmodulin-Binding Proteins/*metabolism ; Muscle, Smooth/enzymology ; Muscles/enzymology ; Myosin-Light-Chain Kinase/metabolism ; Protein Conformation ; Spectrometry, Fluorescence ; Tryptophan
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  • 78
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Racker, E -- New York, N.Y. -- Science. 1987 Feb 27;235(4792):959-61.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2434995" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteria/metabolism ; Cloning, Molecular ; Crystallization ; Humans ; Ion Channels/physiology ; Membrane Proteins/genetics/*physiology ; Mitochondria/metabolism ; Mutation ; Protein Conformation ; Receptors, Cell Surface/physiology
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  • 79
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-10-16
    Description: Chromatographic retention is determined by a relatively small number of amino acids located in a chromatographic contact region on the surface of a polypeptide. This region is determined by the mode of separation and the amino acid distribution within the polypeptide. The contact area may be as small as a few hundred square angstroms in bioaffinity chromatography. In contrast, the contact region in ion exchange, reversed phase, hydrophobic interaction and the other nonbioaffinity separation modes is much broader, ranging from one side to the whole external surface of a polypeptide. Furthermore, structural changes that alter the chromatographic contact region will alter chromatographic properties. Thus, although immunosorbents can be very useful in purifying proteins of similar primary structure, they will be ineffective in discriminating between small, random variations within a structure. Nonbioaffinity columns complement affinity columns in probing a much larger portion of solute surface and being able to discriminate between protein variants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Regnier, F E -- GM25431/GM/NIGMS NIH HHS/ -- GM33644/GM/NIGMS NIH HHS/ -- GM34759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Oct 16;238(4825):319-23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Purdue University, West Lafayette, IN 47907.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3310233" target="_blank"〉PubMed〈/a〉
    Keywords: Adsorption ; Amino Acids ; Chemical Phenomena ; Chemistry ; *Chromatography ; Chromatography, Affinity ; Chromatography, High Pressure Liquid ; Chromatography, Ion Exchange ; Protein Conformation ; Protein Denaturation ; *Proteins ; Recombinant Proteins ; Surface Properties
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  • 80
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-08-28
    Description: Adenosine monophosphate is required for the activation of glycogen phosphorylase b and for release of the inhibition of phosphorylase a by glucose. Two molecules of adenosine monophosphate (AMP) bind to symmetry related sites at the subunit interface of the phosphorylase dimer. Adenosine triphosphate (ATP) binds to the same site, but does not promote catalytic activity. The structure of glucose-inhibited phosphorylase a bound to AMP and also of the complex formed with glucose and ATP is described. Crystallographic refinement of these complexes reveals that structural changes are associated with AMP but not ATP binding. The origin of these effects can be traced to different effector binding modes exhibited by AMP and ATP, respectively. The conformational changes associated with AMP binding traverse multiple paths in the enzyme and link the effector and catalytic sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sprang, S -- Goldsmith, E -- Fletterick, R -- DK31507-05/DK/NIDDK NIH HHS/ -- GM00085-05/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Aug 28;237(4818):1012-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3616621" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Binding Sites ; Enzyme Activation ; Phosphorylase a/*metabolism ; Phosphorylases/*metabolism ; Protein Conformation
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  • 81
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-12-18
    Description: Interleukin-2 is an effector protein that participates in modulating the immune response; it has become a focal point for the study of lymphokine structure and function. The three-dimensional structure of the interleukin molecule has been solved to 3.0 angstrom resolution. Interleukin-2 has a novel alpha-helical tertiary structure that suggests one portion of the molecule forms a structural scaffold, which underlies the receptor binding facets of the molecule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brandhuber, B J -- Boone, T -- Kenney, W C -- McKay, D B -- A1-00631/PHS HHS/ -- A1-19762/PHS HHS/ -- New York, N.Y. -- Science. 1987 Dec 18;238(4834):1707-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3500515" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Interleukin-2/isolation & purification ; Mice ; Models, Molecular ; Protein Conformation ; Solvents ; X-Ray Diffraction
