Biophysical studies of protein denaturation with sodium dodecyl sulfate

The wide variety of biophysical properties of proteins makes the study of proteomics more difficult than that of genomics. The objective of this thesis is to develop new tools for use in proteomics using a detailed understanding of the interactions between proteins and sodium dodecyl sulfate (SDS). In particular, it uses bovine carbonic anhydrase II (BCA) as a model system. Chapter 1 reviews the use of BCA as a model protein for studies of denaturation. Chapter 2 examines the role of the Zn(II) cofactor in the refolding of BCA after SDS denaturation.; Chapter 3 uses chemically modified BCA. Complete acetylation of BCA with acetic anhydride converts all of its 18 lysine-epsilon-NH3 + groups to lysine-epsilon-NHCOCH3 groups, and generates BCA-Ac18. SDS at concentrations above ∼10 mM denatures both BCA and BCA-Ac18; when SDS is removed by dialysis, both proteins refold to the native form. BCA-Ac18 is kinetically more stable than BCA to denaturation with SDS (chapter 4), although some differences are seen for other denaturants (chapter 5). These studies suggest that large differences in the net charge have no significant influence on the structure, the ability to refold, or the rate of refolding of the protein and raise the broader question of why proteins have charged residues on their surface, outside of the region of the active site.; When the acetylation of the lysine-epsilon-NH3+ groups on proteins is incomplete, mixtures of species---charge ladders---differing by discrete charge units arise. Chapter 6 demonstrates the generation of hydrophobic charge ladders using a variety of proteins and various acylating reagents, and uses them to investigate the relative importance of charge and hydrophobicity in partitioning proteins in two polymer solutions. Chapter 7 describes a study of the interaction of BCA with SDS using charge ladders to determine the relative importance of hydrophobicity and electrostatics, and develops a quantitative model of the interaction to support the experimental findings.; Finally, chapter 8 exploits this understanding of the protein-SDS interaction to differentiate proteins based on the kinetics of SDS denaturation and demonstrates how the results of detailed biophysical studies can be utilized to develop new techniques for proteomics.