title: Type VIa β-turn-fused helix N-termini: A novel helix N-cap motif containing cis proline.
abstract: 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 (αRor PPII) often appears at the N-cap position (N0) of helices. The N-cap cisPro(αR) 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(αR) residue at the helix N-cap, directed opposite to the N→C helical axis, participates in long-range interactions. We hypothesize that the cisPro(αR) 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.
authors.affiliation: Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
authors.forename: Rubin
authors.initials: R
authors.lastname: Dasgupta
authors.affiliation: Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
authors.forename: Himal K
authors.initials: HK
authors.lastname: Ganguly
authors.affiliation: Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
authors.forename: E K
authors.initials: EK
authors.lastname: Modugula
authors.affiliation: Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
authors.forename: Gautam
authors.initials: G
authors.lastname: Basu
mesh_terms: D000595:Amino Acid Sequence; D030562:Databases, Protein; D006860:Hydrogen Bonding; D007536:Isomerism; D009682:Magnetic Resonance Spectroscopy; D010456:Peptides, Cyclic / Q000138:chemical synthesis / Q000737:chemistry*; D011392:Proline / Q000737:chemistry*; D017433:Protein Structure, Secondary
chemical_list: D010456:Peptides, Cyclic; D011392:Proline
keywords: cis Proline; helix N-cap; sequence motif