scholarly journals Toward Temperature-Dependent Coarse-Grained Potentials of Side-Chain Interactions for Protein Folding Simulations. II. Molecular Dynamics Study of Pairs of Different Types of Interactions in Water at Various Temperatures

2012 ◽  
Vol 116 (23) ◽  
pp. 6844-6853 ◽  
Author(s):  
Emil Sobolewski ◽  
Stanisław Ołdziej ◽  
Marta Wiśniewska ◽  
Adam Liwo ◽  
Mariusz Makowski
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Coarse Grained ◽  
Side Chain ◽  
Temperature Dependent ◽  
Different Types ◽  
Folding Simulations

PathMolD-AB: Spatiotemporal pathways of protein folding using parallel molecular dynamics with a coarse-grained model

2020 ◽  
Vol 87 ◽  
pp. 107301
Author(s):  
Leandro Takeshi Hattori ◽  
Bruna Araujo Pinheiro ◽  
Rafael Bertolini Frigori ◽  
César Manuel Vargas Benítez ◽  
Heitor Silvério Lopes
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Parallel Molecular Dynamics

Protein folding simulations: From coarse-grained model to all-atom model

IUBMB Life ◽  
2009 ◽  
Vol 61 (6) ◽  
pp. 627-643 ◽  
Author(s):  
Jian Zhang ◽  
Wenfei Li ◽  
Jun Wang ◽  
Meng Qin ◽  
Lei Wu ◽  
...  
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Atom Model ◽  
Folding Simulations

scholarly journals Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

2010 ◽  
Vol 114 (13) ◽  
pp. 4471-4485 ◽  
Author(s):  
Gia G. Maisuradze ◽  
Patrick Senet ◽  
Cezary Czaplewski ◽  
Adam Liwo ◽  
Harold A. Scheraga
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Force Field ◽  
Coarse Grained ◽  
Coarse Grained Molecular Dynamics

scholarly journals The contribution of the ankyrin repeat domain of TRPV1 as a thermal module

2019 ◽  
Author(s):  
E. Ladrón-de-Guevara ◽  
G. E. Rangel-Yescas ◽  
D. A. Fernández-Velasco ◽  
A. Torres-Larios ◽  
T. Rosenbaum ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Ankyrin Repeat ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Temperature Dependent ◽  
Trpv1 Channels ◽  
Repeat Domain ◽  
Ankyrin Repeat Domain ◽  
Coarse Grained Molecular Dynamics

AbstractThe TRPV1 cation non-selective ion channel plays an essential role in thermosensation and perception of other noxious stimuli. TRPV1 can be activated by low pH, high temperature or naturally occurring pungent molecules such as allicin, capsaicin or resiniferatoxin. Its noxious thermal sensitivity makes it an important participant as a thermal sensor in mammals. However, details of the mechanism of channel activation by increases in temperature remain unclear. Here we used a combination of approaches to try to understand the role of the ankyrin repeat domain (ARD) in channel behavior. First, a computational modeling approach by coarse-grained molecular dynamics simulation of the whole TRPV1 embedded in a phosphatidylcholine (POPC) and phosphatidylethanolamine (POPE) membrane provides insight into the dynamics of this channel domain. Global analysis of the structural ensemble shows that the ankyrin repeat domain is a region that sustains high fluctuations during dynamics at different temperatures. We then performed biochemical and thermal stability studies of the purified ARD by means of circular dichroism and tryptophan fluorescence and demonstrate that this region undergoes structural changes at similar temperatures that lead to TRPV1 activation. Our data suggest that the ARD is a dynamic module and that it may participate in controlling the temperature sensitivity of TRPV1.Statement of SignificanceThis work demonstrates that the temperature-dependent dynamics of the ankyrin repeat domain (ARD) of TRPV1 channels, as probed by coarse-grained molecular dynamics, corresponds to the experimentally determined dynamics of an isolated ARD domain. These results show that this region of TRPV1 channels undergoes significant conformational change as a function of increased temperature and suggest that it participates in the temperature-dependent structural changes that lead to channel opening.

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