Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding.
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.
Wang
Jin
J
State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130021, People's Republic of China. jinwang@sprynet.com
Verkhivker
Gennady M
GM
D015195:Drug Design; D057927:Hydrophobic and Hydrophilic Interactions; D008954:Models, Biological; D008956:Models, Chemical; D008968:Molecular Conformation; D011485:Protein Binding; D017510:Protein Folding; D055672:Static Electricity; D013816:Thermodynamics