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  • 1
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    Docking phospholipase A2 on membranes using electrostatic potential-modulated spin relaxation magnetic resonance (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-04-16
    Description: A method involving electron paramagnetic resonance spectroscopy of a site-selectively spin-labeled peripheral membrane protein in the presence and absence of membranes and of a water-soluble spin relaxant (chromium oxalate) has been developed to determine how bee venom phospholipase A2 sits on the membrane. Theory based on the Poisson-Boltzmann equation shows that the rate of spin relaxation of a protein-bound nitroxide by a membrane-impermeant spin relaxant depends on the distance (up to tens of angstroms) from the spin probe to the membrane. The measurements define the interfacial binding surface of this secreted phospholipase A2.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443684/" 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/PMC3443684/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Y -- Nielsen, R -- Murray, D -- Hubbell, W L -- Mailer, C -- Robinson, B H -- Gelb, M H -- GM32681/GM/NIGMS NIH HHS/ -- HL36235/HL/NHLBI NIH HHS/ -- P30 ES07033/ES/NIEHS NIH HHS/ -- R01 CA052874/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1998 Mar 20;279(5358):1925-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Biochemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9506941" target="_blank"〉PubMed〈/a〉
    Keywords: Bee Venoms/chemistry ; Binding Sites ; Chromates ; Electron Spin Resonance Spectroscopy ; *Glycerophospholipids ; Liposomes ; Membrane Proteins/analysis/*chemistry/genetics/metabolism ; *Membranes, Artificial ; Models, Molecular ; Mutation ; Oxalates ; Phosphatidic Acids ; Phospholipases A/analysis/*chemistry/genetics/metabolism ; Phospholipases A2 ; Spin Labels ; Surface Properties
    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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  • 2
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    Parasitology. Drugs to combat tropical protozoan parasites (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-07-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gelb, Michael H -- Hol, Wim G J -- New York, N.Y. -- Science. 2002 Jul 19;297(5580):343-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Chemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12130767" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Antimalarials/chemistry/pharmacology/therapeutic use ; *Antiprotozoal Agents/chemistry/pharmacology/therapeutic use ; Chagas Disease/drug therapy/parasitology ; Chemistry, Pharmaceutical ; Combinatorial Chemistry Techniques ; Computational Biology ; Databases, Factual ; Drug Design ; Drug Resistance ; Genomics ; Humans ; Leishmania/drug effects/genetics/metabolism ; Leishmaniasis/drug therapy/parasitology ; Malaria/drug therapy/parasitology ; Plasmodium falciparum/drug effects/genetics/metabolism ; Plasmodium vivax/drug effects/genetics ; *Trypanocidal Agents/chemistry/pharmacology/therapeutic use ; Trypanosoma brucei brucei/drug effects/genetics/metabolism ; Trypanosoma cruzi/drug effects/genetics/metabolism ; Trypanosomiasis, African/drug therapy/parasitology
    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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  • 3
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    Identification of geranylgeranyl-modified proteins in HeLa cells (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-01-19
    Description: Previous studies have shown that animal cells contain isoprenoid-modified proteins and that one of these proteins, lamin B, contains a thioether-linked farnesyl group that is attached to cysteine. In the present study, a novel isoprenoid-modification was identified by labeling HeLa cells with [3H]mevalonic acid and analyzing proteolytic digests of the total cell protein. Radioactive fragments were purified from these digests and treated with Raney nickel. The released, labeled material was analyzed by gas-liquid chromatography (GC) and mass spectrometry (MS). This approach revealed that an all-trans geranylgeranyl group was a major isoprenoid modification.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3442113/" 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/PMC3442113/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Farnsworth, C C -- Gelb, M H -- Glomset, J A -- R01 HL036235/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Jan 19;247(4940):320-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute Laboratory, University of Washington, Seattle 98195.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2296721" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatography, Gel ; Chromatography, Ion Exchange ; Diterpenes/*metabolism ; Gas Chromatography-Mass Spectrometry ; HeLa Cells/metabolism ; Humans ; Mevalonic Acid/metabolism ; Molecular Structure ; Nickel ; Peptide Fragments ; Proteins/*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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  • 4
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    Interfacial catalysis: the mechanism of phospholipase A2 (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-12-14
