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  • Binding Sites
  • American Association for the Advancement of Science (AAAS)  (97)
  • American Association of Petroleum Geologists (AAPG)
  • 1985-1989  (97)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (97)
  • American Association of Petroleum Geologists (AAPG)
Years
Year
  • 1
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    Triggering of allostery in an enzyme by a point mutation: ornithine transcarbamoylase (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-08-04
    Description: The origin of allostery is an unanswered question in the evolution of complex regulatory proteins. Anabolic ornithine transcarbamoylase, a trimer of identical subunits, is not an allosteric enzyme per se. However, when the active-site residue arginine-106 of the Escherichia coli enzyme is replaced with a glycine through site-directed mutagenesis, the resultant mutant enzyme manifests substrate cooperativity that is absent in the wild-type enzyme. Both homotropic and heterotropic interactions occur in the mutant enzyme. The initial velocity saturation curves of the substrates, carbamoyl phosphate and L-ornithine, conform to the Hill equation. The observed cooperativity depends on substrate but not enzyme concentration. The finding underscores the possibility that a single mutation of the enzyme in the cell could turn transcarbamoylation into a regulatory junction in the biosynthesis of L-arginine and urea.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuo, L C -- Zambidis, I -- Caron, C -- DK01721/DK/NIDDK NIH HHS/ -- DK38089/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 4;245(4917):522-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Metcalf Center for Science and Engineering, Boston University, MA 02215.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2667139" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Binding Sites ; Carbamyl Phosphate/metabolism ; Escherichia coli/*enzymology ; Glycine ; Kinetics ; Macromolecular Substances ; *Mutation ; Ornithine/metabolism ; Ornithine Carbamoyltransferase/*genetics/metabolism ; Structure-Activity Relationship ; Zinc/pharmacology
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  • 2
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    The MHC-binding and gp120-binding functions of CD4 are separable (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-08-18
    Description: CD4 is a cell surface glycoprotein that is thought to interact with nonpolymorphic determinants of class II major histocompatibility (MHC) molecules. CD4 is also the receptor for the human immunodeficiency virus (HIV), binding with high affinity to the HIV-1 envelope glycoprotein, gp120. Homolog-scanning mutagenesis was used to identify CD4 regions that are important in class II MHC binding and to determine whether the gp120 and class II MHC binding sites of CD4 are related. Class II MHC binding was abolished by mutations in each of the first three immunoglobulin-like domains of CD4. The gp120 binding could be abolished without affecting class II MHC binding and vice versa, although at least one mutation examined reduced both functions significantly. These findings indicate that, while there may be overlap between the gp120 and class II MHC binding sites of CD4, these sites are distinct and can be separated. Thus it should be possible to design CD4 analogs that can block HIV infectivity but intrinsically lack the ability to affect the normal immune response by binding to class II MHC molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lamarre, D -- Ashkenazi, A -- Fleury, S -- Smith, D H -- Sekaly, R P -- Capon, D J -- New York, N.Y. -- Science. 1989 Aug 18;245(4919):743-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire d'Immunologie, Institut de Recherches Cliniques de Montreal, Quebec, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2549633" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens, Surface ; Binding Sites ; DNA, Recombinant ; HIV/*metabolism ; HIV Envelope Protein gp120 ; HLA-DP Antigens/immunology ; Histocompatibility Antigens Class II/*immunology ; Humans ; Hybridomas ; Mice ; Molecular Sequence Data ; Mutation ; Receptors, HIV ; Receptors, Virus/genetics/immunology/*metabolism ; Retroviridae Proteins/immunology/*metabolism ; Rosette Formation ; Structure-Activity Relationship ; T-Lymphocytes/immunology/metabolism ; Transfection
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  • 3
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    The DNA binding domain of the rat liver nuclear protein C/EBP is bipartite (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    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
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    Defining the inside and outside of a catalytic RNA molecule (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-07-21
    Description: Ribozymes are RNA molecules that catalyze biochemical reactions. Fe(II)-EDTA, a solvent-based reagent which cleaves both double- and single-stranded RNA, was used to investigate the structure of the Tetrahymena ribozyme. Regions of cleavage alternate with regions of substantial protection along the entire RNA molecule. In particular, most of the catalytic core shows greatly reduced cleavage. These data constitute experimental evidence that an RNA enzyme, like a protein enzyme, has an interior and an exterior. Determination of positions where the phosphodiester backbone of the RNA is on the inside or on the outside of the molecule provides major constraints for modeling the three-dimensional structure of the Tetrahymena ribozyme. This approach should be generally informative for structured RNA molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Latham, J A -- Cech, T R -- GM 11227-03/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Jul 21;245(4915):276-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2501870" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autoradiography ; Base Sequence ; Binding Sites ; Crystallography ; Edetic Acid ; Electrophoresis, Polyacrylamide Gel ; Ferrous Compounds ; Molecular Sequence Data ; Molecular Structure ; *Nucleic Acid Conformation ; *RNA Splicing ; RNA, Catalytic ; RNA, Fungal/analysis ; *RNA, Ribosomal/analysis/metabolism ; RNA, Transfer, Phe/analysis ; Tetrahymena/*genetics
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  • 5
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    Three-dimensional solution structure of a single zinc finger DNA-binding domain (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 6
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    Mouse lymph node homing receptor cDNA clone encodes a glycoprotein revealing tandem interaction domains (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-03-03
    Description: Isolation of a clone encoding the mouse lymph node homing receptor reveals a deduced protein with an unusual protein mosaic architecture, containing a separate carbohydrate-binding (lectin) domain, an epidermal growth factor-like (EGF) domain, and an extracellular precisely duplicated repeat unit, which preserves the motif seen in the homologous repeat structure of complement regulatory proteins and other proteins. The receptor molecule is potentially highly glycosylated, and contains an apparent transmembrane region. Analysis of messenger RNA transcripts reveals a predominantly lymphoid distribution in direct relation to the cell surface expression of the MEL-14 determinant, and the cDNA clone is shown to confer the MEL-14 epitope in heterologous cells. The many novel features, including ubiquitination, embodied in this single receptor molecule form the basis for numerous approaches to the study of cell-cell interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siegelman, M H -- van de Rijn, M -- Weissman, I L -- AI09022/AI/NIAID NIH HHS/ -- OIG43551/PHS HHS/ -- New York, N.Y. -- Science. 1989 Mar 3;243(4895):1165-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Stanford University School of Medicine, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2646713" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal ; Base Sequence ; Binding Sites ; Carbohydrate Metabolism ; Cell Membrane/metabolism ; DNA/*genetics ; Epidermal Growth Factor ; Glycosylation ; Lymph Nodes/*metabolism ; Membrane Glycoproteins/*genetics ; Mice ; Molecular Sequence Data ; Oligonucleotide Probes ; RNA, Messenger/genetics ; Receptors, Lymphocyte Homing ; Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; Transcription, Genetic
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  • 7
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    Structural origins of high-affinity biotin binding to streptavidin (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 8
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    The role of cis-acting promoter elements in tissue-specific albumin gene expression (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-04-21
    Description: The mouse albumin gene promoter has six closely spaced binding sites for nuclear proteins that are located between the TATA motif and nucleotide position -170. In vitro transcription with liver or spleen nuclear extracts of templates containing either mutated or polymerized albumin promoter elements establishes a hierarchy of the different protein binding sites for tissue-specific albumin gene transcription. The HNF-1 and C/EBP binding sites strongly activate transcription in a tissue-specific manner. The NF-Y binding site has a lower activation potential and is less specific, being equally efficient in liver and spleen nuclear extracts. The remaining elements are relatively weak activator sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maire, P -- Wuarin, J -- Schibler, U -- New York, N.Y. -- Science. 1989 Apr 21;244(4902):343-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departement de Biologie Moleculaire, Sciences II, Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2711183" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; CCAAT-Enhancer-Binding Proteins ; Carrier Proteins/metabolism/pharmacology ; Cell Nucleus/metabolism ; DNA-Binding Proteins/*metabolism ; Dicarboxylic Acid Transporters ; *Gene Expression Regulation/drug effects ; Liver/metabolism/ultrastructure ; Mice ; Nuclear Proteins/metabolism/pharmacology ; *Promoter Regions, Genetic ; Serum Albumin/*genetics ; Spleen/metabolism/ultrastructure ; Templates, Genetic ; Transcription Factors ; Transcription, Genetic/drug effects
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  • 9
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    NCI team remodels key AIDS virus enzyme (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 10
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    Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-12-01
    Description: A single-site mutant of Escherichia coli glutaminyl-synthetase (D235N, GlnRS7) that incorrectly acylates in vivo the amber suppressor supF tyrosine transfer RNA (tRNA(Tyr] with glutamine has been described. Two additional mutant forms of the enzyme showing this misacylation property have now been isolated in vivo (D235G, GlnRS10; I129T, GlnRS15). All three mischarging mutant enzymes still retain a certain degree of tRNA specificity; in vivo they acylate supE glutaminyl tRNA (tRNA(Gln] and supF tRNA(Tyr) but not a number of other suppressor tRNA's. These genetic experiments define two positions in GlnRS where amino acid substitution results in a relaxed specificity of tRNA discrimination. The crystal structure of the GlnRS:tRNA(Gln) complex provides a structural basis for interpreting these data. In the wild-type enzyme Asp235 makes sequence-specific hydrogen bonds through its side chain carboxylate group with base pair G3.C70 in the minor groove of the acceptor stem of the tRNA. This observation implicates base pair 3.70 as one of the identity determinants of tRNA(Gln). Isoleucine 129 is positioned adjacent to the phosphate of nucleotide C74, which forms part of a hairpin structure adopted by the acceptor end of the complexed tRNA molecule. These results identify specific areas in the structure of the complex that are critical to accurate tRNA discrimination by GlnRS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perona, J J -- Swanson, R N -- Rould, M A -- Steitz, T A -- Soll, D -- New York, N.Y. -- Science. 1989 Dec 1;246(4934):1152-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2686030" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Aspartic Acid ; Binding Sites ; Crystallization ; Escherichia coli/*enzymology/genetics ; Glutamine/metabolism ; Hydrogen Bonding ; Isoleucine ; Molecular Structure ; *Mutation ; RNA, Transfer, Gln/metabolism ; RNA, Transfer, Tyr ; Structure-Activity Relationship ; Substrate Specificity ; Suppression, Genetic
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  • 11
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    Function of a bacterial activator protein that binds to transcriptional enhancers (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-02-03
    Description: The nitrogen regulatory (NtrC) protein of enteric bacteria, which binds to sites that have the properties of transcriptional enhancers, is known to activate transcription by a form of RNA polymerase that contains the NtrA protein (sigma 54) as sigma factor (referred to as sigma 54-holoenzyme). In the presence of adenosine triphosphate, the NtrC protein catalyzes isomerization of closed recognition complexes between sigma 54-holoenzyme and the glnA promoter to open complexes in which DNA in the region of the transcription start site is locally denatured. NtrC is not required subsequently for maintenance of open complexes or initiation of transcription.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Popham, D L -- Szeto, D -- Keener, J -- Kustu, S -- GM38361/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Feb 3;243(4891):629-35.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, University of California, Berkley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2563595" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/analogs & derivatives/metabolism/pharmacology ; *Bacterial Proteins ; Base Sequence ; Binding Sites ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/*metabolism ; DNA-Directed RNA Polymerases/metabolism ; Deoxyribonuclease I ; *Enhancer Elements, Genetic ; Glutamate-Ammonia Ligase/genetics ; Heparin/pharmacology ; Molecular Sequence Data ; Mutation ; PII Nitrogen Regulatory Proteins ; Phosphorylation ; Promoter Regions, Genetic ; Salmonella typhimurium/*genetics ; Sigma Factor/metabolism ; *Trans-Activators ; Transcription Factors ; *Transcription, Genetic
