Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations.

ABSTRACT: Structural fluctuations of a protein are essential for the function of native proteins and for protein folding. To understand how the main chain in the native state of a protein fluctuates on different time scales, we examined the rotational correlation functions (RCFs), C(t), of the backbone N-H bonds and of the dihedral angles γ built on four consecutive C(α) atoms. Using molecular dynamics simulations of a model α/β protein (VA3) in its native state, we demonstrate that these RCFs decay as stretched exponentials, ln[C(t)] ≈ D(α)t(α) with a constant D(α) and an exponent α (0 < α < 0.35) varying with the free-energy profiles (FEPs) along the amino acid sequence. The probability distributions of the fluctuations of the main chain computed at short time scale (1 ps) were identical to those

SUBMITTER: Cote Y 

PROVIDER: S-EPMC2993386 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature