Over the past forty years, mechanistic studies of protein folding have focused primarily on proteins fewer than 300 amino acids in length with quite simple folding reactions. Nevertheless, these studies have provided crucial insights into the driving forces and mechanisms of the folding of all proteins, including large proteins with many domains and complex folding reactions. In addition, there is growing recognition that conformational changes coupled to protein functions are mechanistically similar to protein folding reactions. The long term goal of our research is to understand how to use our knowledge based on biophysical studies of simple systems to deduce the folding mechanisms of much more complex proteins and to do so in the context of their function and cellular environment. Specifically, we plan to use conventional kinetic methods such as stopped-flow and temperature-jump fluorescence to measure the folding kinetics of RNase P protein when it binds ligands, particularly its cognate RNA. We also plan to extend our studies on the B domain of protein A (BdpA) to include the A, C, D and E domains so as to understand the global folding this important pathogenicity factor in the bacterium Staphylococcus aureus. Finally, we have developed an experimental approach to study unfolded proteins under physiological conditions and plan to exploit this method to study the unfolded forms of monomeric;repressor and BdpA. We plan to collect a variety of spectroscopic and biophysical data on these model denatured ensembles and compare the ensemble-averaged properties with those of statistical mechanical models of each system. Our goal is to provide a more accurate picture of the significantly populated conformations in these ensembles so that they can be used in our mechanistic models of the folding reaction.

Public Health Relevance

These studies are important because many protein domains have been observed to sample their unfolded states tens or hundreds of times every second, making the unfolded form as relevant to function as the folded form. The biological significance of our proposed studies rests on the relevance of recurrent and complex folding reactions to the regulation and function of proteins in the cell. A detailed understanding of protein-ligand interactions and the myriad biological phenomena that result from them requires a thermodynamic and kinetic description.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM081666-03
Application #
8004924
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Wehrle, Janna P
Project Start
2008-12-01
Project End
2012-11-30
Budget Start
2010-12-01
Budget End
2011-11-30
Support Year
3
Fiscal Year
2011
Total Cost
$393,265
Indirect Cost
Name
Duke University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705
Qi, Yang; Martin, Jeffrey W; Barb, Adam W et al. (2018) Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics. J Mol Biol 430:3412-3426
Daniels, Kyle G; Suo, Yang; Oas, Terrence G (2015) Conformational kinetics reveals affinities of protein conformational states. Proc Natl Acad Sci U S A 112:9352-7
Mosley, Pamela L; Daniels, Kyle G; Oas, Terrence G (2015) Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein Determined by Nuclear Magnetic Resonance-Based Histidine pKa Measurements. Biochemistry 54:5379-88
Deis, Lindsay N; Wu, Qinglin; Wang, You et al. (2015) Suppression of conformational heterogeneity at a protein-protein interface. Proc Natl Acad Sci U S A 112:9028-33
Capp, Jo A; Hagarman, Andrew; Richardson, David C et al. (2014) The statistical conformation of a highly flexible protein: small-angle X-ray scattering of S. aureus protein A. Structure 22:1184-1195
Daniels, Kyle G; Tonthat, Nam K; McClure, David R et al. (2014) Ligand concentration regulates the pathways of coupled protein folding and binding. J Am Chem Soc 136:822-5
Deis, Lindsay N; Pemble 4th, Charles W; Qi, Yang et al. (2014) Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. Structure 22:1467-77
Isom, Daniel G; Marguet, Philippe R; Oas, Terrence G et al. (2011) A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity. Proteins 79:1034-47
Kahsai, Alem W; Xiao, Kunhong; Rajagopal, Sudarshan et al. (2011) Multiple ligand-specific conformations of the ?2-adrenergic receptor. Nat Chem Biol 7:692-700
Chang, Yu-Chu; Oas, Terrence G (2010) Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand. Biochemistry 49:5086-96

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