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Conformational analyses of collagen-like Co -Glycine/L-proline oligopeptides by quantum chemical calculation (QCC): Sequence effects on conformations and intra-molecular hydrogen bonds

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Abstract

The sequence effects on the conformations and intra-molecular hydrogen bonds (NH···OC: H-bond) of collagen-like co-peptides (single chains) were analyzed using co-glycine (G)/L-proline (P) oligopeptides (6- and 9-mer, G/P = 1/2 mol), by QCC [B3LYP/6-31G(d,p)], with homo-oligopeptides. Each sequence was specified using three kinds of basic triplets of GPP, PGP, and PPG. The conformations (dihedral angles: φn/ψn) varied depending on the sequences. The conformation types of each unit were classified in the following three groups: φ/ψ of g−/g + (shorter polyproline II helical structure: P-like) with H-bond, g−/t + (polyproline II helical structure: PPII) with no H-bond, and φ/ψ of t−/g + with no H-bond. All H-bonds that have seven-membered ring were formed between units separated by one peptide. The positions and number (Nh) of H-bonds varied depending on the sequences. The H-bonds between CO of proline and NH of glycine unit were newly formed. The co-peptides that have no GPP triplet in N-end side (CH3CO-GPP) were found to be more stable than the corresponding blend models due to the formations of newly formed H-bonds. From the comparison with the structures observed for triple helix of collagen in other works and the findings (the existence of the CO group that have no H-bond), it was inferred that collagen may be formed by conformational rearrangement from P-like (single chain) to PPII (triple helix) and may be stabilized by inter-molecular hydrogen bonding between the residual CO groups and water molecules.

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Authors and Affiliations

  1. Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Naka-cho, Koganei, Tokyo, 184-8588, Japan

    Minoru Kobayashi

  2. Department of Advanced Material and Chemical Engineering, Halla University, Wonju, 220-712, Korea

    Jae Ho Sim

  3. Graduate School of Technical Management, Tokyo University of Agriculture and Technology, Naka-cho, Koganei, Tokyo, 184-8588, Japan

    Hisaya Sato

Authors
  1. Minoru Kobayashi
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  2. Jae Ho Sim
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  3. Hisaya Sato
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Correspondence to Minoru Kobayashi.

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Kobayashi, M., Sim, J.H. & Sato, H. Conformational analyses of collagen-like Co -Glycine/L-proline oligopeptides by quantum chemical calculation (QCC): Sequence effects on conformations and intra-molecular hydrogen bonds . Polym. Bull. 79, 6627–6644 (2022). https://doi.org/10.1007/s00289-021-03805-8

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  • DOI: https://doi.org/10.1007/s00289-021-03805-8

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