Type VIa β-turn-fused helix N-termini: A novel helix N-cap motif containing cis proline

Helix N-capping motifs often form hydrogen bonds with terminal amide groups which otherwise would be free. Also, without an amide hydrogen, proline (trans) is over-represented at helix N-termini (N1 position) because this naturally removes the need to hydrogen bond one terminal amide. However, the preference of cisPro, vis-à-vis helix N-termini, is not known. We show that cisPro (α_R or PP_II ) often appears at the N-cap position (N0) of helices. The N-cap cisPro(α_R ) is associated with a six-residue sequence motif - X_(-2) -X_(-1) -cisPro-X₍₁₎ -X₍₂₎ -X₍₃₎ - with preference for Glu/Gln at X_(-1) , Phe/Tyr/Trp at X₍₁₎ and Ser/Thr at X₍₃₎ . The motif, formed by the fusion of a helix and a type VIa β-turn, contains a hydrogen bond between the side chain of X_(-1) and the side chain/backbone of X₍₃₎ , a α-helical hydrogen bond between X_(-2) and X₍₂₎ and stacking interaction between cisPro and an aromatic residue at X₍₁₎ . NMR experiments on peptides containing the motif and its variants showed that local interactions associated with the motif, as found in folded proteins, were not enough to significantly tilt the cis/trans equilibrium towards cisPro. This suggests that some other evolutionary pressure must select the cisPro motif (over transPro) at helix N-termini. Database analysis showed that >C = O of the pre-cisPro(α_R ) residue at the helix N-cap, directed opposite to the N→C helical axis, participates in long-range interactions. We hypothesize that the cisPro(α_R ) motif is preferred at helix N-termini because it allows the helix to participate in long-range interactions that may be structurally and functionally important.