SPICA Force Field for Proteins and Peptides

Abstract

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the Surface Property fItting Coarse grAined (SPICA) 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) simulations with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. An elastic network model was adopted to maintain the secondary structure within a single chain. The side-chain analogues reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable association free energy (potential of mean force) in water compared to those from AA MD. A series of peptides/proteins adsorbed onto or penetrated into the membrane simulated by the CG MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins as comparable to those in the orientations of proteins in membranes (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 the good performance of the SPICA FF.

Substantial Effect of Terminal Groups in cis-Polyisoprene: A Multiscale Molecular Dynamics Simulation Study

“…Over the last two decades, many coarse-grained models − ,− ,− and all-atom models ,,,− have been developed to cover this range. Two approaches have been broadly utilized to reproduce the physiochemical properties of polymers by CG force field parametrization, which are a bottom-up approach ,,− and a top-down approach. − In the case of the bottom-up approach, all-atom MD data is extensively reproduced for CG force field parametrization. The Boltzmann inversion method, ,, force-matching method, and inverse Monte Carlo method , have used the bottom-up approach for CG force field parametrization.…”

Local Molecular Field Theory for Coulomb Interactions in Aqueous Solutions

“…Similarly, we anticipate that the SS model could be of great use to the coarse-grained (CG) modeling community. In addition to the computational gain achieved by removing long-range interactions within the SS model, CG models effectively integrate out many of the short-range, atomic-scale details that can cause small errors when using universal effective interactions. ,− As a result of removing these atomic-scale details, we anticipate the SS model to be even more accurate for CG models.…”

Development of a coarse-grained model for surface-functionalized gold nanoparticles: towards an accurate description of their aggregation behavior

“…All the MD simulations with the SPICA force field [32][33][34]36,48 were performed using the LAMMPS package 49 . Only a new bead (CD) had to be introduced to account for and mimic the physicochemical properties of the grafting points at the surface of the gold core.…”