The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition

PLoS Comput Biol. 2015 Apr 17;11(4):e1004212. doi: 10.1371/journal.pcbi.1004212. eCollection 2015 Apr.

Abstract

We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology
  • Kinetics*
  • Ligands*
  • Models, Theoretical*
  • Protein Binding / physiology*
  • Statistical Distributions
  • Thermodynamics

Substances

  • Ligands

Grants and funding

JW thanks National Science Foundation for support. This work is supported by the National Natural Science Foundation of China (Grants 11174105, 91227114, 91430217 and 21190040). This work is also funded by Science and Technology Development Plan of Jilin Province (20130101179Jc) and Jilin province public computing platform. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.