Intramolecular alpha-helix-beta-structure-random coil transition in polypeptides. II. Dynamic case

The conformational changes of polypeptides which are capable of forming the alpha-helix. beta-structure and random coil (or the unordered) conformations are discussed. The kinetics of this system are studied as the time evolution of the probabilities describing the conformational states of the system. The time behavior of the average numbers of the alpha-helix and the beta-structure reveals the existence of intermediate states which are not found and not stable at equilibrium. These intermediates make the kinetics of this system more complex. Such situations can occur in protein folding and unfolding processes in such a way that a conformation absent in the tertiary structure appears in the intermediate stages and disappears finally, and the time course of the reaction is described by the sum of two or more exponential terms, in other words, the protein folding and unfolding processes display multiphasic kinetics. These intermediates, which are formed by short-range interactions, may usually be destroyed but sometimes can be stabilized by medium- and long-range interactions and remain stable for a fairly long time in the process of renaturation in real proteins.