Raman optical activity of tetra-alanine in the poly(l-proline) II type peptide conformation. 2017

Masakazu Furuta, and Tomotsumi Fujisawa, and Hiroyasu Urago, and Takahiro Eguchi, and Takahito Shingae, and Satoshi Takahashi, and Ewan W Blanch, and Masashi Unno
Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840-8502, Japan. unno@cc.saga-u.ac.jp.

The poly(l-proline) II (PPII) helix is considered to be a major conformation in disordered polypeptides and unfolded proteins in aqueous solution. The PPII conformation can be identified by using Raman optical activity (ROA), which measures the different intensities of right- and left-circularly polarized Raman scattered light from chiral molecules and provides information on stereochemistry associated with vibrational motions. In the present study, we used tetra-alanine (Ala4) as a model system, since its central amide bond adopts the PPII conformation. The predominance of the PPII conformation was supported by 11 ns molecular dynamics (MD) simulations at 300 K. The MD snapshots were used for subsequent quantum mechanical/molecular mechanical (QM/MM) calculations to compute the Raman and ROA spectra. The present MD + QM/MM analysis leads to a good agreement between the observed and simulated spectra, allowing us to assign most of the spectral features including the ROA band near 1320 cm-1, which has been used as a marker for the PPII conformation. This positive ROA band has three components. The lower frequency component near 1310 cm-1 arises from an internal peptide bond, whereas the higher frequency components around 1320-1335 cm-1 appear due to N- and C-terminal peptide groups. The MD + QM/MM calculations also reproduced the electronic circular dichroism spectra of Ala4. The present results provide a satisfactory framework for future investigations of unfolded/disordered proteins as well as peptides in solutions by chiral spectroscopic methods.

UI MeSH Term Description Entries
D009904 Optical Rotation The rotation of linearly polarized light as it passes through various media. Optical Activity,Activity, Optical,Rotation, Optical
D010455 Peptides Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are considered to be larger versions of peptides that can form into complex structures such as ENZYMES and RECEPTORS. Peptide,Polypeptide,Polypeptides
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D002942 Circular Dichroism A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Circular Dichroism, Vibrational,Dichroism, Circular,Vibrational Circular Dichroism
D000409 Alanine A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM. Abufène,Alanine, L-Isomer,L-Alanine,Alanine, L Isomer,L Alanine,L-Isomer Alanine
D013059 Spectrum Analysis, Raman Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light. Raman Spectroscopy,Analysis, Raman Spectrum,Raman Optical Activity Spectroscopy,Raman Scattering,Raman Spectrum Analysis,Scattering, Raman,Spectroscopy, Raman
D014732 Vibration A continuing periodic change in displacement with respect to a fixed reference. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Vibrations
D056004 Molecular Dynamics Simulation A computer simulation developed to study the motion of molecules over a period of time. Molecular Dynamics Simulations,Molecular Dynamics,Dynamic, Molecular,Dynamics Simulation, Molecular,Dynamics Simulations, Molecular,Dynamics, Molecular,Molecular Dynamic,Simulation, Molecular Dynamics,Simulations, Molecular Dynamics
D058767 Protein Unfolding Conformational transitions of the shape of a protein to various unfolded states. Unfolding, Protein

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