Simplified protein models: predicting folding pathways and structure using amino acid sequences.
Phys Rev Lett
; 111(2): 028103, 2013 Jul 12.
Article
en En
| MEDLINE
| ID: mdl-23889448
ABSTRACT
We demonstrate the ability of simultaneously determining a protein's folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing nativelike substructures or "foldons." Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that nativelike propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the molecular dynamics study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Proteínas
/
Simulación de Dinámica Molecular
/
Aminoácidos
/
Modelos Químicos
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Phys Rev Lett
Año:
2013
Tipo del documento:
Article
País de afiliación:
Estados Unidos