Molecular Recognition of PPARγ by Kinase Cdk5/p25: Insights from a Combination of Protein–Protein Docking and Adaptive Biasing Force Simulations

2015 ◽  
Vol 119 (26) ◽  
pp. 8330-8339 ◽  
Author(s):  
Melina Mottin ◽  
Paulo C. T. Souza ◽  
Munir S. Skaf
Keyword(s):  
Molecular Recognition ◽  
Protein Docking ◽  
Adaptive Biasing ◽  
Adaptive Biasing Force

Adaptive biasing force method for scalar and vector free energy calculations

2008 ◽  
Vol 128 (14) ◽  
pp. 144120 ◽  
Author(s):  
Eric Darve ◽  
David Rodríguez-Gómez ◽  
Andrew Pohorille
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Force Method ◽  
Adaptive Biasing ◽  
Adaptive Biasing Force

scholarly journals The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

2014 ◽  
Vol 119 (3) ◽  
pp. 1129-1151 ◽  
Author(s):  
Jeffrey Comer ◽  
James C. Gumbart ◽  
Jérôme Hénin ◽  
Tony Lelièvre ◽  
Andrew Pohorille ◽  
...  
Keyword(s):  
Force Method ◽  
Adaptive Biasing ◽  
Adaptive Biasing Force

Free energy profiles of ion permeation and doxorubicin translocation in TolC

2014 ◽  
Vol 13 (04) ◽  
pp. 1450031 ◽  
Author(s):  
Beibei Wang ◽  
Jingwei Weng ◽  
Wenning Wang
Keyword(s):  
Outer Membrane ◽  
Transport Mechanism ◽  
Ion Permeation ◽  
Energy Profiles ◽  
Extracellular Loops ◽  
Gate Opening ◽  
Gating Mechanism ◽  
Adaptive Biasing ◽  
Adaptive Biasing Force ◽  
Potential Of Mean Forces

The outer membrane protein TolC of Escherichia coli forms a channel-tunnel pore spanning the periplasmic space and outer membrane, serving as the main exit duct for bacteria multidrug resistance and protein export. Many aspects of the transport mechanism of TolC are still unclear. Here, we have investigated the substrate permeability and gating mechanism of TolC by calculating the potential of mean forces (PMFs) for transporting sodium ion and doxorubicin through TolC using the adaptive biasing force (ABF) method. The transport mechanism is turned out to be substrate dependent. It is found that the periplasmic gate is required to open for the passage of both Na + and doxorubicin, but the conformational gating does not lead to permeation barrier for Na + at this region. The extracellular loops and K283 residues cause permeation barriers for Na + at the extracellular entrance, but not for doxorubicin due to the extensive interactions between the drug molecule and the protein. TolC exhibits high conformational flexibility during the transport of Na +, while doxorubicin seems to be able to stabilize TolC in the resting state with the periplasmic gate closed. The association of the TolC docking domain of AcrB does not lower the permeation barrier for doxorubicin at the periplasmic gate, while the gate opening induces the dissociation of the TolC–AcrB complex.

scholarly journals Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method

2016 ◽  
Vol 121 (15) ◽  
pp. 3676-3685 ◽  
Author(s):  
Adrien Lesage ◽  
Tony Lelièvre ◽  
Gabriel Stoltz ◽  
Jérôme Hénin
Keyword(s):  
Free Energies ◽  
Extended System ◽  
Force Method ◽  
Adaptive Biasing ◽  
Adaptive Biasing Force

scholarly journals Analysis of an Adaptive Biasing Force method based on self-interacting dynamics

2020 ◽  
Vol 25 (0) ◽  
Author(s):  
Michel Benaïm ◽  
Charles-Edouard Bréhier ◽  
Pierre Monmarché
Keyword(s):  
Force Method ◽  
Adaptive Biasing ◽  
Adaptive Biasing Force
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