Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions.
Biophys J
; 91(5): 1868-86, 2006 Sep 01.
Article
em En
| MEDLINE
| ID: mdl-16766618
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 properties follow well-defined power laws that are expected for generic polymers in the EV limit. The average available volume is filled inefficiently, and cavities of all sizes are found within the interiors of denatured proteins. All properties characterized from simulated ensembles match predictions from rigorous field theories. We use our results to resolve between conflicting proposals for structure in ensembles for highly denatured states.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Desnaturação Proteica
/
Solventes
/
Algoritmos
/
Modelos Moleculares
/
Complexos Multiproteicos
/
Modelos Químicos
Tipo de estudo:
Diagnostic_studies
/
Prognostic_studies
Idioma:
En
Revista:
Biophys J
Ano de publicação:
2006
Tipo de documento:
Article
País de afiliação:
Estados Unidos