Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments

Abstract

We propose the replica permutation with solute tempering (RPST) by combining the replica-permutation method (RPM) and the replica exchange with solute tempering (REST). Temperature permutations are performed among more than two replicas in RPM, whereas temperature exchanges are performed between two replicas in the replica-exchange method (REM). The temperature transition in RPM occurs more efficiently than in REM. In REST, only the temperatures of the solute region, the solute temperatures, are exchanged to reduce the number of replicas compared to REM. Therefore, RPST is expected to be an improved method taking advantage of these methods. For comparison, we applied RPST, REST, RPM, and REM to two amyloid-β(16–22) peptides in explicit water. We calculated the transition ratio and the number of tunneling events in the temperature space and the number of dimerization events of amyloid-β(16–22) peptides. The results indicate that, in RPST, the number of replicas necessary for frequent random walks in the temperature and conformational spaces is reduced compared to the other three methods. In addition, we focused on the dimerization process of amyloid-β(16–22) peptides. The RPST simulation with a relatively small number of replicas shows that the two amyloid-β(16–22) peptides form the intermolecular antiparallel β-bridges due to the hydrophilic side-chain contact between Lys and Glu and hydrophobic side-chain contact between Leu, Val, and Phe, which stabilizes the dimer of the peptides.