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1 Ontario Cancer Institute and Department of Medical Biophysics,
2 Department of Biochemistry,
3 Structural Genomics Consortium, and
4 Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
5 Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
6 Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
7 Laboratory of Biochemistry, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
8 School of Biochemistry and Microbiology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
9 Department of Biochemistry, Umea University, S-901 87 Umea, Sweden
10 Department of Chemistry, State University of New York, Stony Brook, New York 11794, USA
11 Département de Biochimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
12 Dipartimento di Scienze Biochimiche, Universita’ degli Studi di Firenze, 50134 Firenze, Italy
13 Department of Physics, University of Florida, Gainesville, Florida 32611, USA
14 Institute of Molecular Biology, Department of Protein Chemistry, DK-1353 Copenhagen, Denmark
15 Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
16 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
17 European Molecular Biology Laboratory, Heidelberg D-69012 Germany
18 Biochemistry and Cell Biology Department and Chemistry Department, Rice University, Houston, Texas 77251, USA
19 Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
(RECEIVED October 28, 2004; FINAL REVISION November 26, 2004; ACCEPTED November 26, 2004)
Recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. These difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the difficulty of obtaining correct and complete sequence and structural details for the characterized constructs. The lack of a single approach to data analysis and error estimation, or even of a common set of units and reporting standards, further hinders comparative studies of folding. In an effort to overcome these problems, we define here a "consensus" set of experimental conditions (25°C at pH 7.0, 50 mM buffer), data analysis methods, and data reporting standards that we hope will provide a benchmark for experimental studies. We take the first step in this initiative by describing the folding kinetics of 30 apparently two-state proteins or protein domains under the consensus conditions. The goal of our efforts is to set uniform standards for the experimental community and to initiate an accumulating, self-consistent data set that will aid ongoing efforts to understand the folding process.
Keywords: two-state; protein folding; kinetics; chevron plots; equilibrium
Abbreviations: GuHCl, guanidine hydrochloride • tris, tris hydroxymethylaminoethane • HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid • TCEP, tris(2-carboxyethyl)phosphine • CD, circular dichroism
Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041205405.
Reprint requests to: Kevin W. Plaxco, Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; e-mail: kwp{at}chem.ucsb.edu; fax: (805) 893-4120.
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