The empirical valence bond as an effective strategy for computer-aided enzyme design
The ability of the empirical valence bond (EVB) to be used in screening active site residues in enzyme design is explored in a preliminary way. This validation is done by comparing the ability of this approach to evaluate the catalytic contributions of various residues in chorismate mutase. It is de...
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| Veröffentlicht in: | Biotechnology journal 2009-04, Vol.4 (4), p.495-500 |
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| container_title | Biotechnology journal |
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| creator | Vardi-Kilshtain, Alexandra Roca, Maite Warshel, Arieh |
| description | The ability of the empirical valence bond (EVB) to be used in screening active site residues in enzyme design is explored in a preliminary way. This validation is done by comparing the ability of this approach to evaluate the catalytic contributions of various residues in chorismate mutase. It is demonstrated that the EVB model can serve as an accurate tool in the final stages of computer‐aided enzyme design (CAED). The ability of the model to predict quantitatively the catalytic power of enzymes should augment the capacity of current approaches for enzyme design. |
| doi_str_mv | 10.1002/biot.200800299 |
| format | Article |
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This validation is done by comparing the ability of this approach to evaluate the catalytic contributions of various residues in chorismate mutase. It is demonstrated that the EVB model can serve as an accurate tool in the final stages of computer‐aided enzyme design (CAED). The ability of the model to predict quantitatively the catalytic power of enzymes should augment the capacity of current approaches for enzyme design.</description><identifier>ISSN: 1860-6768</identifier><identifier>EISSN: 1860-7314</identifier><identifier>DOI: 10.1002/biot.200800299</identifier><identifier>PMID: 19229886</identifier><language>eng</language><publisher>Weinheim: WILEY-VCH Verlag</publisher><subject>Amino Acid Substitution ; Arginine - metabolism ; Binding Sites ; Catalysis ; Chorismate Mutase - chemistry ; Chorismate Mutase - genetics ; Chorismate Mutase - metabolism ; Computer Simulation ; Computer-Aided Design ; Dimerization ; Enzyme Activation ; Enzyme design ; Enzymes - chemistry ; Enzymes - genetics ; Kinetics ; Models, Chemical ; Models, Molecular ; Pre-organization effect ; Static Electricity ; Structure-Activity Relationship ; Thermodynamics ; Transition-state stabilization ; Valine - metabolism ; Water - chemistry</subject><ispartof>Biotechnology journal, 2009-04, Vol.4 (4), p.495-500</ispartof><rights>Copyright © 2009 WILEY‐VCH Verlag GmbH & Co. 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The ability of the model to predict quantitatively the catalytic power of enzymes should augment the capacity of current approaches for enzyme design.</description><subject>Amino Acid Substitution</subject><subject>Arginine - metabolism</subject><subject>Binding Sites</subject><subject>Catalysis</subject><subject>Chorismate Mutase - chemistry</subject><subject>Chorismate Mutase - genetics</subject><subject>Chorismate Mutase - metabolism</subject><subject>Computer Simulation</subject><subject>Computer-Aided Design</subject><subject>Dimerization</subject><subject>Enzyme Activation</subject><subject>Enzyme design</subject><subject>Enzymes - chemistry</subject><subject>Enzymes - genetics</subject><subject>Kinetics</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Pre-organization effect</subject><subject>Static Electricity</subject><subject>Structure-Activity Relationship</subject><subject>Thermodynamics</subject><subject>Transition-state stabilization</subject><subject>Valine - metabolism</subject><subject>Water - chemistry</subject><issn>1860-6768</issn><issn>1860-7314</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUtvEzEUhS1ERR-wZYm8YjfBr_FjgwRRaStVLYugsrNsz53UMDMO9iQ0_HqmShTaFSvbuud898gHobeUzCgh7IOPaZwxQvT0MOYFOqFakkpxKl7u71JJfYxOS_lBiKg5Ea_QMTWMGa3lCVos7gFDv4o5BtfhjetgCIB9GhrsCnYDhraFMMYN4DJmN8Jyi9uUcUj9aj1CrlxsoMEw_Nn2gBsocTm8Rket6wq82Z9n6NuX88X8srq-vbiaf7qugpj2V0Y2QmjigTdN7U2twQhHPCFOqNY5N2UFHpzkpq2NUUpLRqn3hHnNKSWSn6GPO-5q7XtoAgxTws6ucuxd3trkon0-GeK9XaaNZVLRWrEJ8H4PyOnXGspo-1gCdJ0bIK2LZaSujaZ6Es52wpBTKRnawxJK7GMR9rEIeyhiMrx7Gu2ffP_zk8DsBL9jB9v_4Oznq9vFU3i188YywsPB6_JPKxVXtb27ubDzG_Hd3F1-tXP-F2whpcE</recordid><startdate>200904</startdate><enddate>200904</enddate><creator>Vardi-Kilshtain, Alexandra</creator><creator>Roca, Maite</creator><creator>Warshel, Arieh</creator><general>WILEY-VCH Verlag</general><general>WILEY‐VCH Verlag</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>5PM</scope></search><sort><creationdate>200904</creationdate><title>The empirical valence bond as an effective strategy for computer-aided enzyme design</title><author>Vardi-Kilshtain, Alexandra ; Roca, Maite ; Warshel, Arieh</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4229-96d4480be3dd5b958e94a0b00a47faaa304e3ca639f5997786211bb02b8311063</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Amino Acid Substitution</topic><topic>Arginine - metabolism</topic><topic>Binding Sites</topic><topic>Catalysis</topic><topic>Chorismate Mutase - chemistry</topic><topic>Chorismate Mutase - genetics</topic><topic>Chorismate Mutase - metabolism</topic><topic>Computer Simulation</topic><topic>Computer-Aided Design</topic><topic>Dimerization</topic><topic>Enzyme Activation</topic><topic>Enzyme design</topic><topic>Enzymes - chemistry</topic><topic>Enzymes - genetics</topic><topic>Kinetics</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Pre-organization effect</topic><topic>Static Electricity</topic><topic>Structure-Activity Relationship</topic><topic>Thermodynamics</topic><topic>Transition-state stabilization</topic><topic>Valine - metabolism</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vardi-Kilshtain, Alexandra</creatorcontrib><creatorcontrib>Roca, Maite</creatorcontrib><creatorcontrib>Warshel, Arieh</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biotechnology journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vardi-Kilshtain, Alexandra</au><au>Roca, Maite</au><au>Warshel, Arieh</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The empirical valence bond as an effective strategy for computer-aided enzyme design</atitle><jtitle>Biotechnology journal</jtitle><addtitle>Biotechnology Journal</addtitle><date>2009-04</date><risdate>2009</risdate><volume>4</volume><issue>4</issue><spage>495</spage><epage>500</epage><pages>495-500</pages><issn>1860-6768</issn><eissn>1860-7314</eissn><abstract>The ability of the empirical valence bond (EVB) to be used in screening active site residues in enzyme design is explored in a preliminary way. 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| fulltext | fulltext |
| identifier | ISSN: 1860-6768 |
| ispartof | Biotechnology journal, 2009-04, Vol.4 (4), p.495-500 |
| issn | 1860-6768 1860-7314 |
| language | eng |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Amino Acid Substitution Arginine - metabolism Binding Sites Catalysis Chorismate Mutase - chemistry Chorismate Mutase - genetics Chorismate Mutase - metabolism Computer Simulation Computer-Aided Design Dimerization Enzyme Activation Enzyme design Enzymes - chemistry Enzymes - genetics Kinetics Models, Chemical Models, Molecular Pre-organization effect Static Electricity Structure-Activity Relationship Thermodynamics Transition-state stabilization Valine - metabolism Water - chemistry |
| title | The empirical valence bond as an effective strategy for computer-aided enzyme design |
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