Influence of ordered backbone structure on protein folding. A study of some simple models

Four series of model molecules, each of which contains a coil section and one or two sections of fixed ordered backbone structure, have been examined to locate their low-energy conformations in water. The four series are: helix-coil, helix-coil-helix, extended-coil, and extended-coil-extended. In each series, the length of the coil is allowed to vary from four to ten residues, while the nuclei (ordered backbone structures) are held fixed at six residues. By comparing these molecules, it is observed that the low-energy conformations of those containing two nuclei can be regarded as being derived from low-energy conformations of molecules containing one nucleus. This suggests that folding of proteins containing preformed nuclei proceeds through interactions between the nuclei and adjacent non-regular sections of the chain rather than between nuclei. It is also observed that helices are better promoters of globularity than extended strands. These results are compared with those from recent studies of various aspects of protein folding.