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  • 12
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    Identification of a zinc finger protein that binds to the sterol regulatory element (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-08-11
    Description: Cholesterol balance in mammalian cells is maintained in part by sterol-mediated repression of gene transcription for the low density lipoprotein receptor and enzymes in the cholesterol biosynthetic pathway. A promoter sequence termed the sterol regulatory element (SRE) is essential for this repression. With the use of an oligonucleotide containing the SRE to screen a human hepatoma complementary DNA expression library, a clone for a DNA binding protein was isolated that binds to the conserved SRE octanucleotide in both a sequence-specific and a single-strand--specific manner. This protein contains seven highly conserved zinc finger repeats that exhibit striking sequence similarity to retroviral nucleic acid binding proteins (NBPs). We have designated the protein "cellular NBP" (CNBP). CNBP is expressed in a wide variety of tissues, is up regulated by sterols, and exhibits binding specificity that correlates with in vivo function. These properties are consistent with a role in sterol-mediated control of transcription.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rajavashisth, T B -- Taylor, A K -- Andalibi, A -- Svenson, K L -- Lusis, A J -- HL30568/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 11;245(4918):640-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of California, Los Angeles 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2562787" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Carcinoma, Hepatocellular/metabolism ; Cholesterol/biosynthesis ; DNA/*metabolism ; DNA Probes ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression Regulation/*drug effects ; Humans ; Hydroxymethylglutaryl CoA Reductases/genetics ; Liver Neoplasms/metabolism ; Metalloproteins/genetics/*metabolism ; Molecular Sequence Data ; Promoter Regions, Genetic ; *RNA-Binding Proteins ; Receptors, LDL/genetics ; *Regulatory Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; Sterols/*pharmacology ; Tumor Cells, Cultured
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  • 13
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    Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-12-01
    Description: The crystal structure of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) complexed with its cognate glutaminyl transfer RNA (tRNA(Gln] and adenosine triphosphate (ATP) has been derived from a 2.8 angstrom resolution electron density map and the known protein and tRNA sequences. The 63.4-kilodalton monomeric enzyme consists of four domains arranged to give an elongated molecule with an axial ratio greater than 3 to 1. Its interactions with the tRNA extend from the anticodon to the acceptor stem along the entire inside of the L of the tRNA. The complexed tRNA retains the overall conformation of the yeast phenylalanine tRNA (tRNA(Phe] with two major differences: the 3' acceptor strand of tRNA(Gln) makes a hairpin turn toward the inside of the L, with the disruption of the final base pair of the acceptor stem, and the anticodon loop adopts a conformation not seen in any of the previously determined tRNA structures. Specific recognition elements identified so far include (i) enzyme contacts with the 2-amino groups of guanine via the tRNA minor groove in the acceptor stem at G2 and G3; (ii) interactions between the enzyme and the anticodon nucleotides; and (iii) the ability of the nucleotides G73 and U1.A72 of the cognate tRNA to assume a conformation stabilized by the protein at a lower free energy cost than noncognate sequences. The central domain of this synthetase binds ATP, glutamine, and the acceptor end of the tRNA as well as making specific interactions with the acceptor stem.2+t is〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rould, M A -- Perona, J J -- Soll, D -- Steitz, T A -- New York, N.Y. -- Science. 1989 Dec 1;246(4934):1135-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2479982" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/*metabolism ; Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Anticodon ; Base Composition ; Base Sequence ; Binding Sites ; Biological Evolution ; Chemistry, Physical ; Crystallization ; Escherichia coli/*enzymology/genetics ; Molecular Sequence Data ; Molecular Structure ; Nucleic Acid Conformation ; Physicochemical Phenomena ; RNA, Bacterial/*metabolism ; RNA, Fungal ; RNA, Transfer, Amino Acid-Specific/*metabolism ; RNA, Transfer, Gln/*metabolism ; X-Ray Diffraction
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  • 14
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    Control of enzyme activity by an engineered disulfide bond (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-02-10
    Description: A novel approach to the control of enzyme catalysis is presented in which a disulfide bond engineered into the active-site cleft of bacteriophage T4 lysozyme is capable of switching the activity on and off. Two cysteines (Thr21----Cys and Thr142----Cys) were introduced by oligonucleotide-directed mutagenesis into the active-site cleft. These cysteines spontaneously formed a disulfide bond under oxidative conditions in vitro, and the catalytic activity of the oxidized (cross-linked) T4 lysozyme was completely lost. On exposure to reducing agent, however, the disulfide bond was rapidly broken, and the reduced (non-cross-linked) lysozyme was restored to full activity. Thus an enzyme has been engineered such that redox potential can be used to control catalytic activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsumura, M -- Matthews, B W -- GM21967/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Feb 10;243(4892):792-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2916125" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromatography, High Pressure Liquid ; DNA Mutational Analysis ; *Disulfides ; Models, Molecular ; Muramidase/*physiology ; *Protein Engineering ; Recombinant Proteins ; Structure-Activity Relationship ; T-Phages/enzymology
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  • 15
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    Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-07-28
    Description: The cloning of genes encoding mammalian DNA binding transcription factors for RNA polymerase II has provided the opportunity to analyze the structure and function of these proteins. This review summarizes recent studies that define structural domains for DNA binding and transcriptional activation functions in sequence-specific transcription factors. The mechanisms by which these factors may activate transcriptional initiation and by which they may be regulated to achieve differential gene expression are also discussed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mitchell, P J -- Tjian, R -- New York, N.Y. -- Science. 1989 Jul 28;245(4916):371-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biochemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2667136" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Cloning, Molecular ; DNA-Binding Proteins/*genetics/metabolism ; Gene Expression Regulation ; Molecular Sequence Data ; Protein Processing, Post-Translational ; RNA Polymerase II/*genetics/metabolism ; Repetitive Sequences, Nucleic Acid ; Transcription Factors/*genetics/metabolism ; *Transcription, Genetic
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  • 16
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    DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-06-23
    Description: The multiprotein-DNA complexes that participate in bacteriophage lambda site-specific recombination were used to study the combined effect of protein-induced bending and protein-mediated looping of DNA. The protein integrase (Int) is a monomer with two autonomous DNA binding domains of different sequence specificity. Stimulation of Int binding and cleavage at the low affinity core-type DNA sites required interactions with the high affinity arm-type sites and depended on simultaneous binding of the sequence-specific DNA bending protein IHF (integration host factor). The bivalent DNA binding protein is positioned at high affinity sites and directed, by a DNA bending protein, to interactions with distant lower affinity sites. Assembly of this complex is independent of protein-protein interactions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892171/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892171/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moitoso de Vargas, L -- Kim, S -- Landy, A -- AI-13544/AI/NIAID NIH HHS/ -- GM-33928/GM/NIGMS NIH HHS/ -- R01 GM033928/GM/NIGMS NIH HHS/ -- R01 GM062723/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Jun 23;244(4911):1457-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology and Medicine, Brown University, Providence, RI 02912.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2544029" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/metabolism/*pharmacology ; Bacteriophage lambda/enzymology/*genetics ; Binding Sites ; DNA Nucleotidyltransferases/*metabolism ; DNA Restriction Enzymes ; DNA Transposable Elements ; DNA, Bacterial/genetics/*metabolism ; DNA, Viral/genetics/*metabolism ; DNA-Binding Proteins/metabolism ; Integrases ; Integration Host Factors ; Mutation ; Nucleic Acid Conformation/*drug effects ; Recombination, Genetic
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  • 17
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    Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution (1989)
    American Association for the Advancement of Science (AAAS)
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    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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  • 18
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    In vivo footprinting of a muscle specific enhancer by ligation mediated PCR (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-11-10
    Description: In vivo protein-DNA interactions at the developmentally regulated enhancer of the mouse muscle creatine kinase (MCK) gene were examined by a newly developed polymerase chain reaction (PCR) footprinting procedure. This ligation mediated, single-sided PCR technique permits the exponential amplification of an entire sequence ladder. Several footprints were detected in terminally differentiated muscle cells where the MCK gene is actively transcribed. None were observed in myogenic cells prior to differentiation or in nonmuscle cells. Two footprints appear to correspond to sites that can bind the myogenic regulator MyoD1 in vitro, whereas two others represent muscle specific use of apparently general factors. Because MyoD1 is synthesized by undifferentiated myoblasts, these data imply that additional regulatory mechanisms must restrict the interaction between this protein and its target site prior to differentiation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mueller, P R -- Wold, B -- GM35526/GM/NIGMS NIH HHS/ -- RR07003/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1989 Nov 10;246(4931):780-6.〈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/2814500" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cell Line ; Creatine Kinase/*genetics ; DNA/*analysis/metabolism ; DNA-Binding Proteins/genetics/metabolism ; *Enhancer Elements, Genetic ; *Gene Amplification ; Gene Expression ; Genes, Regulator ; Mice ; Molecular Sequence Data ; Muscles/*enzymology ; *Polymerase Chain Reaction ; Protein Binding ; Protein Processing, Post-Translational ; Templates, Genetic ; Transcription Factor AP-2 ; Transcription Factors/genetics/metabolism
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  • 19
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    Domain separation in the activation of glycogen phosphorylase a (1989)
    American Association for the Advancement of Science (AAAS)
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    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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  • 20
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    Mutant potassium channels with altered binding of charybdotoxin, a pore-blocking peptide inhibitor (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-09-22
    Description: The inhibition by charybdotoxin of A-type potassium channels expressed in Xenopus oocytes was studied for several splicing variants of the Drosophila Shaker gene and for several site-directed mutants of this channel. Charybdotoxin blocking affinity is lowered by a factor of 3.5 upon replacing glutamate-422 with glutamine, and by a factor of about 12 upon substituting lysine in this position. Replacement of glutamate-422 by aspartate had no effect on toxin affinity. Thus, the glutamate residue at position 422 of this potassium channel is near or in the externally facing mouth of the potassium conduction pathway, and the positively charged toxin is electrostatically focused toward its blocking site by the negative potential set up by glutamate-422.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉MacKinnon, R -- Miller, C -- AR 19826/AR/NIAMS NIH HHS/ -- GM 31768/GM/NIGMS NIH HHS/ -- NS 07292/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1989 Sep 22;245(4924):1382-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02254.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2476850" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Charybdotoxin ; DNA Mutational Analysis ; Drosophila melanogaster ; Ions ; Membrane Proteins/genetics/metabolism/ultrastructure ; Potassium Channels/*metabolism/ultrastructure ; Scorpion Venoms/*metabolism ; Structure-Activity Relationship ; Transfection ; Xenopus laevis
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  • 21
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    The diageotropica mutant of tomato lacks high specific activity auxin binding sites (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-07-07
    Description: Tomato plants homozygous for the diageotropica (dgt) mutation exhibit morphological and physiological abnormalities which suggest that they are unable to respond to the plant growth hormone auxin (indole-3-acetic acid). The photoaffinity auxin analog [3H]5N3-IAA specifically labels a polypeptide doublet of 40 and 42 kilodaltons in membrane preparations from stems of the parental variety, VFN8, but not from stems of plants containing the dgt mutation. In roots of the mutant plants, however, labeling is indistinguishable from that in VFN8. These data suggest that the two polypeptides are part of a physiologically important auxin receptor system, which is altered in a tissue-specific manner in the mutant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hicks, G R -- Rayle, D L -- Lomax, T L -- DCB-8718731/DC/NIDCD NIH HHS/ -- New York, N.Y. -- Science. 1989 Jul 7;245:52-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331-2902.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11537490" target="_blank"〉PubMed〈/a〉
