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Published online before print April 9, 2004, 10.1110/ps.03587604
Protein Science (2004), 13:1173-1181. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Critical nucleation size in the folding of small apparently two-state proteins

Yawen Bai1, Hongyi Zhou2 and Yaoqi Zhou2

1 Laboratory of Biochemistry, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
2 Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, University at Buffalo, State University of New York, Buffalo, New York 14214, USA

(RECEIVED December 18, 2003; FINAL REVISION February 5, 2004; ACCEPTED February 5, 2004)



Abstract

For apparently two-state proteins, we found that the size (number of folded residues) of a transition state is mostly encoded by the topology, defined by total contact distance (TCD) of the native state, and correlates with its folding rate. This is demonstrated by using a simple procedure to reduce the native structures of the 41 two-state proteins with native TCD as a constraint, and is further supported by analyzing the results of eight proteins from protein engineering studies. These results support the hypothesis that the major rate-limiting process in the folding of small apparently two-state proteins is the search for a critical number of residues with the topology close to that of the native state.

Keywords: topology; total contact distance; folding rate; nucleation size

Reprint requests to: Yawen Bai, Laboratory of Biochemistry, National Cancer Institute, NIH, Building 37, Room 6114E, Bethesda, MD 20892, USA; e-mail: yawen{at}helix.nih.gov; fax: (301) 402-3095; or Yaoqi Zhou, Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, University at Buffalo, State University of New York, 124 Sherman Hall, Buffalo, NY 14214, USA; e-mail: yqzhou{at}buffalo.edu; fax: (716) 829-2344.

Article published ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03587604.


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