Profile

Professor,
Department of Biochemistry and Molecular Biology

Phone: (409) 772-0723
Fax: (409) 772- 0725
Email: mpettitt@utmb.edu

1. Bacteriophages, found in bacteria-rich locations like rivers and soil, are nature's machinery for viral infection of bacteria. Their genetic material, DNA or RNA, single- or double-stranded, are carried in protein-based capsids and released into the bacteria. Understanding the biophysical basis of the biological process which transfers a viral genome to infect a cell is important to the cellular machinery and many disease related fields. Predicting the thermodynamic pressures including the osmotic pressure necessary to confine DNA in a specific volume, like a phage, is a problem with implications in genomics, nanotechnology, infection, phage therapies and therapeutic delivery. DNA, a charged elastic polymer, undergoes over 250-fold compaction when packed into a capsid overcoming an unfavorable thermodynamic barrier by using ATP. How DNA overcomes the unfavorable thermodynamic barrier to enter and pack inside a capsid depends on the interplay of many different intermolecular interactions. Combined with experimental data, coarse-grained models and multi-scale techniques are being employed to model the structure and, consequently, the thermodynamics of DNA confined by surfaces. 
2. Phase transitions in protein solutions. How and why proteins fold is a problem that has implications for protein design and therapeutics. Several groups have had some success in describing some aspects of the problem, such as folding a sequence. However, the discovery that proteins do not always necessarily fold into a single stable structure calls for a redefinition of both the folding problem itself and the mechanisms we use to describe it. We consider commonly used concepts of protein folding in relation to solubility and phase transitions in solution. The formation of many non-enveloped cellular structures are governed by the underlying rules of solubility.
3. Thermodynamics and kinetics in liquid solutions especially aqueous systems. Most difficult is the question of how multicomponent systems including crowding, cosolvents and ions affect proteins and nucleic acids in solution. Given correlations and statistical thermodynamics the relations to experimental observables on the effects ions and osmolytes have on biomacromolecules in solution should then be understandable. At the technical level we are working on activity models and diagramatic expansion.
4. Theory and computational methods to investigate solution systems with couplings and correlations at many disparate length and time scales. There are many problems for which atomic correlations do not provide a direct link to macroscopic properties. Connecting meso scale averaging procedures to the atomic and macro levels via multiscale methods is important for biological/materials applications.
   

1. “Twist-Induced Defects of the P-SSP7 Genome Revealed by Modeling Cryo-EM Density" J. Phys.Chem. B 119(15), 4937-43 (2015); Qian Wang, Christopher G. Myers, B.M. Pettitt. DOI:10.1021/acs.jpcb.5b00865
2. "Secondary analysis of the NCI-60 whole exome sequencing data indicates Propionibacterium acnes genomic material in Leukemia (RPMI-8226) and Glioblastoma (SF-295, SF-539, and SNB-1) cell lines",Plos one, 10(6), e0127799 (2015) Mark Rojas, Georgiy Golovko, Kamil Khanipov, Levent Albayrak,B.M. Pettitt, Alex Strongin, Yuriy Fofanov. PMCID: PMC4454691
3. “Force field dependent solution properties of glycine oligomers", Journal of Computational Chemistry,
   36(17), 1275-1285 (2015). Justin Drake, B.M. Pettitt. PMCID: PMC4450816 
4. “Dynamic equilibria between contact and solvent-separated states of interfacial ion pairs in protein-
   DNA complexes", J. Phys. Chem. Lett. 6, 27332737(2015); Chuanying Chen, Alexandre Esadze,
   Levani Zandarashvili, Dan Nguyen, B.M. Pettitt, and Junji Iwahara. DOI 10.1021/acs.jpclett.5b0113
5. “Examining the Assumptions Underlying Continuum-Solvent Models", J. Chem. Theo. Comp., 11,
   45934600 (2015) Robert C. Harris, B.M. Pettitt. DOI: 10.1021/acs.jctc.5b00684 
6. “DNA shape versus sequence variations in the protein binding process", Biophys. J. 110, 534544 (2016);
   Chuanying Chen, B.M. Pettitt. 
7. “Protein Collapse Driven Against Solvation Free Energy, Without H-bonds, Protein Science 25, 103110
   (2016); Deepti Karandur, Robert C. Harris and B.M. Pettitt. 
8. ”Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-
   Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide" J. Phys. Chem. B, 120 69-76
   (2016); Dheeraj Tomar, Valery Weber, B.M. Pettitt, Dilipkumar Asthagiri. 
9. “Sequence Affects the Cyclization of DNA minicircles", J. Phys. Chem. Lett. 7, 10421046 (2016); Qian
   Wang and B.M. Pettitt. DOI: 10.1021/acs.jpclett.6b00246 
10. “Solute-Solvent Energetics Based on Proximal Distribution Functions", J. Phys. Chem. B (2016);
    Shu-Ching Ou and B.M. Pettitt. DOI:10.1021/acs.jpcb.6b01898 
11. “The Contribution of Electrostatic Interactions to the Collapse of Oligoglycine in Water", Cond. Mat.
    Phys. 19(2) 23802: 110 (2016); Deepti Karandur, B.M. Pettitt.