Analysis on long-range residue-residue communication using molecular dynamics: Analysis of Long-Range Residue-Residue Communication
Sangwook Wu, Lee G. Pedersen, Chang Jun Lee · Carolina Digital Repository (University of North Carolina at Chapel Hill) · 2020
We investigated the possibility of inter-residue communication of side chains in barstar, an 89 residue protein, employing mutual information theory. The normalized mutual information (NMI) of the dihedral angles of the side chains was obtained from all-atom molecular dynamics simulations. The accumulated NMI from an explicit solvent equilibrated trajectory (600-ns) with free backbone exhibits a parabola–shaped distribution over the inter–residue distances (0 ~ 36 Å): smaller at the end regimes but larger in the middle regime. This analysis, plus several other measures, does not find unusual long-range communication for free backbone in explicit solvent simulations.