Orientation determination in the 3D reconstruction of icosahedral viruses using a parallel computer

ABSTRACT

Three dimensional image reconstruction from cryo-electron micrographs allows the capsid structures of icosahedral viruses to be studied. The most computationally demanding stages of the reconstruction process are those that find and refine the orientations of the virus particles. We have devised and implemented parallel solutions to the problem of determining these orientations. By enabling determination of the orientations of far more particles than previously had been possible, parallel processing methods have contributed to improvements in the quality of recent reconstructions.

REFERENCES

• 1: Baker, T.S., Newcomb, W.W., Booy, F.P., Brown, J.C., and Steven, A.C., "Three-dimensional structures of maturable and abortive capsids of equine herpesvirus 1 from cryo-electron microscopy," J. Virology64, 563-573 (1990).
• 2: Baker, T.S., Drak, J., and Bina, M., "Reconstruction of the three-dimensional structure of simian virus 40 and visualization of the chromatin core," Proc. Natl. Acad. Sci. USA85, 422-426 (1988).
• 3: Baker, T.S., Drak, J., and Bina, M., "The capsid of small papova viruses contains 72 pentameric capsomers: direct evidence from cryo-electron microscopy of simian virus 40," Biophys. J.55, 243-253 (1989).
• 4: Booy, F.P., Trus, B.L., Newcomb, W.W., Brown, J.C., Conway, J.F., and Steven, A.C., "Finding a needle in a haystack: detection of a small protein (the 12 FDa VP26) in a large complex (the 200 MDa capsid of herpes simplex virus), Proc. Natl. Acad. Sci. USA91: 5652-5656 (1994).
• 5: Booy, F.P., Newcomb, W.W., Trus, B.L., Brown, J.C., Baker, T.S., and Steven, A.C., "Liquid-crystalline, phage-like packaging of encapsidated DNA in herpes simplex virus," Cell64, 1007-1015 (1991).
• 6: Conway, J.F., Trus, B.L., Booy, F.P., Newcomb, W.W., Brown, J.C., and Steven, A.C., "The effects of radiation damage on the structure of frozen hydrated HSV1 capsids," J. Struct. Biol.111: 222-233 (1993).
• 7: Crowther, R.A., "Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs," Phil. Trans. Roy. Soc. Lond. B.261, 221-230 (1971).
• 8: Crowther, R.A., "The reconstruction of a three-dimensional structure from projections and its application to electron microscopy," Proc. Roy. Soc. Lond. A.317, 319-340 (1970).
• 9: Crowther, R.A., Amos, L.A., Finch, J.T., DeRosier, D.J., and Klug, A., "Three dimensional reconstructions of spherical viruses by Fourier synthesis from electron micrographs," Nature226, 421-425 (1970).
• 10: Fuller, S.D., "The T=4 envelope of Sinbis virus is organized by interactions with a complementary T=3 capsid," Cell48, 923-934 (1987).
• 11: Martino, R.L., Johnson, C.A., Yap, T.K., Suh, E.B., Pfeifer, J.C., Hodoscek, M., and Brooks, B.R., "Highly parallel computing at the National Institutes of Health," Supercomputing USA/Pacific 91 Conference, 110-111 (1991).
• 12: Nelder, J.A., and Mead, R., "A simplex method for function minimization," Computer Journal 7, 308-313 (1965).
• 13: Newcomb, W.W., Trus, B.L., Booy, F.P., Steven, A.C., Wall, J.S., and Brown, J.C., "Structure of herpes simplex virus capsid: molecular composition of the pentons and the triplexes," J. Mol. Biol.232, 499-511 (1993).
• 14: Saxton, W.O., and Baumeister, W., "The correlation averaging of a regularly arranged bacterial cell envelope protein," J. Microscopy127, part 2, 127-138 (1982).
• 15: Trus, B.L., Newcomb, W.W., Booy, F.P., Brown, J.C., and Steven, A.C., "Distinct monoclonal antibodies separately label the hexons or the pentons of herpes simplex virus capsid," Proc. Natl. Acad. Sci. USA89, 11508-11512 (1992).
• 16: Trus, B.L. and Steven, A.C., "Digital image processing of electron micrographs - the PIC System," Ultramicroscopy6, 383-386 (1981).