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  • 82
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-01-16
    Description: A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure (for example, approximately 2000 minima were sampled in a 300-picosecond trajectory). This is expected to have important consequences for the interpretation of the activity of transport proteins and enzymes. Different minima correspond to changes in the relative orientation of the helices coupled with side-chain rearrangements that preserve the close packing of the protein interior. The conformational space sampled by the simulation is similar to that found in the evolutionary development of the globins. Glasslike behavior is expected at low temperatures. The minima obtained from the trajectory do not satisfy certain criteria for ultrametricity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elber, R -- Karplus, M -- New York, N.Y. -- Science. 1987 Jan 16;235(4786):318-21.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3798113" target="_blank"〉PubMed〈/a〉
    Keywords: Models, Structural ; Motion ; *Myoglobin ; Protein Conformation ; Thermodynamics
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  • 83
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-09-25
    Description: The aspartate receptor of Escherichia coli and Salmonella typhimurium is a cell surface sensory transducer that binds extracellular aspartate and sends a transmembrane signal to the inside of the bacterium. The flexibility and allostery of this receptor was examined by placing sulfhydryl groups as potential cross-linking sites at targeted locations in the protein. Seven different mutant receptors were constructed, each containing a single cysteine residue at a different position in the primary structure. Intramolecular disulfide bond formation within oligomers of these mutant receptors is shown to trap structural fluctuations and to detect ligand-induced changes in structure. The results indicate that the receptor oligomer has a flexible, dynamic structure which undergoes a global change upon aspartate binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Falke, J J -- Koshland, D E Jr -- New York, N.Y. -- Science. 1987 Sep 25;237(4822):1596-600.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2820061" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacterial Proteins/*physiology ; *Chemotaxis ; Cloning, Molecular ; Cysteine ; Disulfides ; Macromolecular Substances ; Membrane Proteins/*physiology ; Mutation ; Protein Conformation ; *Receptors, Amino Acid ; Receptors, Neurotransmitter/*physiology ; Structure-Activity Relationship
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  • 84
    Publication Date: 1987-05-08
    Description: beta-lactamases are enzymes that protect bacteria from the lethal effects of beta-lactam antibiotics, and are therefore of considerable clinical importance. The crystal structure of beta-lactamase from the Gram-positive bacterium Staphylococcus aureus PC1 has been determined at 2.5 angstrom resolution. It reveals a molecule of novel topology, made up of two closely associated domains. The active site is located at the interface between the domains, with the key catalytic residue Ser70 at the amino terminus of a buried helix. Examination of the disposition of the functionally important residues within the active site depression leads to a model for the binding of a substrate and a functional analogy to the serine proteases. The unusual topology of the secondary structure units is relevant to questions concerning the evolutionary relation to the beta-lactam target enzymes of the bacterial cell wall.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herzberg, O -- Moult, J -- New York, N.Y. -- Science. 1987 May 8;236(4802):694-701.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3107125" target="_blank"〉PubMed〈/a〉
    Keywords: *Anti-Bacterial Agents/metabolism ; Binding Sites ; Biological Evolution ; Catalysis ; Crystallization ; Drug Resistance, Microbial ; Endopeptidases ; Models, Molecular ; Polyethylene Glycols ; Protein Conformation ; Serine ; Serine Endopeptidases ; Solvents ; Staphylococcus aureus/*enzymology ; *beta-Lactamases/metabolism ; beta-Lactams
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  • 85
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-12-04