    Keywords: Affinity Labels ; Azides/*metabolism ; Binding Sites ; Hypocotyl/cytology/genetics/metabolism/ultrastructure ; Indoleacetic Acids/*analysis/*metabolism ; Intracellular Membranes/chemistry/metabolism/ultrastructure ; Lycopersicon esculentum/cytology/*genetics/metabolism/ultrastructure ; Microsomes/ultrastructure ; *Mutation ; Photolysis ; *Plant Growth Regulators ; Plant Proteins ; Plant Roots/cytology/genetics/metabolism/ultrastructure ; Receptors, Cell Surface/analysis/genetics/metabolism ; Time Factors
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  • 22
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    Identification by ENDOR of Trp191 as the free-radical site in cytochrome c peroxidase compound ES (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-08-18
    Description: The chemical identity of the amino acid free-radical site that represents one of the two oxidizing equivalents stored in the H2O2-oxidized intermediate (compound ES) of the mitochondrial heme enzyme, cytochrome c peroxidase (CcP) has been sought for almost a quarter of a century. Site-directed mutagenesis alone cannot yield this answer. Low-temperature 35-gigahertz (Q-band) electron nuclear double resonance (ENDOR) spectroscopy was used to examine compound ES prepared from proteins containing specifically deuterated methionine or tryptophan, as well as the amino acid replacement Trp51----Phe. The results definitely identify the site of the radical in compound ES as tryptophan, most likely Trp191.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sivaraja, M -- Goodin, D B -- Smith, M -- Hoffman, B M -- GM-33804/GM/NIGMS NIH HHS/ -- GM-41049/GM/NIGMS NIH HHS/ -- HL-13531/HL/NHLBI NIH HHS/ -- R01 GM041049/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 18;245(4919):738-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Northwestern University, Evanston, IL 60208.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2549632" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Cytochrome-c Peroxidase/genetics ; Electron Spin Resonance Spectroscopy ; Escherichia coli/enzymology ; Free Radicals ; Mutation ; Oxidation-Reduction ; *Peroxidases/genetics ; Recombinant Proteins ; *Tryptophan
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  • 23
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    Calicheamicin gamma 1I and DNA: molecular recognition process responsible for site-specificity (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-05-12
    Description: Calicheamicin gamma 1I is a recently discovered diyne-ene-containing antitumor antibiotic that cleaves DNA in a double-stranded fashion, a rarity among drugs, at specific sequences. It is proposed that the cutting specificity is due to a combination of the complementarity of the diyne-ene portion of the aglycone with DNA secondary structures and stabilization by association of the thiobenzoate-carbohydrate tail with the minor groove.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zein, N -- Poncin, M -- Nilakantan, R -- Ellestad, G A -- New York, N.Y. -- Science. 1989 May 12;244(4905):697-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cyanamid Company, Medical Research Division, Lederle Laboratories, Pearl River, NY 10965.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2717946" target="_blank"〉PubMed〈/a〉
    Keywords: *Aminoglycosides ; Animals ; Anti-Bacterial Agents/*metabolism ; Antibiotics, Antineoplastic ; Base Sequence ; Benzoates ; Binding Sites ; Carbohydrates ; Cattle ; Computer Simulation ; DNA/*metabolism ; Enediynes ; Models, Molecular ; Molecular Structure ; Nucleic Acid Conformation ; Structure-Activity Relationship
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  • 24
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    Leucine repeats and an adjacent DNA binding domain mediate the formation of functional cFos-cJun heterodimers (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-03-31
    Description: The discovery that the AP-1 family of enhancer binding factors includes a complex of the cellular Fos (cFos) and cellular Jun (cJun) proteins established a direct and important link between oncogenesis and transcriptional regulation. Homodimeric cJun protein synthesized in vitro is capable of binding selectively to AP-1 recognition sites, whereas the cFos polypeptide is not. When cotranslated, the cFos and cJun proteins can form a stable, heterodimeric complex with the DNA binding properties of AP-1/cJun. The related proteins Jun B and vJun are also able to form DNA binding complexes with cFos. Directed mutagenesis of the cFos protein reveals that a leucine repeat structure is required for binding to cJun, in a manner consistent with the proposed function of the "leucine zipper." A novel domain adjacent to, but distinct from, the leucine repeat of cFos is required for DNA binding by cFos-cJun heterodimers. Thus experimental evidence is presented that leucine repeats can mediate complex formation between heterologous proteins and that promotes further understanding of the molecular mechanisms underlying the function of two proto-oncogene products.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Turner, R -- Tjian, R -- New York, N.Y. -- Science. 1989 Mar 31;243(4899):1689-94.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biochemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2494701" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Chromatography, Affinity ; DNA/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression Regulation ; Humans ; *Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Mutation ; Oncogenes ; Protein Biosynthesis ; 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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    Parallel association of Fos and Jun leucine zippers juxtaposes DNA binding domains (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Direct Bronsted analysis of the restoration of activity to a mutant enzyme by exogenous amines (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-03-17
    Description: A true Bronsted analysis of proton transfer in an enzyme mechanism is made possible by the chemical rescue of an inactive mutant of aspartate aminotransferase, where the endogenous general base, Lys258, is replaced with Ala by site-directed mutagenesis. Catalytic activity is restored to this inactive mutant by exogenous amines. The eleven amines studied generate a Bronsted correlation with beta of 0.4 for the transamination of cysteine sulfinate, when steric effects are included in the regression analysis. Localized mutagenesis thus allows the classical Bronsted analysis of transition-state structure to be applied to enzyme-catalyzed reactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toney, M D -- Kirsch, J F -- GM07232/GM/NIGMS NIH HHS/ -- GM35393/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Mar 17;243(4897):1485-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2538921" target="_blank"〉PubMed〈/a〉
    Keywords: Amines ; Aspartate Aminotransferases/*metabolism ; Binding Sites ; Catalysis ; Escherichia coli/enzymology ; Kinetics ; Lysine ; Mutation ; Protons
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    The structure of the "second genetic code" (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-12-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waldrop, M M -- New York, N.Y. -- Science. 1989 Dec 1;246(4934):1122.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2479981" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/*metabolism ; Binding Sites ; Escherichia coli/*enzymology/genetics ; Molecular Structure ; RNA, Bacterial/*metabolism ; RNA, Transfer, Amino Acid-Specific/*metabolism ; RNA, Transfer, Gln/*metabolism
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    Molecular modeling of the HIV-1 protease and its substrate binding site (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 29
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    Signal transduction by the platelet-derived growth factor receptor (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-03-24
    Description: When platelet-derived growth factor (PDGF) binds to its receptor on a quiescent fibroblast or smooth muscle cell, it stimulates a remarkably diverse group of biochemical responses, including changes in ion fluxes, activation of several kinases, alterations in cell shape, increased transcription of a number of genes, and stimulation of enzymes that regulate phospholipid metabolism. These and other reactions culminate, hours later, in DNA replication and cell division. How does the receptor for PDGF recognize and bind its specific ligand and then transduce this signal across the cell membrane via a single membrane-spanning region? Which of the immediate cellular responses are directly involved in the biochemical pathways that lead to DNA synthesis? How does the PDGF receptor trigger a diverse group of responses? Recent studies of the PDGF receptor have provided insight into these issues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, L T -- HL-32898/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1989 Mar 24;243(4898):1564-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Francisco 94143-0724.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2538922" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Gene Expression Regulation ; Humans ; Membrane Proteins/physiology/ultrastructure ; Molecular Structure ; Platelet-Derived Growth Factor/*physiology ; Protein-Tyrosine Kinases/physiology ; Receptors, Cell Surface/*physiology/ultrastructure ; Receptors, Platelet-Derived Growth Factor
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    Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease (1989)
    American Association for the Advancement of Science (AAAS)
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    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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    Functionally distinct NF-kappa B binding sites in the immunoglobulin kappa and IL-2 receptor alpha chain genes (1989)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1989-04-28
    Description: The interleukin-2 receptor alpha (IL-2R alpha) chain gene contains a sequence similar to the immunoglobulin (Ig) kappa (kappa) enhancer NF-kappa B binding site. This site, which is bound by the nuclear protein, NF-kappa B, is critical for Ig kappa gene expression. The major T cell nuclear factor that binds to the IL-2R alpha site in vitro appears indistinguishable from NF-kappa B. NF-kappa B binds to IL-2R alpha and kappa sequences with similar affinities; however, only the kappa site potently activates transcription from heterologous promoters. Thus, high-affinity NF-kappa B binding in vitro cannot be equated with transcriptional activation in vivo. Mutation of the NF-kappa B binding site in the context of an IL-2 R alpha promoter construct markedly diminished promoter activity in human T cell lymphotropic virus type I (HTLV-I)-transformed MT-2 cells but not in phorbol myristate acetate-stimulated Jurkat T cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cross, S L -- Halden, N F -- Lenardo, M J -- Leonard, W J -- New York, N.Y. -- Science. 1989 Apr 28;244(4903):466-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2497520" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cell Line, Transformed ; DNA-Binding Proteins/*metabolism ; *Enhancer Elements, Genetic ; *Gene Expression Regulation ; HIV-1/genetics ; HeLa Cells ; Human T-lymphotropic virus 1 ; Humans ; Immunoglobulin kappa-Chains/*genetics ; Mice ; Molecular Sequence Data ; Mutation ; NF-kappa B ; Promoter Regions, Genetic ; Receptors, Interleukin-2/*genetics ; T-Lymphocytes/metabolism ; Tetradecanoylphorbol Acetate/pharmacology ; Transcription Factors/*metabolism ; Transcription, Genetic
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    Cellular transcription factors and regulation of IL-2 receptor gene expression by HTLV-I tax gene product (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-07-01
    Description: Expression of the interleukin-2 receptor (IL-2R alpha) gene is activated by the transcriptional activator protein, Tax (previously referred to as the tat gene product), encoded by the human T-cell leukemia virus (HTLV-I). Multiple protein binding sites for specific DNA-protein interactions were identified over the upstream IL-2R alpha transcriptional regulatory sequences. However, only one region, which includes the sequence motif GGGGAATCTCCC, was required for activation by both the tax gene product and mitogenic stimulation. Remarkably, this sequence also bound the nuclear factor NF kappa B, which is important for induction of kappa-immunoglobulin gene expression. A model is presented whereby regulation of cellular gene expression by the HTLV-I tax gene product occurs via an indirect mechanism that may involve a post-translational modification of preexistent cellular transcription factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ruben, S -- Poteat, H -- Tan, T H -- Kawakami, K -- Roeder, R -- Haseltine, W -- Rosen, C A -- New York, N.Y. -- Science. 1988 Jul 1;241(4861):89-92.〈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/2838905" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Cell Line ; DNA/genetics/metabolism ; Deltaretrovirus/*genetics ; Gene Expression Regulation/*drug effects ; Gene Products, tat ; Immunoglobulin kappa-Chains/genetics ; Mutation ; Plasmids ; Promoter Regions, Genetic ; Receptors, Immunologic/*genetics ; Receptors, Interleukin-2 ; Regulatory Sequences, Nucleic Acid ; Transcription Factors/genetics/metabolism/*pharmacology
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    Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences (1988)
    American Association for the Advancement of Science (AAAS)
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    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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    HIV-infected cells are killed by rCD4-ricin A chain (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-11-25
