REFINEMENT OF HERPESVIRUS B-CAPSID STRUCTURE ON PARALLEL SUPERCOMPUTERS

Electron cryomicroscopy and icosahedral reconstruction are used to obt ain the three-dimensional structure of the 1250-Angstrom-diameter herp esvirus B-capsid. The centers and orientations of particles in focal p airs of 400-kV, spot-scan micrographs are determined and iteratively r efined by common-lines-based local and global refinement procedures. W e describe the rationale behind choosing shared-memory multiprocessor computers for executing the global refinement, which is the most compu tationally intensive step in the reconstruction procedure. This refine ment has been implemented on three different shared-memory supercomput ers. The speedup and efficiency are evaluated by using test data sets with different numbers of particles and processors. Using this paralle l refinement program, we refine the herpesvirus B-capsid from 355-part icle images to 13-Angstrom resolution. The map shows new structural fe atures and interactions of the protein subunits in the three distinct morphological units: penton, hexon, and tripler of this T = 16 icosahe dral particle.