    Description: The major coat protein of bacteriophage M13 is synthesized as a precursor, the procoat, with a typical leader (signal) sequence of 23 residues at its NH2-terminus. A fusion protein that contains the NH2-terminal 141 residues of cytoplasmic ribulokinase and all but the first ten residues of M13 procoat was made. The fusion protein inserts into the plasma membrane of Escherichia coli and is processed by leader peptidase to give rise to a leader peptide of 155 residues and the mature coat protein of 50 residues. The NH2-terminus of the leader peptide remains in the cytoplasm and is protected from protease added to the medium outside of the cell. This indicates that M13 procoat inserts into the membrane as a loop structure and that the NH2-terminus of a leader peptide remains within the cytoplasm during membrane insertion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuhn, A -- New York, N.Y. -- Science. 1987 Dec 4;238(4832):1413-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Microbiology Department, University of Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3317833" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Capsid/*metabolism ; Coliphages/*metabolism ; Escherichia coli/metabolism ; Membrane Proteins/*metabolism ; Molecular Sequence Data ; Protein Conformation ; Protein Precursors/metabolism ; Protein Processing, Post-Translational ; Protein Sorting Signals/metabolism ; Recombinant Fusion Proteins/metabolism
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  • 86
    Publication Date: 1987-11-20
    Description: Complementary DNA and genomic clones were isolated and sequenced corresponding to rat and human synaptophysin (p38), a major integral membrane protein of synaptic vesicles. The deduced amino acid sequences indicate an evolutionarily highly conserved protein that spans the membrane four times. Both amino and carboxyl termini face the cytoplasm, with the latter containing ten copies of a tyrosine-rich pentapeptide repeat. The structure of synaptophysin suggests that the protein may function as a channel in the synaptic vesicle membrane, with the carboxyl terminus serving as a binding site for cellular factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sudhof, T C -- Lottspeich, F -- Greengard, P -- Mehl, E -- Jahn, R -- New York, N.Y. -- Science. 1987 Nov 20;238(4830):1142-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular Genetics, University of Texas Health Science Center, Dallas 75235.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3120313" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cloning, Molecular ; *Membrane Proteins/genetics ; Molecular Sequence Data ; Protein Conformation ; Rats ; Solubility ; Synaptic Vesicles/ultrastructure ; Synaptophysin
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  • 87
    Publication Date: 1987-02-13
    Description: A monoclonal antibody bound to a protein antigen slows the rate of chemical modification of amino acid residues located at the epitope. By comparing the degree of acetylation of 18 lysine and 7 threonine residues in free and antibody-bound horse cytochrome c, a discontiguous, conformational epitope was characterized on this protein antigen. The new approach is particularly suitable to probe discontiguous and conformational epitopes, which are difficult to analyze by other procedures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burnens, A -- Demotz, S -- Corradin, G -- Binz, H -- Bosshard, H R -- New York, N.Y. -- Science. 1987 Feb 13;235(4790):780-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2433768" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/*immunology ; *Antigen-Antibody Complex ; Cytochrome c Group/*immunology ; Epitopes/*immunology ; Horses ; Humans ; Models, Molecular ; Protein Conformation ; Species Specificity
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  • 88
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-02-13
    Description: The Hin recombinase binds to specific sites on DNA and mediates a recombination event that results in DNA inversion. In order to define the DNA-binding domain of the Hin protein two peptides 31 and 52 amino acids long were synthesized. Even though the 31mer encompassed the sequence encoding the putative helix-coil-helix-binding domain, it was not sufficient for binding to the 26-base pair DNA crossover site. However, the 52mer specifically interacted with the site and also effectively inhibited the Hin-mediated recombination reaction. The 52mer bound effectively to both the 26-base pair complete site and to a 14-base pair "half site." Nuclease and chemical protection studies with the 52mer helped to define the DNA base pairs that contributed to the specificity of binding. The synthetic peptide provides opportunities for new approaches to the study of the nature of protein-DNA interaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bruist, M F -- Horvath, S J -- Hood, L E -- Steitz, T A -- Simon, M I -- GM-09534-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Feb 13;235(4790):777-80.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3027895" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemical synthesis/metabolism ; Base Composition ; DNA/*metabolism ; DNA Nucleotidyltransferases/*metabolism ; Peptides/chemical synthesis ; Protein Binding ; Protein Conformation
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  • 89
    Publication Date: 1987-11-06
