title: Intramolecular backbone···backbone hydrogen bonds in polypeptide conformations. The other way around: ɛ-turn.
abstract: In this study, we performed a detailed literature survey of the ɛ-turn in peptides and proteins. This three-dimensional structural feature is characterized by an eleven-membered pseudo-cycle closed by an intramolecular backbone…backbone H-bond. Interestingly, in this motif the direction of the N-H…O = C H-bond runs opposite to that of the much more popular and extensively investigated α-, β-, and γ-turns. We did not authenticate unequivocally the ɛ-turn main-chain reversal topology in any linear short peptide. However, it is frequently observed in small cyclic peptides formed by four, five, and six amino acid residues with stringent geometric requirements. Rather surprisingly, ɛ-turns do occur in proteins, although to a relatively moderate extent, as an isolated feature or in the turn segment of hairpin motifs based on two antiparallel, pleated β-strands. Moreover, the ɛ-turn may also host not only the seven-membered, intramolecularly H-bonded, pseudo-cycle termed γ-turn, either of the classic or inverse type, but also one (or even two) cis peptide bond(s) or a β-bulge conformation. Based on their ϕ, ψ backbone torsion angles, we were able to classify the protein ɛ-turns in six different families. Conformational energy computations using the DFT methodology were also performed on the ɛ-turns adopted by the amino acid triplet -Gly-Gly-Gly- (Gly is the most commonly found residue at each of the three positions in our analysis of proteins). Again, in this computational study, six families of turns were identified, but only some of them resemble rather closely those extracted from our investigation on proteins.
authors.affiliation: Department of Chemistry, University of Padova, Padova, 35131, Italy.|Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova, 35131, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Toniolo
authors.affiliation: Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova, 35131, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Crisma
authors.affiliation: Department of Chemistry, University of Padova, Padova, 35131, Italy.|Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova, 35131, Italy.
authors.forename: Fernando
authors.initials: F
authors.lastname: Formaggio
authors.affiliation: Departament d'Enginyeria Quimica, ETSEIB, Universitat Politècnica de Catalunya, Barcelona, 08028, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Alemán
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Chandrasekharan
authors.initials: C
authors.lastname: Ramakrishnan
authors.affiliation: National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India.
authors.forename: Neha
authors.initials: N
authors.lastname: Kalmankar
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Padmanabhan
authors.initials: P
authors.lastname: Balaram
mesh_terms: D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D007536:Isomerism; D009682:Magnetic Resonance Spectroscopy; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry
chemical_list: D009842:Oligopeptides; D010455:Peptides; D010456:Peptides, Cyclic; D011506:Proteins; C035647:glycyl-glycyl-glycine
keywords: NMR; X-ray diffraction; conformational energy calculations; peptide turns; solution conformation