Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions.

ABSTRACT: Our focus is on an appropriate theoretical framework for describing highly denatured proteins. In high concentrations of denaturants, proteins behave like polymers in a good solvent and ensembles for denatured proteins can be modeled by ignoring all interactions except excluded volume (EV) effects. To assay conformational preferences of highly denatured proteins, we quantify a variety of properties for EV-limit ensembles of 23 two-state proteins. We find that modeled denatured proteins can be best described as follows. Average shapes are consistent with prolate ellipsoids. Ensembles are characterized by large correlated fluctuations. Sequence-specific conformational preferences are restricted to local length scales that span five to nine residues. Beyond local length scales, chain properti

SUBMITTER: Tran HT 

PROVIDER: S-EPMC1544316 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature