Sequence Preference of α-Helix N-Terminal Tetrapeptide

Abstract

The α-helix is the most abundant secondary structure in proteins. Due to the specific i, i+4 hydrogen bond pattern, the two termini have unsatisfied hydrogen bonds, and are less constrained; in order to compensate for this, specific residues are preferred for the terminal positions. However, a naive combination of the statistically-preferred residues for each position may not result in a stable N-terminal helical sequence. In order to provide a set of preferable N-terminal peptides for α-helix design, we have studied the N-terminal tetrapeptide sequence motifs that are favorable for helix formation using statistical analysis and atomistic simulations. A set of tetrapeptide sequences including TEEE and TPEE were found to be favorable motifs. In addition to forming more hydrogen bonds in the helical conformation, the favorable motifs also tended to form more capping boxes. To empirically test our predictions, we obtained 10 peptides with different N-terminal motifs and measured their α-helical content by circular dichroism spectroscopy. The experimental results agreed qualitatively with the statistical and simulation results. Furthermore, some of the suggested preferable tetrapeptide sequences have been successfully applied in de novo protein design.

Computational design and optimization of novel d‐peptide TNFα inhibitors

“…The sequence of DHPT‐9 was optimized to increase its helicity and reduce entropy loss upon TNFα binding. As N‐cap plays important role in stabilizing helical secondary structure, we replaced the N‐terminal sequence of DHPT‐9 with a top‐ranking N‐cap sequence, TEEE . To enhance helix propensity and reduce hydrophobic exposure of the designed peptides, two noninterfacial residues L16 and D20 were selected for optimization (Fig.…”