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  • Protein Conformation  (17)
  • American Association for the Advancement of Science (AAAS)  (17)
  • American Physical Society
  • Elsevier
  • 2005-2009  (17)
  • 2005  (17)
Collection
Publisher
  • American Association for the Advancement of Science (AAAS)  (17)
  • American Physical Society
  • Elsevier
Years
  • 2005-2009  (17)
Year
  • 1
    Publication Date: 2005-11-15
    Description: The primary event that initiates vision is the light-induced 11-cis to all-trans isomerization of retinal in the visual pigment rhodopsin. Despite decades of study with the traditional tools of chemical reaction dynamics, both the timing and nature of the atomic motions that lead to photoproduct production remain unknown. We used femtosecond-stimulated Raman spectroscopy to obtain time-resolved vibrational spectra of the molecular structures formed along the reaction coordinate. The spectral evolution of the vibrational features from 200 femtoseconds to 1 picosecond after photon absorption reveals the temporal sequencing of the geometric changes in the retinal backbone that activate this receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kukura, Philipp -- McCamant, David W -- Yoon, Sangwoon -- Wandschneider, Daniel B -- Mathies, Richard A -- EY-02051/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2005 Nov 11;310(5750):1006-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16284176" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle ; Chemistry, Physical ; Energy Transfer ; Hydrogen/chemistry ; Isomerism ; *Light ; Models, Chemical ; Models, Molecular ; Photochemistry ; Photons ; Physicochemical Phenomena ; Protein Conformation ; Retinaldehyde/*chemistry ; Rhodopsin/*chemistry ; Spectrum Analysis, Raman ; Time Factors ; *Vision, Ocular
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2005-07-16
    Description: Apolipoprotein L-I is the trypanolytic factor of human serum. Here we show that this protein contains a membrane pore-forming domain functionally similar to that of bacterial colicins, flanked by a membrane-addressing domain. In lipid bilayer membranes, apolipoprotein L-I formed anion channels. In Trypanosoma brucei, apolipoprotein L-I was targeted to the lysosomal membrane and triggered depolarization of this membrane, continuous influx of chloride, and subsequent osmotic swelling of the lysosome until the trypanosome lysed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perez-Morga, David -- Vanhollebeke, Benoit -- Paturiaux-Hanocq, Francoise -- Nolan, Derek P -- Lins, Laurence -- Homble, Fabrice -- Vanhamme, Luc -- Tebabi, Patricia -- Pays, Annette -- Poelvoorde, Philippe -- Jacquet, Alain -- Brasseur, Robert -- Pays, Etienne -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):469-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Parasitology, IBMM, Universite Libre de Bruxelles, 12, rue des Profs Jeener et Brachet, B6041 Gosselies, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020735" target="_blank"〉PubMed〈/a〉
    Keywords: 4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid/pharmacology ; Amino Acid Sequence ; Animals ; Anions/metabolism ; Apolipoproteins/*chemistry/genetics/*metabolism/pharmacology ; Cells, Immobilized ; Chlorides/metabolism ; Colicins/chemistry/pharmacology ; Escherichia coli/drug effects/growth & development ; Humans ; Intracellular Membranes/drug effects/*metabolism/ultrastructure ; Ion Channels/metabolism ; Lipid Bilayers/chemistry ; Lipoproteins, HDL/*chemistry/genetics/*metabolism/pharmacology ; Lysosomes/drug effects/*metabolism/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Permeability ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/metabolism ; Trypanosoma brucei brucei/drug effects/*metabolism/ultrastructure
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2005-11-15
    Description: We have identified a small-molecule inhibitor of tumor necrosis factor alpha (TNF-alpha) that promotes subunit disassembly of this trimeric cytokine family member. The compound inhibits TNF-alpha activity in biochemical and cell-based assays with median inhibitory concentrations of 22 and 4.6 micromolar, respectively. Formation of an intermediate complex between the compound and the intact trimer results in a 600-fold accelerated subunit dissociation rate that leads to trimer dissociation. A structure solved by x-ray crystallography reveals that a single compound molecule displaces a subunit of the trimer to form a complex with a dimer of TNF-alpha subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Molly M -- Smith, Annemarie Stroustrup -- Oslob, Johan D -- Flanagan, William M -- Braisted, Andrew C -- Whitty, Adrian -- Cancilla, Mark T -- Wang, Jun -- Lugovskoy, Alexey A -- Yoburn, Josh C -- Fung, Amy D -- Farrington, Graham -- Eldredge, John K -- Day, Eric S -- Cruz, Leslie A -- Cachero, Teresa G -- Miller, Stephan K -- Friedman, Jessica E -- Choong, Ingrid C -- Cunningham, Brian C -- New York, N.Y. -- Science. 2005 Nov 11;310(5750):1022-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sunesis Pharmaceuticals, Incorporated, 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16284179" target="_blank"〉PubMed〈/a〉