    Description: Cytochrome c and cytochrome b5 form an electrostatically associated electron transfer complex. Computer models of this and related complexes that were generated by docking the x-ray structures of the individual proteins have provided insight into the specificity and mechanism of electron transfer reactions. Previous static modeling studies were extended by molecular dynamics simulations of a cytochrome c-cytochrome b5 intermolecular complex. The simulations indicate that electrostatic interactions at the molecular interface results in a flexible association complex that samples alternative interheme geometries and molecular conformations. Many of these transient geometries appear to be more favorable for electron transfer than those formed in the initial model complex. Of particular interest is a conformational change that occurred in phenylalanine 82 of cytochrome c that allowed the phenyl side chain to bridge the two cytochrome heme groups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wendoloski, J J -- Matthew, J B -- Weber, P C -- Salemme, F R -- New York, N.Y. -- Science. 1987 Nov 6;238(4828):794-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Central Research and Development Department, E. I. du Pont de Nemours and Company, Wilmington, DE 19898.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2823387" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Graphics ; Cytochrome b Group/*metabolism ; Cytochrome c Group/*metabolism ; Cytochromes b5 ; Electron Transport ; Kinetics ; Models, Molecular ; Protein Binding ; Protein Conformation
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  • 90
    Publication Date: 1987-08-21
    Description: The structure of the Asn102 mutant of trypsin was determined in order to distinguish whether the reduced activity of the mutant at neutral pH results from an altered active site conformation or from an inability to stabilize a positive charge on the active site histidine. The active site structure of the Asn102 mutant of trypsin is identical to the native enzyme with respect to the specificity pocket, the oxyanion hole, and the orientation of the nucleophilic serine. The observed decrease in rate results from the loss of nucleophilicity of the active site serine. This decreased nucleophilicity may result from stabilization of a His57 tautomer that is unable to accept the serine hydroxyl proton.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sprang, S -- Standing, T -- Fletterick, R J -- Stroud, R M -- Finer-Moore, J -- Xuong, N H -- Hamlin, R -- Rutter, W J -- Craik, C S -- AM26081/AM/NIADDK NIH HHS/ -- AM31507/AM/NIADDK NIH HHS/ -- GM24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Aug 21;237(4817):905-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3112942" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Asparagine ; Aspartic Acid ; Binding Sites ; Cattle ; Computer Simulation ; Crystallography ; Histidine ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Protein Conformation ; Rats ; Serine ; Structure-Activity Relationship ; *Trypsin
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  • 91
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-09-25
    Description: Previous experimental results along with the structural modeling presented indicate that a nucleotide fold starts in the amino-terminal part of Escherichia coli isoleucyl-transfer RNA synthetase, a single chain polypeptide of 939 amino acids. Internal deletions were created in the region of the nucleotide fold. A set of deletions that collectively span 145 contiguous amino acids yielded active enzymes. Further extensions of the deletions yielded inactive or unstable proteins. The three-dimensional structure of an evidently homologous protein suggests that the active deletions lack portions of a segment that connects two parts of the nucleotide fold. Therefore, the results imply that removal of major sections of the polypeptide that connects these two parts of the fold does not result in major perturbation of the nucleotide binding site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Starzyk, R M -- Webster, T A -- Schimmel, P -- GM23562/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Sep 25;237(4822):1614-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3306924" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Amino Acyl-tRNA Synthetases ; Bacterial Proteins ; Binding Sites ; Escherichia coli/enzymology ; Hydrogen Bonding ; *Isoleucine-tRNA Ligase ; *Methionine-tRNA Ligase ; Protein Conformation ; RNA, Transfer/*metabolism ; Structure-Activity Relationship ; Transfer RNA Aminoacylation
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  • 92
    Publication Date: 1987-10-16
