Modeling (Semi) Unstructured Proteins

By Michael Colvin

University of California - Merced

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The past century has seen tremendous progress in determining the biochemical and biophysical processes that constitute life. One exciting consequence of this understanding is the possibility of developing mathematical models of biological function that are accurate and even predictive. My research uses a wide range of simulation methods to model biological systems at different levels. Much of my research uses molecular modeling to study biochemical problems, with a particular emphasis on modeling the activity of DNA-binding food mutagens and anticancer drugs. These methods involve computing the structures and energetics of biomolecules using either quantum or classical mechanics and often requires the use of supercomputers. Other molecular modeling projects include studying synthetic analogs to nucleic acids and exotic nucleic acid structures, the function of DNA-processing multiprotein complexes and the mechanism of cytochrome P450 and other enzymes. More recently, my research interests have expanded to include simulations of biophysical and cellular processes using equations that describe the system as continuous (and sometime stochastic) dynamical systems. These projects include simulating the formation mutagenic compounds during cooking, the operation of the nuclear pore complex, and the cell fate decisions. These projects offer a wide range of research projects for students interested in the application of mathematics and computers to understand the living world.


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University of Illinois at Urbana-Champaign.

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1. Leininger, M.L., I.M.B. Nielsen, M.E. Colvin, C.L. Janssen (2002) Complete Basis Set MP2 Binding Energies for Stacked Uracil Dimers Journal of Physical Chemistry A 106: 3850-3854.
2. Grossman, J.C., M.E. Colvin, N.L. Tran, S.G. Louie, M.L. Cohen (2002) Aromaticity and Hydrogenation Patterns in Highly Strained Fullerenes. Chemical Physics Letters 356: 247-253.
3. Nguyen, D.H., M.E. Colvin, Y. Yen, R.E. Feeney, W.H. Fink, (2002) The Dynamics, Structure, and Free Energy Profile of Proline-Containing Antifreeze Glycoprotein Biophysical Journal 82: 2892-2905.
4. Sasaki, J.C., R.S. Fellers, M.E. Colvin (2002) Metabolic Oxidation of Carcinogenic Arylamines by P-450 Monooxygenases: Theoretical Support for the One Electron Transfer Mechanism Mutation Research 506-507: 79-89.
5. Venclovas, C., M.E. Colvin, M.P. Thelen, (2002) Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process Protein Science 11: 2403-2416.
6. Colvin, M.E., J.N. Quong (2002) DNA-Alkylating Events Associated with Nitrogen Mustard Based Anticancer Drugs and Metabolic Byproduct Acrolein Advances in DNA Sequence-Specific Agents Vol. 4; G.B. Jones, ed., Elsevier, New York, 29-46.
7. Mundy, C.J., M.E., Colvin, A.A. Quong, (2002) Irradiated Guanine: A Car-Parrinello molecular dynamics study of dehydrogenation in the presence of an OH radical Journal Physical Chemistry A 106: 10063-10071.
8. Wheelock, C.E., M.E. Colvin, I. Uemura, M.M. Olmstead, J.R. Sanborn, Y. Nakagawa, B.D. Hammock (2002) Use of ab initio calculations to predict the biological potency of carboxylesterase inhibitors. Journal of Medicinal Chemistry 45: 5576-5593.
9. Tran, N.L., M. Colvin, S. Gronert, and W. Wu (2003) Catalysis of decarboxylation by an adjacent negative charge: a theoretical approach. Bioorganic Chemistry 31: 271-277.
10. M.D. Winthrop, S.J. DeNardo, H. Albrecht, G.R. Mirick, L.A. Kroger, K.R. Lamborn, C. Venclovas, M.E. Colvin, P.A. Burke, G.L. DeNardo (2003) Selection and Characterization of Anti-MUC-1 scFvs Intended for Targeted Therapy Clinical Cancer Research 9: 3845sE853s.
11. J.R. Keefe, S. Gronert, M.E. Colvin, N.L. Tran (2003) Identity Proton Transfer Reactions from C-H, N-H, and O-H Acids. An ab initio, DFT, and CPCM-B3LYP Aqueous Solvent Model Study Journal of the American Chemical Society 125: 11730-11745.
12. D.H. Nguyen, T. Dieckmann, M.E. Colvin and W.H. Fink (2004) Dynamics Studies of a Malachite Green-RNA Complex Revealing the Origin of the Red-Shift and Energetic Contributions of Stacking Interactions Journal of Physical Chemistry B 108: 1279-1286.
13. Y. Wu, C.J. Mundy, M.E. Colvin and R. Car (2004) On the mechanisms of OH radical induced DNA base damage: A comparative quantum chemical and Car-Parrinello molecular dynamics study Journal of Physical Chemistry A 108: 2922-2929.
14. J.S. Felton, M.G. Knize, L.M. Bennett, M.A. Malfatti, M.E. Colvin, K.S. Kulp (2004) Impact of environmental exposures on the mutagenicity/carcinogenicity of heterocyclic amines Toxicology 198: 135-145.
15. D.H. Nguyen, M.E. Colvin, Y.Yeh, R.E. Feeney, and W.H. Fink (2004) Intermolecular Interaction Studies of Winter Flounder Antifreeze Protein Revealing the Existence of Thermally Accessible Binding State Biopolymers 75: 109-117.
16. J.B. Springer, Y.H. Chang, K.I. Koo, O.M. Colvin, M.E. Colvin, M.E. Dolan, S.M. Delaney, J.L. Flowers, S.M. Ludeman (2004) 1,3- versus 1,5-Intramolecular Alkylation Reactions in Isophosphoramide and Phosphoramide Mustards Chemical Research in Toxicology 17: 1217-1226.
17. E.Y. Lau, F.C. Lightstone, and M.E. Colvin (2005) Dynamics of DNA Encapsulated in a Hydrophobic Nanotube Chemical Physics Letters (in press).
18. T.A. Sulchek, R.W. Friddle, K. Langry, E.Y. Lau, H. Albrecht, T.V. Ratto, S.J. DeNardo, M.E. Colvin, and A. Noy (2005) Dynamic force spectroscopy of parallel individual Mucin1–antibody bonds Proceedings of the National Academy of Sciences (in press).
19. M.G. Knize, F.T. Hatch, M.J. Tanga, E.Y. Lau, and M.E.Colvin (2005) A QSAR for the Mutagenic Potencies of Twelve 2-Amino-trimethylimidazopyridine Isomers: Structural, QuantumChemical, and Hydropathic Factors Environmental and Molecular Mutagenesis (in press).

Cite this work

Researchers should cite this work as follows:

  • Nano-Bio Workshop and nanoHUB Summer School,
    NCSA, University of Illinois at Urbana-Champaign, July 30-31, 2007
  • Michael Colvin (2008), "Modeling (Semi) Unstructured Proteins,"

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NCSA, University of Illinois at Urbana-Champaign, IL