Proteins vibrational circular dichroism

UNFOLDED PEPTIDES AND PROTEINS STUDIED WITH INFRARED ABSORPTION AND VIBRATIONAL CIRCULAR DICHROISM SPECTRA... 

Vibrational circular dichroism involves IR absorption bands. The technique has been applied to sugars,110 oligosaccharides,111 proteins,112 and nucleic acids.113 The related vibrational Raman optical activity has also been applied to polyribonucleotides.114... 

Baumruk V. Pancoska P. Keiderling TA. Prediction of secondary structure using statistical analysis of electronic and vibrational circular dichroism and Fourier transform infrared spectra of proteins in H2O. J Mol Biol 1996 259 774-791. 

Shanmugam G, Polavarapu PL (2004) Vibrational circular dichroism spectra of protein films thermal denaturation of bovine serum albumin. Biophys Chem 111 73-77... 

Bour and Keiderling (1993) report ah initio simulation of the vibrational circular dichroism of coupled peptides in the amide I and II region. Using the MFP model and the 4-3IG basis set they were able to reproduce the VCD sign pattern and the relative intensities of spectra of proteins in the a-helical, /)-sheet 3io-helical and polyproline II conformations. 

Keiderling TA and Xu Q (2002) Unfolded peptides and proteins studied with infrared absorption and vibrational circular dichroism spectra. Advances in Protein Chemistry 62 111-161. 

Keiderling, T.A. Protein and peptide secondary structure and conformational determination with vibrational circular dichroism. Curr. Opin. Chem. Biol. 6, 682-688 (2002)... 

Pancoska, P., Wang, L., Keiderling, T.A. Frequency analysis of infrared absorption and vibrational circular dichroism of proteins in D2O solution. Protein Sci. 2, 411 19 (1993)... 

Bormett, R.W., Asher, S.A., Larkin, P.J., Gustafson, W.G., Ragunathan, N., et al. Selective examination of heme protein azide ligand-distal globin interactions by vibrational circular dichroism. J. Am. Chem. Soc. 114, 6864—6867 (1992)... 

Optical measurements (/) such as Raman Scattering, Fluorescence techniques. Vibrational Circular Dichroism, (VCD), Optical Rotational Dispersion (ORD), Raman Optical Activity (ROA) and infrared absorption spectroscopy can overcome many of the obstacles mentioned above due to the fact that optical techniques are non-invasive and can monitor proteins in their native environment and with accurate time resolution. One disadvantage is the low sensitivity. However, the use of Surface Enhanced Raman Scattering (SERS), techniques (2-4) means that proteins can be observed down to the single molecule level. Thus, optical teclmiques hold great promise for the future investigation of protein dynamics processes provided that proteins can be maintained in a suitable and controllable sample cell. 

Keiderling TA (1994) Vibrational circular dichroism spectroscopy of peptides and proteins. In Nakanishi K, Berova N and Woody RW (eds) Circular Dichroism -Principles and Applications, pp 597-521. New York VCH. 

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. 

Although X-ray crystallography, NMR, and circular dichroism are extremely valuable techniques for determining the structure of crystalline proteins or proteins in solution, they cannot be used to study proteins adsorbed on surfaces. Vibrational spectroscopy (infrared and Raman) appears to be the best approach available for bridging the gap between adsorbed proteins and proteins in solution. 

Circular dichroism (CD) spectroscopy is widely used to determine the amount of a-helix, y3-pleated sheet, and random coil structures in a protein molecule. The principle of CD is based on the fact that asymmetrical structures absorb light in an asymmetrical manner. Natural light vibrates in all planes perpendicular to its direction of travel but its plane of polarization can be fixed to possess either left or right orientation. However, in circular polarization the direction of polarization rotates with the frequency of the light. If the rotation is clockwise, it is called right circularly polarized light and if counterclockwise it is called left circularly polarized light. 

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