We have developed a computational procedure for determining high resolution structures of large icosahedral virus particles. The thrust of the procedure is to determine accurately the centers and orientations of particles in focal-pairs of 400 kV, spot-scan micrographs by iterative common-lines-based local and global refinement. We choose shared-memory multiprocessor computers for executing the global refinement, which is the most computationally-intensive step in the reconstruction procedure. The speedup and efficiency of our parallel codes are evaluated on two different computer architectures. We show that parallel computing permits the reconstruction of large icosahedral viruses at higher resolutions than was previously practical and has allowed us to refine the 9 ? structure of herpesvirus B-capsid from hundreds of noisy, close-to-focus images. The map shows the sub-domain features of the protein subunits, which exhibit differences at quasi-equivalent positions and reveals large variations in the numbers and locations of contact points between penton/hexon subunits and their adjacent triplexes. This extensive conformational switching of proteins represents departures from the pattern predicted by the Caspar-Klug theory and presumably reflects structural compromises made to keep this large capsid stable.
| Bucero, Marta Abril; Bajaj, Chandrajit; Mourrain, Bernard (2016) On the construction of general cubature formula by flat extensions. Linear Algebra Appl 502:104-125 |
| Ebeida, Mohamed S; Rushdi, Ahmad A; Awad, Muhammad A et al. (2016) Disk Density Tuning of a Maximal Random Packing. Comput Graph Forum 35:259-269 |
| Wensel, Theodore G; Zhang, Zhixian; Anastassov, Ivan A et al. (2016) Structural and molecular bases of rod photoreceptor morphogenesis and disease. Prog Retin Eye Res 55:32-51 |
| Baker, Mariah R; Fan, Guizhen; Serysheva, Irina I (2015) Single-Particle Cryo-EM of the Ryanodine Receptor Channel in an Aqueous Environment. Eur J Transl Myol 25:4803 |
| Rushdi, Ahmad A; Mitchell, Scott A; Bajaj, Chandrajit L et al. (2015) Robust All-quad Meshing of Domains with Connected Regions. Procedia Eng 124:96-108 |
| Edwards, John; Daniel, Eric; Pascucci, Valerio et al. (2015) Approximating the Generalized Voronoi Diagram of Closely Spaced Objects. Comput Graph Forum 34:299-309 |
| Wensel, Theodore G; Gilliam, Jared C (2015) Three-dimensional architecture of murine rod cilium revealed by cryo-EM. Methods Mol Biol 1271:267-92 |
| Jeter, Cameron B; Patel, Saumil S; Morris, Jeffrey S et al. (2015) Oculomotor executive function abnormalities with increased tic severity in Tourette syndrome. J Child Psychol Psychiatry 56:193-202 |
| Zhang, Qin; Cha, Deukhyun; Bajaj, Chandrajit (2015) Quality Partitioned Meshing of Multi-Material Objects. Procedia Eng 124:187-199 |
| Baker, Mariah R; Fan, Guizhen; Serysheva, Irina I (2015) Single-particle cryo-EM of the ryanodine receptor channel in an aqueous environment. Eur J Transl Myol 25:35-48 |
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