Proteins, structure secondary

Most proteins have a characteristic secondary and tertiary structure and this arises from the alternative spatial distributions of the chains. 

FIGURE 10.14 Polypeptide chain configuration. The two amide planes (shown in broken lines) are connected by C and to each other by twist angles ( ) /. The two planes are coplanar when ( ) = / = 0. 

Reliable secondary structures can enhance the prediction of higher order protein structure, and to a limited extent, secondary-structure motifs can even suggest specific fold structures. Sometimes these secondary structures provide insight into function. Definition of Secondary Structure of Proteins (DSSP), Integrated Sequence-Structure Database (ISSD), Protein Secondary Structure Database (PSSD), and CATH are covered in this section (see Table 2.2). 

PSSD http //ibc.ut.ac.ir/pssd/about.html CATH http //www.cathdb.info/ 

PSSD is a database that incorporates sequences of secondary-structure elements for all proteins with three-dimensional structures defined by experimental methods (such as NMR-Spectroscopy or X-Ray Crystallography) and for which structural data exist in the Brookhaven protein databank. 

In addition to various studies on protein composition and distribution within the plant tissue [72], the influence of protein secondary structure on global crop attributes, such as nutritive values, baking quality, or digestive behavior, achieved increasing interest. 

The secondary structure of endosperm protein as either a-helix or sheet is generally identified by the line shape and position of the amide I (a-helix 1650 cm , -sheet 1630 cm ) or amide II band coupled with band modeling processes. 

In 1998, Wolkers et al. [73] identified changes in the protein secondary structure in association with desiccation tolerance of developing maize embryos by SR-IMS. The same technique was used by Yu et al. for comparison of the protein secondary structure of various grains with those of feathers. Feathers contain more than 80% of -folded protein, whereas grain is mainly composed of a-helix structured protein that is located in higher concentrations only in the endosperm [63, 74]. 

Wetzel and coworkers used SR-IMS to discriminate different wheat cultivars based on their protein secondary structure. The ratio of a-helix to -sheet was determined to range from 1.4 to 2.2 for hard and 1.0 for soft wheat cultivars, respectively [75, 76]. Studying the protein content and composition during grain development pointed out an increase in a-helix protein during ripening. 

By combination of FT-IR hyperspectral imaging and multivariate curve resolution (MCR) analysis, Budevska et al. [77] could identify two separate corn storage proteins, the so-called zeins in maize seed sections. By univariate analysis, these proteins could not be separated from the entire protein complex caused by superimposition of the corresponding amide I signals around 1656 cm .  

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Chi Z H, Chen X G, Holtz J S W and Asher S A 1998 UV resonance Raman-selective amide vibrational enhancement quantitative methodology for determining protein secondary structure Biochemistry 27 2854-64... 

Rost B and C Sander 1993. Prediction of Protein Secondary Structure at Better than 70% Accurt journal of Molecular Biology 232 584-599. 

Secondary structure (Section 27 19) The conformation with respect to nearest neighbor ammo acids m a peptide or pro tern The a helix and the pleated 3 sheet are examples of protein secondary structures... 

JE Gibrat, J Garnier, B Robson. Eurther developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J Mol Biol 198 425-443, 1987. 

LH Holley, M Karplus. Protein secondary structure prediction with a neural network. Proc Natl Acad Sci USA 86 152-156, 1989. 

AL Delcher, S Kasif, HR Goldberg, WH Hsu. Protein secondary structure modelling with probabilistic networks. Intelligent Systems m Molecular Biology 1 109-117, 1993. 

JM Chandoma, M Karplus. The importance of larger data sets for protein secondary structure prediction with neural networks. Protein Sci 5 768-774, 1996. 

GE Arnold, AK Dunker, SJ Johns, RJ Douthart. Use of conditional probabilities for determining relationships between ammo acid sequence and protein secondary structure. Proteins 12 382-399, 1992. 

P Stolorz, A Lapedes, Y Xia. Predicting protein secondary structure using neural net and statistical methods. J Mol Biol 225 363-377, 1992. 

Barton, G.J. Protein secondary structure prediction. Curr. Opin. Struct. Biol. 5 372-376, 1995. 

Rost, B., Sander, C., Schneider, R. Redefining the goals of protein secondary structure prediction. /. Mol. Biol. 

