Concepts and misconcepts in the analysis of simple kinetics of protein folding

Unusually simple two-state kinetics characterizes the folding of a number of small proteins possessing a variety secondary structures. This limits dramatically the number of experimentally resolvable parameters that may characterize this process and also suggests the possibility to describe it based on simple theories borrowed from the field of ordinary chemical reactions. An attempt is made to critically evaluate the basic concepts, which are in the background of this approach. We demonstrate their limitations, which may cast doubt on the interpretation of experimental data. It is shown also that, in contrast to provisions of transition state theory, the simple kinetics of protein folding does not correlate with folded state stability or with the size of the folding unit. Moreover, the folding kinetics exhibits anomalous dependence on temperature and pressure and surprisingly strong dependence on solvent viscosity. The possible role in folding of fluctuations, relaxations and gradient dynamics is discussed. Being overlooked or underestimated, these mechanisms may determine the rate and specificity of the process.