    Description: Inhomogeneous broadening of the 760-nanometer photoproduct band of carboxymyoglobin at cryogenic temperatures has been demonstrated with a dynamic hole burning technique. Line-shape changes and frequency shifts in this spectral band are generated by ligand recombination and are shown not to be the result of structural relaxation below 60 K. The observation of dynamic hole burning exposes the relation between the structural disorder responsible for the inhomogeneous broadening and the well-known distributed ligand rebinding kinetics. The findings provide direct evidence for the functional relevance of conformational substrates in myoglobin rebinding. In addition, a general protocol for evaluating the relative contributions of structural relaxation and hole burning to the spectral changes accompanying rebinding in hemeproteins is presented.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Campbell, B F -- Chance, M R -- Friedman, J M -- HL-18708/HL/NHLBI NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- New York, N.Y. -- Science. 1987 Oct 16;238(4825):373-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉AT&T Bell Laboratories, Murray Hill, NJ 07974.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3659921" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carbon Monoxide/metabolism ; Kinetics ; Myoglobin/*metabolism ; Photochemistry ; Protein Binding ; Protein Conformation ; Spectrophotometry ; Spectrophotometry, Infrared ; Temperature
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  • 93
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-07-24
    Description: A novel approach to engineering enzyme specificity is presented in which a catalytic group from an enzyme is first removed by site-directed mutagenesis causing inactivation. Activity is then partially restored by substrates containing the missing catalytic functional group. Replacement of the catalytic His with Ala in the Bacillus amyloliquefaciens subtilisin gene (the mutant is designated His64Ala) by site-directed mutagenesis reduces the catalytic efficiency (kcat/Km) by a factor of a million when assayed with N-succinyl-L-Phe-L-Ala-L-Ala-L-Phe-p-nitroanilide (sFAAF-pNA). Model building studies showed that a His side chain at the P2 position of a substrate bound at the active site of subtilisin could be virtually superimposed on the catalytic His side chain of this serine protease. Accordingly, the His64Ala mutant hydrolyzes a His P2 substrate (sFAHF-pNA) up to 400 times faster than a homologous Ala P2 or Gln P2 substrate (sFAAF-pNA or sFAQF-pNA) at pH 8.0. In contrast, the wild-type enzyme hydrolyzes these three substrates with similar catalytic efficiencies. Additional data from substrate-dependent pH profiles and hydrolysis of large polypeptides indicate that the His64Ala mutant enzyme can recover partially the function of the lost catalytic histidine from a His P2 side chain on the substrate. Such "substrate-assisted catalysis" provides a new basis for engineering enzymes with very narrow and potentially useful substrate specificities. These studies also suggest a possible functional intermediate in the evolution of the catalytic triad of serine proteases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, P -- Wells, J A -- New York, N.Y. -- Science. 1987 Jul 24;237(4813):394-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3299704" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Enzymes/*metabolism ; Models, Molecular ; Molecular Conformation ; Mutation ; Protein Binding ; Protein Conformation ; Substrate Specificity ; Subtilisins/genetics/*metabolism
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  • 94
    Publication Date: 1987-06-05
    Description: The v-sis oncogene encodes a platelet-derived growth factor (PDGF)-related product whose transforming activity is mediated by its functional interaction with the PDGF receptor. PDGF, as well as processed forms of the v-sis gene product, is a disulfide-linked dimer with eight conserved cysteine residues in the minimum region necessary for biologic activity. Site-directed mutagenesis of the v-sis gene revealed that each conserved cysteine residue was required directly or indirectly for disulfide-linked dimer formation. However, substitution of serine for cysteine codons at any of four positions had no detrimental effect on transforming activity of the encoded v-sis protein. These results establish that interchain disulfide bonds are not essential in order for this protein to act as a functional ligand for the PDGF receptor. The remaining four substitutions of serine for cysteine each inactivated transforming function of the molecule. In each case this was associated with loss of a conformation shown to involve intramolecular disulfide bonds. These studies provide insight into the role of individual cysteine residues in determining the structure of the sis/PDGF molecule critical for biological activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giese, N A -- Robbins, K C -- Aaronson, S A -- New York, N.Y. -- Science. 1987 Jun 5;236(4806):1315-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3035718" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Polyomavirus Transforming ; Antigens, Viral, Tumor/analysis/*physiology ; Cell Transformation, Viral ; Cross Reactions ; Cysteine ; *Genes, Viral ; Mutation ; Oncogene Proteins, Viral/analysis/*physiology ; *Oncogenes ; Platelet-Derived Growth Factor/analysis/physiology ; Protein Conformation ; Protein Processing, Post-Translational ; Receptors, Cell Surface/metabolism ; Receptors, Platelet-Derived Growth Factor ; Retroviridae/*genetics ; Sarcoma Virus, Woolly Monkey/*genetics ; Serine ; Transfection
