Conformational space search of Neuromedin C using replica exchange molecular dynamics and molecular dynamics

Abstract

The present study involves the utilization of replica exchange molecular dynamics (REMD) methodology to explore the conformational space of Neuromedin C (NMC) using implicit (REMD(implicit) ) and explicit (REMD(explicit) ) water models. Comparison of the structures obtained from these simulations indicate that REMD(explicit) trajectory display a greater tendency to induce β-turns and bent structures as compared to those obtained from the REMD(implicit) simulation. Moreover, two additional MD trajectories performed using Langevin (MD(Lang) ) and Berendsen (MD(Berend) ) algorithms under generalized born (GB) solvent conditions were also suitably competent to sample similar kinds of conformations, although the extent of beta turns was low compared to those observed in REMD(explicit) simulation. Finally, the comparison of results obtained from all the trajectories and those derived from the NMR studies of Ni(II) complex of NMC indicates that the REMD under explicit conditions is more efficient in sampling the conformations, and show good agreement with the experimental results.