Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations

2010 ◽  
Vol 79 (1) ◽  
pp. 271-281 ◽  
Author(s):  
Weihua Li ◽  
Jie Shen ◽  
Guixia Liu ◽  
Yun Tang ◽  
Tyuji Hoshino
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome P450 ◽  
Molecular Dynamics Simulations ◽  
Steered Molecular Dynamics ◽  
Human Cytochrome ◽  
Cytochrome P450 2A6 ◽  
Random Acceleration ◽  
Dynamics Simulations

Exploring the different ligand escape pathways in acylaminoacyl peptidase by random acceleration and steered molecular dynamics simulations

RSC Advances ◽  
2016 ◽  
Vol 6 (13) ◽  
pp. 10987-10996 ◽  
Author(s):  
Hanyong Jin ◽  
Jingxuan Zhu ◽  
Yang Dong ◽  
Weiwei Han
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Steered Molecular Dynamics ◽  
Prolyl Oligopeptidase ◽  
Acylaminoacyl Peptidase ◽  
Random Acceleration ◽  
Dynamics Simulations

Acylaminoacyl peptidase (APH, EC 3.4.19.1) is a novel class of serine-type protease belonging to the prolyl oligopeptidase (POP) family.

Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations

2016 ◽  
Vol 18 (7) ◽  
pp. 5622-5629 ◽  
Author(s):  
Yuzhen Niu ◽  
Shuyan Li ◽  
Dabo Pan ◽  
Huanxiang Liu ◽  
Xiaojun Yao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Residence Time ◽  
Computational Study ◽  
Steered Molecular Dynamics ◽  
The Difference ◽  
Random Acceleration ◽  
Dynamics Simulations

Random acceleration and steered molecular dynamics simulations reveal the unbinding pathway of B-RAF inhibitors and the difference in the residence time.

scholarly journals Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2

2016 ◽  
Vol 18 (44) ◽  
pp. 30344-30356 ◽  
Author(s):  
Petr Jeřábek ◽  
Jan Florián ◽  
Václav Martínek
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Cytochrome P450 ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Cytochrome P450 1A2 ◽  
Structure And Dynamics ◽  
Human Cytochrome ◽  
Membrane Bound ◽  
Dynamics Simulations

The structure and dynamics of the membrane-bound full-length human cytochrome P450 1A2 (CYP1A2) in aqueous solution determined by coarse-grained and all-atom molecular dynamics simulations.

scholarly journals Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects

2013 ◽  
Vol 4 ◽  
pp. 429-440 ◽  
Author(s):  
Hlengisizwe Ndlovu ◽  
Alison E Ashcroft ◽  
Sheena E Radford ◽  
Sarah A Harris
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Steered Molecular Dynamics ◽  
Mechanical Failure ◽  
Structural Defects ◽  
Dynamics Simulations

We examine how the different steric packing arrangements found in amyloid fibril polymorphs can modulate their mechanical properties using steered molecular dynamics simulations. Our calculations demonstrate that for fibrils containing structural defects, their ability to resist force in a particular direction can be dominated by both the number and molecular details of the defects that are present. The simulations thereby suggest a hierarchy of factors that govern the mechanical resilience of fibrils, and illustrate the general principles that must be considered when quantifying the mechanical properties of amyloid fibres containing defects.

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