the effect of nonnative interactions on the energy landscapes of frustrated model proteins外来的影响蛋白质在沮丧的能源景观模型的相互作用.pdfVIP

Hindawi Publishing Corporation Journal of Atomic, Molecular, and Optical Physics Volume 2012, Article ID 192613, 9 pages doi:10.1155/2012/192613 Research Article The Effect of Nonnative Interactions on the Energy Landscapes of Frustrated Model Proteins Mark T. Oakley,1 David J. Wales,2 and Roy L. Johnston1 1 School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK 2 University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK Correspondence should be addressed to Mark T. Oakley, m.t.oakley@bham.ac.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. 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 Go-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 λ ≤ 0.9, the energy landscape is funnelled. The fastest mean first encounter time for the global ¯ minimum does no