Vibration spectra of proteins

The concept of transferability and a detailed understanding of these amide modes provides the basis for quantitative estimation of secondary structure for unknown proteins and polypeptides. The quantitative methods currently used to analyze vibrational spectra of proteins can be classified into two categories (1) methods based on decomposition of band contours into underlying components characterized by distinct frequencies, and (2) methods based on principles of pattern recognition. 

The normal-mode calculations on glucagon and BPTI demonstrate that, in order to analyze the vibrational spectra of proteins, we need to be able to predict more than just a density of vibrational states. In particular, we need to know what IR and Raman intensities are to be expected for a normal vibration. While a calculation of Raman intensities has yet to be done, important progress has been made in calculating IR intensities of amide and backbone modes of the polypeptide chain (Cheam and Krimm, 1985). 

The application of normal-mode analysis to the study of vibrational spectra of proteins is in its infancy, and we may expect this area to develop significantly. In this connection, certain general studies will be useful the nature of vibrations in combined a and jS structures the extent of localization of modes in structures which contain hinge regions the correlation of the calculated spectrum of a protein with that obtained from a sum of its constituent secondary structural components. 

The consistent force field (CFF) was developed to yield consistent accuracy of results for conformations, vibrational spectra, strain energy, and vibrational enthalpy of proteins. There are several variations on this, such as the Ure-Bradley version (UBCFF), a valence version (CVFF), and Lynghy CFF. The quantum mechanically parameterized force field (QMFF) was parameterized from ah initio results. CFF93 is a rescaling of QMFF to reproduce experimental results. These force fields use five to six valence terms, one of which is an electrostatic term, and four to six cross terms. 

The C—S and S—S stretch vibrations of disulfides (Edsall et al., 1950) can be observed in the Raman spectra of proteins, but their interpretation is still somewhat controversial (see, for example, Klis and Siemion, 1978 Spiro and Gaber, 1977). Using series of model compounds, Van Wart et al. (1973) have related S—S stretch frequency to the xs (C/3—S—S—Cfi ) dihedral angle, while Sugeta et al. (1972, 1973) have related the S—S frequency to the x (Car—Cj8—S—S) di-... 

More discussions on vibrational spectra of peptides and proteins are found in Refs. 15-18. 

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. 

The vibrational spectra of molecules dissolved in water are different in significant ways from the spectra of these molecules in the gas phase. The study of water solution spectra is particularly important for molecules of biological significance because their structure and properties are often determined by the presence or absence of water. Computational techniques have been developed that relate computationally determined structure and associated properties such as force constants to experimental information such as vibrational frequencies. Experimental vibrational studies have been used to elucidate information about such problems as the secondary structure of proteins in water solution. A brief review of the computational and experimental techniques is presented. Our work, which builds on the essential combination of theoretical and experimental information, is then reviewed to outline our ideas about using computational studies to investigate the complicated problems of amino acids and proteins in water solution. Finally some suggestions are presented to show how computational techniques can enhance the use of experimental techniques, such as isotopic substitution for the study of complicated molecules. 

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. 

Vander Meulen and Ressler (1980) measured the near-lR spectra of proteins in aqueous solution and compared them with the spectra of protein films. Brown et al. (1983) reported multiple internal reflectance spectra of hydrated films of carbonmonoxy and oxy forms of hemoglobin. This work was extended by Findsen et al. (1986), who, using resonance Raman scattering, measured the effects of hydration on the equilibrium and dynamic properties of hemoglobin and its carbonmonoxy complex. There was a substantial effect of hydration on the CO vibration, but no significant effect on the vibrational properties of the heme protein. 

The absorption spectra of proteins and polypeptides are now much better understood as a result of the vibrational analyses given by Miyazawa (1960, 1962, 1963), but it is still true that structures are more often used to test the interpretation of spectra rather than the reverse. Transition moment directions and coupling effects, however, are now sufficiently well understood for infrared dichroism measurements to provide at least a semiquantitative evaluation of some features of a model. 

Detailed analyses of the vibrational spectra of raacromolecules, however, have provided a deeper understanding of structure and interactions in these systems (Krimm, 1960). An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in A -methylacetamide (Miyazawa et al., 1958), and the characterization of several specific amide vibrations in polypeptide systems (Miyazawa, 1962, 1967). Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins (see, for example, Pezolet et al., 1976 Lippert et al., 1976 Williams and Dunker, 1981 Williams, 1983). 

Table 1. Vibrational energy-spectra of protein with three channels in cm ...

Rimai L, Gill D and Parson JL (1971) Raman spectra of dilute solutions of some stereoisomers ofvitamin A-type molecules. J Am Chem Soc 93 1353-1357 Rimai L, Heyde ME and Gill D (1973) Vibrational spectra of some carotenoids and related linear polyenes. A Raman spectroscopic study. J Am Chem Soc 95 4493 501 Robert B (1983) Etude par diffusion Raman de resonance de complexes proteine-pigment antennes des RhodospiiiUales. These Doct. 3eme Cycle, Universite Pierre et Marie Curie, Paris... 

Spectra of proteins and nucleic acids. Most proteins have a strong light absorption band at 280 nm (35,700 cm ) which arises from the aromatic amino acids tryptophan, tyrosine, and phenylalanine (Fig. 3-14). The spectrum of phenylalanine resembles that of toluene (Fig. 23-7)whose 0-0 band comes at 37.32 x 10 cm. The vibrational structure of phenylalanine can be seen readily in the spectra of many proteins (e.g., see Fig. 23-llA). The spectrum of tyrosine is also similar (Fig. 3-13), but the 0-0 peak is shifted to a lower energy of 35,500 cm (in water). Progressions with spacings of 1200 and 800 cm are prominent. The low-energy band of tryptophan consists of two overlapping transitions and The Lb transition has well-resolved vibrational subbands, whereas those of the La transition are more diffuse. Tryptophan derivatives in hydrocarbon solvents show 0-0 bands for both of these transitions at approximately... 

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