Literature DB >> 18802578

QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate.

Anna L Bowman1, Ian M Grant, Adrian J Mulholland.   

Abstract

Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations indicate that the reaction of native HEWL with its natural substrate involves a covalent intermediate, in contrast to the 'textbook' mechanism for this seminal enzyme.

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Year:  2008        PMID： 18802578     DOI： 10.1039/b810099c

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN： 1359-7345            Impact factor:   6.222


  13 in total

Review 1.  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

2.  Free energy study of the catalytic mechanism of Trypanosoma cruzi trans-sialidase. From the Michaelis complex to the covalent intermediate.

Authors:  Gustavo Pierdominici-Sottile; Nicole A Horenstein; Adrian E Roitberg
Journal:  Biochemistry       Date:  2011-10-27       Impact factor: 3.162

Review 3.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Proteins       Date:  2010-05-01

4.  The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions.

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Faraday Discuss       Date:  2010       Impact factor: 4.008

5.  A computational and experimental study of O-glycosylation. Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2.

Authors:  Hansel Gómez; Raúl Rojas; Divya Patel; Lawrence A Tabak; José M Lluch; Laura Masgrau
Journal:  Org Biomol Chem       Date:  2014-05-07       Impact factor: 3.876

6.  QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase.

Authors:  Caroline S Pereira; Rodrigo L Silveira; Munir S Skaf
Journal:  J Chem Inf Model       Date:  2021-03-24       Impact factor: 4.956

7.  QM/MM Study of the Fosfomycin Resistance Mechanism Involving FosB Enzyme.

Authors:  Anderson H Lima; José Rogério A Silva; Cláudio Nahum Alves; Jerônimo Lameira
Journal:  ACS Omega       Date:  2021-05-03

8.  Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

Authors:  Richard Lonsdale; Simon Hoyle; Daniel T Grey; Lars Ridder; Adrian J Mulholland
Journal:  Biochemistry       Date:  2012-02-10       Impact factor: 3.162

9.  Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes.

Authors:  Gerhard König; Phillip S Hudson; Stefan Boresch; H Lee Woodcock
Journal:  J Chem Theory Comput       Date:  2014-02-11       Impact factor: 6.006

10.  QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes.

Authors:  Emilio Lence; Marc W van der Kamp; Concepción González-Bello; Adrian J Mulholland
Journal:  Org Biomol Chem       Date:  2018-06-20       Impact factor: 3.876
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