Raman spectroscopy side chain vibrations

Raman spectroscopy is a vibrational spectroscopic technique which can be a useful probe of protein structure, since both intensity and frequency of vibrational motions of the amino acid side chains or polypeptide backbone are sensitive to chemical changes and the microenvironment around the functional groups. Thus, it can monitor changes related to tertiary structure as well as secondary structure of proteins. An important advantage of this technique is its versatility in application to samples which may be in solution or solid, clear or turbid, in aqueous or organic solvent. Since the concentration of proteins typically found in food systems is high, the classical dispersive method based on visible laser Raman spectroscopy, as well as the newer technique known as Fourier-transform Raman spectroscopy which utilizes near-infrared excitation, are more suitable to study food proteins (Li-Chan et aL, 1994). In contrast the technique based on ultraviolet excitation, known as resonance Raman spectroscopy, is more commonly used to study dilute protein solutions. 

In addition to the structural information on proteins that is obtained from the vibrations of the polypeptide backbone, the vibrations of the side chains can also give valuable information on the environment of the side chain and sometimes on the accessibility to protons and deuterons. The ability to probe the accessibility of the side chains of a protein is one of the important features of Raman spectroscopy for the study of protein dynamics. 

Using time-resolved Raman spectroscopy, Kitagawa and coworkers investigated the vibrational relaxation of the V4 and v-, modes of the heme following photoexcitation in wild-type sperm whale Mb and its modifications, in which one or the other isopropionate side chain is selectively replaced by a methyl group [64]. Both modified hemes have similar relaxation rate (1.5 + 0.1 ps for the V4 mode and 4.9 0.3 ps for the... 

Vibrational spectroscopy is an important tool to obtain information about the secondary structure of proteins [827]. The ability to relate protein conformations to infrared vibrational bands was established very early in the pioneering work of Elhot and Ambrose before any detailed X-ray results were available [828]. Vibrational circular dichroism (VCD) provides sensitive data about the main chain conformation [829, 830]. The Raman optical activity (ROA) signal results from sampling of different modes but is especially sensitive to aromatic side chains [831, 832]. A theoretical prediction for the ROA phenomenon was developed by Barron and Buckingham [833, 834], and the first ROA spectra were measured by Barron, Bogaard and Buckingham [835, 836]. First ab initio predictions were provided by Polavarapu [837]. In 2003, Jalkanen et al. showed that DPT approaches in combination with explicit water molecules and a continuum model reproduce the experimental spectra much better [838]. DFT-based approaches to VCD spectra were, for example, pioneered by Stephens et al. [839]. To extract the local structural information provided by ROA, Hudecova et al. [721] developed multiscale QM/MM simulation techniques. 

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