Connecting cluster dynamics and protein folding

The relaxation dynamics of clusters can be interpreted in terms of the topographies of their potential surfaces. Systems with short-range potentials have sawtooth-like potential surfaces with small drops in energy from one local minimum to the next and few-body motions as the clusters move from one minimum to another; such systems readily take on amorphous structures. These are called “glass-formers". Systems with long-range forces have potentials whose topographies are like rough staircases, with some large drops in energy from one minimum to the next; their well-to-well passages involve very collective motions and such systems are excellent structure-seekers. They find their way to well-ordered, highly selective structures under almost all circumstances. These characteristics generalize to describe the potential surfaces and folding behavior of polypeptides and proteins. The forces are effective long-range forces due to the polymer chain. Staircase topographies emerge both from direct sampling of potential surfaces and from the inversion of the kinetics generated by a much more aaabstract topological model, from which folding pathways can be inferred. Received 4 December 2000