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Published online before print September 9, 2005, 10.1110/ps.051402705
Protein Science (2005), 14:2658-2667. Published by Cold Spring Harbor Laboratory Press. Copyright © 2005 The Protein Society
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Three-state protein folding: Experimental determination of free-energy profile

Ekaterina N. Baryshnikova, Bogdan S. Melnik, Alexei V. Finkelstein, Gennady V. Semisotnov and Valentina E. Bychkova

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia

(RECEIVED February 9, 2005; FINAL REVISION June 18, 2005; ACCEPTED July 6, 2005)

When considering protein folding with a transient intermediate, a difficulty arises as to determination of the rates of separate transitions. Here we overcome this problem, using the kinetic studies of the unfolding/refolding reactions of the three-state protein apomyoglobin as a model. Amplitudes of the protein refolding kinetic burst phase corresponding to the transition from the unfolded (U) to intermediate (I) state, that occurs prior to the native state (N) formation, allow us to estimate relative populations of the rapidly converting states at various final urea concentrations. On the basis of these proportions, a complicated experimental chevron plot has been deconvolved into the urea-dependent rates of the I{leftrightarrow}N and U{leftrightarrow}N transitions to give the dependence of free energies of the main transition state and of all three (N, I, and U) stable states on urea concentration.

Keywords: protein folding; folding intermediates; tryptophan fluorescence; chevron plot; stopped-flow; apomyoglobin

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051402705.

Reprint requests to: Valentina E. Bychkova, Institute of Protein Research (Moscow office), Room 104, Vavilova Street 34, Moscow, GSP 1, 117334, Russia; e-mail: bychkova{at}vega.protres.ru; fax: +7-095-135-9984.


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