    Description: A chemical description of the action of phospholipase A2 (PLA2) can now be inferred with confidence from three high-resolution x-ray crystal structures. The first is the structure of the PLA2 from the venom of the Chinese cobra (Naja naja atra) in a complex with a phosphonate transition-state analogue. This enzyme is typical of a large, well-studied homologous family of PLA2S. The second is a similar complex with the evolutionarily distant bee-venom PLA2. The third structure is the uninhibited PLA2 from Chinese cobra venom. Despite the different molecular architectures of the cobra and bee-venom PLA2s, the transition-state analogue interacts in a nearly identical way with the catalytic machinery of both enzymes. The disposition of the fatty-acid side chains suggests a common access route of the substrate from its position in the lipid aggregate to its productive interaction with the active site. Comparison of the cobra-venom complex with the uninhibited enzyme indicates that optimal binding and catalysis at the lipid-water interface is due to facilitated substrate diffusion from the interfacial binding surface to the catalytic site rather than an allosteric change in the enzyme's structure. However, a second bound calcium ion changes its position upon the binding of the transition-state analogue, suggesting a mechanism for augmenting the critical electrophile.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443688/" 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/PMC3443688/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, D L -- White, S P -- Otwinowski, Z -- Yuan, W -- Gelb, M H -- Sigler, P B -- GM22324/GM/NIGMS NIH HHS/ -- HL36235/HL/NHLBI NIH HHS/ -- R01 HL036235/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 14;250(4987):1541-6.〈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/2274785" target="_blank"〉PubMed〈/a〉
    Keywords: Bee Venoms/analysis ; Binding Sites ; Calcium/metabolism ; Catalysis ; Chemistry, Physical ; Cobra Venoms/analysis ; Models, Molecular ; Molecular Structure ; Organophosphonates/metabolism ; Phospholipases A/chemistry/*metabolism ; Phospholipases A2 ; Phospholipids/metabolism ; Physicochemical Phenomena ; Protein Conformation ; X-Ray Diffraction
    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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  • 5
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    Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-12-14
    Description: The 2.0 angstroms crystal structure of a complex containing bee-venom phospholipase A2 (PLA2) and a phosphonate transition-state analogue was solved by multiple isomorphous replacement. The electron-density map is sufficiently detailed to visualize the proximal sugars of the enzyme's N-linked carbohydrate and a single molecule of the transition-state analogue bound ot its active center. Although bee-venom PLA2 does not belong to the large homologous Class I/II family that encompasses most other well-studied PLA2s, there is segmental sequence similarity and conservation of many functional substructures. Comparison of the bee-venom enzyme with other phospholipase structures provides compelling evidence for a common catalytic mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, D L -- Otwinowski, Z -- Gelb, M H -- Sigler, P B -- GM22324/GM/NIGMS NIH HHS/ -- HL36235/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 14;250(4987):1563-6.〈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/2274788" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bee Venoms/*analysis ; Binding Sites ; Calcium/metabolism ; Carbohydrate Metabolism ; Catalysis ; Chemistry, Physical ; Crystallization ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; Phosphatidylethanolamines/*metabolism ; Phospholipases A/*chemistry/metabolism ; Phospholipases A2 ; Physicochemical Phenomena ; 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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  • 6
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    Crystal structure of cobra-venom phospholipase A2 in a complex with a transition-state analogue (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-12-14
    Description: The crystal structure of a complex between a phosphonate transition-state analogue and the phospholipase A2 (PLA2) from Naja naja atra venom has been solved and refined to a resolution of 2.0 angstroms. The identical stereochemistry of the two complexes that comprise the crystal's asymmetric unit indicates both the manner in which the transition state is stabilized and how the hydrophobic fatty acyl chains of the substrate are accommodated by the enzyme during interfacial catalysis. The critical features that suggest the chemistry of binding and catalysis are the same as those seen in the crystal structure of a similar complex formed with the evolutionarily distant bee-venom PLA2.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉White, S P -- Scott, D L -- Otwinowski, Z -- Gelb, M H -- Sigler, P B -- GM22324/GM/NIGMS NIH HHS/ -- HL 36235/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 14;250(4987):1560-3.〈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/2274787" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bee Venoms/analysis ; Binding Sites ; Calcium/metabolism ; Catalysis ; Chemistry, Physical ; Cobra Venoms/*analysis ; Crystallization ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; Phosphatidylethanolamines/*metabolism ; Phospholipases A/*chemistry/metabolism ; Phospholipases A2 ; Physicochemical Phenomena ; 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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  • 7
