The ultimate speed limit to protein folding is conformational searching. 2007

Kingshuk Ghosh, and S Banu Ozkan, and Ken A Dill
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA.

More than a dozen proteins are known to be ultrafast folders. In addition to being fast, their kinetics is unusual. Like traditional rate processes, fast folding proteins have activation barriers at low temperatures, but unlike traditional processes, they have negative activation energies at high temperatures. We develop a model of ultrafast folders that joins a macroscopic mass-action model with a microscopic energy landscape description; we call it the Thruway Search Model. We find good agreement with experimental rates and equilibria on 13 ultrafast folders. The observed folding rates are found to be proportional to the number of microscopic folding routes: fast-folding proteins have more parallel microscopic routes on energy landscapes. At high temperatures, where traditional barriers are small, the remaining bottleneck is a search through denatured conformations to find thruway routes to the native state. Negative activation arises because increasing temperature expands the denatured ensemble, broadening the search, slowing the folding to the native state. We find that the upper estimate of the free energy barriers are positive but small, as little as 0.5 kT.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D013816 Thermodynamics A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed) Thermodynamic
D017510 Protein Folding Processes involved in the formation of TERTIARY PROTEIN STRUCTURE. Protein Folding, Globular,Folding, Globular Protein,Folding, Protein,Foldings, Globular Protein,Foldings, Protein,Globular Protein Folding,Globular Protein Foldings,Protein Foldings,Protein Foldings, Globular

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