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 95
    Publication Date: 1987-01-23
    Description: The atomic structure of thymidylate synthase from Lactobacillus casei was determined at 3 angstrom resolution. The native enzyme is a dimer of identical subunits. The dimer interface is formed by an unusual association between five-stranded beta sheets present in each monomer. Comparison of known sequences with the Lactobacillus casei structure suggests that they all have a common core structure around which loops are inserted or deleted in different sequences. Residues from both subunits contribute to each active site. Two arginine side chains can contribute to binding phosphate on the substrate. The side chains of several conserved amino acids can account for other determinants of substrate binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hardy, L W -- Finer-Moore, J S -- Montfort, W R -- Jones, M O -- Santi, D V -- Stroud, R M -- AI 19358/AI/NIAID NIH HHS/ -- CA41323/CA/NCI NIH HHS/ -- GM 24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Jan 23;235(4787):448-55.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3099389" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography ; Deoxyuracil Nucleotides/metabolism ; Lactobacillus casei/enzymology ; Models, Molecular ; Protein Conformation ; Structure-Activity Relationship ; *Thymidylate Synthase/antagonists & inhibitors
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
    Publication Date: 1987-01-09
    Description: The structure of Mengo virus, a representative member of the cardio picornaviruses, is substantially different from the structures of rhino- and polioviruses. The structure of Mengo virus was solved with the use of human rhinovirus 14 as an 8 A resolution structural approximation. Phase information was then extended to 3 A resolution by use of the icosahedral symmetry. This procedure gives promise that many other virus structures also can be determined without the use of the isomorphous replacement technique. Although the organization of the major capsid proteins VP1, VP2, and VP3 of Mengo virus is essentially the same as in rhino- and polioviruses, large insertions and deletions, mostly in VP1, radically alter the surface features. In particular, the putative receptor binding "canyon" of human rhinovirus 14 becomes a deep "pit" in Mengo virus because of polypeptide insertions in VP1 that fill part of the canyon. The minor capsid peptide, VP4, is completely internal in Mengo virus, but its association with the other capsid proteins is substantially different from that in rhino- or poliovirus. However, its carboxyl terminus is located at a position similar to that in human rhinovirus 14 and poliovirus, suggesting the same autocatalytic cleavage of VP0 to VP4 and VP2 takes place during assembly in all these picornaviruses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luo, M -- Vriend, G -- Kamer, G -- Minor, I -- Arnold, E -- Rossmann, M G -- Boege, U -- Scraba, D G -- Duke, G M -- Palmenberg, A C -- New York, N.Y. -- Science. 1987 Jan 9;235(4785):182-91.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3026048" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Viral ; Antiviral Agents/metabolism ; Binding Sites ; Capsid ; Crystallography ; Macromolecular Substances ; *Mengovirus/analysis/ultrastructure ; Poliovirus ; Protein Conformation ; Receptors, Virus ; Rhinovirus
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  • 97
    Publication Date: 1987-03-13
    Description: It is a generally accepted principle of biology that a protein's primary sequence is the main determinant of its tertiary structure. However, the mechanism by which a protein proceeds from an unfolded, disordered state to a folded, relatively well-ordered, native conformation is obscure. Studies have been initiated to examine the "genetics" of protein folding, with mutants of bovine pancreatic trypsin inhibitor (BPTI) being used to explore the nature of the specific intramolecular interactions that direct this process. Previous work with BPTI chemically modified at cysteines 14 and 38 indicated that transient disulfide bond formation by these residues contributed to efficient folding at 25 degrees C. In the present work, mutants of BPTI in which these cysteines were replaced by alanines or threonines were made and the mutant proteins were produced by a heterologous Escherichia coli expression system. At 25 degrees C in vitro, the refolding behavior of these mutants was characterized by a pronounced lag. However, when expressed at 37 degrees C in E. coli, or when refolded at 37 degrees or 52 degrees C in vitro, the mutant proteins folded readily into the native conformation, albeit at a rate somewhat slower than that exhibited by wild-type BPTI. These results indicate that, at physiological temperatures, BPTI lacking cysteines 14 and 38 can refold quantitatively.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marks, C B -- Naderi, H -- Kosen, P A -- Kuntz, I D -- Anderson, S -- New York, N.Y. -- Science. 1987 Mar 13;235(4794):1370-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2435002" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Aprotinin/genetics ; *Cysteine ; Disulfides ; Escherichia coli/genetics ; Mutation ; Protein Conformation ; Temperature