    Description: The gp120 envelope glycoprotein of the human immunodeficiency virus (HIV), which is expressed on the surface of many HIV-infected cells, binds to the cell surface molecule CD4. Soluble derivatives of recombinant CD4 (rCD4) that bind gp120 with high affinity are attractive vehicles for targeting a cytotoxic reagent to HIV-infected cells. Soluble rCD4 was conjugated to the active subunit of the toxin ricin. This conjugate killed HIV-infected H9 cells but was 1/1000 as toxic to uninfected H9 cells (which do not express gp120) and was not toxic to Daudi cells (which express major histocompatibility class II antigens, the putative natural ligand for cell surface CD4). Specific killing of infected cells can be blocked by rgp120, rCD4, or a monoclonal antibody to the gp120 binding site on CD4.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Till, M A -- Ghetie, V -- Gregory, T -- Patzer, E J -- Porter, J P -- Uhr, J W -- Capon, D J -- Vitetta, E S -- CA-09082/CA/NCI NIH HHS/ -- CA-28149/CA/NCI NIH HHS/ -- CA-41081/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1988 Nov 25;242(4882):1166-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, 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/2847316" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Differentiation, T-Lymphocyte/*administration & dosage/immunology ; Binding Sites ; Cell Line ; Cell Survival ; Electrophoresis, Polyacrylamide Gel ; HIV/*immunology ; HIV Envelope Protein gp120 ; Histocompatibility Antigens Class II/immunology ; Humans ; Recombinant Proteins/administration & dosage/immunology ; Retroviridae Proteins/*immunology/metabolism ; Ricin/metabolism/*pharmacology ; T-Lymphocytes/immunology/microbiology/physiology
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    Identification of a putative regulator of early T cell activation genes (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-07-08
    Description: Molecules involved in the antigen receptor-dependent regulation of early T cell activation genes were investigated with the use of functional sequences of the T cell activation-specific enhancer of interleukin-2 (IL-2). One of these sequences forms a protein complex, NFAT-1, specifically with nuclear extracts of activated T cells. This complex appeared 10 to 25 minutes before the activation of the IL-2 gene. Studies with inhibitors of protein synthesis indicated that the time of synthesis of the activator of the IL-2 gene in Jurkat T cells corresponds to the time of appearance of NFAT-1. NFAT-1, or a very similar protein, bound functional sequences of the long terminal repeat (LTR) of the human immunodeficiency virus type 1; the LTR of this virus is known to be stimulated during early T cell activation. The binding site for this complex activated a linked promoter after transfection into antigen receptor-activated T cells but not other cell types. These characteristics suggest that NFAT-1 transmits signals initiated at the T cell antigen receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaw, J P -- Utz, P J -- Durand, D B -- Toole, J J -- Emmel, E A -- Crabtree, G R -- CA 01048/CA/NCI NIH HHS/ -- CA 39612/CA/NCI NIH HHS/ -- HL 33942/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1988 Jul 8;241(4862):202-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Stanford University, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3260404" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA-Binding Proteins/*physiology ; *Enhancer Elements, Genetic ; HIV/genetics ; Humans ; In Vitro Techniques ; Interleukin-2/genetics ; *Lymphocyte Activation ; Nuclear Proteins/*physiology ; Receptors, Antigen, T-Cell/*physiology ; *Regulatory Sequences, Nucleic Acid ; T-Lymphocytes/*physiology ; Transcription Factors/*physiology
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    Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    The gramicidin pore: crystal structure of a cesium complex (1988)
    American Association for the Advancement of Science (AAAS)
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    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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    Alpha-2-antiplasmin: a serpin with two separate but overlapping reactive sites (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-08-05
    Description: Although the proteinase inhibitor alpha-2-antiplasmin (alpha 2AP) is known to control the activity of plasmin through rapid formation of stable complexes, it also efficiently inactivates chymotrypsin. These interactions are shown to occur at adjacent, overlapping sites so that plasmin attacks the inhibitor at an Arg364-Met365 peptide bond, while chymotrypsin interacts at a Met365-Ser366 sequence one residue downstream. Thus, a naturally occurring plasma serine proteinase inhibitor can have multiple specificities through interactions at adjacent sites. It also illustrates the potential flexibility of the reactive site loop in this class of inhibitors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Potempa, J -- Shieh, B H -- Travis, J -- New York, N.Y. -- Science. 1988 Aug 5;241(4866):699-700.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, Jagiellonian University, Cracow, Poland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2456616" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Carboxypeptidase B ; Carboxypeptidases/metabolism ; Carboxypeptidases A ; Chromatography, Gel ; Chromatography, High Pressure Liquid ; Chymotrypsin/antagonists & inhibitors/metabolism ; Electrophoresis, Polyacrylamide Gel ; Humans ; Molecular Sequence Data ; Peptide Fragments/metabolism ; Protease Inhibitors ; alpha-2-Antiplasmin/*metabolism
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    DNA binding by proteins (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Intron existence predated the divergence of eukaryotes and prokaryotes (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-11-25
    Description: Nucleotide sequences for the nuclear genes encoding chloroplast (GapA and GapB) and cytosolic (GapC) glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) from Arabidopsis thaliana were determined. Comparison of nucleotide sequences indicates that the divergence of chloroplast and cytosolic GAPDH genes preceded the divergence of prokaryotes and eukaryotes. In addition, some intron-exon junctions are conserved among GapB, GapC, and chicken GAPDH genes. These results provide evidence at the molecular level to support the idea that introns existed before the divergence of prokaryotes and eukaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shih, M C -- Heinrich, P -- Goodman, H M -- New York, N.Y. -- Science. 1988 Nov 25;242(4882):1164-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, MA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3055302" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; *Biological Evolution ; *Cells ; Chickens/genetics ; Chloroplasts/enzymology ; Cytosol/enzymology ; Escherichia coli/genetics ; *Eukaryotic Cells ; Exons ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics/metabolism ; *Introns ; Molecular Sequence Data ; NAD/metabolism ; NADP/metabolism ; Plants/genetics ; *Prokaryotic Cells
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    A specific amino acid binding site composed of RNA (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-06-24
    Description: A specific, reversible binding site for a free amino acid is detectable on the intron of the Tetrahymena self-splicing ribosomal precursor RNA. The site selects arginine among the natural amino acids, and prefers the L- to the D-amino acid. The dissociation constant is in the millimolar range, and amino acid binding is at or in the catalytic rG splicing substrate site. Occupation of the G site by L-arginine therefore inhibits splicing by inhibiting the binding of rG, without inhibition of later reactions in the splicing reaction sequence. Arginine binding specificity seems to be directed at the side chain and the guanidino radical, and the alpha-amino and carboxyl groups are dispensable for binding. The arginine site can be placed within the G site by structural homology, with consequent implications for RNA-amino acid interaction, for the origin of the genetic code, for control of RNA activities, and for further catalytic capabilities for RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yarus, M -- R37 GM30881/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Jun 24;240(4860):1751-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3381099" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arginine/*metabolism ; Binding Sites ; Catalysis ; Genetic Code ; Guanosine Triphosphate/metabolism ; Kinetics ; Magnesium/metabolism ; Models, Molecular ; *RNA Splicing ; RNA, Ribosomal/*physiology ; Structure-Activity Relationship ; Tetrahymena
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    Zipping up DNA binding proteins (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-06-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J L -- New York, N.Y. -- Science. 1988 Jun 24;240(4860):1732.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3381097" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *DNA-Binding Proteins ; Leucine ; Structure-Activity Relationship
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    The DNA-binding properties of the major regulatory protein alpha 4 of herpes simplex viruses (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-03-25
    Description: The transition from the expression of alpha, the first set of five herpes simplex virus genes expressed after infection, to beta and gamma genes, expressed later in infection, requires the participation of infected cell protein 4 (alpha 4), the major viral regulatory protein. The alpha 4 protein is present in complexes formed by proteins extracted from infected cells and viral DNA fragments derived from promoter domains. This report shows that the alpha 4 protein forms specific complexes with DNA fragments derived from 5' transcribed noncoding domains of late (gamma 2) genes whose expression requires viral DNA synthesis as well as functional alpha 4 protein. Some of the DNA fragments to which alpha 4 binds do not contain homologs of the previously reported DNA binding site consensus sequence, suggesting that alpha 4 may recognize and interact with more than one type of DNA binding site. The alpha 4 proteins can bind to DNA directly. A posttranslationally modified form of the alpha 4 protein designated alpha 4c differs from the alpha 4a and alpha 4b forms with respect to its affinity for DNA fragments differing in the nucleotide sequences of the binding sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Michael, N -- Spector, D -- Mavromara-Nazos, P -- Kristie, T M -- Roizman, B -- AI124009/AI/NIAID NIH HHS/ -- CA08494/CA/NCI NIH HHS/ -- CA19264/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1988 Mar 25;239(4847):1531-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marjorie B. Kovler Viral Oncology Laboratories, University of Chicago, IL 60637.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2832940" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA, Viral/*metabolism ; DNA-Binding Proteins ; Electrophoresis, Polyacrylamide Gel ; Gene Expression Regulation ; Genes, Viral ; *Immediate-Early Proteins ; Immunoassay ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; Simplexvirus/*analysis/genetics ; Transcription Factors ; Viral Proteins/*metabolism
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    A specific, highly active malate dehydrogenase by redesign of a lactate dehydrogenase framework (1988)
    American Association for the Advancement of Science (AAAS)
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    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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    Many transcription factors interact synergistically with steroid receptors (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-12-09
    Description: Progesterone (PRE) or glucocorticoid receptor (GRE) DNA binding sites are often found clustered with binding sites for other transcription factors. Individual protein binding sites were tested without the influence of adjacent factors by analyzing isolated combinations of several transcription factor binding sites with PREs or GREs. All show strong synergistic effects on steroid induction. The degree of synergism is inversely related to the strength of the GRE. Thus, a steroid responsive unit can be composed of several modules that, if positioned correctly, act synergistically.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schule, R -- Muller, M -- Kaltschmidt, C -- Renkawitz, R -- New York, N.Y. -- Science. 1988 Dec 9;242(4884):1418-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck Institut fur Biochemie, Martinsried, Federal Republic of Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3201230" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Cloning, Molecular ; Genes ; HeLa Cells/metabolism ; Humans ; Molecular Sequence Data ; Plasmids ; Receptors, Glucocorticoid/*genetics/metabolism ; Receptors, Progesterone/*genetics/metabolism ; Transcription Factors/*genetics/metabolism ; Transfection
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    Insights into enzyme function from studies on mutants of dihydrofolate reductase (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-03-04
    Description: Kinetic analysis and protein mutagenesis allow the importance of individual amino acids in ligand binding and catalysis to be assessed. A kinetic analysis has shown that the reaction catalyzed by dihydrofolate reductase is optimized with respect to product flux, which in turn is predetermined by the active-site hydrophobic surface. Protein mutagenesis has revealed that specific hydrophobic residues contribute 2 to 5 kilocalories per mole to ligand binding and catalysis. The extent to which perturbations within this active-site ensemble may affect catalysis is discussed in terms of the constraints imposed by the energy surface for the reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benkovic, S J -- Fierke, C A -- Naylor, A M -- GM24129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1988 Mar 4;239(4844):1105-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park 16802.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3125607" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemical Phenomena ; Chemistry ; Escherichia coli/enzymology ; Kinetics ; Lactobacillus casei/enzymology ; *Mutation ; Structure-Activity Relationship ; Tetrahydrofolate Dehydrogenase/genetics/*metabolism ; Thermodynamics
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    Site of G protein binding to rhodopsin mapped with synthetic peptides from the alpha subunit (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins (1988)
    American Association for the Advancement of Science (AAAS)
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    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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    Three-dimensional structure at 0.86 A of the uncomplexed form of the transmembrane ion channel peptide gramicidin A (1988)
    American Association for the Advancement of Science (AAAS)
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    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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    Microtubule-associated protein MAP2 shares a microtubule binding motif with tau protein (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-11-11
    Description: The microtubule-associated protein MAP2 is a prominent large-sized component of purified brain microtubules that, like the 36- to 38-kilodalton tau proteins, bears antigenic determinants found in association with the neurofibrillary tangles of Alzheimer's disease. The complete sequence of mouse brain MAP2 was determined from a series of overlapping cloned complementary DNAs. The sequence of the carboxyl-terminal 185 amino acids is very similar (67 percent) to a corresponding region of tau protein, and includes a series of three imperfect repeats, each 18 amino acids long and separated by 13 or 14 amino acids. A subcloned fragment spanning the first two of the 18-amino acid repeats was expressed as a polypeptide by translation in vitro. This polypeptide copurified with microtubules through two successive cycles of polymerization and depolymerization, whereas a control polypeptide derived from the amino-terminal region of MAP2 completely failed to copurify. These data imply that the carboxyl-terminal domain containing the 18-amino acid repeats constitutes the microtubule binding site in MAP2. The occurrence of these repeats in tau protein suggests that these may be a general feature of microtubule binding proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lewis, S A -- Wang, D H -- Cowan, N J -- New York, N.Y. -- Science. 1988 Nov 11;242(4880):936-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, New York University Medical Center, NY 10016.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3142041" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; DNA/genetics ; Mice ; Microtubule-Associated Proteins/genetics/*metabolism ; Microtubules/*metabolism ; Molecular Sequence Data ; Molecular Weight ; Nerve Tissue Proteins ; Protein Biosynthesis ; Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; Tubulin/metabolism ; tau Proteins
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    Recognition of a DNA operator by the repressor of phage 434: a view at high resolution (1988)
    American Association for the Advancement of Science (AAAS)
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    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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    Mutant Trp repressors with new DNA-binding specificities (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Autologous peptides constitutively occupy the antigen binding site on Ia (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-11-18
    Description: Low molecular weight material associated with affinity-purified class II major histocompatibility complex (MHC) molecules of mouse (Ia) had the expected properties of peptides bound to the antigen binding site of Ia. Thus, the low molecular weight material derived from the I-Ad isotype was efficient in inhibiting the binding of 125I-labeled I-Ad-specific peptide to I-Ad, but did not significantly inhibit the binding of an I-Ed-specific peptide to I-Ed; the reciprocal isotype-specific inhibition was demonstrated with low molecular weight material derived from I-Ed. The inhibitory material was predominantly peptide in nature, as shown by its susceptibility to protease digestion. It was heterogeneous as measured by gel filtration (mean molecular weight approximately 3000), and when characterized by high-performance liquid chromatography, it eluted over a wide concentration of solvent. Such self peptide-MHC complexes may have broad significance in the biology of T cell responses, including generation of the T cell repertoire, the specificity of mixed lymphocyte responses, and the immune surveillance of self and nonself antigens in peripheral lymphoid tissues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buus, S -- Sette, A -- Colon, S M -- Grey, H M -- AI09758/AI/NIAID NIH HHS/ -- AI18634/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1988 Nov 18;242(4881):1045-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, National Jewish Center for Immunology and Respiratory Medicine, Denver, CO 80206.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3194755" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autoantigens/immunology ; Binding Sites ; Chromatography, High Pressure Liquid ; Histocompatibility Antigens Class II/isolation & purification/*metabolism ; Mice ; Molecular Weight ; Ovalbumin/metabolism ; Peptides/*metabolism
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    Localization of an Arg-Gly-Asp recognition site within an integrin adhesion receptor (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-10-07
    Description: Many adhesive interactions are mediated by Arg-Gly-Asp (RGD) sequences within adhesive proteins. Such RGD sequences are frequently recognized by structurally related heterodimers that are members of the integrin family of adhesion receptors. A region was found in the platelet RGD receptor, gpIIb/IIIa, to which an RGD peptide becomes chemically cross-linked. This region corresponds to residues 109 to 171 of gpIIIa. This segment is conserved among the beta subunits of the integrins (76 percent identity of sequence), indicating that it may play a role in the adhesive functions of this family of receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉D'Souza, S E -- Ginsberg, M H -- Burke, T A -- Lam, S C -- Plow, E F -- HL16411/HL/NHLBI NIH HHS/ -- HL28235/HL/NHLBI NIH HHS/ -- HL38292/HL/NHLBI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1988 Oct 7;242(4875):91-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Research Institute of Scripps Clinic, La Jolla, California 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3262922" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Blood Platelets/immunology ; Humans ; Integrins ; Membrane Glycoproteins/genetics/*metabolism ; Molecular Sequence Data ; Platelet Membrane Glycoproteins/genetics/metabolism ; Protein Binding ; Receptors, Immunologic/*metabolism ; *Receptors, Peptide
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    Three-dimensional structure of an oncogene protein: catalytic domain of human c-H-ras p21 (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Evidence from cassette mutagenesis for a structure-function motif in a protein of unknown structure (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    The design of molecular hosts, guests, and their complexes (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-05-06
    Description: The origins, definitions, tools, and guiding principles of host-guest chemistry are developed. Perching, nesting, and capsular complexes are exemplified through molecular model and crystal structure comparisons. The degree of preorganization of a host for binding is a central determinant of its binding power. Complementarity of binding site placement in host and guest is a central determinant of structural recognition in complexation. Examples are given of chiral recognition in complexation, of partial transacylase mimics, of caviplexes, and of a synthetic molecular cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cram, D J -- New York, N.Y. -- Science. 1988 May 6;240(4853):760-7.〈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/3283937" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Binding Sites ; Chemical Phenomena ; Chemistry ; Crystallization ; Enzymes ; *Models, Chemical ; Models, Molecular ; Nucleic Acids ; Thermodynamics
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    Genetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Point mutations in the human vitamin D receptor gene associated with hypocalcemic rickets (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-12-23
    Description: Hypocalcemic vitamin D-resistant rickets is a human genetic disease resulting from target organ resistance to the action of 1,25-dihydroxyvitamin D3. Two families with affected children homozygous for this autosomal recessive disorder were studied for abnormalities in the intracellular vitamin D receptor (VDR) and its gene. Although the receptor displays normal binding of 1,25-dihydroxyvitamin D3 hormone, VDR from affected family members has a decreased affinity for DNA. Genomic DNA isolated from these families was subjected to oligonucleotide-primed DNA amplification, and each of the nine exons encoding the receptor protein was sequenced for a genetic mutation. In each family, a different single nucleotide mutation was found in the DNA binding domain of the protein; one family near the tip of the first zinc finger (Gly----Asp) and one at the tip of the second zinc finger (Arg----Gly). The mutant residues were created in vitro by oligonucleotide directed point mutagenesis of wild-type VDR complementary DNA and this cDNA was transfected into COS-1 cells. The produced protein is biochemically indistinguishable from the receptor isolated from patients.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hughes, M R -- Malloy, P J -- Kieback, D G -- Kesterson, R A -- Pike, J W -- Feldman, D -- O'Malley, B W -- New York, N.Y. -- Science. 1988 Dec 23;242(4886):1702-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2849209" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Calcitriol/metabolism ; Cell Line ; Cell Line, Transformed ; Codon ; DNA/genetics/metabolism ; Exons ; Female ; Gene Amplification ; Homozygote ; Humans ; Hypocalcemia/*genetics ; Immunoblotting ; Male ; Molecular Sequence Data ; *Mutation ; Receptors, Calcitriol ; Receptors, Steroid/*genetics/metabolism ; Rickets/*genetics ; Transfection
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    Escherichia coli aspartate transcarbamylase: the relation between structure and function (1988)
    American Association for the Advancement of Science (AAAS)
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    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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    Tertiary structure of plant RuBisCO: domains and their contacts (1988)
    American Association for the Advancement of Science (AAAS)
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    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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    The steroid and thyroid hormone receptor superfamily (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-05-13
    Description: Analyses of steroid receptors are important for understanding molecular details of transcriptional control, as well as providing insight as to how an individual transacting factor contributes to cell identity and function. These studies have led to the identification of a superfamily of regulatory proteins that include receptors for thyroid hormone and the vertebrate morphogen retinoic acid. Although animals employ complex and often distinct ways to control their physiology and development, the discovery of receptor-related molecules in a wide range of species suggests that mechanisms underlying morphogenesis and homeostasis may be more ubiquitous than previously expected.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Evans, R M -- New York, N.Y. -- Science. 1988 May 13;240(4854):889-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92138-9216.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3283939" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; DNA/metabolism ; Gene Expression Regulation ; Humans ; Receptors, Steroid/genetics/*physiology ; Receptors, Thyroid Hormone/genetics/*physiology
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    The Fos complex and Fos-related antigens recognize sequence elements that contain AP-1 binding sites (1988)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1988-03-04
    Description: The Fos protein complex and several Fos-related antigens bind directly or indirectly to a common sequence element that is similar to the consensus binding site for HeLa cell activator protein 1 (AP-1). This element is present in a negative regulatory sequence in the differentiation-sensitive adipocyte gene, aP2; in a transcriptional enhancer for the Gibbon ape leukemia virus; and in a region of the human immunodeficiency virus (HIV) long terminal repeat partially characterized as a negative regulatory element. The protein level and binding activity of Fos and Fos-related antigens increase rapidly after calcium ionophore treatment of a CD4+ human lymphoblast cell line, H9. These data suggest that several proteins may associate with the AP-1 binding site. Moreover, temporally regulated control of the level of each protein could represent a mechanism for modulation of these putative mediators of gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Franza, B R Jr -- Rauscher, F J 3rd -- Josephs, S F -- Curran, T -- New York, N.Y. -- Science. 1988 Mar 4;239(4844):1150-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, NY 11724.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2964084" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Calcimycin/pharmacology ; Cell Line ; Chemical Precipitation ; Dna ; Electrophoresis, Polyacrylamide Gel ; Enhancer Elements, Genetic ; HIV/genetics ; Humans ; Immunoassay ; Immunosorbent Techniques ; Molecular Sequence Data ; Proto-Oncogene Proteins/analysis/genetics/immunology/*metabolism ; Proto-Oncogene Proteins c-fos ; Proto-Oncogenes ; Regulatory Sequences, Nucleic Acid ; Repetitive Sequences, Nucleic Acid ; T-Lymphocytes, Helper-Inducer/cytology/drug effects
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    Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Mapping the main immunogenic region and toxin-binding site of the nicotinic acetylcholine receptor (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-01-02
