Broad Substrate Specificity and Catalytic Mechanism ofPseudomonas stutzeril-Rhamnose Isomerase: Insights from QM/MM Molecular Dynamics Simulations†

Ruibo Wu; Hujun Xie; Yirong Mo; Zexing Cao

doi:10.1021/jp901093g

Broad Substrate Specificity and Catalytic Mechanism ofPseudomonas stutzeril-Rhamnose Isomerase: Insights from QM/MM Molecular Dynamics Simulations†

The Journal of Physical Chemistry A ◽

10.1021/jp901093g ◽

2009 ◽

Vol 113 (43) ◽

pp. 11595-11603 ◽

Cited By ~ 5

Author(s):

Ruibo Wu ◽

Hujun Xie ◽

Yirong Mo ◽

Zexing Cao

Keyword(s):

Molecular Dynamics ◽

Substrate Specificity ◽

Molecular Dynamics Simulations ◽

Catalytic Mechanism ◽

Broad Substrate Specificity ◽

Dynamics Simulations

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Unraveling cGAS catalytic mechanism upon DNA activation through molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/d1cp00378j ◽

2021 ◽

Author(s):

Jordi Soler ◽

Pedro Paiva ◽

Maria Joao Joao Ramos ◽

Pedro Alexandrino Fernandes ◽

Marie Brut

Keyword(s):

Molecular Dynamics ◽

Dna Binding ◽

Molecular Dynamics Simulations ◽

Cyclic Gmp ◽

Catalytic Mechanism ◽

System P ◽

Dynamics Simulations ◽

Cyclic Dinucleotide

Cyclic GMP-AMP Synthase (cGAS) is activated upon DNA binding and catalyzes the synthesis of 2’,3’-cGAMP from GTP and ATP. This cyclic dinucleotide is a messenger that triggers the autoimmune system...

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Structural explanation for the tunable substrate specificity of an E. coli nucleoside hydrolase: insights from molecular dynamics simulations

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-018-0178-y ◽

2018 ◽

Vol 32 (12) ◽

pp. 1375-1388

Author(s):

Stefan A. P. Lenz ◽

Stacey D. Wetmore

Keyword(s):

Molecular Dynamics ◽

Substrate Specificity ◽

Molecular Dynamics Simulations ◽

Structural Explanation ◽

E Coli ◽

Nucleoside Hydrolase ◽

Dynamics Simulations

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Active Site Gating and Substrate Specificity of Butyrylcholinesterase and Acetylcholinesterase: Insights from Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp112030p ◽

2011 ◽

Vol 115 (27) ◽

pp. 8797-8805 ◽

Cited By ~ 33

Author(s):

Lei Fang ◽

Yongmei Pan ◽

Jennifer L. Muzyka ◽

Chang-Guo Zhan

Keyword(s):

Molecular Dynamics ◽

Substrate Specificity ◽

Molecular Dynamics Simulations ◽

Active Site ◽

Dynamics Simulations

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Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: Pathway prediction and reconciliation of X-ray crystallographic and NMR solution data

Protein Science ◽

10.1110/ps.062356406 ◽

2006 ◽

Vol 15 (11) ◽

pp. 2544-2551 ◽

Cited By ~ 26

Author(s):

Daniel Trzesniak ◽

Wilfred F. van Gunsteren

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Catalytic Mechanism ◽

X Ray ◽

Pathway Prediction ◽

Dynamics Simulations

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Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2007.03.010 ◽

2007 ◽

Vol 26 (3) ◽

pp. 643-651 ◽

Cited By ~ 28

Author(s):

Ana Negri ◽

Esther Marco ◽

Jiri Damborsky ◽

Federico Gago

Keyword(s):

Molecular Dynamics ◽

Computer Graphics ◽

Molecular Dynamics Simulations ◽

Catalytic Mechanism ◽

Haloalkane Dehalogenase ◽

Dynamics Simulations

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Structure and Molecular Dynamics Simulations of Protein Tyrosine Phosphatase Non-Receptor 12 Provide Insights into the Catalytic Mechanism of the Enzyme

International Journal of Molecular Sciences ◽

10.3390/ijms19010060 ◽

2017 ◽

Vol 19 (1) ◽

pp. 60 ◽

Cited By ~ 2

Author(s):

Hui Dong ◽

Francesco Zonta ◽

Shanshan Wang ◽

Ke Song ◽

Xin He ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Protein Tyrosine Phosphatase ◽

Catalytic Mechanism ◽

Tyrosine Phosphatase ◽

Protein Tyrosine ◽

Dynamics Simulations

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Substrate specificity of cytochrome P450cam forL- andD- norcamphor as studied by molecular dynamics simulations

Journal of Computational Chemistry ◽

10.1002/jcc.540140506 ◽

1993 ◽

Vol 14 (5) ◽

pp. 541-548 ◽

Cited By ~ 7

Author(s):

Michael B. Bass ◽

Rick L. Ornstein

Keyword(s):

Molecular Dynamics ◽

Substrate Specificity ◽

Molecular Dynamics Simulations ◽

Cytochrome P450cam ◽

Dynamics Simulations

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Variation in aspects of cysteine proteinase catalytic mechanism deduced by spectroscopic observation of dithioester intermediates, kinetic analysis and molecular dynamics simulations

Biochemical Journal ◽

10.1042/0264-6021:3570343 ◽

2001 ◽

Vol 357 (2) ◽

pp. 343 ◽

Cited By ~ 5

Author(s):

James D. REID ◽

Syeed HUSSAIN ◽

Suneal K. SREEDHARAN ◽

Tamara S.F. BAILEY ◽

Surapong PINITGLANG ◽

...

Keyword(s):

Molecular Dynamics ◽

Kinetic Analysis ◽

Molecular Dynamics Simulations ◽

Catalytic Mechanism ◽

Cysteine Proteinase ◽

Spectroscopic Observation ◽

Dynamics Simulations

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Insight into the substrate specificity change caused by the Y227H mutation of α-glucosidase III from the European honeybee (Apis mellifera) through molecular dynamics simulations

PLoS ONE ◽

10.1371/journal.pone.0198484 ◽

2018 ◽

Vol 13 (6) ◽

pp. e0198484 ◽

Cited By ~ 3

Author(s):

Pratchaya Pramoj Na Ayutthaya ◽

Chanpen Chanchao ◽

Surasak Chunsrivirot

Keyword(s):

Molecular Dynamics ◽

Apis Mellifera ◽

Substrate Specificity ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations ◽

European Honeybee ◽

Insight Into

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Evaluating substrate specificity of glutathione peroxidase mimic by molecular dynamics simulations and kinetics

Journal of Inclusion Phenomena and Macrocyclic Chemistry ◽

10.1007/s10847-007-9362-8 ◽

2007 ◽

Vol 60 (1-2) ◽

pp. 139-144 ◽

Cited By ~ 4

Author(s):

Shao-Wu Lv ◽

Qing-Chuan Zheng ◽

Ying Mu ◽

Xiao-Guang Wang ◽

Yue-Tong Ji ◽

...

Keyword(s):

Molecular Dynamics ◽

Glutathione Peroxidase ◽

Substrate Specificity ◽

Molecular Dynamics Simulations ◽

Peroxidase Mimic ◽

Dynamics Simulations

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