Aspects of protein reaction dynamics: Deviations from simple behavior

Proteins are complex systems so that their reactions may have characteristics not often observed in small molecules. Two common aspects of small molecule reactions are an exponential time dependence and Arrhenius-like temperature dependence. This review shows that corresponding behavior is not always observed in reactions involving proteins. Bond-making and bond-breaking reactions, as well as conformational changes, which do not involve chemical bonds, are discussed. As examples of bond making, bond breaking reactions, enzyme catalysis by triosephosphate isomerase and ligand binding by myoglobin are considered. Several reactions involving conformational changes are described. They include aromatic side chain rotations, loop/lid opening and closing motions, quaternary structural changes in hemoglobin, and protein folding. In some of these cases, deviations from simple small molecule behavior have been observed, but it is evident that more information is needed for a complete understanding. The protein folding reaction, which is most complex because it involves the entire polypeptide chain, is analyzed in some detail.