A DESCRIPTIVE ANALYSIS OF POPULATIONS OF 3-DIMENSIONAL STRUCTURES CALCULATED FROM PRIMARY SEQUENCES OF PROTEINS BY OSIRIS

Among different ab initio approaches to calculate 3D-structures of pro teins out of primary sequences, a few are using restricted dihedral sp aces and empirical equations of energy as is OSIRIS. All those approac hes were calibrated on a few proteins or fragments of proteins. To opt imize the calculation over a larger diversity of structures, we need f irst to define for each sequence what are good conditions of calculati ons in order to choose a consensus procedure fitting most 3D-structure s best. This requires objective classification of calculated 3D-struct ures. In this work, populations of avian and bovine pancreatic polypep tides (APP, BPP) and of calcium-binding protein (CaBP) are obtained by varying the rate of the angular dynamics of the second step of OSIRIS . Then, 3D-structures are clustered using a nonhierarchical method, SI CLA, using rmsd as a distance parameter. A good clustering was obtaine d for four subpopulations of APP, BPP and CaBP. Each subpopulation was characterized by its barycenter, relative frequency and dispersion. F or the three alpha-helix proteins, after the step I of OSIRIS, most se condary structures were correct but molecules have a few atomic contac ts. Step 2, i.e., the angular dynamics, resolves those atomic contacts and clustering demonstrates that it generates subpopulations of topol ogical conformers as the barycenter topologies show.