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

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.