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
    Publication Date: 1986-11-28
    Description: The three-dimensional structure of favin, the glucose- and mannose-binding lectin of Vicia faba (vetch, broad bean), has been determined at a resolution of 2.8 angstroms by molecular replacement. The crystals contain specifically bound glucose and provide the first high-resolution view of specific saccharide binding in a leguminous lectin. The structure is similar to those of concanavalin A (Con A) and green pea lectin; differences from Con A show that minimal changes are needed to accommodate the cyclic permutation in amino acid sequence between the two molecules. The molecule is an ellipsoidal dimer dominated by extensive beta structures. Each protomer contains binding sites for two divalent metal ions (Mn2+ and Ca2+) and a specific saccharide. Glucose is bound by favin in a cleft in the molecular surface and has noncovalent contacts primarily with two peptide loops, one of which contains several metal ion ligands. The specific carbohydrate-binding site is similar to that of Con A in location and general peptide folding, despite several differences in specific amino acid residues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reeke, G N Jr -- Becker, J W -- AI-11378/AI/NIAID NIH HHS/ -- GM-22663/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Nov 28;234(4780):1108-11.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3775378" target="_blank"〉PubMed〈/a〉
    Keywords: Concanavalin A ; *Lectins ; Plant Lectins ; Plants ; Protein Conformation
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
    Publication Date: 1986-11-07
    Description: Binding of antibodies to effector cells by way of receptors to their constant regions (Fc receptors) is central to the pathway that leads to clearance of antigens by the immune system. The structure and function of this important class of receptors on immune cells is addressed through the molecular characterization of Fc receptors (FcR) specific for the murine immunoglobulin G isotype. Structural diversity is encoded by two genes that by alternative splicing result in expression of molecules with highly conserved extracellular domains and different transmembrane and intracytoplasmic domains. The proteins encoded by these genes are members of the immunoglobulin supergene family, most homologous to the major histocompatibility complex molecule E beta. Functional reconstitution of ligand binding by transfection of individual FcR genes demonstrates that the requirements for ligand binding are encoded in a single gene. These studies demonstrate the molecular basis for the functional heterogeneity of FcR's, accounting for the possible transduction of different signals in response to a single ligand.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ravetch, J V -- Luster, A D -- Weinshank, R -- Kochan, J -- Pavlovec, A -- Portnoy, D A -- Hulmes, J -- Pan, Y C -- Unkeless, J C -- AI 24322/AI/NIAID NIH HHS/ -- GM 36306/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Nov 7;234(4777):718-25.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2946078" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; DNA/genetics ; Gene Expression Regulation ; Histocompatibility Antigens Class II/genetics ; Immunoglobulin G ; Lymphocytes/*physiology ; Macrophages/*physiology ; Membrane Proteins ; Mice ; Protein Conformation ; *Receptors, Fc/genetics ; Receptors, IgG ; Transcription, Genetic ; Transfection
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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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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1986-09-26
    Description: Fusions of the secreted protein alkaline phosphatase to an integral cytoplasmic membrane protein of Escherichia coli showed different activities depending on where in the membrane protein the alkaline phosphatase was fused. Fusions to positions in or near the periplasmic domain led to high alkaline phosphatase activity, whereas those to positions in the cytoplasmic domain gave low activity. Analysis of alkaline phosphatase fusions to membrane proteins of unknown structure may thus be generally useful in determining their membrane topologies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Manoil, C -- Beckwith, J -- New York, N.Y. -- Science. 1986 Sep 26;233(4771):1403-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3529391" target="_blank"〉PubMed〈/a〉
    Keywords: Alkaline Phosphatase/genetics ; Cell Membrane/ultrastructure ; Chromosome Deletion ; Escherichia coli/genetics ; Membrane Proteins/*genetics ; Mutation ; Plasmids ; Protein Conformation ; Recombinant Proteins/analysis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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