ArticleProceedings of the National Academy of Sciences of the United States of America2007
Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.The journal of physical chemistry. B · 2012Article
- A variational model for oligomer-formation process of GNNQQNY peptide from yeast prion protein Sup35.Biophysical journal · 2012Article
- A semi-analytical description of protein folding that incorporates detailed geometrical information.The Journal of chemical physics · 2011Article
- Direct observation of downhill folding of lambda-repressor in a microfluidic mixer.Biophysical journal · 2009Article
- Analysis of oligomeric proteins during unfolding by pH and temperature.Journal of molecular modeling · 2009Article
- How general is the nucleation-condensation mechanism?Proteins · 2008Article
- Capillarity-like growth of protein folding nuclei.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- An experimental survey of the transition between two-state and downhill protein folding scenarios.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Folding domain B of protein A on a dynamically partitioned free energy landscape.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Origins of barriers and barrierless folding in BBL.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
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Abstract
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce minor structural cooperativity are included in the interaction potential. In general, the cooperative folding routes have sharper interfaces between folded and unfolded regions of the folding nucleus and higher free energy barriers. The calculated free energy barriers are strongly correlated with native topology as characterized by contact order. Increasing the rigidity of the folding nucleus changes the local structure of the transition state ensemble nonuniformly across the set of proteins studied. Nevertheless, the calculated prefactors k(0) are found to be relatively uniform across the protein set, with variation in 1/k(0) less than a factor of 5. This direct calculation justifies the common assumption that the prefactor is roughly the same for all small two-state folding proteins. Using the barrier heights obtained from the model and the best-fit monomer relaxation time 30 ns, we find that 1/k(0) approximately 1-5 mus (with average 1/k(0) approximately 4 micros). This model can be extended to study subtle aspects of folding such as the variation of the folding rate with stability or solvent viscosity and the onset of downhill folding.
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