Literature DB >> 18208378

Computational enzymology: modelling the mechanisms of biological catalysts.

Adrian J Mulholland1.   

Abstract

Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and reliable predictions of mechanisms, revolutionizing enzymology.

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Year:  2008        PMID： 18208378     DOI： 10.1042/BST0360022

Source DB:  PubMed          Journal:  Biochem Soc Trans        ISSN： 0300-5127            Impact factor:   5.407


  10 in total

1.  Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase.

Authors:  Maria P Frushicheva; Jie Cao; Zhen T Chu; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-09       Impact factor: 11.205

Review 2.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

3.  Introduction. Biomolecular simulation.

Authors:  Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

4.  Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis.

Authors:  Maria P Frushicheva; Jie Cao; Arieh Warshel
Journal:  Biochemistry       Date:  2011-04-15       Impact factor: 3.162

Review 5.  Computer aided enzyme design and catalytic concepts.

Authors:  Maria P Frushicheva; Matthew J L Mills; Patrick Schopf; Manoj K Singh; Ram B Prasad; Arieh Warshel
Journal:  Curr Opin Chem Biol       Date:  2014-05-08       Impact factor: 8.822

Review 6.  Protein engineering for metabolic engineering: current and next-generation tools.

Authors:  Ryan J Marcheschi; Luisa S Gronenberg; James C Liao
Journal:  Biotechnol J       Date:  2013-04-16       Impact factor: 4.677

7.  The empirical valence bond as an effective strategy for computer-aided enzyme design.

Authors:  Alexandra Vardi-Kilshtain; Maite Roca; Arieh Warshel
Journal:  Biotechnol J       Date:  2009-04       Impact factor: 4.677

8.  Toward accurate screening in computer-aided enzyme design.

Authors:  Maite Roca; Alexandra Vardi-Kilshtain; Arieh Warshel
Journal:  Biochemistry       Date:  2009-04-14       Impact factor: 3.162

9.  Simulating the catalytic effect of a designed mononuclear zinc metalloenzyme that catalyzes the hydrolysis of phosphate triesters.

Authors:  Manoj Kumar Singh; Zhen T Chu; Arieh Warshel
Journal:  J Phys Chem B       Date:  2014-10-13       Impact factor: 2.991

10.  Unraveling the differences of the hydrolytic activity of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase: a quantum mechanics-molecular mechanics modeling study.

Authors:  Juan A Bueren-Calabuig; Gustavo Pierdominici-Sottile; Adrian E Roitberg
Journal:  J Phys Chem B       Date:  2014-05-21       Impact factor: 2.991
  10 in total

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