Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins.
A novel approach for analyzing multiple protein structures is presented. A family of related protein structures may be characterized by an affine model, obtained by applying transformation matrices that permit both rotation and shear. The affine model and transformation matrices can be computed efficiently using a single eigen-decomposition. A novel method for finding correspondences is also introduced. This method matches curvatures along the protein backbone. The algorithm is applied to analyze a set of seven globin structures. Our method identifies 100 corresponding landmarks across all seven structures. Results show that most helices in globins can be identified by high curvature, with the exception of the C and D helices. Analysis of the superposition reveals that globins are most strongly conserved structurally in the mid-regions of the E and G helices.
Wu
T D
TD
Department of Biochemistry, Stanford University, CA 94305, USA.
Schmidler
S C
SC
Hastie
T
T
Brutlag
D L
DL
D000465:Algorithms; D000595:Amino Acid Sequence; D003196:Computer Graphics; D003198:Computer Simulation; D017124:Conserved Sequence; D005914:Globins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012984:Software
D005914:Globins