Mt. O saddle
  • Adjunct Professor, Biomedical Engineering
  • Professor, Medicinal Chemistry

Research Statement

Use and development of biomolecular simulation and computational chemistry methods applied to therapeutic design, delivery and disposition. A key focus is on simulation of nucleic acids, both DNA and RNA, including drug interaction, force field development and structure/dynamics.

Grants, Contracts & Research Gifts

  • Biomolecular simulation for the end-stage refinement of nucleic acids. PI: Cheatham. NIH, 02/01/2009 - 01/31/2013. Total project budget to date: $0.00
  • AMBER force field consortium. PI: Duan (UC Davis). Co-PI(s): Cheatham, Simmerling, Cieplak, Luo, Wang. NIH, 09/27/2008 - 08/31/2012. Total project budget to date: $0.00
  • Insight into biomolecular structure, dynamics and energetics from simulation. PI: Cheatham. NSF TRAC, 07/01/2002 - present. Total project budget to date: $0.00

Languages

  • English, fluent.

Publications

  • P Banas, D Hollas, M Zgarbova, P Jurecka, M Orozco, TE Cheatham, III, J Sponer, and M Otyepka. “Performance of molecular mechanics force fields for RNA simulations. Stability of UUCG and GNRA hairpins.” J. Chem. Theory Comp. 6, 3836-3849 (2010). Published, 10/2010.
  • CD Moore, K Shahrokh, SF Sontum, TE Cheatham, III and GS Yost "Improved Cyp3A4 molecular models accurately predict Phe215 requirement for raloxifene dehydrogentation selectivity.” Biochemistry 49, 9011-9019 (2010). Published, 09/2010.
  • KF Wong, JL Sonnerberg, F Paesani, T Yamamoto, J Vanicek, J Zhang, HB Schlegl, DA Case, TE Cheatham, III, WH Miller, and GA Voth. “Proton transfer studied using a combined ab initio reactive potential energy surface with quantum path integral methodology.” J. Chem. Theory Comp. 6, 2566-2580 (2010). Published, 09/2010.
  • R.B. Paulsen, P.P. Seth, E.E. Swayze, R.H. Griffey, J.J. Skalicky, T.E. Cheatham, III and D.R. Davis "Inhibitor induced structural change in the HCV IRES domain IIa RNA" PNAS 107, 7263-7268 (2010). Published, 04/01/2010.
  • T. Truong, H. Freedman, L. Le, T.E. Cheatham, III, J. Tuszynski, and L. Huynh. “Explicitly-solvated ligand contribution to continuum solvation models for binding free energies: Selectivity of theophylline binding to an RNA aptamer.” J. Phys. Chem. B 114, 2227-2237 (2010). Published, 01/01/2010.
  • R. Lavery, K. Zakrzewska, D.L. Beveridge, T.C. Bishop, D.A. Case, T.E. Cheatham, III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Spackova, and J. Sponer. “A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA”. Nuc. Acids Res. 38, 299-313 (2010). PMCID: 2800215. Published, 01/01/2010.
  • H. Wang, T.E. Cheatham III, P.M. Gannett, and J. Lewis "Differential electronic states observed during the A-B DNA duplex conformational transitions" Soft Matter 5, 685-690 (2009). Published, 01/01/2009.
  • T.S. Han, M.-M. Zhang, A. Walewska, P. Gruszczynski, T.E. Cheatham III, D. Yoshikami, B.M. Olivera, G. Bulaj "Structurally minimized disulfide-deficient mu-conotoxin analogs as sodium channel blockers: Implications for designing conopeptide-based therapeutics" ChemPhysChem 4, 406-414 (2009). Published, 01/01/2009.
  • S.S. Pendley, Y.B. Yu, and T.E. Cheatham III "Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coil proteins". Proteins 74, 612-629 (2009). Published, 01/01/2009.
  • In Suk Joung, Ö Persil Çetinkol, N. V. Hud, and T.E. Cheatham, III. “Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A•A base pairing and a putative structure of the coralyne-induced homo-adenine duplex.” Nuc. Acids Res. 37, 7715-7727 (2009). PMCID: 2794157. Published, 01/01/2009.
  • In Suk Joung, and T.E. Cheatham, III. “Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model specific ion parameters.” J. Phys. Chem. B 113, 13279-13290 (2009). PMCID: 2755304. Published, 01/01/2009.
  • E. Fadrna, N. Spackova, J. Sarzynska, J. Koca, M. Orozco, T.E. Cheatham, III, T. Kulinski, J. Sponer. “Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force field” J. Chem. Theory Comp. 5, 2514-2530 (2009). Published, 01/01/2009.
  • I.S. Joung and T.E. Cheatham III "Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations" J. Phys. Chem. B 112, 9020-9041 (2008). Published, 07/02/2008.
  • D. Svozil, J.E. Sponer, I. Marchan, A. Perez, T.E. Cheatham III, J. Luque, M. Orozco, and J. Sponer "Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids" J. Phys. Chem. B 112, 8188-8197 (2008). Published, 06/18/2008.