LINKSCONTACT
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Research InterestsStructural study of macromolecules (i.e., proteins and nucleic acids) using computational methods including conformational energy calculations, molecular dynamics, Monte Carlo simulations, homology modeling, and other computational techniques Developing algorithms for predicting structures of proteins and nucleic acids utilizing low-resolution structural information derived from small angle scattering, mutagenesis, chemical linking, fluorescence, and other experimental techniques Systems that we have studied include the following: Troponing I/Troponin C complex, homeodomain/DNA complex, c-AMP depenedent protein kinase regularatory/catalytic heterodimer, hemagglutinin of the influenza-B virus, thioredoxin, Fen-1/DNA complex, XPG/DNA complex, a pseudoknot motif (residues 500-545) in 16S RNA, actinomycin D/DNA hairpin, cro/DNA complex, gene V protein/DNA complex, nucleosome, Coli small ribosomal subunit, Thermophilus 70S ribosome. Selected Recent Publications:Sanbonmatsu, K. Y. and Tung, C.-S., 2006, "Large-scale simulations of the ribosome: A new landmark in computational biology." J. Physics. 46: 334-342. Sanbonmatsu, K. Y., Joseph, S. and Tung, C.-S., 2005, "Simulating movement of tRNA into the ribosome during decoding." Proc Natl Acad Sci USA, 102: 15854-15859. Henkelman, G., LaBute, M. X., Tung, C.-S., Fenimore, P. W., McMahon, B. H., 2005, "Conformational dependence of a protein kinase phosphate transfer reaction." Proc Natl Acad Sci, USA 102: 15347-15351. Tung, C.-S., Sanbonmatsu, K., 2004, "Atomic structure of the T. thermophilus 70S ribosome developed in silico." Biophys J 87: 2714-2722. Tung, C.-S., Goodman, J. L., Lu, H., Macken, C. A., 2004, "Homology model of the structure of influenza b haemagglutinin." J. General Virology 85: 3249-3259. Tung, C.-S., Joseph S., Sanbonmatsu, K., 2002, "Homology model of the Escherichia coli 30S ribosome." Nature Structural Biol 9: 750-755. Tung, C.-S., Walsh, D. A., and Trewhella, J., 2002, "Structural Modeling of the Catalytic Subunit-Regulatory Subunit Dimeric Complex of the cAMP-dependent Protein Kinase.", J Biol Chem 277: 12423-12431. Olson W. K., Bansal M., Burley S. K., Dickerson R. E., Gerstein M., Harvey S. C., Heinemann U., Neidle S., Shakked Z., Sklenar H., Suzuki M., Tung C.-S., Westhof E., Wolberger C., Berman H. M., 2001, "A standard reference frame for the description of nucleic acid base-pair geometry." J Mol Biol 313 229-237. Tung CS, Wall ME, Gallagher SC, Trehwhlla J, 2000, "A model of troponin-I in complex with troponin-C using hybrid experimental Data: The inhibitory region is a beta-hairpin." Protein Science, 9: 1312-1326. Tung CS, 1999, "Structrual study of homeodomain Protein-DNA complexes using a homology modeling approach." JBSD 17: 347- 354. Wadkins RM, Vladu B, Tung CS, 1998, "Actinomycin D binds to metastable hairpins in single-stranded DNA." Biochemistry 37: 11915-11923. Tung CS, 1997, "A computational approach to modeling nucleic acid hairpin structures." Biophysics J 72: 876-885. Carter E, Tung CS, 1996, "NAMOT2-a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures." CABIOS 12: 25-30.
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