Literature DB >> 19437047

Recent developments of the quantum chemical cluster approach for modeling enzyme reactions.

Per E M Siegbahn1, Fahmi Himo.   

Abstract

The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent applications have used cluster models much larger than before which have given new modeling insights. One important and rather surprising feature is the fast convergence with cluster size of the energetics of the reactions. Even for reactions with significant charge separation it has in some cases been possible to obtain full convergence in the sense that dielectric cavity effects from outside the cluster do not contribute to any significant extent. Direct comparisons between quantum mechanics (QM)-only and QM/molecular mechanics (MM) calculations for quite large clusters in a case where the results differ significantly have shown that care has to be taken when using the QM/MM approach where there is strong charge polarization. Insights from the methods used, generally hybrid density functional methods, have also led to possibilities to give reasonable error limits for the results. Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II.

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Year:  2009        PMID: 19437047     DOI: 10.1007/s00775-009-0511-y

Source DB:  PubMed          Journal:  J Biol Inorg Chem        ISSN: 0949-8257            Impact factor:   3.358


  39 in total

1.  The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment.

Authors:  G Andrés Cisneros; Min Wang; Peter Silinski; Michael C Fitzgerald; Weitao Yang
Journal:  Biochemistry       Date:  2004-06-08       Impact factor: 3.162

2.  O-O bond formation in the S(4) state of the oxygen-evolving complex in photosystem II.

Authors:  Per E M Siegbahn
Journal:  Chemistry       Date:  2006-12-13       Impact factor: 5.236

3.  A designed synthetic analogue of 4-OT is specific for a non-natural substrate.

Authors:  Norman Metanis; Ehud Keinan; Philip E Dawson
Journal:  J Am Chem Soc       Date:  2005-04-27       Impact factor: 15.419

4.  Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

Authors:  Demian Riccardi; Patricia Schaefer; Yang Yang; Haibo Yu; Nilanjan Ghosh; Xavier Prat-Resina; Peter König; Guohui Li; Dingguo Xu; Hua Guo; Marcus Elstner; Qiang Cui
Journal:  J Phys Chem B       Date:  2006-04-06       Impact factor: 2.991

5.  Highly enantioselective and regioselective biocatalytic azidolysis of aromatic epoxides.

Authors:  J H Spelberg; J E van Hylckama Vlieg; L Tang; D B Janssen; R M Kellogg
Journal:  Org Lett       Date:  2001-01-11       Impact factor: 6.005

6.  The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations.

Authors:  Jan C Schöneboom; Hai Lin; Nathalie Reuter; Walter Thiel; Shimrit Cohen; François Ogliaro; Sason Shaik
Journal:  J Am Chem Soc       Date:  2002-07-10       Impact factor: 15.419

7.  Enantioselective formation and ring-opening of epoxides catalysed by halohydrin dehalogenases.

Authors:  D B Janssen; M Majerić-Elenkov; G Hasnaoui; B Hauer; J H Lutje Spelberg
Journal:  Biochem Soc Trans       Date:  2006-04       Impact factor: 5.407

8.  An autocatalytic mechanism for NiFe-hydrogenase: reduction to Ni(I) followed by oxidative addition.

Authors:  Sten O Nilsson Lill; Per E M Siegbahn
Journal:  Biochemistry       Date:  2009-02-10       Impact factor: 3.162

9.  Characterization of a novel enantioselective halohydrin hydrogen-halide-lyase.

Authors:  T Nakamura; T Nagasawa; F Yu; I Watanabe; H Yamada
Journal:  Appl Environ Microbiol       Date:  1994-04       Impact factor: 4.792

10.  Quantum Chemical Modeling of the Dehalogenation Reaction of Haloalcohol Dehalogenase.

Authors:  Kathrin H Hopmann; Fahmi Himo
Journal:  J Chem Theory Comput       Date:  2008-07       Impact factor: 6.006

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  38 in total

1.  Evaluation and ranking of enzyme designs.

Authors:  Gert Kiss; Daniela Röthlisberger; David Baker; K N Houk
Journal:  Protein Sci       Date:  2010-09       Impact factor: 6.725

Review 2.  A practical guide to modelling enzyme-catalysed reactions.

Authors:  Richard Lonsdale; Jeremy N Harvey; Adrian J Mulholland
Journal:  Chem Soc Rev       Date:  2012-01-26       Impact factor: 54.564

3.  Brønsted-Evans-Polanyi relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory.

Authors:  Rajeev Surendran Assary; Linda J Broadbelt; Larry A Curtiss
Journal:  J Mol Model       Date:  2011-04-27       Impact factor: 1.810

4.  Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics.

Authors:  Mats Linder; Adam Johannes Johansson; Tjelvar S G Olsson; John Liebeschuetz; Tore Brinck
Journal:  J Comput Aided Mol Des       Date:  2012-09-16       Impact factor: 3.686

5.  A quantum-mechanical study of the reaction mechanism of sulfite oxidase.

Authors:  Marie-Céline van Severen; Milica Andrejić; Jilai Li; Kerstin Starke; Ricardo A Mata; Ebbe Nordlander; Ulf Ryde
Journal:  J Biol Inorg Chem       Date:  2014-06-24       Impact factor: 3.358

6.  Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study.

Authors:  Dmytro Bykov; Frank Neese
Journal:  J Biol Inorg Chem       Date:  2010-12-02       Impact factor: 3.358

7.  Differences in the Nature of the Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models.

Authors:  Rui Lai; Qiang Cui
Journal:  J Phys Chem B       Date:  2020-10-08       Impact factor: 2.991

8.  Nuclear inelastic scattering and Mössbauer spectroscopy as local probes for ligand binding modes and electronic properties in proteins: vibrational behavior of a ferriheme center inside a β-barrel protein.

Authors:  Beate Moeser; Adam Janoschka; Juliusz A Wolny; Hauke Paulsen; Igor Filippov; Robert E Berry; Hongjun Zhang; Aleksandr I Chumakov; F Ann Walker; Volker Schünemann
Journal:  J Am Chem Soc       Date:  2012-02-27       Impact factor: 15.419

9.  Mechanism and Structure of γ-Resorcylate Decarboxylase.

Authors:  Xiang Sheng; Yury Patskovsky; Anna Vladimirova; Jeffrey B Bonanno; Steven C Almo; Fahmi Himo; Frank M Raushel
Journal:  Biochemistry       Date:  2018-01-19       Impact factor: 3.162

10.  Predicting the relative binding affinity of mineralocorticoid receptor antagonists by density functional methods.

Authors:  Katarina Roos; Anders Hogner; Derek Ogg; Martin J Packer; Eva Hansson; Kenneth L Granberg; Emma Evertsson; Anneli Nordqvist
Journal:  J Comput Aided Mol Des       Date:  2015-11-16       Impact factor: 3.686

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