Biological membranes that play major roles in diverse functions are composed of numerous lipids and proteins, making them an important target for coarse-grained (CG) molecular dynamics (MD) simulations. Recently, we have developed the CG implicit solvent lipid force field (iSoLF) that has a resolution compatible with the widely used Cα protein representation [D. Ugarte La Torre and S. Takada, J. Chem. Phys. 153, 205101 (2020)]. In this study, we extended it and developed a lipid–protein interaction model that allows the combination of the iSoLF and the Cα protein force field, AICG2+. The hydrophobic–hydrophilic interaction is modeled as a modified Lennard-Jones potential in which parameters were tuned partly to reproduce the experimental transfer free energy and partly based on the free energy profile normal to the membrane surface from previous all-atom MD simulations. Then, the obtained lipid–protein interaction is tested for the configuration and placement of transmembrane proteins, water-soluble proteins, and peripheral proteins, showing good agreement with prior knowledge. The interaction is generally applicable and is implemented in the publicly available software, CafeMol.
Skip Nav Destination
Article navigation
21 October 2021
Research Article|
October 18 2021
Modeling lipid–protein interactions for coarse-grained lipid and Cα protein models
Diego Ugarte La Torre
;
Diego Ugarte La Torre
Department of Biophysics, Graduate School of Science, Kyoto University
, Kyoto, Japan
Search for other works by this author on:
Shoji Takada
Shoji Takada
a)
Department of Biophysics, Graduate School of Science, Kyoto University
, Kyoto, Japan
a)Author to whom correspondence should be addressed: [email protected]
Search for other works by this author on:
a)Author to whom correspondence should be addressed: [email protected]
J. Chem. Phys. 155, 155101 (2021)
Article history
Received:
May 19 2021
Accepted:
September 30 2021
Citation
Diego Ugarte La Torre, Shoji Takada; Modeling lipid–protein interactions for coarse-grained lipid and Cα protein models. J. Chem. Phys. 21 October 2021; 155 (15): 155101. https://doi.org/10.1063/5.0057278
Download citation file:
Pay-Per-View Access
$40.00
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Citing articles via
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
CREST—A program for the exploration of low-energy molecular chemical space
Philipp Pracht, Stefan Grimme, et al.
Dielectric profile at the Pt(111)/water interface
Jia-Xin Zhu, Jun Cheng, et al.
Related Content
Coarse-grained implicit solvent lipid force field with a compatible resolution to the C α protein representation
J. Chem. Phys. (November 2020)
Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers
J. Chem. Phys. (August 2023)
Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase
J. Chem. Phys. (March 2015)
Funneling and frustration in the energy landscapes of some designed and simplified proteins
J. Chem. Phys. (July 2013)
Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations
AIP Advances (January 2015)