Literature DB >> 18401503

High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase.

Marc W van der Kamp1, Francesca Perruccio, Adrian J Mulholland.   

Abstract

High-level ab initio quantum mechanical/molecular mechanical (QM/MM) modelling of citryl-CoA formation in citrate synthase reveals that an arginine residue acts as the proton donor; this proposed new mechanism helps to explain how chemical and large scale conformational changes are coupled in this paradigmatic enzyme.

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Year:  2008        PMID： 18401503     DOI： 10.1039/b800496j

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


  11 in total

1.  Taking Ockham's razor to enzyme dynamics and catalysis.

Authors:  David R Glowacki; Jeremy N Harvey; Adrian J Mulholland
Journal:  Nat Chem       Date:  2012-01-29       Impact factor: 24.427

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.  Insight into the reaction mechanism of cis,cis-muconate lactonizing enzymes: a DFT QM/MM study.

Authors:  Tuanjai Somboon; Matthew Paul Gleeson; Supa Hannongbua
Journal:  J Mol Model       Date:  2011-05-04       Impact factor: 1.810

4.  Examining the Mechanism of Phosphite Dehydrogenase with Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

Authors:  David R Stevens; Sharon Hammes-Schiffer
Journal:  Biochemistry       Date:  2020-02-14       Impact factor: 3.162

5.  Arginine: Its pKa value revisited.

Authors:  Carolyn A Fitch; Gerald Platzer; Mark Okon; Bertrand E Garcia-Moreno; Lawrence P McIntosh
Journal:  Protein Sci       Date:  2015-03-22       Impact factor: 6.725

6.  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

7.  Multiscale analysis of enantioselectivity in enzyme-catalysed 'lethal synthesis' using projector-based embedding.

Authors:  Xinglong Zhang; Simon J Bennie; Marc W van der Kamp; David R Glowacki; Frederick R Manby; Adrian J Mulholland
Journal:  R Soc Open Sci       Date:  2018-02-14       Impact factor: 2.963

8.  Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

Authors:  Stephen A Wells; Marc W van der Kamp; John D McGeagh; Adrian J Mulholland
Journal:  PLoS One       Date:  2015-08-04       Impact factor: 3.240

9.  Chemical rescue and inhibition studies to determine the role of Arg301 in phosphite dehydrogenase.

Authors:  John E Hung; Emily J Fogle; Neha Garg; Jonathan R Chekan; Satish K Nair; Wilfred A van der Donk
Journal:  PLoS One       Date:  2014-01-31       Impact factor: 3.240

10.  An active site-tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase.

Authors:  Jesse R Murphy; Stefano Donini; T Joseph Kappock
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-09-23       Impact factor: 1.056
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