PATTERN-RECOGNITION AND SELF-CORRECTING DISTANCE GEOMETRY CALCULATIONS APPLIED TO MYOHEMERYTHRIN

A topological list, consisting of segments of regular secondary struct ures and a list of buried and solvent accessible residues, is automati cally predicted from multiple aligned sequences in a protein family. T his topological list is translated into geometric constraints for dist ance geometry calculation in torsion angle space. Anew self-correcting distance geometry method detects and eliminates false distance constr aints. In an application to the four-helix bundle protein, myohem-eryt hrin, the right-handed global fold was correctly reproduced with a roo t-mean-square deviation of 2.6 Angstrom, when the topological list was derived from the X-ray structure. A predicted topological list, coupl ed with constraints from the residues in the active site of myohemeryt hrin, predicted the correct fold with a root-mean-square deviation of 4 Angstrom for backbone atoms.