Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

ABSTRACT: Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a proba

SUBMITTER: Boomsma W 

PROVIDER: S-EPMC4183297 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature