The primary goal of this work is the solution of solvation/conformation related design problems of peptides and proteins via the development of new theoretical techniques. In this project we will produce a molecular picture (theory) of peptide conformations and protein properties in solution which is consistent with known thermodynamic and structural data. We will make detailed calculations with our new methods and existing techniques in an attempt to make the most direct possible comparisons with recent and planned structural and biological/biochemical experiments. The problems which focus our work are peptides and proteins of biochemical and medicinal importance including protamines, S. m. endonuclease, myoglobin and T. v. ferredoxin. We hope to contribute to understanding solvent effects on conformational stability and on aggregate stability, primarily in a thermodynamic context. Using theoretical methods we have developed such as grand molecular dynamics, integral equations, and classical density functionals we will quantify the balance between general solution effects (such as screening and solvation) and specific effects due to solvent and ion association in solution in determining the thermodynamics of conformations and macromolecular associations in solution. A goal of this work continues to be the development of new theoretical techniques to solve solvation/conformation related design problems of peptides and proteins. Test cases and applications have been chosen to maximize overlap with existing data or collaborations that will yield data of specific relevance to our goal.
| Seckfort, Danielle; Montgomery Pettitt, B (2018) Price of disorder in the lac repressor hinge helix. Biopolymers :e23239 |
| Dai, Wei; Chen, Muyuan; Myers, Christopher et al. (2018) Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 430:4156-4167 |
| Drake, Justin A; Pettitt, B Montgomery (2018) Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model. Biophys J 114:2799-2810 |
| Sarma, Rahul; Wong, Ka-Yiu; Lynch, Gillian C et al. (2018) Peptide Solubility Limits: Backbone and Side-Chain Interactions. J Phys Chem B 122:3528-3539 |
| 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 |
| Asthagiri, D; Karandur, Deepti; Tomar, Dheeraj S et al. (2017) Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15. J Phys Chem B 121:8078-8084 |
| 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 |
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