Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach.
Non-crystallographic symmetry (NCS) averaging is a well known method for improving the quality of an electron-density map and thus aiding structure determination. Prior methods of NCS-operator determination based on estimated heavy-atom positions are prone to errors arising from inaccuracies in these coordinates or differences in the relative orientations of domains between molecules. In this paper, two real-space methods to determine NCS relationships from initial electron-density maps are presented. A brute-force method identifies matching regions in a map by local density correlation. A feature-based algorithm uses rotation-invariant features to reduce the computational time taken by the brute-force algorithm by filtering out regions that are likely to have dissimilar density patterns. This makes the feature-based algorithm faster and as accurate as the brute-force approach. Neither method requires the positions of heavy atoms or any information regarding the protein sequence. Both methods have been tested on a diverse range of experimentally phased maps and the correct NCS relationships were accurately identified for almost all of the test cases. The NCS operators obtained by the feature-based algorithm were used to perform NCS averaging and an improvement in map correlation was observed for some cases.
Pai
Reetal
R
Department of Computer Science, Texas A and M University, TX, USA. reetalp@cs.tamu.edu
Sacchettini
James
J
Ioerger
Thomas
T
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D004583:Electrons; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009169:Mycobacterium tuberculosis / Q000201:enzymology; D010363:Pattern Recognition, Automated; D050543:Phosphoglycerate Dehydrogenase / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D015203:Reproducibility of Results
D011506:Proteins; D050543:Phosphoglycerate Dehydrogenase