title: Automated prediction of protein association rate constants.
abstract: The association rate constants (k(a)) of proteins with other proteins or other macromolecular targets are a fundamental biophysical property. Observed rate constants span over ten orders of magnitude, from 1 to 10(10) M(-1)s(-1). Protein association can be rate limited either by the diffusional approach of the subunits to form a transient complex, with near-native separation and orientation but without short-range native interactions, or by the subsequent conformational rearrangement to form the native complex. Our transient-complex theory showed promise in predicting k(a) in the diffusion-limited regime. Here, we develop it into a web server called TransComp (http://pipe.sc.fsu.edu/transcomp/) and report on the server's accuracy and robustness based on applications to over 100 protein complexes. We expect this server to be a valuable tool for systems biology applications and for kinetic characterization of protein-protein and protein-nucleic acid association in general.
authors.affiliation: Department of Physics and Institute of Molecular Biophysics, Tallahassee, FL 32306, USA.
authors.forename: Sanbo
authors.initials: S
authors.lastname: Qin
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Pang
authors.forename: Huan-Xiang
authors.initials: HX
authors.lastname: Zhou
mesh_terms: D001665:Binding Sites; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D049490:Systems Biology / Q000379:methods*; D013816:Thermodynamics
chemical_list: D011506:Proteins