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Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates.

Identifieur interne : 000175 ( Ncbi/Merge ); précédent : 000174; suivant : 000176

Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates.

Auteurs : Andrew I. Jewett [États-Unis] ; Vijay S. Pande ; Kevin W. Plaxco

Source :

Journal of molecular biology [ 0022-2836 ] ; 2003.

RBID : pubmed:12547206

Descripteurs français

KwdFr :
- Cinétique, Modèles chimiques, Pliage des protéines, Protéines (), Protéines (métabolisme), Structure tertiaire des protéines, Thermodynamique.
MESH :
- métabolisme : Protéines.
- Cinétique, Modèles chimiques, Pliage des protéines, Protéines, Structure tertiaire des protéines, Thermodynamique.

English descriptors

KwdEn :
- Kinetics, Models, Chemical, Protein Folding, Protein Structure, Tertiary, Proteins (chemistry), Proteins (metabolism), Thermodynamics.
MESH :
- chemical , chemistry : Proteins.
- chemical , metabolism : Proteins.
- Kinetics, Models, Chemical, Protein Folding, Protein Structure, Tertiary, Thermodynamics.

Abstract

The relative folding rates of simple, single-domain proteins, proteins whose folding energy landscapes are smooth, are highly dispersed and strongly correlated with native-state topology. In contrast, the relative folding rates of small, Gō-potential lattice polymers, which also exhibit smooth energy landscapes, are poorly dispersed and insignificantly correlated with native-state topology. Here, we investigate this discrepancy in light of a recent, quantitative theory of two-state folding kinetics, the topomer search model. This model stipulates that the topology-dependence of two-state folding rates is a direct consequence of the extraordinarily cooperative equilibrium folding of simple proteins. We demonstrate that traditional Gō polymers lack the extreme cooperativity that characterizes the folding of naturally occurring, two-state proteins and confirm that the folding rates of a diverse set of Gō 27-mers are poorly dispersed and effectively uncorrelated with native state topology. Upon modestly increasing the cooperativity of the Gō-potential, however, significantly increased dispersion and strongly topology-dependent kinetics are observed. These results support previous arguments that the cooperative folding of simple, single-domain proteins gives rise to their topology-dependent folding rates. We speculate that this cooperativity, and thus, indirectly, the topology-rate relationship, may have arisen in order to generate the smooth energetic landscapes upon which rapid folding can occur.

DOI: 10.1016/s0022-2836(02)01356-6
PubMed: 12547206

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pubmed:12547206

Le document en format XML

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<front><div type="abstract" xml:lang="en">The relative folding rates of simple, single-domain proteins, proteins whose folding energy landscapes are smooth, are highly dispersed and strongly correlated with native-state topology. In contrast, the relative folding rates of small, Gō-potential lattice polymers, which also exhibit smooth energy landscapes, are poorly dispersed and insignificantly correlated with native-state topology. Here, we investigate this discrepancy in light of a recent, quantitative theory of two-state folding kinetics, the topomer search model. This model stipulates that the topology-dependence of two-state folding rates is a direct consequence of the extraordinarily cooperative equilibrium folding of simple proteins. We demonstrate that traditional Gō polymers lack the extreme cooperativity that characterizes the folding of naturally occurring, two-state proteins and confirm that the folding rates of a diverse set of Gō 27-mers are poorly dispersed and effectively uncorrelated with native state topology. Upon modestly increasing the cooperativity of the Gō-potential, however, significantly increased dispersion and strongly topology-dependent kinetics are observed. These results support previous arguments that the cooperative folding of simple, single-domain proteins gives rise to their topology-dependent folding rates. We speculate that this cooperativity, and thus, indirectly, the topology-rate relationship, may have arisen in order to generate the smooth energetic landscapes upon which rapid folding can occur.</div>
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Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates.

Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Links to Exploration step

Le document en format XML

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