Characterization of alanine-rich peptides, Ac-(AAKAA)(n)-GY-NH2 (n=1-4), using vibrational circular dichroism and Fourier transform infrared. Conformational determination and thermal unfolding

Vibrational circular dichroism (VCD) and Fourier transform IR (FTIR) were measured for a series of short alanine-based peptides having the general formula Ac-(AAKAA)(n)-GY-NH2 (n = 1-4) from 5 to 50 degrees C in D2O and at room temperature in both TFE and H2O. In both of these latter solvents, the dominant structural form at the lowest temperature for the longest oligomers is alpha-helical. The same is true for the n = 4 peptide in D2O, but under these more dilute aqueous conditions, the shorter (n = 3) peptides have mixed helix-coil structures and the n = 1 and 2 peptides are random coils, The VCD data do not support the 3(10)-helix as a dominant contributor to the conformation of these oligomers in any of these solvents. These vibrational spectral data are consistent with lower-concentration electronic CD results and additionally indicate increased helical stability at higher concentrations, VCD amide I data for the 22mer (n = 4) in D2O indicate that the peptide undergoes a transition from a highly helical conformation at 5 degrees C to a dominant random coil structure at similar to 45 degrees C with a T-m of similar to 25 degrees C (effective midpoint). Factor analysis of the thermal data showed that three principal components were required to describe both the VCD and FTIR data for the n = 4 peptide in D2O. The transition is characterized by a gradual loss of contribution from a spectral component representing the alpha-helical fraction. The third component is evidence of an optically detected intermediate conformation best viewed as a mixed coil-helix structure resulting from end fraying of the helical peptide as the temperature is increased, The nature of the junction between the interior helix and frayed ends is not determined by these data and could involve local (phi and psi) angles mimicking a 3(10)-helix that would provide consistency with ESR and NMR results from Millhauser and co-workers.