ArticleBiophysical journal2005
Protein folding in high-dimensional spaces: hypergutters and the role of nonnative interactions.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 28 citations in OpenAlex.
- A non-equilibrium approach to allosteric communication.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Article
- The role of high-dimensional diffusive search, stabilization, and frustration in protein folding.Biophysical journal · 2014Article
- Protein folded states are kinetic hubs.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Intermediates: ubiquitous species on folding energy landscapes?Current opinion in structural biology · 2007Review
- A multi-objective evolutionary approach to the protein structure prediction problem.Journal of the Royal Society, Interface · 2006Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilizing interactions, and folding rates themselves, leads to a model of the energy hypersurface that is characterized by the structure of diffusive "hypergutters" as well as the familiar "funnels". Several general predictions result: 1), intermediate subspaces of configurations will always be visited; 2), specific but nonnative interactions may be important in stabilizing these low-dimensional diffusive searches on the folding pathway, as well as native interactions; 3), sequential barriers will commonly be found, even in "two-state" proteins; 4), very early times will show characteristic departures from single-exponential kinetics; and 5), contributions of nonnative interactions to Phi-values and "Chevron plots" are calculable, and may be significant. The example of a three-helix bundle is treated in more detail as an illustration. The model also shows that high-dimensional structures provide conceptual relations between different models of protein folding. It suggests that kinetic strategies for fast folding may be encoded rather generally in nonnative as well as in native interactions. The predictions are related to very recent findings in experiment and simulation.
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