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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM037657-10
Application #
6018677
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1988-08-01
Project End
2001-06-30
Budget Start
1999-07-01
Budget End
2000-06-30
Support Year
10
Fiscal Year
1999
Total Cost
Indirect Cost
Name
University of Houston
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
800771594
City
Houston
State
TX
Country
United States
Zip Code
77204
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
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
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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