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Published online before print August 4, 2004, 10.1110/ps.04713804
Protein Science (2004), 13:2446-2457. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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What can one learn from experiments about the elusive transition state?

Iksoo Chang1,2, Marek Cieplak1,3, Jayanth R. Banavar1 and Amos Maritan4,5

1 Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
2 National Research Laboratory for Computational Proteomics and Biophysics, Department of Physics, Pusan National University, Pusan 609-735, Korea
3 Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
4 INFM and Dipatrimento di Fisica ‘G. Galilei,’ Universitá di Padova, 35131 Padova, Italy
5 The Abdus Salam International Center for Theoretical Physics (ICTP), 34100 Trieste, Italy

(RECEIVED March 1, 2004; FINAL REVISION May 7, 2004; ACCEPTED May 14, 2004)

We present the results of an exact analysis of a model energy landscape of a protein to clarify the idea of the transition state and the physical meaning of the {phi} values determined in protein engineering experiments. We benchmark our findings to various theoretical approaches proposed in the literature for the identification and characterization of the transition state.

Keywords: protein folding; transition state; protein engineering

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04713804.

Reprint requests to: Marek Cieplak, Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland; e-mail: mc{at}ifpan.edu.pl; fax: 48-22-843-0926.


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