The ''3-color, 46-bead'' model of a folding polypeptide is the vehicle for adapting to proteins a mode of analysis used heretofore for atomic clusters, to relate the topography of the potential surface to the dynamics that lead to formation of selected structures. The analysis is based on sequences of stationary points-successive minima, joined by saddles-that rise monotonically in energy from basin bottoms. Like structure-seeking clusters, the potential surface of the model studied here is staircase-like, rather than sawtoothlike, with highly collective motions required for passage from one minimum to the next. The surface has several deep basins whose minima correspond to very similar structures, but which are separated by high energy barriers.A challenge to chemical theory has been finding a way to infer from attainable data at the atomic level why some systems readily form glasses and others fall into very selective structures. It is possible to do this now for atomic clusters by examining sequences of linked stationary points on the potential surface, particularly sequences whose minima rise monotonically from the bottoms of basins on the surface (1-4). The signature of a glass-former seems to be a complex potential with a sawtooth topography-a potential whose successive minima differ little in energy, relative to the heights of the energy barriers that separate them. In contrast, the signature of a ''structure-seeker'' appears to be a complex potential with a staircase topography-a potential some of whose adjacent minima differ considerably in energy, relative to the energy barrier between them. The mechanistic difference between the two, at the atomic level, is that only a very few particles move when a glass-former passes from one local minimum to the next, whereas in a structure-seeker, many particles move in the well-to-well passages, and in some of these, the internal potential energy changes considerably. Examples of glass-formers are such rare-gas clusters as Ar 19 and Ar 55 (2,3,5); an example of a good structure-seeker is (KCl) 32 , which, when quenched (in molecular dynamics simulations) from liquid, finds one of its few hundred rocksalt structures rather than one of its (roughly) 10 13 amorphous structures (6). Only if the cluster is quenched at a rate above 10 13 K͞s-i.e., if the energy is removed during only 5-10 vibrational periods-can this system be trapped in an amorphous structure (6, 7).Even as the results emerged for clusters, it was apparent that the same characteristics might govern the structure-seeking propensities of proteins and other biopolymers. The interatomic forces in proteins differ very much indeed from those between the atoms of clusters, but if the characterization is correct, that difference is irrelevant to the generic issue of why some species are good structure-seekers and others are good glass-formers. The crucial issue is the topography of the potential surface, not the microscopic origin of the forces that give rise to that topography. We therefore undertook...
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