Prediction and Dissection of Widely-Varying Association Rate Constants of Actin-Binding Proteins
Actin is an abundant protein that constitutes a main component of the eukaryotic cytoskeleton. Its polymerization and depolymerization are regulated by a variety of actin-binding proteins. Their functions range from nucleation of actin polymerization to sequestering G-actin in 1:1 complexes. The kinetics of forming these complexes, with rate constants varying at least three orders of magnitude, is critical to the distinct regulatory functions. Previously we have developed a transient-complex theory for computing protein association mechanisms and association rate constants. The transient complex refers to an intermediate in which the two associating proteins have near-native separation and relative orientation but have yet to form short-range specific interactions of the native complex. The association rate constant is predicted as ka = ka0, where ka0 is the basal rate constant for reaching the transient complex by free diffusion, and the Boltzmann factor captures the bias of long-range electrostatic interactions. Here we applied the transient-complex theory to study the association kinetics of seven actin-binding proteins with G-actin. These proteins exhibit three classes of association mechanisms, due to their different molecular shapes and flexibility. The 1000-fold ka variations among them can mostly be attributed to disparate electrostatic contributions. The basal rate constants also showed variations, resulting from the different shapes and sizes of the interfaces formed by the seven actin-binding proteins with G-actin. This study demonstrates the various ways that actin-binding proteins use physical properties to tune their association mechanisms and rate constants to suit distinct regulatory functions. Actin polymerization and depolymerization drive cell motility and are regulated by a variety of actin-binding proteins. The widely-varying rate constants (ka) of the actin-binding proteins associating with G-actin, spanning at least three orders of magnitude, appear to be tuned for their distinct regulatory functions. Here we applied our previously developed transient-complex theory to study the association kinetics of seven actin-binding proteins with G-actin. These proteins exhibit three classes of association mechanisms, due to their different molecular shapes and flexibility. The 1000-fold ka variations among them can mostly be attributed to disparate inter-protein electrostatic interactions. By computing the association mechanisms and quantifying the physical determinants of association rate constants, the present study reveals critical links between the structure and function of the actin-binding proteins.