Principal component analysis of fast-folding λ-repressor mutants

Abstract

Principal component (PC) analysis is carried out on 10 ns simulations of four fast-folding mutants of the λ 6–85-repressor fragment near the native structure. The range of motion along the largest two PCs is seen to be greater for the faster folding mutants in the group. Dynamics along the largest PC and the free energy profile resemble those for Brownian dynamics, the former apparently more than thus far found for other proteins over similar times. These measures, however, do not easily distinguish Brownian from subdiffusive dynamics, which is suggested by the PC eigenvalue distribution.