    Description: The alpha-chain of the nicotinic acetylcholine receptor carries the binding sites both for cholinergic ligands and for most experimentally induced or naturally occurring antibodies to the native receptor. By means of expression cloning in Escherichia coli, fusion proteins were derived from specific fragments of a complementary DNA encoding the mouse alpha-chain, allowing the mapping of the toxin-binding site to residues 160-216 and the main immunogenic region to residues 6-85. This approach permits the independent study of different functional domains of a complex receptor molecule and should be generally applicable to other proteins for which complementary DNA clones are available.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barkas, T -- Mauron, A -- Roth, B -- Alliod, C -- Tzartos, S J -- Ballivet, M -- New York, N.Y. -- Science. 1987 Jan 2;235(4784):77-80.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2432658" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/immunology ; Binding Sites ; Binding, Competitive ; Bungarotoxins/metabolism ; Cloning, Molecular ; Epitopes ; Humans ; Immunosorbent Techniques ; Ligands ; Mice ; Receptors, Nicotinic/genetics/*immunology ; Recombinant Fusion Proteins/immunology ; Species Specificity ; Structure-Activity Relationship
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    Structure of MHC protein solved (1987)
    American Association for the Advancement of Science (AAAS)
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    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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    Selective inactivation of influenza C esterase: a probe for detecting 9-O-acetylated sialic acids (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-06-05
    Description: The influenza C virus (INF-C) hemagglutinin recognizes 9-O-acetyl-N-acetylneuraminic acid. The same protein contains the receptor-destroying enzyme (RDE), which is a 9-O-acetyl-esterase. The RDE was inactivated by the serine esterase inhibitor di-isopropyl fluorophosphate (DFP). [3H]DFP-labeling localized the active site to the heavy chain of the glycoprotein. DFP did not alter the hemagglutination or fusion properties of the protein, but markedly decreased infectivity of the virus, demonstrating that the RDE is important for primary infection. Finally, DFP-treated INF-C bound specifically and irreversibly to cells expressing 9-O-acetylated sialic acids. This provides a probe for a molecule that was hitherto very difficult to study.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muchmore, E A -- Varki, A -- 1-K12-AM01408/AM/NIADDK NIH HHS/ -- R01 GM32373/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Jun 5;236(4806):1293-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3589663" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Animals ; Binding Sites ; Biological Assay ; Hemagglutination Tests ; Influenzavirus C/drug effects/*enzymology ; Isoflurophate/metabolism/*pharmacology ; Mice ; Orthomyxoviridae/*enzymology ; Protein Binding ; Sialic Acids/*analysis ; Viral Proteins/metabolism
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    A subset of yeast snRNA's contains functional binding sites for the highly conserved Sm antigen (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-01-16
    Description: Autoimmune sera of the Sm specificity react with the major class of small nuclear RNA (snRNA)-containing ribonucleoprotein particles (snRNP's) from organisms as evolutionarily divergent as insects and dinoflagellates but have been reported not to recognize snRNP's from yeast. The Sm antigen is thought to bind to a conserved snRNA motif that includes the sequence A(U3-6)G. The hypothesis was tested that yeast also contains functional analogues of Sm snRNA's, but that the Sm binding site in the RNA is more strictly conserved than the Sm antigenic determinant. After microinjection of labeled yeast snRNA's into Xenopus eggs or oocytes, two snRNA's from Saccharomyces cerevisiae become strongly immunoprecipitable with human auto-antibodies known as anti-Sm. These each contain the sequence A(U5-6)G, are essential for viability, and are constituents of the spliceosome. At least six other yeast snRNA's do not become immunoprecipitable and lack this sequence; these non-Sm snRNA's are all dispensable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riedel, N -- Wolin, S -- Guthrie, C -- GM 21119/GM/NIGMS NIH HHS/ -- GM 26875/GM/NIGMS NIH HHS/ -- GM 31286/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Jan 16;235(4786):328-31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2948278" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autoantigens/*metabolism ; Binding Sites ; Protein Binding ; RNA, Small Nuclear/*metabolism ; Ribonucleoproteins/*metabolism ; Ribonucleoproteins, Small Nuclear ; Saccharomyces cerevisiae/*genetics/immunology ; Xenopus laevis ; snRNP Core Proteins
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    Direct evidence for DNA bending at the lambda replication origin (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-04-24
    Description: Replication initiation in bacteriophage lambda appears to require wrapping of origin DNA on an approximately 50 angstrom radius in or around the complex with the initiator protein O. Since short lengths of DNA are not that flexible, it may be that runs of coherently spaced deoxyadenylate residues constitute bend sites in the ori sequence that facilitate the process. Earlier data showed that ori DNA has electrophoretic anomalies characteristic of bend sites and that these are augmented by initiator protein binding. Here origin bending is examined by direct measurement of the ability of polymerized ori sequences to form small circles. The smallest circles observed (84 residues) are compatible with the required radius of curvature. Bend sites within the O protein binding sites, bend sites in the spacers between them, plus the inherent flexibility of non-bent DNA in the origin may all contribute to origin bending. The data also show that a bend site is required for O protein binding to DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zahn, K -- Blattner, F R -- GM 07133/GM/NIGMS NIH HHS/ -- GM 21812/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Apr 24;236(4800):416-22.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2951850" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/*genetics/ultrastructure ; Binding Sites ; *DNA Replication ; *DNA, Viral ; DNA-Binding Proteins/metabolism ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides ; Protein Binding ; Viral Proteins/metabolism ; Virus Replication
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    Saccharomyces cerevisiae has a U1-like small nuclear RNA with unexpected properties (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-09-18
    Description: Previous experiments indicated that only a small subset of the approximately equal to 24 small nuclear RNAs (snRNAs) in Saccharomyces cerevisiae have binding sites for the Sm antigen, a hallmark of metazoan small nuclear ribonucleoproteins (snRNPs) involved in pre-messenger RNA splicing. Antibodies from human serum to Sm proteins were used to show that four snRNAs (snR7, snR14, snR19, and snR20) can be immunoprecipitated from yeast extracts. Three of these four, snR7, snR14, and snR20, have been shown to be analogs of mammalian U5, U4, and U2, respectively. Several regions of significant homology to U1 (164 nucleotides) have now been found in cloned and sequenced snR19 (568 nucleotides). These include ten out of ten matches to the 5' end of U1, the site known to interact with the 5' splice site of mammalian introns. Surprisingly, the precise conservation of this sequence precludes perfect complementarity between snR19 and the invariant yeast 5' junction (GTATGT), which differs from the mammalian consensus at the fourth position (GTPuAGT).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siliciano, P G -- Jones, M H -- Guthrie, C -- GM21119/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Sep 18;237(4821):1484-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3306922" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies ; Autoantigens/metabolism ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Humans ; Nucleic Acid Conformation ; RNA, Fungal/analysis ; RNA, Small Nuclear/*analysis ; *Ribonucleoproteins, Small Nuclear ; Saccharomyces cerevisiae/*genetics ; snRNP Core Proteins
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    Structure of the nucleotide activation switch in glycogen phosphorylase a (1987)
    American Association for the Advancement of Science (AAAS)
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    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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    The catalytic role of the active site aspartic acid in serine proteases (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-08-21
    Description: The role of the aspartic acid residue in the serine protease catalytic triad Asp, His, and Ser has been tested by replacing Asp102 of trypsin with Asn by site-directed mutagenesis. The naturally occurring and mutant enzymes were produced in a heterologous expression system, purified to homogeneity, and characterized. At neutral pH the mutant enzyme activity with an ester substrate and with the Ser195-specific reagent diisopropylfluorophosphate is approximately 10(4) times less than that of the unmodified enzyme. In contrast to the dramatic loss in reactivity of Ser195, the mutant trypsin reacts with the His57-specific reagent, tosyl-L-lysine chloromethylketone, only five times less efficiently than the unmodified enzyme. Thus, the ability of His57 to react with this affinity label is not severely compromised. The catalytic activity of the mutant enzyme increases with increasing pH so that at pH 10.2 the kcat is 6 percent that of trypsin. Kinetic analysis of this novel activity suggests this is due in part to participation of either a titratable base or of hydroxide ion in the catalytic mechanism. By demonstrating the importance of the aspartate residue in catalysis, especially at physiological pH, these experiments provide a rationalization for the evolutionary conservation of the catalytic triad.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Craik, C S -- Roczniak, S -- Largman, C -- Rutter, W J -- GM 10765/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Aug 21;237(4817):909-13.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3303334" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Asparagine ; *Aspartic Acid ; Binding Sites ; Catalysis ; *Endopeptidases ; Hydrogen-Ion Concentration ; Kinetics ; Rats ; Serine Endopeptidases ; Structure-Activity Relationship ; Substrate Specificity
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    Bacterial resistance to beta-lactam antibiotics: crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.5 A resolution (1987)
    American Association for the Advancement of Science (AAAS)
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    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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    YIGSR, a synthetic laminin pentapeptide, inhibits experimental metastasis formation (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-11-20
    Description: The invasion of tumor cells through basement membranes is a critical step in the formation of metastases. The binding of the malignant cells to laminin in the basement membranes allows their attachment and activates their invasiveness. Recently a synthetic nonapeptide from the B1 chain sequence of laminin was identified as a major site for cell binding. A pentapeptide within the nonapeptide sequence was found to reduce the formation of lung colonies in mice injected with melanoma cells and also to inhibit the invasiveness of the cells in vitro.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iwamoto, Y -- Robey, F A -- Graf, J -- Sasaki, M -- Kleinman, H K -- Yamada, Y -- Martin, G R -- New York, N.Y. -- Science. 1987 Nov 20;238(4830):1132-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Developmental Biology and Anomalies, National Institute of Drug Research, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2961059" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Basement Membrane/physiopathology ; Binding Sites ; Cell Adhesion/*drug effects ; *Laminin ; Lung Neoplasms/secondary ; Melanoma, Experimental/pathology/physiopathology ; Mice ; Neoplasm Metastasis/*prevention & control ; Oligopeptides/*chemical synthesis/pharmacology ; Receptors, Immunologic/*drug effects ; Receptors, Laminin ; Structure-Activity Relationship
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    Tinkering with enzymes: what are we learning? (1987)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1987-06-05
    Description: It is now possible, by site-directed mutagenesis of the gene, to change any amino acid residue in a protein to any other. In enzymology, application of this technique is leading to exciting new insights both into the mechanism of catalysis by particular enzymes, and into the basis of catalysis itself. The precise and often delicate changes that are being made in and near the active sites of enzymes are illuminating the interdependent roles of catalytic groups, and are allowing the first steps to be taken toward the rational alteration of enzyme specificity and reactivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knowles, J R -- New York, N.Y. -- Science. 1987 Jun 5;236(4806):1252-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3296192" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Binding Sites ; Catalysis ; Chemistry, Physical ; Enzyme Stability ; Enzymes/*genetics/metabolism ; Mutation ; Physicochemical Phenomena ; Substrate Specificity ; Thermodynamics
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    The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis (1987)
    American Association for the Advancement of Science (AAAS)
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    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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    Evidence for dispensable sequences inserted into a nucleotide fold (1987)
    American Association for the Advancement of Science (AAAS)
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    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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    Atomic structure of thymidylate synthase: target for rational drug design (1987)
    American Association for the Advancement of Science (AAAS)
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    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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  • 79
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    Protein-binding sites in Ig gene enhancers determine transcriptional activity and inducibility (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-06-19