    Keywords: Biotinylation ; Chemistry, Physical ; Crystallography, X-Ray ; Dimerization ; Fluorescence ; Hydrogen/chemistry ; Hydrophobic and Hydrophilic Interactions ; Indoles/chemical synthesis/*chemistry/*pharmacology ; Kinetics ; Mass Spectrometry ; Models, Chemical ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Physicochemical Phenomena ; Protein Conformation ; Protein Subunits/chemistry ; Receptors, Tumor Necrosis Factor, Type I/metabolism ; Tumor Necrosis Factor-alpha/*antagonists & inhibitors/*chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2005-11-15
    Description: The third variable region (V3) of the HIV-1 gp120 envelope glycoprotein is immunodominant and contains features essential for coreceptor binding. We determined the structure of V3 in the context of an HIV-1 gp120 core complexed to the CD4 receptor and to the X5 antibody at 3.5 angstrom resolution. Binding of gp120 to cell-surface CD4 would position V3 so that its coreceptor-binding tip protrudes 30 angstroms from the core toward the target cell membrane. The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408531/" 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/PMC2408531/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chih-chin -- Tang, Min -- Zhang, Mei-Yun -- Majeed, Shahzad -- Montabana, Elizabeth -- Stanfield, Robyn L -- Dimitrov, Dimiter S -- Korber, Bette -- Sodroski, Joseph -- Wilson, Ian A -- Wyatt, Richard -- Kwong, Peter D -- AI24755/AI/NIAID NIH HHS/ -- AI31783/AI/NIAID NIH HHS/ -- AI39429/AI/NIAID NIH HHS/ -- AI40895/AI/NIAID NIH HHS/ -- GM46192/GM/NIGMS NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2005 Nov 11;310(5750):1025-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16284180" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antigens, CD4/chemistry/*metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; HIV Antibodies/immunology ; HIV Envelope Protein gp120/*chemistry/immunology/metabolism ; HIV-1/*chemistry/immunology/metabolism ; Humans ; Hydrogen Bonding ; Immunodominant Epitopes ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/*chemistry/immunology/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, CCR5/chemistry/metabolism ; Receptors, CXCR4/chemistry/metabolism
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  • 5
    Publication Date: 2005-08-27
    Description: Adenosine triphosphate (ATP) hydrolysis in the nitrogenase complex controls the cycle of association and dissociation between the electron donor adenosine triphosphatase (ATPase) (Fe-protein) and its target catalytic protein (MoFe-protein), driving the reduction of dinitrogen into ammonia. Crystal structures in different nucleotide states have been determined that identify conformational changes in the nitrogenase complex during ATP turnover. These structures reveal distinct and mutually exclusive interaction sites on the MoFe-protein surface that are selectively populated, depending on the Fe-protein nucleotide state. A consequence of these different docking geometries is that the distance between redox cofactors, a critical determinant of the intermolecular electron transfer rate, is coupled to the nucleotide state. More generally, stabilization of distinct docking geometries by different nucleotide states, as seen for nitrogenase, could enable nucleotide hydrolysis to drive the relative motion of protein partners in molecular motors and other systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tezcan, F Akif -- Kaiser, Jens T -- Mustafi, Debarshi -- Walton, Mika Y -- Howard, James B -- Rees, Douglas C -- New York, N.Y. -- Science. 2005 Aug 26;309(5739):1377-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 114-96, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16123301" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/metabolism ; Adenosine Triphosphate/analogs & derivatives/chemistry/metabolism ; Azotobacter vinelandii/*enzymology ; Binding Sites ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; Hydrogen Bonding ; Hydrolysis ; Models, Molecular ; Molybdoferredoxin/*chemistry/*metabolism ; Nitrogenase/*chemistry/*metabolism ; Oxidation-Reduction ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Subunits/chemistry/metabolism