Oi Hel ix (Section 27.19) One type of protein secondary structure. It is a right-handed helix characterized by hydrogen bonds between NH and C=0 groups. It contains approximately 3.6 amino acids per turn. 

The conformational changes which have been described so far are probably all relatively small local changes in the structure of H,K-ATPase. This has been confirmed by Mitchell et al. [101] who demonstrated by Fourier transform infrared spectroscopy that a gross change in the protein secondary structure does not occur upon a conformational change from Ei to 3. Circular dichroism measurements, however [102,103], indicated an increase in a-helical structure upon addition of ATP to H,K-ATPase in the presence of Mg and... 

M. Vieth, A. Kolinsky, J. Skolnicek, and A. Sikorski, Prediction of protein secondary structure by neural networks, encoding short and long range patterns of amino acid packing. Acta Biochim. Pol., 39 (1992) 369-392. 

Determination of protein secondary structure has long been a major application of optical spectroscopic studies of biopolymers (Fasman, 1996 Havel, 1996 Mantsch and Chapman, 1996). These efforts have primarily sought to determine the average fractional amount of overall secondary structure, typically represented as helix and sheet contributions, which comprise the extended, coherent structural elements in well-structured proteins. In some cases further interpretations in terms of turns and specific helix and sheet segment types have developed. Only more limited applications of optical spectra to determination of tertiary structure have appeared, and these normally have used fluorescence or near-UV electronic circular dichroism (ECD) of aromatic residues to sense a change in the fold (Haas, 1995 Woody and Dunker, 1996). 

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. 

Kabsch, W., and C. Sander. 1983. Dictionary of Protein Secondary Structure Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Biopol. 22,2577-2637. 

Mason JT, O Leary TJ. Effects of formaldehyde fixation on protein secondary structure a calorimetric and infrared spectroscopic investigation. J. Histochem. Cytochem. 1991 39 225-229. 

The effect of formalin-treatment on the structural properties of RNase A was examined using circular dichroism (CD) spectropolarimetry. A brief introduction to CD spectropolarimetry is provided in Section 15.15.2 for those readers unfamiliar with this biophysical method. The secondary structure of RNase A consists of one long four-stranded anti-parallel p-sheet and three short a-helixes,44 which places RNase A in the a + p structural class of proteins. The effect of a 9-day incubation of RNase A (6.5mg/mL) in 10% formalin on the protein secondary structure was examined with CD spectropolarimetry in the far-UV region (170-240nm) as shown in Figure 15.6a. The resulting... 

This process of cross-linking does not appear have a major effect on protein secondary structure at room temperature. However, cross-links formed by reactions of formaldehyde with proteins retard, but do not eliminate, protein denaturation that occurs when proteins are heated to a temperature of approximately 70°C or above.7... 

Protein folding Glycosylation can effect local protein secondary structure and help direct folding of the polypeptide chain... 

A protein s secondary structure arises from the formation of intra- and inter-molecular hydrogen bonds. All carboxyl group oxygens and amine hydrogens of a polypeptide participate in H-bonding. Protein secondary structure also derives from the fact that although all C-N bonds in peptides have some double bond character and cannot rotate, rotation about the Co-N and Ca-C bonds is possible and is... 

Figure 2.9 Protein secondary structures (many R groups omitted for clarity). (Adapted with permission from Figure 1.19 of Cowan, J. A. Inorganic Biochemistry, An Introduction, 2nd ed., Wiley-VCH, New York, 1997. Copyright 1997, Wiley-VCH.)...

A review by Dong et al. [3.57] provides an overview of how Fourier transform JR spectroscopy can be used to study protein stabilization and to prevent lyophilization- induced protein aggregation. An introduction to the study of protein secondary structures and the processing and interpretation of protein IR spectra is given. 

Wallace, B. A., and Janes, R. W. (2001). Synchrotron radiation circular dichroism spectroscopy of proteins Secondary structure, fold recognition and structural genomics. Curr. Opin. Chem. Biol. 5, 567-571. 

Frishman, D., and Argos, P. (1995). Knowledge-based protein secondary structure assignment. Proteins 23, 566-579. 

Pelton, J. T., and McLean, L. R. (2000). Spectroscopic methods for analysis of protein secondary structure. Anal. Biochem. 277, 167-176. 

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