Smoothing protein energy landscapes by integrating folding models with structure prediction.

ABSTRACT: Decades of work has investigated the energy landscapes of simple protein models, but what do the landscapes of real, large, atomically detailed proteins look like? We explore an approach to this problem that systematically extracts simple funnel models of actual proteins using ensembles of structure predictions and physics-based atomic force fields and sampling. Central to our effort are calculations of a quantity called the relative entropy, which quantifies the extent to which a given set of structure decoys and a putative native structure can be projected onto a theoretical funnel description. We examine 86 structure prediction targets and one coupled folding-binding system, and find that in a majority of cases the relative entropy robustly signals which structures are nearest to native

SUBMITTER: Pritchard-Bell A 

PROVIDER: S-EPMC3207166 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature