scholarly journals Development of the SPICA Coarse-grained Force Field for Lipid Membranes and the Perspective

2020 ◽  
Vol 60 (3) ◽  
pp. 157-161
Author(s):  
Wataru SHINODA
Keyword(s):  
Force Field ◽  
Lipid Membranes ◽  
Coarse Grained

scholarly journals The SPICA Coarse-Grained Force Field for Proteins and Peptides

2021 ◽  
Author(s):  
Shuhei Kawamoto ◽  
Huihui Liu ◽  
Sangjae Seo ◽  
Yusuke Miyazaki ◽  
Mayank Dixit ◽  
...  
Keyword(s):  
Force Field ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Coarse Grained ◽  
Transmembrane Helices ◽  
Free Energies ◽  
Transmembrane Peptides ◽  
Energy Profiles ◽  
Protein Model ◽  
Preliminary Version

ABSTRACTA coarse-grained (CG) model for peptides and proteins was developed as an extension of the SPICA (Surface Property fItting Coarse grAined) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulation with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. The side chain analogs reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable dimerization free energies in water compared to those from AA-MD. A series of peptides/proteins adsorbed or penetrated into the membrane simulated by the CG-MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins comparable to those in the orientation of protein in membrane (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated a good performance of the SPICA FF.

pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model

2019 ◽  
Vol 16 (1) ◽  
pp. 782-793 ◽  
Author(s):  
Yusuke Miyazaki ◽  
Susumu Okazaki ◽  
Wataru Shinoda
Keyword(s):  
Force Field ◽  
Lipid Membranes ◽  
Coarse Grained ◽  
Water Model ◽  
Polar Water

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 A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

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