The last slide from this chemistry class at Stanford treat proteins in terms of Browian motion:
and
Protein association events are ubiquitous in biological sys- sional encounter (3). The determination of whether a
tems. Some protein associations and subsequent responses are reaction or response is diffusion controlled is clearly diffusion controlled in vivo. Hence, it is important to be able to crucial to protein design studies. compute bimolecular diffusional association rates for proteins. Recently, there has been quite a dramatic increase The Brownian dynamics simulation methodology may be used to in the number of experimental measurements of the simulate protein–protein encounter, compute association rates, kinetics of protein–protein interactions (4). This is in and examine their dependence on protein mutation and the na- part due to the recent availability of instruments based ture of the physical environment (e.g., as a function of ionic on surface plasmon resonance (4, 5), which, in princi- strength or viscosity).