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    Crystal structure of bee-venom phospholipase A2: correction (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, D L -- Otwinowski, Z -- Gelb, M H -- Sigler, P B -- New York, N.Y. -- Science. 1991 May 10;252(5007):764.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2028251" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bee Venoms/*chemistry ; Crystallography ; Molecular Sequence Data ; Phospholipases A/*chemistry ; Phospholipases A2
    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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  • 8
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    Structures of free and inhibited human secretory phospholipase A2 from inflammatory exudate (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-11-15
    Description: Phospholipase A2 (PLA2) participates in a wide range of cellular processes including inflammation and transmembrane signaling. A human nonpancreatic secretory PLA2 (hnps-PLA2) has been identified that is found in high concentrations in the synovial fluid of patients with rheumatoid arthritis and in the plasma of patients with septic shock. This enzyme is secreted from certain cell types in response to the proinflammatory cytokines, tumor necrosis factor or interleukin-1. The crystal structures of the calcium-bound form of this enzyme have been determined at physiological pH both in the presence [2.1 angstrom (A) resolution] and absence (2.2 A resolution) of a transition-state analogue. Although the critical features that suggest the chemistry of catalysis are identical to those inferred from the crystal structures of other extracellular PLA2s, the shape of the hydrophobic channel of hnps-PLA2 is uniquely modulated by substrate binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, D L -- White, S P -- Browning, J L -- Rosa, J J -- Gelb, M H -- Sigler, P B -- GM22324/GM/NIGMS NIH HHS/ -- HL36235/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1991 Nov 15;254(5034):1007-10.〈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/1948070" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Calcium/chemistry ; Computer Graphics ; Crystallography ; Extracellular Space/enzymology ; Humans ; Inflammation/*enzymology ; Molecular Sequence Data ; Phospholipases A/antagonists & inhibitors/*ultrastructure ; Phospholipases A2 ; Protein Conformation ; Recombinant Proteins ; Sequence Alignment ; X-Ray Diffraction
    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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  • 9
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    Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-22
    Description: The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241958/" 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/PMC3241958/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siegel, Justin B -- Zanghellini, Alexandre -- Lovick, Helena M -- Kiss, Gert -- Lambert, Abigail R -- St Clair, Jennifer L -- Gallaher, Jasmine L -- Hilvert, Donald -- Gelb, Michael H -- Stoddard, Barry L -- Houk, Kendall N -- Michael, Forrest E -- Baker, David -- R01 GM075962/GM/NIGMS NIH HHS/ -- T32 GM008268/GM/NIGMS NIH HHS/ -- T32 GM008268-24/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):309-13. doi: 10.1126/science.1190239.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20647463" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylamides/chemistry ; Algorithms ; Butadienes/chemistry ; Carbon/*chemistry ; Catalysis ; Catalytic Domain ; Computer Simulation ; *Computer-Aided Design ; Crystallography, X-Ray ; Enzymes/*chemistry/genetics ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Models, Molecular ; Mutagenesis ; Physicochemical Processes ; Protein Conformation ; *Protein Engineering ; Proteins/*chemistry/genetics ; Software ; Stereoisomerism ; Substrate Specificity
    Print ISSN: 0036-8075
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  • 10
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    Protein prenylation, et cetera: signal transduction in two dimensions (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-03-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gelb, M H -- New York, N.Y. -- Science. 1997 Mar 21;275(5307):1750-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA. gelb@chem.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9122679" target="_blank"〉PubMed〈/a〉
    Keywords: *Alkyl and Aryl Transferases ; Animals ; Cell Membrane/metabolism ; GTP-Binding Proteins/*metabolism ; Methylation ; Palmitic Acid/metabolism ; *Protein Prenylation ; *Signal Transduction ; Transferases/chemistry/*metabolism ; ras Proteins/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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