title: Influence of an unnatural amino acid side chain on the conformational dynamics of peptides.
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-NH(2) (PPTP) and Ac-Pra-Ala-NH(2) (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 D(2)O. 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.
authors.affiliation: Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Han
authors.forename: Jianping
authors.initials: J
authors.lastname: Wang
mesh_terms: D000480:Alkynes / Q000737:chemistry*; D005998:Glycine / Q000031:analogs & derivatives* / Q000737:chemistry; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D000480:Alkynes; D010455:Peptides; D012997:Solvents; C009055:propargylglycine; D005998:Glycine