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Protein Science (2006), 15:1638-1652. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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Sequence of events in folding mechanism: Beyond the Go model

Ludovico Sutto1, Guido Tiana1 and Ricardo A. Broglia1,2

1 Department of Physics, University of Milano and INFN, 20133 Milano, Italy
2 The Niels Bohr Institute, 2100 Copenhagen, Denmark

(RECEIVED December 21, 2005; FINAL REVISION April 20, 2006; ACCEPTED April 20, 2006)

Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same way so that the folding features of a protein are determined only by the geometry of its native conformation. We present an extended version of a C{alpha}-based Go model where different residues interact with different energies. The model is used to calculate the thermodynamics of three small proteins (Protein G, Src-SH3, and CI2) and the effect of mutations ({Delta}{Delta}GU-N, {Delta}{Delta}G{ddagger}-N, {Delta}{Delta}G{ddagger}-U, and {varphi}-values) on the wild-type sequence. The model allows us to investigate some of the most controversial areas in protein folding, such as its earliest stages and the nature of the unfolded state, subjects that have lately received particular attention.

Keywords: protein folding; simplified model; mutation free energy


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