    Description: Individual protein-binding sites within the mouse immunoglobulin heavy chain and kappa light chain gene enhancers were altered, making it possible to examine the functional role of the sites during transcription. The E motifs, which bind factors that are present in many if not all cells, mostly behave as transcriptional activating sites. The only known heavy chain enhancer site that binds a lymphocyte-specific factor, the "octamer" site, plays a critical role in transcription but only in a truncated form of the enhancer. In the full enhancer, no one site is crucial because of an apparent functional redundancy. The site in the kappa enhancer that binds a factor specific to mature B cells, kappa B, was crucial to the constitutive activity of the enhancer in B cells. This factor is also inducible in pre-B cells, and the site was necessary for inducibility of the kappa enhancer. Thus, the sites defined by protein binding are important for the functional activity of immunoglobulin enhancers, with the sites that bind proteins restricted in their cellular distribution playing the most important roles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lenardo, M -- Pierce, J W -- Baltimore, D -- New York, N.Y. -- Science. 1987 Jun 19;236(4808):1573-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3109035" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; *Enhancer Elements, Genetic ; *Genes, Regulator ; Immunoglobulin Heavy Chains/*genetics ; Immunoglobulin kappa-Chains/*genetics ; Lymphocytes/immunology ; Mice ; Mice, Inbred BALB C ; Multiple Myeloma/metabolism ; Mutation ; *Transcription, Genetic
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  • 80
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    The atomic structure of Mengo virus at 3.0 A resolution (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 81
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    The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-09-19
    Description: WIN 51711 and WIN 52084 are structurally related, antiviral compounds that inhibit the replication of rhino (common cold) viruses and related picornaviruses. They prevent the pH-mediated uncoating of the viral RNA. The compounds consist of a 3-methylisoxazole group that inserts itself into the hydrophobic interior of the VP1 beta-barrel, a connecting seven-membered aliphatic chain, and a 4-oxazolinylphenoxy group (OP) that covers the entrance to an ion channel in the floor of the "canyon." Viral disassembly may be inhibited by preventing the collapse of the VP1 hydrophobic pocket or by blocking the flow of ions into the virus interior.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, T J -- Kremer, M J -- Luo, M -- Vriend, G -- Arnold, E -- Kamer, G -- Rossmann, M G -- McKinlay, M A -- Diana, G D -- Otto, M J -- New York, N.Y. -- Science. 1986 Sep 19;233(4770):1286-93.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3018924" target="_blank"〉PubMed〈/a〉
    Keywords: Antiviral Agents/metabolism/*pharmacology ; Binding Sites ; Chemical Phenomena ; Chemistry ; Humans ; Isoxazoles/metabolism/pharmacology ; Poliovirus/drug effects/metabolism ; Rhinovirus/*drug effects/metabolism ; X-Ray Diffraction
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  • 82
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    Histones and metal-binding domains (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-12-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saavedra, R A -- New York, N.Y. -- Science. 1986 Dec 19;234(4783):1589.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3787266" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Histones/*metabolism ; Metals/*metabolism
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  • 83
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    On the origin of bacterial resistance to penicillin: comparison of a beta-lactamase and a penicillin target (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-03-21
    Description: Structural data are now available for comparing a penicillin target enzyme, the D-alanyl-D-alanine-peptidase from Streptomyces R61, with a penicillin-hydrolyzing enzyme, the beta-lactamase from Bacillus licheniformis 749/C. Although the two enzymes have distinct catalytic properties and lack relatedness in their overall amino acid sequences except near the active-site serine, the significant similarity found by x-ray crystallography in the spatial arrangement of the elements of secondary structure provides strong support for earlier hypotheses that beta-lactamases arose from penicillin-sensitive D-alanyl-D-alanine-peptidases involved in bacterial wall peptidoglycan metabolism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelly, J A -- Dideberg, O -- Charlier, P -- Wery, J P -- Libert, M -- Moews, P C -- Knox, J R -- Duez, C -- Fraipont, C -- Joris, B -- 10RRO1955-01/RR/NCRR NIH HHS/ -- AI-10925/AI/NIAID NIH HHS/ -- AI-16702/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1986 Mar 21;231(4744):1429-31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3082007" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus cereus/enzymology ; Binding Sites ; Carboxypeptidases/genetics/*metabolism ; Molecular Weight ; *Penicillin Resistance ; Protein Conformation ; *Serine-Type D-Ala-D-Ala Carboxypeptidase ; Streptomyces/enzymology ; X-Ray Diffraction ; beta-Lactamases/genetics/*metabolism
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  • 84
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    Active human-yeast chimeric phosphoglycerate kinases engineered by domain interchange (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-08-15
    Description: Phosphoglycerate kinase (PGK) is a monomeric protein composed of two domains of approximately equal size, connected by a hinge. Substrate-induced conformational change results in the closure of the active site cleft, which is situated between these two domains. In a study of the relations between structure and function of this enzyme, two interspecies hybrids were constructed, each composed of one domain from the human enzyme and one domain from the yeast enzyme. Despite a 35% difference in the amino acid composition between human and yeast PGK, catalytic properties of the hybrid enzymes are very similar to those of the parental proteins. This result demonstrates that the evolutionary substitutions within these two distantly related molecules do not significantly affect formation of the active site cleft, mechanism of domain closure, or enzyme activity itself.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mas, M T -- Chen, C Y -- Hitzeman, R A -- Riggs, A D -- R01 GM31263/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Aug 15;233(4765):788-90.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3526552" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; *Chimera ; *Genes ; *Genes, Fungal ; Genetic Engineering ; Humans ; Kinetics ; Models, Molecular ; Phosphoglycerate Kinase/*genetics/metabolism ; Plasmids ; Protein Conformation ; Protein Multimerization ; Saccharomyces cerevisiae/enzymology/*genetics
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  • 85
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    Catalytic antibodies (1986)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1986-12-19
    Description: Monoclonal antibodies elicited to haptens that are analogs of the transition state for hydrolysis of carboxylic esters behaved as enzymic catalysts with the appropriate substrates. These substrates are distinguished by the structural congruence of both hydrolysis products with haptenic fragments. The haptens were potent inhibitors of this esterolytic activity, in agreement with their classification as transition state analogs. Mechanisms are proposed to account for the different chemical behavior of these antibodies with two types of ester substrates. The generation of an artificial enzyme through transition state stabilization by antibodies was thus demonstrated. These studies indicate a potentially general approach to catalyst design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tramontano, A -- Janda, K D -- Lerner, R A -- GM35318/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Dec 19;234(4783):1566-70.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3787261" target="_blank"〉PubMed〈/a〉
    Keywords: *Antibodies, Monoclonal/immunology ; Binding Sites ; Carboxylic Ester Hydrolases ; *Catalysis ; Chemical Phenomena ; Chemistry ; Esters/immunology/metabolism ; Haptens/immunology ; Hydrolysis ; Kinetics
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  • 86
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    Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-12-19
    Description: The crystal structure of the complex between Eco RI endonuclease and the cognate oligonucleotide TCGCGAATTCGCG provides a detailed example of the structural basis of sequence-specific DNA-protein interactions. The structure was determined, to 3 A resolution, by the ISIR (iterative single isomorphous replacement) method with a platinum isomorphous derivative. The complex has twofold symmetry. Each subunit of the endonuclease is organized into an alpha/beta domain consisting a five-stranded beta sheet, alpha helices, and an extension, called the "arm," which wraps around the DNA. The large beta sheet consists of antiparallel and parallel motifs that form the foundations for the loops and alpha helices responsible for DNA strand scission and sequence-specific recognition, respectively. The DNA cleavage site is located in a cleft that binds the DNA backbone in the vicinity of the scissile bond. Sequence specificity is mediated by 12 hydrogen bonds originating from alpha helical recognition modules. Arg200 forms two hydrogen bonds with guanine while Glu144 and Arg145 form four hydrogen bonds to adjacent adenine residues. These interactions discriminate the Eco RI hexanucleotide GAATTC from all other hexanucleotides because any base substitution would require rupture of at least one of these hydrogen bonds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McClarin, J A -- Frederick, C A -- Wang, B C -- Greene, P -- Boyer, H W -- Grable, J -- Rosenberg, J M -- GM25671/GM/NIGMS NIH HHS/ -- GM33506/GM/NIGMS NIH HHS/ -- RR07084/RR/NCRR NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1986 Dec 19;234(4783):1526-41.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3024321" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Base Composition ; Binding Sites ; Chemistry, Physical ; Crystallization ; DNA/*metabolism ; DNA Restriction Enzymes/*metabolism ; Deoxyribonuclease EcoRI ; Hydrogen Bonding ; Macromolecular Substances ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/metabolism ; Physicochemical Phenomena ; Protein Conformation ; Substrate Specificity
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  • 87
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    Selective chemical catalysis by an antibody (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-12-19
    Description: The immunoglobulin MOPC167, which binds the transition state analog p-nitrophenylphosphorylcholine with high affinity, catalyzed the hydrolysis of the corresponding carbonate 1. MOPC167 catalysis displayed saturation kinetics with catalytic constant (kcat) = 0.4 min-1 and Michaelis constant (Km) = 208 microM, showed substrate specificity, and was inhibited by p-nitrophenylphosphorylcholine. The rate of the reaction was first order in hydroxide ion concentration between pH 6.0 and 8.0. The lower limit for the rate of acceleration of hydrolysis by the antibody above the uncatalyzed reaction was 770. This study begins to define the rules for the generation of catalytic antibodies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pollack, S J -- Jacobs, J W -- Schultz, P G -- New York, N.Y. -- Science. 1986 Dec 19;234(4783):1570-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3787262" target="_blank"〉PubMed〈/a〉
    Keywords: *Antibodies ; Binding Sites ; Carbonates/metabolism ; *Catalysis ; Choline/*analogs & derivatives ; Hydrolysis ; Immunoglobulin A/*metabolism ; Kinetics ; Nitrophenols/metabolism ; Phosphorylcholine/*analogs & derivatives/immunology/metabolism
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  • 88
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    Modification of the active site of alkaline phosphatase by site-directed mutagenesis (1986)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1986-01-10
    Description: The catalytically essential amino acid in the active site of bacterial alkaline phosphatase (Ser-102) has been replaced with a cysteine by site-directed mutagenesis. The resulting thiol enzyme catalyzes the hydrolysis of a variety of phosphate monoesters. The rate-determining step of hydrolysis, however, is no longer the same for catalysis when the active protein nucleophile is changed from the hydroxyl of serine to the thiol of cysteine. Unlike the steady-state kinetics of native alkaline phosphatase, those of the mutant show sensitivity to the leaving group of the phosphate ester.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghosh, S S -- Bock, S C -- Rokita, S E -- Kaiser, E T -- AM 07122-02/AM/NIADDK NIH HHS/ -- New York, N.Y. -- Science. 1986 Jan 10;231(4734):145-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3510454" target="_blank"〉PubMed〈/a〉
    Keywords: *2,4-Dinitrophenol/*analogs & derivatives ; Alkaline Phosphatase/*genetics/metabolism ; Amino Acid Sequence ; Binding Sites ; DNA/genetics ; Dinitrophenols/metabolism ; Escherichia coli/enzymology/genetics ; Kinetics ; Mutation ; Nitrophenols/metabolism ; Organophosphates/metabolism ; Organophosphorus Compounds/metabolism ; Plasmids
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  • 89
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    Crystal structure of Cd,Zn metallothionein (1986)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1986-02-14
    Description: The anomalous scattering data from five Cd in the native protein were used to determine the crystal structure of cadmium, zinc (Cd,Zn) metallothionein isoform II from rat liver. The structure of a 4-Cd cluster was solved by direct methods. A 2.3 A resolution electron density map was calculated by iterative single-wavelength anomalous scattering. The structure is folded into two domains. The amino terminal domain (beta) of residues 1 to 29 enfolds a three-metal cluster of one Cd and two Zn atoms coordinated by six terminal cysteine thiolate ligands and three bridging cysteine thiolates. The carboxyl terminal domain (alpha) of residues 30 to 61 enfolds a 4-Cd cluster coordinated by six terminal and five bridging cysteine thiolates. All seven metal sites have tetrahedral coordination geometry. The domains are roughly spherical, and the diameter is 15 to 20 A; there is limited contact between domains. The folding of alpha and beta is topologically similar but with opposite chirality. Redundant, short cysteine-containing sequences have similar roles in cluster formation in both alpha and beta.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Furey, W F -- Robbins, A H -- Clancy, L L -- Winge, D R -- Wang, B C -- Stout, C D -- GM-36535/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Feb 14;231(4739):704-10.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3945804" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cadmium ; Crystallography ; Cysteine ; *Metallothionein ; Models, Molecular ; Protein Conformation ; Rats ; Solutions ; X-Ray Diffraction ; Zinc
