title: Torsion angle differences as a means of pinpointing local polypeptide chain trajectory changes for identical proteins in different conformational states.
abstract: We discuss a facile and sensitive method of determining conformational differences based on the changes in the phi and psi angle values between chemically identical proteins in different conformations. It complements the conventional r.m.s. deviation technique, but offers some advantages. Two classes of conformational difference can be distinguished by this method: (i) abrupt local trajectory deformations where the chains flanking the locus of deformation remain simultaneously superposable and (ii) localized 'hinge bending' that generates domain shifts, thereby causing only one domain to be superposable on the other at one time. In the second case, the r.m.s. deviation method requires two or more calculations of r.m.s. deviation as a function of sequence after optimal alignment of each domain to demonstrate the superposability of the shifted domains, and hence the conservation of internal domain structure. On the other hand, the method of plotting delta phi and/or delta psi as a function of sequence demonstrates in one graph the superposability of shifted domains, without the prior need to perform rotational and translational alignments whose outcomes vary with the subjective choice of alignment parameters. Also, an analysis of the r.m.s. deviation in C alpha alone will miss torsion angle rotations that happen to preserve C alpha positions. The method pinpoints residues contributing singly to localized, major movements of a conformational change; however, it is insensitive to conformational changes achieved through small, concerted movements spread over a number of residues.(ABSTRACT TRUNCATED AT 250 WORDS)
authors: Department of Medical Biophysics/Ontario Cancer Institute, University of Toronto, Canada.
authors: A P
authors: AP
authors: Korn
authors: D R
authors: DR
authors: Rose
mesh_terms: D000942:Antigens, Bacterial / Q000276:immunology; D003198:Computer Simulation; D004247:DNA / Q000276:immunology; D016333:HIV Protease / Q000737:chemistry; D006454:Hemoglobins / Q000737:chemistry; D006801:Humans; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry; D007074:Immunoglobulin G / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D009844:Oligosaccharides / Q000276:immunology; D011487:Protein Conformation; D012475:Salmonella / Q000276:immunology
chemical_list: D000942:Antigens, Bacterial; D006454:Hemoglobins; D007140:Immunoglobulin Fab Fragments; D007074:Immunoglobulin G; D008024:Ligands; D009844:Oligosaccharides; D004247:DNA; D016333:HIV Protease