Developing Solutes as Probes of Protein and DNA Processes

Solutes have a broad range of effects on biopolymer processes, forming a spectrum from destabilizers like urea to more stabilizing osmolytes like proline, glycine betaine (GB) and KGlutamate to secondary structure inducers like trifluorethanol. To explain these effects and develop these solutes as probes of interface formation and large scale conformational changes in protein and DNA processes, we quantify the thermodynamics of their competition with water to interact with different types of biopolymer surface (e.g. aliphatic and aromatic C, polar and charged O and N) using model compounds displaying one or more surface type. Preferential interactions between the solutes and model compounds relative to their interactions with water are determined by osmometry or solubility and dissected using a novel coarse-grained analysis to obtain interaction potentials quantifying the solute’s interaction with each significant type of biopolymer surface. Microscopic local-bulk partition coefficients Kp for the accumulation or exclusion of the solute in the water of hydration of these surfaces relative to bulk water are obtained. We used model compounds representing protein surface types to obtain Kp values for urea and GB, revealing that urea accumulates moderately at amide O and weakly at aliphatic C, while GB is excluded from both. These results provide both thermodynamic and molecular explanations for the opposite effects of urea and GB on protein stability, as well as deductions about strengths of amide NH - amide O and amide NH - amide N hydrogen bonds relative to hydrogen bonds to water. Urea and GB m-values for protein folding and other protein processes are interpreted and predicted using these interaction potentials or Kp values. We also determine interactions of these solutes with nucleic acid surface types to develop the ability to probe protein-nucleic acid interactions.Supported by NIH GM47022.