Site-selective heat current analysis of α-helical protein with linear-homopolymer-like model

Abstract

Although thermal transport is among the essential biophysical properties of proteins, its relationship with protein structures, dynamics, and functions is still elusive. The structures of folded proteins are highly inhomogeneous, giving rise to an anisotropic and non-uniform flow of thermal energy during conformational fluctuations. To illustrate the nature of proteins, we developed a theoretical framework for analyzing local thermal transport properties based on the autocorrelation function formalism, constructed a linear-homopolymer-like model, and applied it to a small α-helical protein, the villin headpiece subdomain (HP36), using equilibrium molecular dynamics simulations. As a result, the model reproduced the exact value of the protein’s thermal conductivity with an error of less than 1%. Interestingly, the site-selective analysis of the local, residue-wise, thermal conductivity demonstrated its distinct residue-type dependence, i.e., its magnitude decreased in the order of charged, polar, and hydrophobic residues. In addition, the local density dependence of the residue-wise thermal transport property was also discussed.