Issue No. 04 - October-December (2008 vol. 5)
Zeyun Yu , IEEE
Chandrajit Bajaj , IEEE
We present computational solutions to two problemsof macromolecular structure interpretation from reconstructedthree-dimensional electron microscopy (3D-EM) maps of largebio-molecular complexes at intermediate resolution (5A-15A). Thetwo problems addressed are: (a) 3D structural alignment (matching)between identified and segmented 3D maps of structure units(e.g. trimeric configuration of proteins), and (b) the secondarystructure identification of a segmented protein 3D map (i.e.locations of a-helices, b -sheets). For problem (a), we presentan efficient algorithm to correlate spatially (and structurally)two 3D maps of structure units. Besides providing a similarityscore between structure units, the algorithm yields an effectivetechnique for resolution refinement of repeated structure units,by 3D alignment and averaging. For problem (b), we present anefficient algorithm to compute eigenvalues and link eigenvectorsof a Gaussian convoluted structure tensor derived from theprotein 3D Map, thereby identifying and locating secondarystructural motifs of proteins. The efficiency and performanceof our approach is demonstrated on several experimentallyreconstructed 3D maps of virus capsid shells from single-particlecryo-EM, as well as computationally simulated protein structuredensity 3D maps generated from protein model entries in theProtein Data Bank.
Structure Analysis, Alignment, Similarity Measure, Segmentation, Secondary Structure Detection, Skeletonization, Cryo-EM Maps, 3D Reconstruction
Z. Yu and C. Bajaj, "Computational Approaches for Automatic Structural Analysis of Large Biomolecular Complexes," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. , pp. 568-582, 2007.