ABSTRACT
Overview ................................................................................................................ 110 Introduction ............................................................................................................ 110
Bimolecular Association ................................................................................... 110 Diffusional Encounter Complex ................................................................... 111 Bound Complex ............................................................................................ 111
Molecular Diffusion .......................................................................................... 111 Electrostatic Interactions ................................................................................... 112 Reaction Rates ................................................................................................... 113
Theoretical and Computational Approaches .......................................................... 114 Particle-Based Approaches ................................................................................ 114 Density-Distribution Approaches ...................................................................... 116 Electrostatic Enhancement of Association Rates .............................................. 117
Recent Advances in Computational Approaches ................................................... 117 Protein-Protein Interactions .............................................................................. 117
Computation of Association Rates ............................................................... 117 Dissection of the Determinants of Binding .................................................. 117 Quantification of the Encounter Complex .................................................... 118 Induced Fit Phenomena ................................................................................ 119 Crowding Phenomena .................................................................................. 119
Protein-Nucleic Acid Interactions .................................................................... 119 Computation of Association Rates ............................................................... 119 Specificity and Nonspecificity ...................................................................... 120 Chromatin Models ........................................................................................ 121
Outlook .................................................................................................................. 122 Acknowledgments .................................................................................................. 123 References .............................................................................................................. 123
The kinetics of the formation of macromolecular complexes contribute to their biological function. We first describe key features and determinants of bimolecular association kinetics. Then we present an overview of theoretical and computational approaches to calculating kinetic properties. Finally, we discuss recent computational advances with selected examples of protein-nucleic acid and protein-protein complexation.
