Steered molecular dynamics analysis of the role of cofilin in increasing the flexibility of actin filaments

2016 ◽  
Vol 218 ◽  
pp. 27-35 ◽  
Author(s):  
Jae In Kim ◽  
Junpyo Kwon ◽  
Inchul Baek ◽  
Sungsoo Na
Keyword(s):  
Molecular Dynamics ◽  
Actin Filaments ◽  
Steered Molecular Dynamics ◽  
Dynamics Analysis

scholarly journals Steered molecular dynamics simulations reveal the role of Ca2+ in regulating mechanostability of cellulose-binding proteins

2018 ◽  
Vol 20 (35) ◽  
pp. 22674-22680 ◽  
Author(s):  
Melissabye Gunnoo ◽  
Pierre-André Cazade ◽  
Adam Orlowski ◽  
Mateusz Chwastyk ◽  
Haipei Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Proteins ◽  
Mechanical Stability ◽  
Binding Specificity ◽  
Steered Molecular Dynamics ◽  
Dynamics Simulations ◽  
Cellulose Binding ◽  
High Mechanical Stability

Cellulosome nanomachines utilise binding specificity and high mechanical stability in breaking down cellulose.

scholarly journals Ab-initio binding of barnase–barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach

2020 ◽  
Vol 19 (04) ◽  
pp. 2050016
Author(s):  
Mahesh Koirala ◽  
Emil Alexov
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
3D Structure ◽  
Binding Mode ◽  
Steered Molecular Dynamics ◽  
Biological Processes ◽  
Close Proximity ◽  
Ligand Interactions ◽  
Pulling Force

Receptor–ligand interactions are involved in various biological processes, therefore understanding the binding mechanism and ability to predict the binding mode are essential for many biological investigations. While many computational methods exist to predict the 3D structure of the corresponding complex provided the knowledge of the monomers, here we use the newly developed DelPhiForce steered Molecular Dynamics (DFMD) approach to model the binding of barstar to barnase to demonstrate that first-principles methods are also capable of modeling the binding. Essential component of DFMD approach is enhancing the role of long-range electrostatic interactions to provide guiding force of the monomers toward their correct binding orientation and position. Thus, it is demonstrated that the DFMD can successfully dock barstar to barnase even if the initial positions and orientations of both are completely different from the correct ones. Thus, the electrostatics provides orientational guidance along with pulling force to deliver the ligand in close proximity to the receptor.

scholarly journals Evaluation of extensional and torsional stiffness of single actin filaments by molecular dynamics analysis

2010 ◽  
Vol 43 (16) ◽  
pp. 3162-3167 ◽  
Author(s):  
Shinji Matsushita ◽  
Taiji Adachi ◽  
Yasuhiro Inoue ◽  
Masaki Hojo ◽  
Masahiro Sokabe
Keyword(s):  
Molecular Dynamics ◽  
Actin Filaments ◽  
Torsional Stiffness ◽  
Dynamics Analysis

scholarly journals Molecular Dynamics Analysis of Coupling Behaviors Between Extension and Torsion of Actin Filaments

2012 ◽  
Vol 102 (3) ◽  
pp. 372a-373a
Author(s):  
Shinji Matsushita ◽  
Yasuhiro Inoue ◽  
Taiji Adachi
Keyword(s):  
Molecular Dynamics ◽  
Actin Filaments ◽  
Dynamics Analysis

The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study

2016 ◽  
Vol 18 (41) ◽  
pp. 28767-28780 ◽  
Author(s):  
Asmita Gupta ◽  
Manju Bansal
Keyword(s):  
Molecular Dynamics ◽  
Steered Molecular Dynamics ◽  
Sequence Dependent ◽  
Rna Pseudoknot

This work highlights a sequence dependent unfolding pathway of an RNA pseudoknot under force-induced pulling conditions.

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