Structural Comparison of the Wild-Type and Drug-Resistant Mutants of the Influenza A M2 Proton Channel by Molecular Dynamics Simulations

2013 ◽  
Vol 117 (20) ◽  
pp. 6042-6051 ◽  
Author(s):  
Ruo-Xu Gu ◽  
Limin Angela Liu ◽  
Yong-Hua Wang ◽  
Qin Xu ◽  
Dong-Qing Wei
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Influenza A ◽  
Proton Channel ◽  
Drug Resistant ◽  
Wild Type ◽  
Structural Comparison ◽  
Resistant Mutants ◽  
M2 Proton Channel ◽  
Dynamics Simulations

scholarly journals Discovery of Novel Dual Inhibitors of the Wild-Type and the Most Prevalent Drug-Resistant Mutant, S31N, of the M2 Proton Channel from Influenza A Virus

2013 ◽  
Vol 56 (7) ◽  
pp. 2804-2812 ◽  
Author(s):  
Jizhou Wang ◽  
Chunlong Ma ◽  
Jun Wang ◽  
Hyunil Jo ◽  
Belgin Canturk ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Resistant Mutant ◽  
Proton Channel ◽  
Drug Resistant ◽  
Wild Type ◽  
Drug Resistant Mutant ◽  
Dual Inhibitors ◽  
M2 Proton Channel

scholarly journals Exploration of the cofactor specificity of wild-type phosphite dehydrogenase and its mutant using molecular dynamics simulations

RSC Advances ◽  
2021 ◽  
Vol 11 (24) ◽  
pp. 14527-14533
Author(s):  
Kunlu Liu ◽  
Min Wang ◽  
Yubo Zhou ◽  
Hongxiang Wang ◽  
Yudong Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Wild Type ◽  
Cofactor Specificity ◽  
Phosphite Dehydrogenase ◽  
Dynamics Simulations

Phosphite dehydrogenase (Pdh) catalyzes the NAD-dependent oxidation of phosphite to phosphate with the formation of NADH.

Observation of “Ionic Lock” Formation in Molecular Dynamics Simulations of Wild-Type β1and β2Adrenergic Receptors

Biochemistry ◽  
2009 ◽  
Vol 48 (22) ◽  
pp. 4789-4797 ◽  
Author(s):  
Stefano Vanni ◽  
Marilisa Neri ◽  
Ivano Tavernelli ◽  
Ursula Rothlisberger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Wild Type ◽  
Dynamics Simulations

scholarly journals Insights into the Folding and Unfolding Processes of Wild-Type and Mutated SH3 Domain by Molecular Dynamics and Replica Exchange Molecular Dynamics Simulations

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e64886 ◽  
Author(s):  
Wen-Ting Chu ◽  
Ji-Long Zhang ◽  
Qing-Chuan Zheng ◽  
Lin Chen ◽  
Hong-Xing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sh3 Domain ◽  
Replica Exchange ◽  
Wild Type ◽  
Replica Exchange Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Allosteric Communication within the Cytoplasmic Region of the Histidine Kinase CpxA, Revealed by Molecular Dynamics Simulations of the Wild-Type and M228V Proteins

2015 ◽  
Vol 108 (2) ◽  
pp. 184a
Author(s):  
Marlet Martinez ◽  
Nathalie Duclert ◽  
Jean-Michel Betton ◽  
Pedro M. Alzari ◽  
Michael Nilges ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Histidine Kinase ◽  
Wild Type ◽  
Cytoplasmic Region ◽  
Allosteric Communication ◽  
Dynamics Simulations

scholarly journals Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
K. K. Abelak ◽  
D. Bishop-Bailey ◽  
I. Nobeli
Keyword(s):  
Molecular Dynamics ◽  
Arachidonic Acid ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanisms ◽  
Homology Model ◽  
Cytochrome P450 Enzyme ◽  
Wild Type ◽  
Substrate Preferences ◽  
P450 Enzyme ◽  
Dynamics Simulations

Abstract Objectives The data presented here is part of a study that was aimed at characterizing the molecular mechanisms of polyunsaturated fatty acid metabolism by CYP2J2, the main cytochrome P450 enzyme active in the human cardiovasculature. This part comprises the molecular dynamics simulations of the binding of three eicosanoid substrates to wild type and mutant forms of the enzyme. These simulations were carried out with the aim of dissecting the importance of individual residues in the active site and the roles they might play in dictating the binding and catalytic specificity exhibited by CYP2J2. Data description The data comprise: (a) a new homology model of CYP2J2, (b) a number of predicted low-energy complexes of CYP2J2 with arachidonic acid, docosahexaenoic acid and eicosapentaenoic acid, produced with molecular docking and (c) a series of molecular dynamics simulations of the wild type and four mutants interacting with arachidonic acid as well as simulations of the wild type interacting with the two other eicosanoid ligands. The simulations may be helpful in identifying the determinants of substrate specificity of this enzyme and in unraveling the role of individual mutations on its function. They may also help guide the generation of mutants with altered substrate preferences.

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