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  • 6
    Publication Date: 2005-05-14
    Description: Polyglutamylation of tubulin has been implicated in several functions of microtubules, but the identification of the responsible enzyme(s) has been challenging. We found that the neuronal tubulin polyglutamylase is a protein complex containing a tubulin tyrosine ligase-like (TTLL) protein, TTLL1. TTLL1 is a member of a large family of proteins with a TTL homology domain, whose members could catalyze ligations of diverse amino acids to tubulins or other substrates. In the model protist Tetrahymena thermophila, two conserved types of polyglutamylases were characterized that differ in substrate preference and subcellular localization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janke, Carsten -- Rogowski, Krzysztof -- Wloga, Dorota -- Regnard, Catherine -- Kajava, Andrey V -- Strub, Jean-Marc -- Temurak, Nevzat -- van Dijk, Juliette -- Boucher, Dominique -- van Dorsselaer, Alain -- Suryavanshi, Swati -- Gaertig, Jacek -- Edde, Bernard -- New York, N.Y. -- Science. 2005 Jun 17;308(5729):1758-62. Epub 2005 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de Recherches de Biochimie Macromoleculaire, CNRS, 34293 Montpellier, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15890843" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Brain/enzymology ; *Catalytic Domain ; Cilia/physiology ; Humans ; Mice ; Microtubules/metabolism ; Models, Molecular ; Molecular Sequence Data ; Movement ; Peptide Synthases/*chemistry/genetics/isolation & purification/*metabolism ; Phylogeny ; Polyglutamic Acid/*chemistry/genetics/isolation & purification/*metabolism ; Protein Conformation ; Protein Subunits/chemistry/isolation & purification/metabolism ; Recombinant Fusion Proteins/metabolism ; Substrate Specificity ; Tetrahymena thermophila/*enzymology/genetics/metabolism ; Tubulin/*chemistry/genetics/isolation & purification/*metabolism
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  • 7
    Publication Date: 2005-09-24
    Description: The polypyrimidine tract binding protein (PTB) is a 58-kilodalton RNA binding protein involved in multiple aspects of messenger RNA metabolism, including the repression of alternative exons. We have determined the solution structures of the four RNA binding domains (RBDs) of PTB, each bound to a CUCUCU oligonucleotide. Each RBD binds RNA with a different binding specificity. RBD3 and RBD4 interact, resulting in an antiparallel orientation of their bound RNAs. Thus, PTB will induce RNA looping when bound to two separated pyrimidine tracts within the same RNA. This leads to structural models for how PTB functions as an alternative-splicing repressor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oberstrass, Florian C -- Auweter, Sigrid D -- Erat, Michele -- Hargous, Yann -- Henning, Anke -- Wenter, Philipp -- Reymond, Luc -- Amir-Ahmady, Batoul -- Pitsch, Stefan -- Black, Douglas L -- Allain, Frederic H-T -- New York, N.Y. -- Science. 2005 Sep 23;309(5743):2054-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology, Zurich, ETH-Honggerberg, CH-8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16179478" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Exons ; Heterogeneous-Nuclear Ribonucleoproteins/*chemistry/genetics/*metabolism ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Nuclear Proteins/metabolism ; Oligoribonucleotides ; Polypyrimidine Tract-Binding Protein/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; RNA/*chemistry/*metabolism ; Ribonucleoproteins/metabolism
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  • 8
    Publication Date: 2005-11-29
    Description: Complexes between CD1 molecules and self or microbial glycolipids represent important immunogenic ligands for specific subsets of T cells. However, the function of one of the CD1 family members, CD1e, has yet to be determined. Here, we show that the mycobacterial antigens hexamannosylated phosphatidyl-myo-inositols (PIM6) stimulate CD1b-restricted T cells only after partial digestion of the oligomannose moiety by lysosomal alpha-mannosidase and that soluble CD1e is required for this processing. Furthermore, recombinant CD1e was able to bind glycolipids and assist in the digestion of PIM6. We propose that, through this form of glycolipid editing, CD1e helps expand the repertoire of glycolipidic T cell antigens to optimize antimicrobial immune responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de la Salle, Henri -- Mariotti, Sabrina -- Angenieux, Catherine -- Gilleron, Martine -- Garcia-Alles, Luis-Fernando -- Malm, Dag -- Berg, Thomas -- Paoletti, Samantha -- Maitre, Blandine -- Mourey, Lionel -- Salamero, Jean -- Cazenave, Jean Pierre -- Hanau, Daniel -- Mori, Lucia -- Puzo, Germain -- De Libero, Gennaro -- New York, N.Y. -- Science. 