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Phys. Rev. Lett. 90, 188101 (2003) [4 pages]

Energy Landscape Theory, Funnels, Specificity, and Optimal Criterion of Biomolecular Binding

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Jin Wang1,2,3,4 * and Gennady M. Verkhivker5 †
1State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130021, People’s Republic of China
2Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
3Department of Physics, National University of Singapore 2 Science Drive 3 Singapore, 117542 Singapore
4Global Strategic Analytics Unit, Citigroup, One Huntington Quadrangle, Suite 1N16, Melville, New York 11747, USA
5Department of Computational Chemistry, Pfizer Global Research and Development La Jolla, 10777 Science Center Drive, San Diego, California 92121-1111, USA

Received 6 June 2002; published 6 May 2003

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.


©2003 The American Physical Society

URL: http://link.aps.org/doi/10.1103/PhysRevLett.90.188101
DOI: 10.1103/PhysRevLett.90.188101
PACS: 87.10.+e, 87.14.–g, 87.15.–v

* Electronic address: jinwang@sprynet.com
† Electronic address: gennady.verkhivker@pfizer.com

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