Protein secondary structure, methods study

Our band shape methods have made use of the principal component method of factor analysis (Pancoska etal., 1979 Malinowski, 1991) to characterize the protein spectra in terms of a relatively small number of coefficients (loadings) (Pancoska et al., 1994 1995 Baumruk et al., 1996). This approach is similar, in its initial stages, to various methods (Selcon, Variselect, etc.) that have been used for determining protein secondary structure from ECD data (Hennessey and Johnson, 1981 Provencher and Glockner, 1981 Johnson, 1988 Pancoska and Keiderling, 1991 Sreerama and Woody, 1993, 1994 Venyaminov and Yang, 1996). At this point, one can say these traditional quantitative methods have had little impact upon structural studies of denatured proteins. 

In the literature Raman spectroscopy has been used to characterize protein secondary structure using reference intensity profile method (Alix et al. 1985). A set of 17 proteins was studied with this method and results of characterization of secondary structures were compared to the results obtained by x-ray crystallography methods. Deconvolution of the Raman Amide I band, 1630-1700 cm-1, was made to quantitatively analyze structures of proteins. This method was used on a reference set of 17 proteins, and the results show fairly good correlations between the two methods (Alix et al. 1985). 

There is substantial history regarding the application of conventional vibrational spectroscopy methods to study the intact surface of skin, the extracted stratum corneum and the ceramide-cholesterol-fatty acid mixtures that constitute the primary lipid components of the barrier. The complexity of the barrier and the multiple phases formed by the interactions of the barrier components have begun to reveal the role of each of these substances in barrier structure and stability. The use of bulk phase IR to monitor lipid phase behavior and protein secondary structures in the epidermis, as well as in stratum corneum models, is also well established 24-28 In addition, in vivo and ex vivo attenuated total reflectance (ATR) techniques have examined the outer layers of skin to probe hydration levels, drug delivery and percutaneous absorption at a macroscopic level.29-32 Both mid-IR and near-IR spectroscopy have been used to differentiate pathological skin samples.33,34 The above studies, and many others too numerous to mention, lend confidence to the fact that the extension to IR imaging will produce useful results. 

Source Data from Liljas A, Rossmann MG. X-ray studies of protein interactions. Annu Rev Biochem 43 475-505, 1974 Argos P, Schwarz JS, Schwarz J. An assessment of protein secondary structure prediction methods based on amino acid sequence. Biochim Biophys Acta 439 261-273, 1976. 

The present analysis might give rise to a somewhat pessimistic view of the effectiveness of protein secondary structure prediction algorithms. In fact, with the increasing number of proteins with known three-dimensional structure, constant re-evaluation of performance must take place in order to ascertain the validity of the methods. We note that the methods do not have the predictive power claimed by its authors when analyzed consistently using the 148 proteins selected in this study. Moreover, the situation is even worse for the Mathews correlation coefficient, which indicates that the predictions are poorly correlated with the actual structure. 

The analysis of the amide I band to obtain the estimation of protein secondary structure content in terms of percentage helix, j3 strand, and reverse turn that was developed by Williams has proved very successful and has now been used by numerous workers.In this method the amide I region is analyzed as a linear combination of the spectra of the reference proteins whose structures are known. As noted above the Raman spectra of globular proteins in the crystal and in solution are almost identical, reflecting the compact nature of the macromolecules. Thus one may use the fraction of each type of secondary structure determined in the crystalline state by the X-ray diffraction studies for proteins in solution. If there are n reference proteins with the Raman spectrum of each of them represented as normalized intensity measurements at p different wave numbers, then this information is related by the following matrix equation ... 

Native monellin consists of two polypeptide chains, a 45-residue A-chain and a 50-residue B-chain, linked by non-covalent interactions. At neutral pH, it is fairly resistant to heat denaturation with a higher than 80 °C. The crystal structure of native monellin shows a tertiary structure comprising an anti-parallel /1-sheet with five strands and an a-helix. H NMR spectroscopy and hydrogen exchange methods have been used to characterize the alcohol-denaturated state of monellin in order to understand how its secondary structure depends on environmental conditions. " Structural and dynamic studies by NMR have been carried out in order to compare native monellin and a non-sweet analogue in which Asp was replaced by Abu . The three-dimensional structures of the two proteins are found to be very... 

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