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  • 90
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    Active T-cell receptor genes have intron deoxyribonuclease hypersensitive sites (1985)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1985-08-09
    Description: The T-cell receptor beta-chain gene has a nuclease hypersensitive site in several kinds of T cells, which does not appear in B cells expressing immunoglobulins. Conversely, the kappa immunoglobulin gene shows a known hypersensitive site at its enhancer element in B cells, as expected, but this site is absent in T cells. As is the case with immunoglobulin genes, the T-cell receptor site lies within the gene, in the intron separating joining and constant region segments. These nuclease hypersensitive DNA configurations in the introns of active T-cell receptor and immunoglobulin genes may arise from control elements that share ancestry but have diverged to the extent that each normally acts only in lymphoid cells which use the proximal gene product.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bier, E -- Hashimoto, Y -- Greene, M I -- Maxam, A M -- AI 19901/AI/NIAID NIH HHS/ -- CA 22427/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1985 Aug 9;229(4713):528-34.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3927483" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/metabolism ; Base Sequence ; Binding Sites ; Cell Line ; Chromosome Mapping ; Collodion ; Deoxyribonuclease I/*metabolism ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Humans ; Hybridomas ; Immunochemistry ; Immunoglobulin Fragments/*genetics ; Immunoglobulin Heavy Chains/genetics ; Immunoglobulin kappa-Chains/genetics ; Mice ; Receptors, Antigen, T-Cell/*genetics ; T-Lymphocytes/*metabolism ; Transcription, Genetic
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  • 91
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    Bidirectional SV40 transcription mediated by tandem Sp1 binding interactions (1985)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1985-11-01
    Description: The 21-base pair repeat elements of the SV40 promoter contain six tandem copies of the GGGCGG hexanucleotide (GC-box), each of which can bind, with varying affinity, to the cellular transcription factor, Sp1. In vitro SV40 early RNA synthesis is mediated by interaction of Sp1 with GC-boxes I, II, and III, whereas transcription in the late direction is mediated by binding to GC-boxes III, V, and VI.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gidoni, D -- Kadonaga, J T -- Barrera-Saldana, H -- Takahashi, K -- Chambon, P -- Tjian, R -- New York, N.Y. -- Science. 1985 Nov 1;230(4725):511-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2996137" target="_blank"〉PubMed〈/a〉
    Keywords: Autoradiography ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/*metabolism ; Deoxyribonuclease I/metabolism ; Electrophoresis, Polyacrylamide Gel ; Gene Expression Regulation ; Mutation ; Pregnancy Proteins/*metabolism ; RNA, Messenger/analysis ; RNA, Viral/biosynthesis ; Simian virus 40/*genetics ; Sp1 Transcription Factor ; Templates, Genetic ; Transcription Factors/*metabolism ; *Transcription, Genetic
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  • 92
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    A model for fibrinogen: domains and sequence (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-12-20
    Description: Electron microscopy of rotary-shadowed fibrinogen demonstrates that the molecules modified for crystallization by limited cleavage with a bacterial protease retain the major features of the native structure. This evidence, together with image processing and x-ray analysis of the crystals and of fibrin, has been used to develop a three-dimensional low resolution model for the molecule. The data indicate that the two large end domains of the molecule would be composed of the carboxyl-terminus of the B beta chain (proximal) and gamma chain (distal), respectively; the carboxyl-terminus of the A alpha chain would fold back to form an additional central domain. On this basis, the carboxyl-terminal region of each of the three chains of fibrinogen is folded independently into a globular domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weisel, J W -- Stauffacher, C V -- Bullitt, E -- Cohen, C -- AM17346/AM/NIADDK NIH HHS/ -- GM07596-07/GM/NIGMS NIH HHS/ -- HL30954/HL/NHLBI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1985 Dec 20;230(4732):1388-91.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/4071058" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Computers ; Fibrinogen/*metabolism ; Microscopy, Electron ; Models, Molecular ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 93
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    Alterations in L-glutamate binding in Alzheimer's and Huntington's diseases (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-03-22
    Description: Brain sections from patients who had died with senile dementia of the Alzheimer's type (SDAT), Huntington's disease (HD), or no neurologic disease were studied by autoradiography to measure sodium-independent L-[3H]glutamate binding. In brain sections from SDAT patients, glutamate binding was normal in the caudate, putamen, and claustrum but was lower than normal in the cortex. The decreased cortical binding represented a reduction in numbers of binding sites, not a change in binding affinity, and appeared to be the result of a specific decrease in numbers of the low-affinity quisqualate binding site. No significant changes in cortical binding of other ligands were observed. In brains from Huntington's disease patients, glutamate binding was lower in the caudate and putamen than in the same regions of brains from control and SDAT patients but was normal in the cortex. It is possible that development of positron-emitting probes for glutamate receptors may permit diagnosis of SDAT in vivo by means of positron emission tomographic scanning.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greenamyre, J T -- Penney, J B -- Young, A B -- D'Amato, C J -- Hicks, S P -- Shoulson, I -- NS00420/NS/NINDS NIH HHS/ -- NS00464/NS/NINDS NIH HHS/ -- NS17978/NS/NINDS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1985 Mar 22;227(4693):1496-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2858129" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/enzymology/*metabolism ; Autoradiography ; Binding Sites ; Brain/enzymology/*metabolism ; Caudate Nucleus/metabolism ; Cerebral Cortex/metabolism ; Choline O-Acetyltransferase/metabolism ; Glutamates/*metabolism ; Glutamic Acid ; Humans ; Huntington Disease/enzymology/*metabolism ; Putamen/metabolism ; Receptors, Glutamate ; Receptors, Neurotransmitter/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 94
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    Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-10-04
    Description: A 2.7 angstrom resolution x-ray diffraction analysis of a trypsin-modified form of the Escherichia coli elongation factor Tu reveals that the GDP-binding domain has a structure similar to that of other nucleotide-binding proteins. The GDP ligand is located at the COOH-terminal end of the beta sheet and is linked to the protein via a Mg2+ ion salt bridge. The location of the guanine ring is unusual; the purine ring is located on the outer edge of the domain, not deep within a hydrophobic pocket. The amino acids from Pro10 to Arg44 and from Gly59 to Glu190 have been assigned to the electron density with computer graphic techniques, and the resulting model is consistent with all known biochemical data. An analysis of the structure reveals that four regions of the amino acid sequence that are homologous with the family of ras oncogene proteins, termed p21, are located in the vicinity of the GDP-binding site, and most of the invariant amino acids shared by the proteins interact directly with the GDP ligand.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jurnak, F -- GM 26895/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1985 Oct 4;230(4721):32-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3898365" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/*analysis ; Binding Sites ; Chemistry, Physical ; Computers ; Escherichia coli ; Fourier Analysis ; Guanine Nucleotides/*analysis ; Guanosine Diphosphate/*analysis ; Magnesium/metabolism ; *Oncogenes ; Peptide Elongation Factor Tu ; Peptide Elongation Factors/*analysis ; Physicochemical Phenomena ; Protein Conformation ; Trypsin/metabolism ; X-Ray Diffraction
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 95
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    A model for the tertiary structure of p21, the product of the ras oncogene (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-10-04
    Description: A model was developed for the structure of p21, the protein with a molecular weight of 21,000 that is produced by the ras genes. This model predicts that p21 consists of a central core of beta-sheet structure, connected by loops and alpha helices. Four of these loops comprise the guanine nucleotide binding site. The phosphoryl binding region is made up of amino acid sequences from 10 to 16 and from 57 to 63 of p21. The latter sequence may contain a site for magnesium binding. Amino acids defining guanine specificity are Asn-116 and Asp-119, and sequences around amino acid 145 may contribute to guanine binding. The model makes it possible to visualize how oncogenic mutations of p21 affect interaction with guanine nucleotides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCormick, F -- Clark, B F -- la Cour, T F -- Kjeldgaard, M -- Norskov-Lauritsen, L -- Nyborg, J -- New York, N.Y. -- Science. 1985 Oct 4;230(4721):78-82.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3898366" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/analysis ; Animals ; *Aspartate Carbamoyltransferase ; Base Sequence ; Binding Sites ; *Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) ; Cattle ; *Dihydroorotase ; Escherichia coli ; Guanine Nucleotides/metabolism ; Humans ; Macromolecular Substances ; Magnesium/metabolism ; Membrane Proteins/analysis ; Models, Chemical ; *Multienzyme Complexes ; Mutation ; *Oncogenes ; Peptide Elongation Factor Tu ; Peptide Elongation Factors/analysis ; Protein Conformation ; Proteins/*analysis ; RNA, Transfer, Amino Acyl/metabolism ; Saccharomyces cerevisiae ; Transducin
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
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    The 3' splice site of pre-messenger RNA is recognized by a small nuclear ribonucleoprotein (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-12-20
    Description: A component present in splicing extracts selectively binds the 3' splice site of a precursor messenger RNA (pre-mRNA) transcript of a human beta-globin gene. Since this component can be immunoprecipitated by either autoantibodies of the Sm class or antibodies specifically directed against trimethylguanosine, it is a small nuclear ribonucleoprotein (snRNP). Its interaction with the 3' splice site occurs rapidly even at 0 degrees C, does not require adenosine triphosphate, and is altered by certain mutations in the 3' splice site region. Binding is surprisingly insensitive to treatment of the extract with micrococcal nuclease. The U5 particle is the only abundant Sm snRNP with a capped 5' end that is equally resistant to micrococcal nuclease. This suggests that, in addition to the U1 and U2 snRNP's, U5 snRNP's participate in pre-mRNA splicing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chabot, B -- Black, D L -- LeMaster, D M -- Steitz, J A -- GM-26154/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1985 Dec 20;230(4732):1344-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2933810" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Globins/genetics ; Humans ; Nucleic Acid Conformation ; Nucleic Acid Precursors/*genetics/metabolism ; Protein Binding ; RNA Precursors ; *RNA Splicing ; RNA, Messenger/*genetics/metabolism ; Ribonucleoproteins/*genetics/metabolism ; Ribonucleoproteins, Small Nuclear ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
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    The structure of arthropod hemocyanins (1985)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1985-08-09
    Description: Hemocyanins are large multi-subunit copper proteins that transport oxygen in many arthropods and molluscs. Comparison of the amino acid sequence data for seven different subunits of arthropod hemocyanins from crustaceans and chelicerates shows many highly conserved residues and extensive regions of near identity. This correspondence can be matched closely with the three domain structure established by x-ray crystallography for spiny lobster hemocyanin. The degree of identity is particularly striking in the second domain of the subunit that contains the six histidines which ligate the two oxygen-binding copper atoms. The polypeptide architecture of spiny lobster hemocyanin appears to be the same in all arthropods. This structure must therefore be at least as old as the estimated time of divergence of crustaceans and chelicerates, about 540 to 600 million years ago.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Linzen, B -- Soeter, N M -- Riggs, A F -- Schneider, H J -- Schartau, W -- Moore, M D -- Yokota, E -- Behrens, P Q -- Nakashima, H -- Takagi, T -- GM 21314/GM/NIGMS NIH HHS/ -- GM 28410/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1985 Aug 9;229(4713):519-24.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/4023698" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Arachnida/genetics ; *Arthropods/genetics ; Binding Sites ; Biological Evolution ; Chemical Phenomena ; Chemistry ; Copper ; Crustacea/genetics ; *Hemocyanin/genetics ; Models, Molecular ; Protein Conformation ; Species Specificity
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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