A genetic algorithm for the identification of conformationally invariant regions in protein molecules.
Understanding macromolecular function often relies on the comparison of different structural models of a molecule. In such a comparative analysis, the identification of the part of the molecule that is conformationally invariant with respect to a set of conformers is a critical step, as the corresponding subset of atoms constitutes the reference for subsequent analysis for example by least-squares superposition. A method is presented that categorizes atoms in a molecule as either conformationally invariant or flexible by automatic analysis of an ensemble of conformers (e.g. crystal structures from different crystal forms or molecules related by non-crystallographic symmetry). Different levels of coordinate precision, both for different models and for individual atoms, are taken explicitly into account via a modified form of Cruickshank's DPI [Cruickshank (1999), Acta Cryst. D55, 583-601] and are propagated into error-scaled difference distance matrices [Schneider (2000), Acta Cryst. D56, 715-721]. All pairwise error-scaled difference distance matrices are then analysed simultaneously using a genetic algorithm. The algorithm has been tested on several well known examples and has been found to converge rapidly to reasonable results using a standard set of parameters. In addition to the description of the algorithm, a criterion is suggested for testing the identity of two three-dimensional models within experimental error without any explicit superposition.
Schneider
Thomas R
TR
Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany. trs@shelx.uni-ac.gwdg.de
D000465:Algorithms; D000818:Animals; D024442:Aspartate Aminotransferase, Mitochondrial / Q000737:chemistry / Q000235:genetics; D002826:Chorismate Mutase / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry / Q000235:genetics; D008957:Models, Genetic; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D019998:Racemases and Epimerases / Q000737:chemistry / Q000235:genetics; D013552:Swine; D000516:alpha-Amylases / Q000737:chemistry / Q000235:genetics
D007140:Immunoglobulin Fab Fragments; D011506:Proteins; D024442:Aspartate Aminotransferase, Mitochondrial; D000516:alpha-Amylases; D019998:Racemases and Epimerases; D002826:Chorismate Mutase