A descriptive analysis of populations of three-dimensional structures calculated from primary sequences of proteins by OSIRIS.
Among different ab initio approaches to calculate 3D-structures of proteins out of primary sequences, a few are using restricted dihedral spaces and empirical equations of energy as is OSIRIS. All those approaches were calibrated on a few proteins or fragments of proteins. To optimize the calculation over a larger diversity of structures, we need first to define for each sequence what are good conditions of calculations in order to choose a consensus procedure fitting most 3D-structures best. This requires objective classification of calculated 3D-structures. In this work, populations of avian and bovine pancreatic polypeptides (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, SICLA, using rmsd as a distance parameter. A good clustering was obtained for four subpopulations of APP, BPP and CaBP. Each subpopulation was characterized by its barycenter, relative frequency and dispersion. For the three alpha-helix proteins, after the step 1 of OSIRIS, most secondary structures were correct but molecules have a few atomic contacts. Step 2, i.e., the angular dynamics, resolves those atomic contacts and clustering demonstrates that it generates subpopulations of topological conformers as the barycenter topologies show.
INSERM U10, Hôp. C. Bernard-X. Bichat, Paris, France. benhabil@infobiogen.fr
N
N
Benhabilès
X
X
Gallet
A
A
Thomas-Soumarmon
R
R
Brasseur
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001717:Birds; D002135:Calcium-Binding Proteins / Q000737:chemistry; D002417:Cattle; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010191:Pancreatic Polypeptide / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
D002135:Calcium-Binding Proteins; D011506:Proteins; D010191:Pancreatic Polypeptide