FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W1968739731> ?p ?o ?g. }

• W1968739731 endingPage "4107" @default.
• W1968739731 startingPage "4097" @default.
• W1968739731 abstract "The steric effect, exerted by enzymes on their reacting substrates, has been considered as a major factor in enzyme catalysis. In particular, it has been proposed that enzymes catalyze their reactions by pushing their reacting fragments to a catalytic configuration which is sometimes called near attack configuration (NAC). This work uses computer simulation approaches to determine the relative importance of the steric contribution to enzyme catalysis. The steric proposal is expressed in terms of well defined thermodynamic cycles that compare the reaction in the enzyme to the corresponding reaction in water. The SN2 reaction of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10, which was used in previous studies to support the strain concept is chosen as a test case for this proposal. The empirical valence bond (EVB) method provides the reaction potential surfaces in our studies. The reliability and efficiency of this method make it possible to obtain stable results for the steric free energy. Two independent strategies are used to evaluate the actual magnitude of the steric effect. The first applies restraints on the substrate coordinates in water in a way that mimics the steric effect of the protein active site. These restraints are then released and the free energy associated with the release process provides the desired estimate of the steric effect. The second approach eliminates the electrostatic interactions between the substrate and the surrounding in the enzyme and in water, and compares the corresponding reaction profiles. The difference between the resulting profiles provides a direct estimate of the nonelectrostatic contribution to catalysis and the corresponding steric effect. It is found that the nonelectrostatic contribution is about −0.7 kcal/mol while the full “apparent steric contribution” is about −2.2 kcal/mol. The apparent steric effect includes about −1.5 kcal/mol electrostatic contribution. The total electrostatic contribution is found to account for almost all the observed catalytic effect (∼−6.1 kcal/mol of the −6.8 calculated total catalytic effect). Thus, it is concluded that the steric effect is not the major source of the catalytic power of haloalkane dehalogenase. Furthermore, it is found that the largest component of the apparent steric effect is associated with the solvent reorganization energy. This solvent-induced effect is quite different from the traditional picture of balance between the repulsive interaction of the reactive fragments and the steric force of the protein." @default.
• W1968739731 created "2016-06-24" @default.
• W1968739731 creator A5004433843 @default.
• W1968739731 creator A5021716572 @default.
• W1968739731 creator A5076781251 @default.
• W1968739731 creator A5088665303 @default.
• W1968739731 date "2002-03-20" @default.
• W1968739731 modified "2023-10-12" @default.
• W1968739731 title "How Much Do Enzymes Really Gain by Restraining Their Reacting Fragments?" @default.
• W1968739731 cites W1974167806 @default.
• W1968739731 cites W1980066100 @default.
• W1968739731 cites W1982122835 @default.
• W1968739731 cites W1985071657 @default.
• W1968739731 cites W1993916927 @default.
• W1968739731 cites W1997082598 @default.
• W1968739731 cites W1999970382 @default.
• W1968739731 cites W2004303971 @default.
• W1968739731 cites W2008873087 @default.
• W1968739731 cites W2010100725 @default.
• W1968739731 cites W2020180057 @default.
• W1968739731 cites W2022189885 @default.
• W1968739731 cites W2023556976 @default.
• W1968739731 cites W2032718131 @default.
• W1968739731 cites W2046997698 @default.
• W1968739731 cites W2053520864 @default.
• W1968739731 cites W2056167405 @default.
• W1968739731 cites W2068502964 @default.
• W1968739731 cites W2078998588 @default.
• W1968739731 cites W2082176114 @default.
• W1968739731 cites W2089380173 @default.
• W1968739731 cites W2090504201 @default.
• W1968739731 cites W2091237955 @default.
• W1968739731 cites W2107025108 @default.
• W1968739731 cites W2108772880 @default.
• W1968739731 cites W2139982366 @default.
• W1968739731 cites W2156060143 @default.
• W1968739731 cites W2325113402 @default.
• W1968739731 cites W2950002563 @default.
• W1968739731 cites W2953289392 @default.
• W1968739731 cites W4246242479 @default.
• W1968739731 doi "https://doi.org/10.1021/ja012230z" @default.
• W1968739731 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/11942849" @default.
• W1968739731 hasPublicationYear "2002" @default.
• W1968739731 type Work @default.
• W1968739731 sameAs 1968739731 @default.
• W1968739731 citedByCount "119" @default.
• W1968739731 countsByYear W19687397312012 @default.
• W1968739731 countsByYear W19687397312013 @default.
• W1968739731 countsByYear W19687397312014 @default.
• W1968739731 countsByYear W19687397312015 @default.
• W1968739731 countsByYear W19687397312016 @default.
• W1968739731 countsByYear W19687397312017 @default.
• W1968739731 countsByYear W19687397312018 @default.
• W1968739731 countsByYear W19687397312019 @default.
• W1968739731 countsByYear W19687397312020 @default.
• W1968739731 countsByYear W19687397312021 @default.
• W1968739731 countsByYear W19687397312022 @default.
• W1968739731 countsByYear W19687397312023 @default.
• W1968739731 crossrefType "journal-article" @default.
• W1968739731 hasAuthorship W1968739731A5004433843 @default.
• W1968739731 hasAuthorship W1968739731A5021716572 @default.
• W1968739731 hasAuthorship W1968739731A5076781251 @default.
• W1968739731 hasAuthorship W1968739731A5088665303 @default.
• W1968739731 hasConcept C111368507 @default.
• W1968739731 hasConcept C127313418 @default.
• W1968739731 hasConcept C147597530 @default.
• W1968739731 hasConcept C161790260 @default.
• W1968739731 hasConcept C178790620 @default.
• W1968739731 hasConcept C181199279 @default.
• W1968739731 hasConcept C185592680 @default.
• W1968739731 hasConcept C201194858 @default.
• W1968739731 hasConcept C21951064 @default.
• W1968739731 hasConcept C2777289219 @default.
• W1968739731 hasConcept C41183919 @default.
• W1968739731 hasConcept C69118441 @default.
• W1968739731 hasConcept C71240020 @default.
• W1968739731 hasConcept C96765332 @default.
• W1968739731 hasConceptScore W1968739731C111368507 @default.
• W1968739731 hasConceptScore W1968739731C127313418 @default.
• W1968739731 hasConceptScore W1968739731C147597530 @default.
• W1968739731 hasConceptScore W1968739731C161790260 @default.
• W1968739731 hasConceptScore W1968739731C178790620 @default.
• W1968739731 hasConceptScore W1968739731C181199279 @default.
• W1968739731 hasConceptScore W1968739731C185592680 @default.
• W1968739731 hasConceptScore W1968739731C201194858 @default.
• W1968739731 hasConceptScore W1968739731C21951064 @default.
• W1968739731 hasConceptScore W1968739731C2777289219 @default.
• W1968739731 hasConceptScore W1968739731C41183919 @default.
• W1968739731 hasConceptScore W1968739731C69118441 @default.
• W1968739731 hasConceptScore W1968739731C71240020 @default.
• W1968739731 hasConceptScore W1968739731C96765332 @default.
• W1968739731 hasIssue "15" @default.
• W1968739731 hasLocation W19687397311 @default.
• W1968739731 hasLocation W19687397312 @default.
• W1968739731 hasOpenAccess W1968739731 @default.
• W1968739731 hasPrimaryLocation W19687397311 @default.
• W1968739731 hasRelatedWork W1972323689 @default.
• W1968739731 hasRelatedWork W1980221804 @default.

• next