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Tim Baker e-mail: tsb@chem.ucsd.edu |
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The primary thrust of our research is to image viruses and gain insights about how they interact with their hosts, replicate, and mature. We use the tools of cryo-electron microscopy (CryoEM) and three-dimensional (3D), image-reconstruction to observe viruses or virus-like particles and examine intermolecular interactions at sub-nanometer resolutions. At such resolution, it is possible to discern and distinguish viral components (protein, nucleic acid, lipid, carbohydrate) and even visualize secondary structural details such as alpha-helices and beta-sheets in proteins. Viruses currently under investigation include bacteriophages phi-29 and P22; gemini viruses, several partitiviruses, parvoviruses (human bocavirus and several serotypes of adeno-associated viruses both as native virions and complexed with neutralizing antibodies and receptor molecules), reoviruses, a tetravirus, two distinct totiviruses, and several, large dsDNA viruses that infect algae and insects; and a family of small, enveloped, ssRNA viruses that include members that are serious human pathogens and have been listed as possible agents of bio-terrorism.
Samples for CryoEM are flash frozen so quickly that they are preserved in a thin layer of non-crystalline ice. They are maintained in this state in the transmission electron microscope, which is cooled to either liquid nitrogen or liquid helium temperatures. Two state-of-the-art, computer-controlled microscopes are available for this work. They greatly assist the researcher in collecting the tens of thousands of virus images that are often required to obtain high-resolution 3D reconstructions.
Computer reconstruction techniques are continuously being developed to more effectively and efficiently extract usable information from the noisy image data. With help from San Diego Supercomputer Center staff, we have developed a new system (AUTO3DEM) that automates much of the tedious steps in the 3D reconstruction process. We often are now able to obtain reconstructions at sub-nanometer resolution in a few days or less after the images are recorded.
Ochoa, W. F., W. M. Havens, R. S. Sinkovits, M. L. Nibert, S. A. Ghabrial, and T. S. Baker (2008). Partitivirus Structure Reveals a 120-Subunit, Helix-Rich Capsid with Distinctive Surface Arches Formed by Quasisymmetric Coat-Protein Dimers. Structure 16(5):776-786.
Tang, J., W. F. Ochoa, R. S. Sinkovits, B. T. Poulos, S. A. Ghabrial, D. V. Lightner, T. S. Baker, and M. L. Nibert (2008). Infectious myonecrosis virus has a totivirus-like, 120-subunit capsid, but with fiber complexes at the fivefold axes. Proc. Natl. Acad. Sci. USA 105:17526–17531.
Tang, J., N. Olson, P. J. Jardine, S. Grimes, D. L. Anderson, and T. S. Baker (2008). DNA Poised for Release in Bacteriophage phi-29. Structure 16(6):935-943.
Ghabrial, S. A., W. F. Ochoa, T. S. Baker, and M. L. Nibert (2008). Partitiviruses: General features. 3rd ed. In Encyclopedia of Virology (Mahy, B. W. J., and M. H. V. Van Regenmortel, Eds.), Vol. 4, pp. 68-75. 5 vols. Elsevier, Oxford.
Yan, X., Z. Yu, P Zhang, A. J. Battisti, H. A. Holdaway, P. R. Chipman, C. Bajaj, M. Bergoin, M. G. Rossmann and T. S. Baker (2008). The capsid proteins of a large icosahedral dsDNA virus. J. Mol. Biol. In press.
Yan, X., R. S. Sinkovits, and T. S. Baker (2007). AUTO3DEM--an automated and high throughput program for image reconstruction of icosahedral particles. J. Struct. Bio. 157(1):73-82.
Yan X., K. A. Dryden, J. Tang, and T. S. Baker (2007) Ab initio random model method facilitates 3D reconstruction of icosahedral particles. J. Struct. Bio. 157:211-225.
Tim Baker received his Ph.D. from UCLA and was a Jane Coffin Childs postdoctoral fellow at Cambridge University, a NIH Postdoctoral Fellow and the Charles A. King Trust Postdoctoral Fellow at Brandeis University. From 1983-2004, he was on the Faculty of Purdue University where he earned the Herbert Newby McCoy Award for Scientific Achievement and a NIH NIGMS MERIT award. He received a joint faculty appointment in Biological Sciences and Chemistry & Biochemistry at UCSD in 2004.