Residue Level Quantification of Protein Stability in Living Cells Public Deposited

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  • March 19, 2019
Creator
  • Monteith, William
    • Affiliation: College of Arts and Sciences, Department of Chemistry
Abstract
  • The intracellular milieu differs from the dilute conditions in which most biophysical and biochemical studies are performed. This difference has led both experimentalists and theoreticians to tackle the challenging task of understanding how the intracellular environment affects the properties of biopolymers. Despite a growing number of in-cell studies, there is a lack of quantitative, residue-level information about equilibrium thermodynamic protein stability under non-perturbing conditions. My dissertation addresses this void by describing the use of NMR-detected hydrogen-deuterium exchange of quenched cell lysates to measure individual opening free energies of the 56-amino acid B1 domain of protein G (GB1) in living <italic>Escherichia coli</italic> cells without adding destabilizing co-solutes or heat. Comparisons to dilute solution data (pH 7.6 and 37 °C) show that opening free energies increase by as much as 1.14 ±0.05 kcal/mol in cells. Importantly, I also show that homogeneous protein crowders destabilize GB1, highlighting the challenge of recreating the cellular interior. These findings are discussed in terms of hard-core excluded volume effects, charge-charge GB1-crowder interactions and other factors. The quenched lysate method is applied further in mutational studies of GB1 to make the first quantification of non-specific protein-protein interactions in cells. I show that a surface mutation in GB1 is 10-times more destabilizing in <italic>E. coli</italic> than in buffer. The results indicate that quinary interactions between surface exposed residues and cytoplasmic proteins can play a key role in determining the native stability of a protein, whereas such a role is absent in buffer alone. The methods developed and applied throughout this work should prove useful for extension to other globular proteins in efforts to gain a more complete understanding of the effects of the intracellular environment on protein chemistry.
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  • In Copyright
Advisor
  • Thompson, Nancy
  • Pielak, Gary J.
  • Campbell, Sharon
  • Spremulli, Linda
  • Berkowitz, Max
Degree
  • Doctor of Philosophy
Degree granting institution
  • University of North Carolina at Chapel Hill Graduate School
Graduation year
  • 2014
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  • Chapel Hill, NC
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