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Monte Pettitt University of Houston Department: Chemistry, Computer Science, Physics, Biology and Biochemistry Address: Fleming Bldg. Rm. 232 4800 Calhoun Houston TX 77204-5003 Phone: 713-743-2709 Fax: 713-743-2709 Email: pettitt@uh.edu Web:

Education

B.S. Chemistry, University of Houston (1975); B.S. Mathematics, University of Houston (1975)
Ph.D. Theoretical Chemistry, University of Houston (1980)
Post Doc in Theoretical Chemistry, UT Austin (1980-82); NIH Post Doc, Harvard, (1983-85)

Honors

Alfred P. Sloan Fellow 1989-1993
Teaching Excellence Award, University of Houston 1992
Fellow of the American Physical Society, 1993
Alumni Outstanding Faculty Award, University of Houston 1999
Distinguished Alumni Award, University of Houston 2000
Robert A. Welch Lecturer in Chemistry, 2001
American Chemical Society Local Section Award 2002
ALA achievement award 2003
AAAS Fellow 2008

Research Topic

Development of methods for calculating structure and conformational equilibria of biomolecules in aqueous environments.

Research Description

The solution environment as well as the sequence are known to determine the conformation, kinetic and thermodynamic behavior of polymers. It is widely appreciated for biopolymers that biological activity is usually found within a narrow range of solvent and salt concentration. Formulating hypotheses to explain this sensitivity is a unifying goal for the studies in the laboratory. The physical sensitivity is also reflected in a parameter sensitivity in theories and simulations of these systems which must be accounted for in any physical interpretations. Projects in this laboratory bring theoretical and calculational approaches to bear to an array of problems.
An area of considerable interest to us is how the presence of a surface, either, dielectric or metallic, affects the binding affinities between targets and probes. This is an important problem for optimizing DNA chips and Protein-chips. We have both theoretical and computational work which shows how one can optimize such surface effects to gain the most sensitivity in a DNA analysis.

1) Development of methods for calculating structure and conformational equilibria of biomolecules in aqueous environments.
(2) Stability and thermodynamics of DNA/RNA structures in solution and on surfaces both dielectric and metallic.

(3) Peptide/Protein folding via solution stability criteria. Theory of biomolecular solutions.

(4) Structural and thermodynamic description of molecular fluids, including water, ions, and biomolecular solutes .

(5) Development of theoretical techniques for the description of the thermodynamics and structure of biomolecules as anisotropic fluids.

(6) Development of computer simulation methodology for biotechnology.

Selected Publications

• Makarov, V., Feig, M., Andrews, K.A. and Pettitt, B.M. (1998). Diffusion of Solvent around Biomolecular Solutes: a Molecular Dynamics Simulation Study. Biophys. J. 75: 1.
• Feig, M. and Pettitt, B.M. (1998). Crystallographic Water Sites from a Theoretical Perspective. Structure 6: 1351.
• Feig, M. and Pettitt, B.M. (1999). Modeling Consistent with Experiment: High Resolution Hydration patterns in Correlation with DNA Sequence and Conformation. J. Mol. Biol. 286: 1075.
• M. Feig, M. Abdullah, L. Johnsson, and B. M. Pettitt. (1999). Large Scale Distributed Data Repository: Design of a Molecular Dynamics Trajectory Database. Future Generation Computer Systems 16: 101.
• Feig, M. and Pettitt, B.M. (2000). A Molecular Simulation Picture of DNA Hydration around A- and B-DNA. Biopolymers 48: 199.
• Vainrub, A. and Pettitt, B.M. (2003). Sensitive quantitative nucleic acid detection using oligonucleotide microarrays. J. Am. Chem. Soc. 125: 7798-7799.
• Vainrub, A. and Pettitt, B.M. (2003). Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics. Biopolymers 68: 265-270.
• Marlow, G.E. and Pettitt, B.M. (2003). Simulation of the bis-(penicillamine) enkephalin in ammonium chloride solution: a comparison with sodium chloride. Biopolymers 68: 192-209.
• "The Melting Pathway for oligomeric DNA via molecular dynamics simulation", Bio- phys. J. 95 5618-5626 (2008); Ka-Yiu Wong, and B.M. Pettitt.
• "An Integral Equation Study of the Hydrophobic Interaction between Graphene Plates" J. Chem. Theory Comp. 4 1928-1939 (2008); Jesse Howard, John Perkyns, Niharendu Choudhury, B.M. Pettitt.
• "Advantage of Being a Dimer for Serratia marcescens Endonuclease" J. Phys. Chem. B 113 511-521 (2009); Chuanying Chen, Kurt Krause, and B.M. Pettitt.
• "Osmolyte solutions and protein folding" F1000 Biology Reports, 1:41 2009; C.Y. Hu, B.M. Pettitt and J. Roesgen
• "Salt Effects on Surface Tethered Peptides in Solution", J. Phys. Chem. 113 (28), 94729478(2009); Jun Feng, Ka-Yiu Wong, Gillian Lynch, Xiaolian Gao, B.M. Pettitt.
• "Osmolyte influence on protein stability: perspectives from theory and experiments", in Modeling of Solvent Environments, ed. M. Feig (2009), J Wiley, NY NY; Hu, C., J. Roesgen, and B.M. Pettitt.

Lab Members

Current Graduate Students
Current Post Docs

Lab Photos

Last edited on: September 10, 2009