Flap opening dynamics in HIV-1 protease explored with a coarse-grained model

2007 ◽  
Vol 157 (3) ◽  
pp. 606-615 ◽  
Author(s):  
Valentina Tozzini ◽  
Joanna Trylska ◽  
Chia-en Chang ◽  
J. Andrew McCammon
Keyword(s):  
Coarse Grained ◽  
Coarse Grained Model ◽  
Hiv 1

scholarly journals Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model

2006 ◽  
Vol 90 (11) ◽  
pp. 3880-3885 ◽  
Author(s):  
Chia-En Chang ◽  
Tongye Shen ◽  
Joanna Trylska ◽  
Valentina Tozzini ◽  
J. Andrew McCammon
Keyword(s):  
Brownian Dynamics ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Hiv 1

A coarse grained model for the dynamics of flap opening in HIV-1 protease

2005 ◽  
Vol 413 (1-3) ◽  
pp. 123-128 ◽  
Author(s):  
Valentina Tozzini ◽  
J. Andrew McCammon
Keyword(s):  
Coarse Grained ◽  
Coarse Grained Model ◽  
Hiv 1

3D structure stability of the HIV-1 TAR RNA in ion solutions: A coarse-grained model study

2019 ◽  
Vol 151 (16) ◽  
pp. 165101
Author(s):  
Ben-Gong Zhang ◽  
Hua-Hai Qiu ◽  
Jian Jiang ◽  
Jie Liu ◽  
Ya-Zhou Shi
Keyword(s):  
3D Structure ◽  
Coarse Grained ◽  
Structure Stability ◽  
Coarse Grained Model ◽  
Model Study ◽  
Tar Rna ◽  
Hiv 1

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

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