Solvation Effects and Driving Forces for Protein Thermodynamic And Kinetic Cooperativity: How Adequate Is Native-Centric Topological Modeling?

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dc.creatorKaya, Huseyin
dc.creatorChan, Hue Sun
dc.date2002-12-04
dc.date2002-12-12
dc.date.accessioned2026-07-07T02:48:33Z
dc.date.available2026-07-07T02:48:33Z
dc.descriptionWhat energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of continuum Langevin dynamics models of chymotrypsin inhibitor 2. We find that residue-based additive Gō-like contact energies, although native-centric, are by themselves insufficient for proteinlike calorimetric two-state cooperativity. Further native biases by local conformational preferences are necessary for proteinlike thermodynamics. Kinetically, however, even models with both contact and local native-centric energies do not produce simple two-state chevron plots. Thus a model protein's thermodynamic cooperativity is not sufficient for simple two-state kinetics. The models tested appear to have increasing internal friction with increasing native stability, leading to chevron rollovers that typify kinetics that are commonly referred to as non-two-state. The free energy profiles of these models are found to be sensitive to the choice of native contacts and the presumed spatial ranges of the contact interactions. Motivated by explicit-water considerations, we explore recent treatments of solvent granularity that incorporate desolvation free energy barriers into effective implicit-solvent intraprotein interactions. This additional feature reduces both folding and unfolding rates vis-à-vis that of the corresponding models without desolvation barriers, but the kinetics remain non-two-state. Taken together, our observations suggest that interaction mechanisms
dc.description44 pages, 12 postscript figures, corrected typos (will appear on JMB)
dc.identifierhttps://arxiv.org/abs/cond-mat/0212105
dc.identifierhttp://arxiv.org/abs/cond-mat/0212105
dc.identifierJournal of Molecular Biology 326 (2003) 911-931
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/20448
dc.subjectStatistical Mechanics
dc.subjectSoft Condensed Matter
dc.subjectQuantitative Biology
dc.titleSolvation Effects and Driving Forces for Protein Thermodynamic And Kinetic Cooperativity: How Adequate Is Native-Centric Topological Modeling?
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