Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations

摘要

The conformational ensembles of a disordered peptide, polyglutamine Q15, over a wide temperature range were sampled using multiple replicates of conventional molecular dynamics (cMD) simulations as well as two enhanced sampling methods, temperature replica exchange (TREMD) and replica exchange with solute tempering (REST). The radius of gyration, asphericity, secondary structure, and hydrogen bonding patterns were used for the comparison of the sampling methods. Overall, the three sampling methods generated similar conformational ensembles, with progressive collapse at higher temperatures. Although accumulating the longest simulation time (90 μs), cMD at room temperature missed a small subspace that was sampled by both TREMD and REST. This subspace was high in α-helical content and separated from the main conformational space by an energy barrier. REST used less simulation time than TREMD (36 μs versus 42 μs), and this gap is expected to widen significantly for larger disordered proteins. We conclude that REST is the method of choice for conformational sampling of intrinsically disordered proteins.