Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins.

ABSTRACT: The folding specificity of proteins can be simulated using simplified structural models and knowledge-based pair-potentials. However, when the same models are used to simulate systems that contain many proteins, large aggregates tend to form. In other words, these models cannot account for the fact that folded, globular proteins are soluble. Here we show that knowledge-based pair-potentials, which include explicitly calculated energy terms between the solvent and each amino acid, enable the simulation of proteins that are much less aggregation-prone in the folded state. Our analysis clarifies why including a solvent term improves the foldability. The aggregation for potentials without water is due to the unrealistically attractive interactions between polar residues, causing artificial clu

SUBMITTER: Abeln S 

PROVIDER: S-EPMC3030183 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature