The goal of this project is to provide a molecular picture (theory) of peptide conformations and properties in solution which is consistent with known thermodynamic and structural data. We will make detailed calculations with our new methods in an attempt to make the most direct possible comparisons with recent and planned structural and biological/biochemical experiments. We will consider the relation of thermodynamics and allowed conformations of peptides to their solution environment and salt concentration. Using theoretical methods we will quantify the balance between general solution effects (such as screening and solvation) and specific effects due to molecular association in solutions of peptides in determining the thermodynamics in solution. This will be applied to covalently constrained peptides and peptido mimetics of biochemical and medicinal importance. A goal of this work continues to be the development of new theoretical techniques to solve solvation/conformation related design problems of peptides. 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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