Coarse-Grained Simulation Study of the Association of Selected Dipeptides.

ABSTRACT: The association of 55 dipeptides extracted from aggregation-prone regions of selected proteins was studied by means of multiplexed replica-exchange molecular dynamics simulations with the coarse-grained UNRES model of polypeptide chains. Each simulation was carried out with 320 dipeptide molecules in a periodic box at 0.24 mol/dm³ concentration, in the 260-370 K temperature range. The temperature profiles of the degree of association, distributions of dipeptide cluster size, and structures of clusters were examined. It has been found that the dipeptides composed of strongly nonpolar (aromatic or aliphatic) residues associate nearly completely at all temperatures to form tight clusters, while those composed of charged or polar residues exhibited no or residual association. The di

SUBMITTER: Lesniewski M 

PROVIDER: S-EPMC11664597 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature