REDUCED MOLECULAR REPRESENTATIONS AND THEIR ROLE IN PROTEIN-STRUCTUREPREDICTION

The technique of nonlinear mapping is shown to permit two-dimensional representations of protein structure. The resulting diagrams retain di stance geometry information to a distance matrix root mean square (dmr ms) accuracy of about 3.0 Angstrom, and in a striking manner maintain the fold and secondary structural features of the three-dimensional en tity. By assuming a consistent carbon alpha to carbon alpha distance, we make a further reduction to a one-dimensional angle plot which itse lf retains distance relationships to an accuracy not appreciably worse than the two-dimensional plot. It is possible to go from one dimensio n to two, and hence to three without complications arising from chiral ity by using a sign convention and inspecting the overall three-dimens ional structure which may need inverting. There are numerous possible applications of this approach but the hope is that it will provide a b asis for going from a one-dimensional gene sequence to a tertiary prot ein structure. (C) 1997 Elsevier Science B.V.