Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates.
Identifieur interne : 003225 ( Main/Exploration ); précédent : 003224; suivant : 003226Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates.
Auteurs : Andrew I. Jewett [États-Unis] ; Vijay S. Pande ; Kevin W. PlaxcoSource :
- Journal of molecular biology [ 0022-2836 ] ; 2003.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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
Affiliations:
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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></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><noCountry><name sortKey="Pande, Vijay S" sort="Pande, Vijay S" uniqKey="Pande V" first="Vijay S" last="Pande">Vijay S. Pande</name><name sortKey="Plaxco, Kevin W" sort="Plaxco, Kevin W" uniqKey="Plaxco K" first="Kevin W" last="Plaxco">Kevin W. Plaxco</name></noCountry><country name="États-Unis"><region name="Californie"><name sortKey="Jewett, Andrew I" sort="Jewett, Andrew I" uniqKey="Jewett A" first="Andrew I" last="Jewett">Andrew I. 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