Biogels. On comparison of structure differences in anti-parallel and parallel complexes of the $H-(RADA)_4-OH$ peptides

Water based solution of the $H-(RADA)_4-OH$ peptide tend to self-assemble into bi-layered fibrils composed of two hydrophilic layers and hydrophobic one in between of them. Bio gels of the $H-(RADA)_4-OH$ peptides are considered as an extra cellular matrix for culturing cells of different types, a prominent source of synthetic scaffolds for regenerative medicine and tissue engineering. We have designed two types of bi-layered protofilament structure, which layers are formed either of parallel or anti-parallel peptide chains, then used the method of molecular dynamics to study these peptide complexes (AMBER package v.11 and ff03 force field at 300K). It was pointed out, that the most stable complex consists of anti-parallel peptides with the lowest free energy estimated by the generalized Born approach and the least deviation of atoms coordinates values. Analysis of the results gave insight into the factors, which influence on the initial stage of the $H-(RADA)_4-OH$ self-assembly mechanism.