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Journal of Atomic, Molecular, and Optical Physics
Volume 2012 (2012), Article ID 192613, 9 pages
http://dx.doi.org/10.1155/2012/192613
Research Article

The Effect of Nonnative Interactions on the Energy Landscapes of Frustrated Model Proteins

1School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
2University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK

Received 15 November 2011; Accepted 27 January 2012

Academic Editor: Jan Petter Hansen

Copyright © 2012 Mark T. Oakley et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The 46- and 69-residue BLN model proteins both exhibit frustrated folding to β-barrel structures. We study the effect of varying the strength of nonnative interactions on the corresponding energy landscapes by introducing a parameter λ, which scales the potential between the BLN (λ=1) and Gō-like (λ=0) limits. We study the effect of varying λ on the efficiency of global optimisation using basin-hopping and genetic algorithms. We also construct disconnectivity graphs for these proteins at selected values of λ. Both methods indicate that the potential energy surface is frustrated for the original BLN potential but rapidly becomes less frustrated as λ decreases. For values of λ0.9, the energy landscape is funnelled. The fastest mean first encounter time for the global minimum does not correspond to the Gō model: instead, we observe a minimum when the favourable nonnative interactions are still present to a small degree.