title: Refinement of herpesvirus B-capsid structure on parallel supercomputers.
abstract: Electron cryomicroscopy and icosahedral reconstruction are used to obtain the three-dimensional structure of the 1250-A-diameter herpesvirus B-capsid. The centers and orientations of particles in focal pairs of 400-kV, spot-scan micrographs are determined and iteratively refined by common-lines-based local and global refinement procedures. We describe the rationale behind choosing shared-memory multiprocessor computers for executing the global refinement, which is the most computationally intensive step in the reconstruction procedure. This refinement has been implemented on three different shared-memory supercomputers. The speedup and efficiency are evaluated by using test data sets with different numbers of particles and processors. Using this parallel refinement program, we refine the herpesvirus B-capsid from 355-particle images to 13-A resolution. The map shows new structural features and interactions of the protein subunits in the three distinct morphological units: penton, hexon, and triplex of this T = 16 icosahedral particle.
authors.affiliation: Texas Center for Advanced Molecular Computation, University of Houston, 77204-3476, USA.
authors.forename: Z H
authors.initials: ZH
authors.lastname: Zhou
authors.forename: W
authors.initials: W
authors.lastname: Chiu
authors.forename: K
authors.initials: K
authors.lastname: Haskell
authors.forename: H
authors.initials: H
authors.lastname: Spears
authors.forename: J
authors.initials: J
authors.lastname: Jakana
authors.forename: F J
authors.initials: FJ
authors.lastname: Rixon
authors.forename: L R
authors.initials: LR
authors.lastname: Scott
mesh_terms: D002213:Capsid / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D005615:Freezing; D008854:Microscopy, Electron; D008958:Models, Molecular; D011487:Protein Conformation; D018139:Simplexvirus / Q000737:chemistry* / Q000648:ultrastructure