Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods.

ABSTRACT: Computer simulations of protein unfolding substantially help to interpret force-extension curves measured in single-molecule atomic force microscope (AFM) experiments. Standard all-atom (AA) molecular dynamics simulations (MD) give a good qualitative mechanical unfolding picture but predict values too large for the maximum AFM forces with the common pulling speeds adopted here. Fine tuned coarse-grain MD computations (CG MD) offer quantitative agreement with experimental forces. In this paper we address an important methodological aspect of MD modeling, namely the impact of numerical noise generated by random assignments of bead velocities on maximum forces (F(max)) calculated within the CG MD approach. Distributions of CG forces from 2000 MD runs for several model proteins rich in β struc

SUBMITTER: Mikulska K 

PROVIDER: S-EPMC3964301 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature