PMID: 12786043Jun 6, 2003Paper

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

Physical Review Letters
Jin Wang, Gennady M Verkhivker

Abstract

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.

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Citations

Apr 14, 2010·Journal of Molecular Modeling·Claudio Carra, Francis A Cucinotta
May 7, 2011·Journal of the American Chemical Society·Yibing ShanDavid E Shaw
Aug 23, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jin WangErkang Wang
May 31, 2008·Proceedings of the National Academy of Sciences of the United States of America·Giorgio ColomboGennady Verkhivker
Feb 18, 2010·Proceedings of the National Academy of Sciences of the United States of America·Anat BurgerPeter G Wolynes
Sep 19, 2012·Proceedings of the National Academy of Sciences of the United States of America·Davit A Potoyan, Garegin A Papoian
Sep 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jin WangVitor B P Leite
Jun 12, 2013·Proceedings of the National Academy of Sciences of the United States of America·Xiakun ChuJin Wang
Feb 27, 2013·Proceedings of the National Academy of Sciences of the United States of America·Fang BaiHualiang Jiang
Jun 27, 2013·Proceedings of the National Academy of Sciences of the United States of America·Michael J HarmsJoseph W Thornton
Sep 18, 2013·Proceedings of the National Academy of Sciences of the United States of America·Yong WangJin Wang
Feb 25, 2009·Bioinformatics·Anatoly M Ruvinsky, Ilya A Vakser
Mar 12, 2013·Bioinformatics·Zhiqiang YanJin Wang
Dec 17, 2011·BMC Evolutionary Biology·Johan A GrahnenDavid A Liberles
Nov 28, 2012·The AAPS Journal·Xiliang ZhengJin Wang
Jul 15, 2006·PLoS Computational Biology·Jin WangH Peter Lu
Nov 23, 2006·PLoS Computational Biology·Jin WangZhirong Sun
Jan 5, 2012·PLoS Computational Biology·Rui ChangWei Wang
May 27, 2009·International Journal of Molecular Sciences·Zaizhi LaiCunxin Wang
Aug 21, 2009·The Journal of Chemical Physics·Wei MinBiman Bagchi
Dec 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Diego U FerreiroPeter G Wolynes
Apr 9, 2010·Proceedings of the National Academy of Sciences of the United States of America·Ignacio E SánchezGonzalo de Prat-Gay
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Jul 5, 2005·Biophysical Journal·Jin WangErkang Wang
Jul 5, 2015·Journal of Computer-aided Molecular Design·Heloisa dos Santos Muniz, Alessandro S Nascimento
Jun 3, 2008·Biophysical Journal·Anatoly M Ruvinsky, Ilya A Vakser

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