Topological and energetic factors: what determines the structural details of the transition state ensemble and "on-route" intermediates for protein folding? An investigation for small globular proteins

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dc.creatorClementi, Cecilia
dc.creatorNymeyer, Hugh
dc.creatorOnuchic, Jose' Nelson
dc.date2000-03-28
dc.date.accessioned2026-07-07T02:37:13Z
dc.date.available2026-07-07T02:37:13Z
dc.descriptionRecent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the topological control of the folding process, we study the folding of simplified models of five small globular proteins constructed using a Go-like potential in order to retain the information about the native structures but drastically reduce the energetic frustration and energetic heterogeneity among residue-residue native interactions. By comparing the structure of the transition state ensemble experimentally determined by Phi-values and of the intermediates with the ones obtained using our models, we show that these energetically unfrustrated models can reproduce the global experimentally known features of the transition state ensembles and "on-route" intermediates, at least for the analyzed proteins. This result clearly indicates that, as long as the protein sequence is sufficiently minimally frustrated, topology plays a central role in determining the folding mechanism.
dc.description25 pages, 10 color figures. Journal of Molecular Biology, in press
dc.identifierhttps://arxiv.org/abs/cond-mat/0003460
dc.identifierhttp://arxiv.org/abs/cond-mat/0003460
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/16204
dc.subjectStatistical Mechanics
dc.subjectQuantitative Biology
dc.titleTopological and energetic factors: what determines the structural details of the transition state ensemble and "on-route" intermediates for protein folding? An investigation for small globular proteins
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