Energetics of [alpha]-helix formation in peptides and proteins

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.In title on title page, "[alpha]" appears as the lower-case Greek letter. Vita.Includes bibliographical references (p. 289-303).This thesis focuses on the energetics of !-helix formation in peptides and proteins. The [alpha]-helix is the most prevalent type of secondary structure found in proteins, and has arguably dominated our thinking about protein structure since its discovery, as it plays an important role in the early stages of protein folding. The intrinsic helical propensities of the natural amino acids make a very important contribution to secondary structure formation during these earliest folding events of peptides and proteins, whether studied in isolation in vitro, or during the co-translational folding of the nascent polypeptide chain during protein biogenesis in vivo. The energetics of helical propensities have been studied intensively over the last four decades in both peptides and proteins, but fundamental controversies remain to date, as essential experimental parameters, such as temperature or pH, have largely been ignored in the past. A new approach is needed that yields a revised helical propensity scale for the natural amino acids, if these intrinsic properties are to be incorporated and used in algorithms that predict peptide and protein structure and stability in applications of molecular modeling, protein engineering and design, or medicinal chemistry. In this thesis, context- and temperature-dependences of the helical propensities are explicitly explored both in optimized peptide and protein models, and a revised scale of intrinsic helical propensities is derived. The groundwork for helical propensity assignments in a peptide model is laid by rigorous characterization of spaced, solubilized polyalanine peptides as the ideal host to study intrinsic helical propensities in a solvent-exposed, context-free model.(cont.) Building upon this foundation, temperature dependent intrinsic helical propensities are assigned for the 20 natural amino acids and selected unnatural amino acids, and specifically, the first set of intrinsic helical propensities of the natural amino acids relevant to the human physiological condition is introduced. For selected amino acids, the temperature- and context-dependence of the helical propensities is explored in a hydrophobic polynorvaline peptide model applicable to the environment found in helices in the interior of a protein as part of the hydrophobic core. A strong increase in helical propensity concurrently with measurement temperature is observed for selected non-polar and charged residues, which correlate well with recent findings hypothesizing that a selected set of seven amino acids is preferentially incorporated into protein helices of thermophilic organisms. An additional piece of evidence demonstrates that there are no fundamental differences between the helical propensities in peptides and proteins. Studies in carefully tailored peptide and protein model systems at solvent-exposed sites free of context-dependent side chain or backbone interactions show the helical propensities of the natural amino acids to be equivalent in both systems, if assigned at the same measurement temperature. Taken together, these results are expected to become the new 'gold standard' for the energetics of intrinsic helical propensities of the natural amino acids.by Christina Reinhold Schubert.Ph.D