MARTINI-based Coarse-grained Model for Poly(alpha-peptoid)s

TL;DR

This paper introduces a MARTINI-compatible coarse-grained model for poly(alpha-peptoid)s, enabling efficient simulation of their structural and solvation properties with good transferability across different molecules.

Contribution

The paper develops a new CG model for poly(alpha-peptoid)s based on the MARTINI force field, demonstrating transferability and accurate prediction of key properties.

Findings

CG model accurately predicts radius of gyration for various chain lengths

Model successfully predicts hydration and solvation free energies

Studied coil-globule transition in diblock polypeptoids

Abstract

In this paper, we present a new coarse-grained (CG) model for poly (alpha-peptoid)s that is compatible with the MARTINI CG FF. In the proposed model, CG poly (alpha-peptoid) is composed by a CG backbone (here we select polysarcosine as the backbone) and side chain beads. The CG model of the backbone (polysarcosine) in a solvent is first developed and then extended to poly (alpha-peptoid)s with different side groups that can be obtained from MARTINI FF. We demonstrate that our CG model has good transferability. For example, the CG potentials for polysarcosine can be transferred to predict hydration free energy of other peptoids. Also, the CG polypeptoid model accurately predicts the radius of gyration over a wide range of chain lengths and the solvation free energy for relatively short peptoid molecules in good solvents. We use the CG model to study sequenced diblock polypeptoid in binary solvent mixtures and compare the results with the experimentally observed coil-globule transition.