Developing Solutes as Quantitative Probes of Protein and Nucleic Acid Processes

Solutes have a broad range of effects on noncovalent self-assembly processes of proteins and nucleic acids. Urea is a general destabilizer; osmolytes proline and glycine betaine (GB) stabilize protein and protein-nucleic acid assemblies; trifluorethanol (TFE) induces extended &agr;-helices, and the physiological salt KGlutamate (KGlu) is typically much more stabilizing than the laboratory salt KCl.;To explain these effects and develop these solutes as probes of interface formation and large scale conformational changes in biopolymer processes, we quantify the thermodynamics of their competition with water to interact with model compounds displaying biopolymer surface types (aliphatic and aromatic C, polar and charged O and N). Preferential interactions between these solutes and model compounds are determined by osmometry, solubility, micelle formation or two-phase distribution assays. Interpreted using analysis based on the solute partitioning model, these data yield interaction potentials (&agr;-values) quantifying the interaction of the solute with a unit area of each surface type and partition coefficients Kp quantifying the local accumulation or exclusion of the solute at these surfaces. &agr;-Values allow the effects of these solutes on a process to be predicted or interpreted in terms of information about the surface buried.;Kp values reveal that the different effects of these solutes on protein folding result from their characteristically different interactions with aliphatic C and amide O groups that account for most of the surface buried in folding. Urea accumulates moderately at amide O and weakly at aliphatic C, while GB and proline are moderately to strongly excluded from both, and glutamate is more excluded from both than chloride. TFE accumulates at aliphatic C, and is strongly excluded from amide surface, explaining why it converts both globular and unfolded proteins to &agr;-helices. Use of combinations of these solute allows one to probe the steps of protein processes in which large-scale folding occurs. From &agr;- or Kp-values, the widely different effectiveness of these solutes as osmolytes and on assembly or precipitation of proteins can also be predicted from structural information. We also determine interactions of urea with nucleic acid surface types to develop the ability to probe protein-nucleic acid interactions.