N-Capping Motifs Promote Interaction of Amphipathic Helical Peptides with Hydrophobic Surfaces and Drastically Alter Hydrophobicity Values of Individual Amino Acids

Abstract

Capping rules, which govern interactions of helical peptides with hydrophobic surfaces, were never established before due to lack of methods for the direct measurement of polypeptide structure on the interphase boundary. We employed proteomic techniques and peptide retention modeling in reversed-phase chromatography to generate a data set sufficient for amino acid population analysis at helix ends. We found that interactions of amphipathic helical peptides with a hydrophobic C18 phase are induced by a unique motif featuring hydrophobic residues in the N1 and N2 positions adjacent to the N-cap (Asn, Asp, Ser, Thr, Gly), followed by Glu, Gln, or Asp in position N3 to complete a capping box. A favorable N-capping arrangement prior to amphipathic helix may result in the highest hydrophobicity (retention on C18 columns) of Asp/Asn (or Glu/Gln) peptide analogues among all naturally occurring amino acids when placed in N-cap or N3 position, respectively. These results contradict all previously reported hydrophobicity scales and provide new insights into our understanding of the phenomenon of hydrophobic interactions.

Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis

“…Finding sequence specific factors, which affect peptide physico-chemical properties (electrophoretic mobility in our case), is a key process applied in our modeling approach [6, 14, 16]. It is based on repetitive application of following steps:…”

“…In case of CE – this is a direct induction effect of acidic residues on the apparent basicity of N- terminal amino group. Correct prediction of peptide helicity is another key development, which will improve prediction modeling for both RP-HPLC [16] and CE.…”

Chromatographic behavior of peptides containing oxidized methionine residues in proteomic LC–MS experiments: Complex tale of a simple modification

“…Multiple studies in the 1990's demonstrated such behavior using designed model peptides [39][40][41] and led to establishing separate hydrophobicity scales for random coil and helical conformations of peptides upon interaction with RP sorbents [42]. The arrival of proteomic techniques provides chromatographers with access to thousands of peptides with secondary structures that providing a significant contribution to their RP LC retention [31]. These studies will continue the search for a better understanding the underlying mechanisms, and ultimately, to more accurate prediction of peptide retention properties.…”

“…Recently we demonstrated that similar to helices in proteins, amphipathic helical structures upon interaction with hydrophobic C18 phase are stabilized by N-cap box motifs [31]. This motif consists of four residues with each position showing different preferences for individual residues.…”

“…The first (N-cap, according to Richardson and Richardson's terminology [32]) position is preferable for Asn, Asp, Ser, Thr, and Gly. Second (N1) and third (N2) positions are favoring hydrophobic residues [31]. Forth (N3) position is predominantly occupied by Glu, Gln and Asp.…”