2005 Nov 25;310(5752):1321-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INSERM, U725, Etablissement Francais du Sang-Alsace, F-67065 Strasbourg, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16311334" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; *Antigen Presentation ; Antigen-Presenting Cells/immunology ; Antigens, Bacterial/*immunology/*metabolism ; Antigens, CD1/chemistry/genetics/immunology/*metabolism ; Cell Line, Tumor ; Dendritic Cells/enzymology/immunology ; Glycolipids/*immunology/metabolism ; Humans ; Hydrogen-Ion Concentration ; Lymphocyte Activation ; Models, Molecular ; Mycobacterium tuberculosis/immunology ; Phosphatidylinositols/*immunology/*metabolism ; Protein Conformation ; Recombinant Proteins/immunology/metabolism ; Solubility ; T-Lymphocytes/immunology ; Transfection ; alpha-Mannosidase/immunology
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  • 9
    Publication Date: 2005-01-18
    Description: Amyloid fibrils commonly exhibit multiple distinct morphologies in electron microscope and atomic force microscope images, often within a single image field. By using electron microscopy and solid-state nuclear magnetic resonance measurements on fibrils formed by the 40-residue beta-amyloid peptide of Alzheimer's disease (Abeta(1-40)), we show that different fibril morphologies have different underlying molecular structures, that the predominant structure can be controlled by subtle variations in fibril growth conditions, and that both morphology and molecular structure are self-propagating when fibrils grow from preformed seeds. Different Abeta(1-40) fibril morphologies also have significantly different toxicities in neuronal cell cultures. These results have implications for the mechanism of amyloid formation, the phenomenon of strains in prion diseases, the role of amyloid fibrils in amyloid diseases, and the development of amyloid-based nano-materials.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petkova, Aneta T -- Leapman, Richard D -- Guo, Zhihong -- Yau, Wai-Ming -- Mattson, Mark P -- Tycko, Robert -- New York, N.Y. -- Science. 2005 Jan 14;307(5707):262-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD 20892-0520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15653506" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amyloid beta-Peptides/*chemistry/toxicity/*ultrastructure ; Animals ; Cells, Cultured ; Chemistry, Physical ; Hippocampus/cytology ; Humans ; Hydrogen Bonding ; Microscopy, Atomic Force ; Microscopy, Electron, Transmission ; Molecular Structure ; Neurons/cytology/drug effects ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/*chemistry/toxicity/*ultrastructure ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Rats
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  • 10
    Publication Date: 2005-01-08
    Description: The P1 lysozyme Lyz is secreted to the periplasm of Escherichia coli and accumulates in an inactive membrane-tethered form. Genetic and biochemical experiments show that, when released from the bilayer, Lyz is activated by an intramolecular thiol-disulfide isomerization, which requires a cysteine in its N-terminal SAR (signal-arrest-release) domain. Crystal structures confirm the alternative disulfide linkages in the two forms of Lyz and reveal dramatic conformational differences in the catalytic domain. Thus, the exported P1 endolysin is kept inactive by three levels of control-topological, conformational, and covalent-until its release from the membrane is triggered by the P1 holin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Min -- Arulandu, Arockiasamy -- Struck, Douglas K -- Swanson, Stephanie -- Sacchettini, James C -- Young, Ry -- GM27099/GM/NIGMS NIH HHS/ -- GM62410/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):113-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15637279" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage P1/*enzymology ; Binding Sites ; Catalytic Domain ; Cell Membrane/enzymology ; Chemistry, Physical ; Crystallography, X-Ray ; Cysteine/chemistry ; Enzyme Activation ; Escherichia coli/enzymology/virology ; Isomerism ; Lipid Bilayers ; Models, Molecular ; Molecular Sequence Data ; Muramidase/*chemistry/genetics/*metabolism ; Mutation ; Physicochemical Phenomena ; Protein Conformation ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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