Lifson-Roig nucleation for alpha-helices in trifluoroethanol: context has a strong effect on the helical propensity of amino acids.

We have investigated the effect of substituting each of 19 common amino acids (excluding P) at the X position in the peptide acetyl-Y-VAEAK-TSXSR-VAEAK-NH(2). This very different peptide is of interest because, in previous work, we showed that nucleation in the strong alpha-helix-forming pentamers VAEAK was unable to propagate the helix structure through the sequence TSDSR, which is neither a helix-forming sequence nor a breaker, but is indifferent to helix formation. Substitution in the center of the indifferent sequence reveals an interesting measure of the helical propensity for the 19 amino acids. CD spectra were measured in various mixtures of buffer and 2,2,2-trifluoroethanol (TFE), and then analyzed for helix propensity of the amino acids using the Lifson-Roig model. However, the nucleation parameter in the Lifson-Roig model has never been measured for TFE. We have empirically found that the nucleation parameter for a solvent can be determined from the data normally used to determine only the propagation parameters. The results of the analysis of the CD show that most amino acids are excellent or good helix formers in 90% TFE, while amino acids D, W, F and G are poor helix formers for the indifferent pentamer sequence. The helix propensity of the 19 amino acids is quite different from the helix propensity measured in other peptide sequences, demonstrating the context dependence of this property. The results as a function of alcohol concentration confirm that the relative order of helical propensity of amino acids changes with solvent environment. Clearly, the prediction of alpha-helical secondary structure from protein sequence requires more than a single helical propensity for each amino acid.