title: Rate Constants and Mechanisms of Protein-Ligand Binding.
abstract: Whereas protein-ligand binding affinities have long-established prominence, binding rate constants and binding mechanisms have gained increasing attention in recent years. Both new computational methods and new experimental techniques have been developed to characterize the latter properties. It is now realized that binding mechanisms, like binding rate constants, can and should be quantitatively determined. In this review, we summarize studies and synthesize ideas on several topics in the hope of providing a coherent picture of and physical insight into binding kinetics. The topics include microscopic formulation of the kinetic problem and its reduction to simple rate equations; computation of binding rate constants; quantitative determination of binding mechanisms; and elucidation of physical factors that control binding rate constants and mechanisms.
authors.affiliation: Department of Physics, Florida State University, Tallahassee, Florida 32306; email: hzhou4@fsu.edu.|Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Pang
authors.affiliation: Department of Physics, Florida State University, Tallahassee, Florida 32306; email: hzhou4@fsu.edu.|Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306.
authors.forename: Huan-Xiang
authors.initials: HX
authors.lastname: Zhou
mesh_terms: D000465:Algorithms; D006801:Humans; D007700:Kinetics; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D011506:Proteins
keywords: binding mechanism; binding rate constant; conformational selection; dock and coalesce; induced fit; reactive flux