The primary goal of this proposal is to provide a molecular picture of the basis for the profound effects of cellular crowding and nonideal solution effects in general on biology via the development of new theoretical techniques in conjunction with simulation to provide a molecular picture (theory) of the aspects of the free energy surface that govern protein interfaces and associations in solution. In this project we will produce a molecular picture (theory) of protein interfaces and properties in nonideal solution which are consistent with known and coming thermodynamic and structural data. Test cases including Sm endonuclease and insulin and applications have been chosen to maximize overlap with existing data or collaborations that will yield data of specific relevance to our goal. We will make extensive use of concentration variables in our theoretical and computational studies. Biology rarely uses temperature differences as a mechanism to drive processes;nature more often uses solution composition (concentration of salt, osmolytes, other biomolecules, etc) to affect changes in biological conformation and state of aggregation. We seek to provide a better understanding of these effects.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
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Wehrle, Janna P
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University of Houston
Schools of Arts and Sciences
United States
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Kolawole, Abimbola O; Smith, Hong Q; Svoboda, Sophia A et al. (2017) Norovirus Escape from Broadly Neutralizing Antibodies Is Limited to Allostery-Like Mechanisms. mSphere 2:
Zhang, Cheng; Drake, Justin A; Ma, Jianpeng et al. (2017) Optimal updating magnitude in adaptive flat-distribution sampling. J Chem Phys 147:174105
Ou, Shu-Ching; Drake, Justin A; Pettitt, B Montgomery (2017) Nonpolar Solvation Free Energy from Proximal Distribution Functions. J Phys Chem B 121:3555-3564
Chen, Chuanying; Pettitt, B Montgomery (2016) DNA Shape versus Sequence Variations in the Protein Binding Process. Biophys J 110:534-544
Zhang, Cheng; Lai, Chun-Liang; Pettitt, B Montgomery (2016) Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace. Mol Simul 42:1079-1089
Dyer, Kippi M; Perkyns, John S; Pettitt, B Montgomery (2016) Dielectric behavior for saline solutions from renormalized diagrammatically proper interaction site model theory. J Phys Condens Matter 28:414006
Harris, Robert C; Pettitt, B Montgomery (2016) Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins. J Phys Condens Matter 28:083003
Ou, Shu-Ching; Pettitt, B Montgomery (2016) Solute-Solvent Energetics Based on Proximal Distribution Functions. J Phys Chem B 120:8230-7
Tomar, Dheeraj S; Weber, Valéry; Pettitt, B Montgomery et al. (2016) 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
Karandur, Deepti; Harris, Robert C; Pettitt, B Montgomery (2016) Protein collapse driven against solvation free energy without H-bonds. Protein Sci 25:103-10

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