Analysis of secondary structures in nucleic acid binding proteins and nuclear magnetic resonance investigation of helix propagation and residual motions in proteins

This thesis involves analyses of 32-helices, alpha-helices and of the change in residual entropy of a protein upon chemical modification. Part of the long-term goal of understanding the formation, function and stability of proteins requires that all conformations be accurately assigned and structurally understood. By a statistical analysis of 258 nucleic acid binding proteins from the protein data bank, 5% of their amino acids were found to exist as 32-helices. The third K homology domain, Epstein-Barr nuclear antigen-1 and the homeodomain from the Drosophila paired protein contained 32-helices involved in nucleic acid recognition. Contact maps of these three proteins show that the 32-helical motif is capable of both specific and non-specific recognition and binding of nucleotides.; Once all conformational structures are accurately assigned, their natural diversity of sequence and environment in proteins can be explored to understand how they are formed. alpha-Helix formation in various mixtures of 2,2,2-trifluoroethanol (TFE), a known helix-inducing solvent, can be used to predict whether a sequence will form a helix at the protein core vs. the solvent-exposed protein surface. Nuclear magnetic resonance spectroscopy of a TFE solvated peptide composed of two helix-favoring pentapeptides flanking a helix-indifferent pentapeptide shows that the structure adopts N-terminal and C-terminal helices separated by two non-helical residues in the indifferent sequence. The initation of two nucleation events in this short peptide and the inability of the helix to propagate through the indifferent sequence (neither event is predicted by current models) indicates that, in addition to environment, there is a strong sequence context dependence for helix formation.; Enzymatic function can be tied directly to the internal motions identified as the residual entropy of protein structure. The use of chemical modification as a method of irreversibly trapping a mimic of the catalytic intermediate in thioredoxin function shows that these motions are substantial and are not necessarily localized to the active site. The observed increase in fast motions identifies obvious structures known to be important in the redox mechanism and several unobvious structures that could indicate regions possibly coupled to protein function. Together these results identify important properties for understanding protein structure and function.