Literature DB >> 12069618

The incorporation of quantum effects in enzyme kinetics modeling.

Donald G Truhlar1, Jiali Gao, Cristobal Alhambra, Mireia Garcia-Viloca, José Corchado, Maria Luz Sánchez, Jordi Villà.   

Abstract

We present an overview of new procedures for including quantum mechanical effects in enzyme kinetics. Quantum effects are included in three ways: (1) The electronic structure of the atoms in the catalytic center is treated quantum mechanically in order to calculate a realistic potential energy surface for the bond rearrangement process. (2) The discrete nature of quantum mechanical vibrational energies is incorporated in the treatment of nuclear motion for computing the potential of mean force. (3) Multidimensional tunneling contributions are included. These procedures are illustrated by applications to proton abstractions catalyzed by enolase and methylamine dehydrogenase and hydride-transfer reactions by alcohol dehydrogenase and xylose isomerase.

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Year:  2002        PMID: 12069618     DOI: 10.1021/ar0100226

Source DB:  PubMed          Journal:  Acc Chem Res        ISSN: 0001-4842            Impact factor:   22.384


  46 in total

1.  Molecular dynamics and protein function.

Authors:  M Karplus; J Kuriyan
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-03       Impact factor: 11.205

2.  Nonperfect synchronization of reaction center rehybridization in the transition state of the hydride transfer catalyzed by dihydrofolate reductase.

Authors:  Jingzhi Pu; Shuhua Ma; Mireia Garcia-Viloca; Jiali Gao; Donald G Truhlar; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2005-10-26       Impact factor: 15.419

3.  Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals.

Authors:  Jingzhi Pu; Jiali Gao; Donald G Truhlar
Journal:  Chemphyschem       Date:  2005-09-05       Impact factor: 3.102

Review 4.  Mechanisms and free energies of enzymatic reactions.

Authors:  Jiali Gao; Shuhua Ma; Dan T Major; Kwangho Nam; Jingzhi Pu; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

Review 5.  Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.

Authors:  Jingzhi Pu; Jiali Gao; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

Review 6.  Modeling kinetics of subcellular disposition of chemicals.

Authors:  Stefan Balaz
Journal:  Chem Rev       Date:  2009-05       Impact factor: 60.622

7.  Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer.

Authors:  Katarzyna Świderek; Kemel Arafet; Amnon Kohen; Vicent Moliner
Journal:  J Chem Theory Comput       Date:  2017-02-22       Impact factor: 6.006

8.  Barrier compression and its contribution to both classical and quantum mechanical aspects of enzyme catalysis.

Authors:  Sam Hay; Linus O Johannissen; Michael J Sutcliffe; Nigel S Scrutton
Journal:  Biophys J       Date:  2010-01-06       Impact factor: 4.033

Review 9.  Catalytic efficiency of enzymes: a theoretical analysis.

Authors:  Sharon Hammes-Schiffer
Journal:  Biochemistry       Date:  2012-12-20       Impact factor: 3.162

10.  Evolutionary basis for the coupled-domain motions in Thermus thermophilus leucyl-tRNA synthetase.

Authors:  Kristina Mary Ellen Weimer; Brianne Leigh Shane; Michael Brunetto; Sudeep Bhattacharyya; Sanchita Hati
Journal:  J Biol Chem       Date:  2009-02-02       Impact factor: 5.157

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