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.
| 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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