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Refinement of herpesvirus B-capsid structure on parallel supercomputers.

Z H Zhou·W Chiu·K Haskell·H Spears·J Jakana·F J Rixon·L R Scott
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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.

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CapsidComputer SimulationFreezingMicroscopy, ElectronModels, MolecularProtein ConformationSimplexvirusJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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Z H Zhou, W Chiu, K Haskell, H Spears, J Jakana, F J Rixon, L R Scott. 1998. Refinement of herpesvirus B-capsid structure on parallel supercomputers.. https://doi.org/10.1016/s0006-3495(98)77816-6

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