Abhinav Kumar, Ph.D.

University of Washington
Dept. of Biomolecular Structure
Health Sciences Center, K-428
Box 357742, Seattle, WA-98195

Phone: (206) 685 7047
Fax: (206) 685 7002
akumar@u.washington.edu

Education	Doctor of Philosophy in Structural Biology Department of Biological Sciences Purdue University, West Lafayette, IN December, 1997 Master of Science in Physics Indian Institute of Technology, Kanpur, India May, 1989 Bachelor of Science in Physics St. Stephen's College, Delhi University, India July, 1987
Employment Experiences	Mar 1998 - present: Associate in the laboratory of Prof. Wim G.J. Hol, at HHMI, Biomolecular Structure Center, University of Washington, Seattle, WA. Oct 1997 - Mar 1998: Research Associate in the laboratory of Prof. John E. Johnson at The Scripps Research Institute, La Jolla, CA 1992 - 1997: Teaching and Research Assistant in Department of Biological Sciences, Purdue University, W. Lafayette, IN, and The Scripps Research Institute, La Jolla, CA 1989 - 1992: Lecturer in Physics at Delhi University, India. Responsibility: teaching undergraduate courses in physics.
Qualifications	Have been trained in X-ray crystallography, Electron Microscopy, Structural Biology, Virology and various aspects of Biochemistry and Molecular Biology. Molecular Biology and Biochemistry Experience in many aspects of Molecular Biology and Protein Chemistry including cloning/subcloning and insertion of genes into vectors, design and construction of synthetic genes and subsequent insertion into vectors, overexpression of foreign genes in E. coli. (including techniques to induce expression of soluble proteins), purification of soluble and insoluble proteins (including refolding) by batch methods, affinity-tagging, chromatography, electrophoresis etc., biophysical characterization with techniques like gel electrophoresis including native, IEF and SDS PAGE, CD spectroscopy, Dynamic Light Scattering, and chromatographic methods including gel filtration. Crystallography and Electron Microscopy Extensive training in protein crystallography with experience in most aspects of structure determination and structure analysis including crystallization, data collection and processing, structure determination by Molecular Replacement and MAD methods, model building and refinement etc. Have extensive experience and familiarity with standard program packages like CCP4, CNS/XPLOR, O, Solve, Sharp etc. Have been involved in theoretical studies in certain areas of crystallography like Phase determination in MIR cases (Kumar and Rossmann, 1996, Acta. Cryst., D 52: 518-520) and data generation using NCS operators in sparse data situations (unpublished). Have been involved in using Electron Microscopic information to generate initial low resolution phases Computation Extensive computer skill in Unix environment including shell script, awk, Perl and programming languages like FORTRAN and C. A few of the programs authored by me: MASK_OVERLAP: A program to check/edit the existence of any possible overlaps in a mask arising from NCS and/or Crystal symmetry operators. DEALPDB: A general utility program to perform a series of operations on a set of pdb coordinates in an interactive or batch mode. DEALMAP: A general utility program to perform a series of operations on a map file in an interactive or batch mode. MATRIX: A general-purpose matrix manipulation program. A small package of 2D image manipulation programs for Electron Microscopic analysis. A set of Web-based Perl programs for Molecular Biology applications.
Publications	Abhinav Kumar, Claudia Roach, Irwin S. Hirsh, Stewart Turley, Stéphane deWalque, Paul A. M. Michels, Wim G. J. Hol , "An Unexpected Extended Conformation for the Third TPR Motif of the Peroxin PEX5 from Trypanosoma brucei.", J Mol Biol., 2001 Mar 16; 307(1):271-282. Medline Link Opalka N, Tihova M, Brugidou C, Kumar A, Beachy RN, Fauquet CM, Yeager M, 2000,"Structure of native and expanded sobemoviruses by electron cryo-microscopy and image reconstruction", J Mol Biol., 303(2):197-211. Medline Link Abhinav Kumar, Arnthor Aevarsson, and Wim G.J. Hol, 1999, "Multi-Protein Assemblies with Point Group Symmetry", In Perspectives in Structural Biology, 449-466, Ed. M. Vijayan, N. Yathindra, A. S. Kolaskar, Indian Academy of Sciences and Universities Press (India) Limited. David M. Belnap, Abhinav Kumar, Jon T. Folk, Thomas J. Smith, and Timothy S. Baker, 1999, "Low-Resolution Density Maps from Atomic Models: How Stepping `Back' Can Be a Step `Forward'", Journal of Structural Biology, 125: 166-175. Medline Link JSB Link Vijay S. Reddy, Heidi A. Giesing, Ryan T. Morton, Abhinav Kumar, Carol Beth Post, Charles L. Brooks III, and John E. Johnson, 1998,"Energetics of Quasi-equivalence: Computational Analysis of Protein-Protein Interactions in Icosahedral Viruses", Biophysical Journal, 74: 546-558. Medline Link Abhinav Kumar, Vijay S. Reddy, Vidadi Yusibov, Paul R. Chipmann, Yasuo Hata, Ignacio Fita, Keiichi Fukuyama, Michael G. Rossmann, L. Sue Loesch-Fries, Timothy S. Baker and John E. Johnson, 1997, "The Structure of Alfalfa Mosaic Virus Capsid Protein Assembled as a T=1 Icosahedral Particle at 4.0 Å Resolution", J. Virology, 71: 7911-7916. Medline Link Vidadi Yusibov, Abhinav Kumar, Adam North, John E. Johnson and L. Sue Loesch-Fries, 1996, "Purification, characterization, assembly and crystallization of assembled alfalfa mosaic virus coat protein expressed in Escherichia coli.", Journal of General Virology, 77: 567-73. Medline Link Abhinav Kumar and Michael G. Rossmann, 1996, "Phase Combination",Acta. Cryst. D 52: 518-520.