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Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides

Authors

  • Chen Han,

    1. Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 (China), Fax: (+86) 010-62563167
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  • Jianping Wang

    Corresponding author
    1. Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 (China), Fax: (+86) 010-62563167
    • Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 (China), Fax: (+86) 010-62563167
    Search for more papers by this author

Abstract

In this work, a non-natural amino acid, H-propargylglycine-OH (Pra), is chosen to examine the side-chain effect on the backbone conformation of small peptides. The conformations of two synthesized Pra-containing tripeptides, Ac-Pra-Pra-NH2 (PPTP) and Ac-Pra-Ala-NH2 (PATP), are examined by infrared (IR) spectroscopy in combination with molecular dynamics (MD) simulations and quantum chemical computations. By analyzing the joint distributions of backbone torsional angles, several significant conformations can be identified for the two tripeptides solvated in D2O. At room temperature, 44 % of PPTP exists in the α-α conformation and 33 % of PATP exists in the α-polyproline-II conformation. Larger structural inhomogeneity is seen in both cases by MD simulations at elevated temperatures. Thus even a small side chain, such as the propargyl group can significantly alter the peptide backbone conformations. The results suggest that there is no overwhelming conformational propensity of the Pra residue in short peptides. IR spectra simulated in the amide-I region using two different methods, reasonably reproduce the experimental IR spectra and their temperature dependence.

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