Literature DB >> 12481026

Ten-nanosecond molecular dynamics simulation of the motions of the horse liver alcohol dehydrogenase.PhCH2O- complex.

Jia Luo1, Thomas C Bruice.   

Abstract

Molecular dynamics simulations have been carried out for a period of 10 ns with the dimeric enzyme horse liver alcohol dehydrogenase (HLADH) present as the reactive complex HLADH.NAD+. PhCH2O-. Cross-correlation analysis of the trajectory was carried out with the latter from 500 ps to 10 ns. The resulting cross-correlation map allowed the identification of the correlated and anticorrelated motions, which involve the entire protein. Anticorrelated and correlated motions are carried into the active site-aligned residues.

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Year:  2002        PMID： 12481026      PMCID： PMC139189          DOI： 10.1073/pnas.262667599

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  9 in total

1.  Three-dimensional structure of horse liver alcohol dehydrogenase at 2-4 A resolution.

Authors:  H Eklund; B Nordström; E Zeppezauer; G Söderlund; I Ohlsson; T Boiwe; B O Söderberg; O Tapia; C I Brändén; A Akeson
Journal:  J Mol Biol       Date:  1976-03-25       Impact factor: 5.469

2.  Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations.

Authors:  T Ichiye; M Karplus
Journal:  Proteins       Date:  1991

3.  A link between protein structure and enzyme catalyzed hydrogen tunneling.

Authors:  B J Bahnson; T D Colby; J K Chin; B M Goldstein; J P Klinman
Journal:  Proc Natl Acad Sci U S A       Date:  1997-11-25       Impact factor: 11.205

4.  Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase.

Authors:  Stavros Caratzoulas; Joshua S Mincer; Steven D Schwartz
Journal:  J Am Chem Soc       Date:  2002-04-03       Impact factor: 15.419

5.  Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode.

Authors:  F Colonna-Cesari; D Perahia; M Karplus; H Eklund; C I Brädén; O Tapia
Journal:  J Biol Chem       Date:  1986-11-15       Impact factor: 5.157

6.  Dynamic structures of horse liver alcohol dehydrogenase (HLADH): results of molecular dynamics simulations of HLADH-NAD(+)-PhCH(2)OH, HLADH-NAD(+)-PhCH(2)O(-), and HLADH-NADH-PhCHO.

Authors:  J Luo; T C Bruice
Journal:  J Am Chem Soc       Date:  2001-12-05       Impact factor: 15.419

7.  Structures of horse liver alcohol dehydrogenase complexed with NAD+ and substituted benzyl alcohols.

Authors:  S Ramaswamy; H Eklund; B V Plapp
Journal:  Biochemistry       Date:  1994-05-03       Impact factor: 3.162

8.  General base catalysis in a glutamine for histidine mutant at position 51 of human liver alcohol dehydrogenase.

Authors:  T Ehrig; T D Hurley; H J Edenberg; W F Bosron
Journal:  Biochemistry       Date:  1991-01-29       Impact factor: 3.162

9.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991
  9 in total
  16 in total

1.  Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis.

Authors:  R August Estabrook; Jia Luo; Matthew M Purdy; Vyas Sharma; Paul Weakliem; Thomas C Bruice; Norbert O Reich
Journal:  Proc Natl Acad Sci U S A       Date:  2005-01-18       Impact factor: 11.205

2.  Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping.

Authors:  Jia Luo; Thomas C Bruice
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-19       Impact factor: 11.205

3.  A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations.

Authors:  Bethany L Kormos; Anne M Baranger; David L Beveridge
Journal:  J Struct Biol       Date:  2006-11-10       Impact factor: 2.867

4.  Atomistic insights into the lung cancer-associated L755P mutation in HER2 resistance to lapatinib: a molecular dynamics study.

Authors:  Bei Yang; Haiping Zhang; Hao Wang
Journal:  J Mol Model       Date:  2015-01-27       Impact factor: 1.810

Review 5.  Hydrogen tunneling in enzymes and biomimetic models.

Authors:  Joshua P Layfield; Sharon Hammes-Schiffer
Journal:  Chem Rev       Date:  2013-12-20       Impact factor: 60.622

6.  Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase.

Authors:  Steven Hayward; Akio Kitao
Journal:  Biophys J       Date:  2006-05-19       Impact factor: 4.033

7.  Anticorrelated motions as a driving force in enzyme catalysis: the dehydrogenase reaction.

Authors:  Jia Luo; Thomas C Bruice
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-26       Impact factor: 11.205

8.  Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins.

Authors:  Albert S Song; Taylor A Poor; Luciano A Abriata; Theodore S Jardetzky; Matteo Dal Peraro; Robert A Lamb
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-22       Impact factor: 11.205

Review 9.  Conformational changes and catalysis by alcohol dehydrogenase.

Authors:  Bryce V Plapp
Journal:  Arch Biochem Biophys       Date:  2009-07-05       Impact factor: 4.013

10.  Cleavage, Downregulation, and Aggregation of Serum Amyloid A.

Authors:  Wenhua Wang; Prabir Khatua; Ulrich H E Hansmann
Journal:  J Phys Chem B       Date:  2020-01-30       Impact factor: 2.991
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