scholarly journals SAFT-γ Force Field for the Simulation of Molecular Fluids. 5. Hetero-Group Coarse-Grained Models of Linear Alkanes and the Importance of Intramolecular Interactions

2018 ◽  
Vol 122 (39) ◽  
pp. 9161-9177 ◽  
Author(s):  
Sadia Rahman ◽  
Olga Lobanova ◽  
Guadalupe Jiménez-Serratos ◽  
Carlos Braga ◽  
Vasilios Raptis ◽  
...  
Keyword(s):  
Force Field ◽  
Intramolecular Interactions ◽  
Coarse Grained ◽  
Molecular Fluids ◽  
Linear Alkanes

SAFT-γ Force Field for the Simulation of Molecular Fluids: 2. Coarse-Grained Models of Greenhouse Gases, Refrigerants, and Long Alkanes

2013 ◽  
Vol 117 (9) ◽  
pp. 2717-2733 ◽  
Author(s):  
Carlos Avendaño ◽  
Thomas Lafitte ◽  
Claire S. Adjiman ◽  
Amparo Galindo ◽  
Erich A. Müller ◽  
...  
Keyword(s):  
Greenhouse Gases ◽  
Force Field ◽  
Coarse Grained ◽  
Molecular Fluids

scholarly journals SAFT-γ Force Field for the Simulation of Molecular Fluids. 1. A Single-Site Coarse Grained Model of Carbon Dioxide

2011 ◽  
Vol 115 (38) ◽  
pp. 11154-11169 ◽  
Author(s):  
Carlos Avendaño ◽  
Thomas Lafitte ◽  
Amparo Galindo ◽  
Claire S. Adjiman ◽  
George Jackson ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Force Field ◽  
Single Site ◽  
Coarse Grained ◽  
Molecular Fluids ◽  
Coarse Grained Model

scholarly journals SAFT-γ force field for the simulation of molecular fluids: 8. Hetero-segmented coarse-grained models of perfluoroalkylalkanes assessed with new vapour–liquid interfacial tension data

2016 ◽  
Vol 114 (18) ◽  
pp. 2597-2614 ◽  
Author(s):  
Pedro Morgado ◽  
Olga Lobanova ◽  
Erich A. Müller ◽  
George Jackson ◽  
Miguel Almeida ◽  
...  
Keyword(s):  
Interfacial Tension ◽  
Force Field ◽  
Coarse Grained ◽  
Molecular Fluids

SAFT-γ force field for the simulation of molecular fluids: 4. A single-site coarse-grained model of water applicable over a wide temperature range

2015 ◽  
Vol 113 (9-10) ◽  
pp. 1228-1249 ◽  
Author(s):  
Olga Lobanova ◽  
Carlos Avendaño ◽  
Thomas Lafitte ◽  
Erich A. Müller ◽  
George Jackson
Keyword(s):  
Force Field ◽  
Wide Temperature Range ◽  
Single Site ◽  
Coarse Grained ◽  
Molecular Fluids ◽  
Temperature Range ◽  
Coarse Grained Model

scholarly journals Martini Coarse-Grained Force Field: Extension to RNA

2017 ◽  
Vol 113 (2) ◽  
pp. 246-256 ◽  
Author(s):  
Jaakko J. Uusitalo ◽  
Helgi I. Ingólfsson ◽  
Siewert J. Marrink ◽  
Ignacio Faustino
Keyword(s):  
Force Field ◽  
Field Extension ◽  
Coarse Grained

scholarly journals A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

2018 ◽  
Vol 39 (28) ◽  
pp. 2360-2370 ◽  
Author(s):  
Adam K. Sieradzan ◽  
Artur Giełdoń ◽  
Yanping Yin ◽  
Yi He ◽  
Harold A. Scheraga ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Force Fields ◽  
Coarse Grained ◽  
Protein Nucleic Acid ◽  
New Protein

scholarly journals Residue-Level Contact Reveals Modular Domain Interactions of PICK1 Are Driven by Both Electrostatic and Hydrophobic Forces

2021 ◽  
Vol 7 ◽  
Author(s):  
Amy O. Stevens ◽  
Yi He
Keyword(s):  
Hydrophobic Interactions ◽  
Pdz Domain ◽  
Md Simulations ◽  
Intramolecular Interactions ◽  
Coarse Grained ◽  
Scaffolding Protein ◽  
Concave Surface ◽  
Stable Complex ◽  
Bar Domain ◽  
C Terminus

PICK1 is a multi-domain scaffolding protein that is uniquely comprised of both a PDZ domain and a BAR domain. While previous experiments have shown that the PDZ domain and the linker positively regulate the BAR domain and the C-terminus negatively regulates the BAR domain, the details of internal regulation mechanisms are unknown. Molecular dynamics (MD) simulations have been proven to be a useful tool in revealing the intramolecular interactions at atomic-level resolution. PICK1 performs its biological functions in a dimeric form which is extremely computationally demanding to simulate with an all-atom force field. Here, we use coarse-grained MD simulations to expose the key residues and driving forces in the internal regulations of PICK1. While the PDZ and BAR domains do not form a stable complex, our simulations show the PDZ domain preferentially interacting with the concave surface of the BAR domain over other BAR domain regions. Furthermore, our simulations show that the short helix in the linker region can form interactions with the PDZ domain. Our results reveal that the surface of the βB-βC loop, βC strand, and αA-βD loop of the PDZ domain can form a group of hydrophobic interactions surrounding the linker helix. These interactions are driven by hydrophobic forces. In contrast, our simulations reveal a very dynamic C-terminus that most often resides on the convex surface of the BAR domain rather than the previously suspected concave surface. These interactions are driven by a combination of electrostatic and hydrophobic interactions.

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