Secondary structures globular proteins

Provencher, S.W. andGlockner, J. 1981. Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20 33-37. 

V. 1. Lim. Structural principles of die globular organisation of proton chains. A stereochemical theory rf globular protein secondary structure. J. MoL BioL 88 857-872(1974). 

A. Relative >robabUitles of amino add residueOi ( urreiice in dift erent globular protein secondary structures ... 

The P structure is one of the most important secondary structures in proteins. It occurs in about 80% of the soluble globular proteins whose structures have been determined. In many cases almost the entire protein is made up of P structure. Single strands of extended polypeptide chain are sometimes present within globular proteins but more often a chain folds back on itself to form a hairpin loop. A second fold may be added to form an antiparallel "P meander"102 and additional folds to form P sheets. Beta structures are found in silk fibers (Box 2-B) as well as in soluble proteins. 

We began the discussion of globular protein tertiary structure by pointing out that the secondary and tertiary structure is determined by the primary structure and that this is probably a reflection of the fact that the native folded conformation is the most stable structure that can be formed. If this is so, then it should be possible to predict a protein s structure from its primary sequence. At this juncture, such predictions remain an elusive goal. However, most proteins are made of a limited number of domains, which tend to reappear in many different proteins. Since this is the case, it may be possible to predict the structures of many proteins in the future by using the information accumulated from x-ray diffraction studies of related proteins. 

A type of protein secondary structure where the chain is neither curled into an a helix nor lined up in a pleated sheet. In a globular protein, the kinks that fold the molecule into its globular shape are usually segments of random coil. (p. 1192)... 

A rapid FTIR method for the direct determination of the casein/whey ratio in milk has also been developed [26]. This method is unique because it does not require any physical separation of the casein and whey fractions, but rather makes use of the information contained in the whole spectrum to differentiate between these proteins. Proteins exhibit three characteristic absorption bands in the mid-infrared spectrum, designated as the amide I (1695-1600 cm-i), amide II (1560-1520 cm-i) and amide III (1300-1230 cm >) bands, and the positions of these bands are sensitive to protein secondary structure. From a structural viewpoint, caseins and whey proteins differ substantially, as the whey proteins are globular proteins whereas the caseins have little secondary structure. These structural differences make it possible to differentiate these proteins by FTIR spectroscopy. In addition to their different conformations, other differences between caseins and whey proteins, such as their differences in amino acid compositions and the presence of phosphate ester linkages in caseins but not whey proteins, are also reflected in their FTIR spectra. These spectroscopic differences are illustrated in Figure 15, which shows the so-called fingerprint region in the FTIR spectra of sodium caseinate and whey protein concentrate. Thus, FTIR spectroscopy can provide a means for quantitative determination of casein and whey proteins in the presence of each other. 

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 ... 

Gamier J, D Osguthorpe and B Robson 1978. Analysis of the Accuracy and ImpUcatiotrs of Simple Mel for Predicting the Secondary Structure of Globular Proteins. Journal of Mokadar Biology 120 97-i... 

Nlng Q and T J Sejnowsld 1988. Predicting the Secondary Structure of Globular Proteins Using Neural Network Models. Journal of Molecular Biology 202 865-888. 

Hydrogen bonding stabilizes some protein molecules in helical forms, and disulfide cross-links stabilize some protein molecules in globular forms. We shall consider helical structures in Sec. 1.11 and shall learn more about ellipsoidal globular proteins in the chapters concerned with the solution properties of polymers, especially Chap. 9. Both secondary and tertiary levels of structure are also influenced by the distribution of polar and nonpolar amino acid molecules relative to the aqueous environment of the protein molecules. Nonpolar amino acids are designated in Table 1.3. 

MJ McGregor, SA Islam, MJE Sternberg. Analysis of the relationship between side-chain conformation and secondary structure m globular proteins. J Mol Biol 198 295-310, 1987. 

N Qian, TJ Sejnowski. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 202 865-884, 1988. 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

Gamier, J., Osguthorpe, D.J., Robson, B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. 

Figure 26.5 (a) The o-helical secondary structure of proteins is stabilized by hydrogen bonds between the N—H group of one residue and the C=0 group four residues away, (b) The structure of myoglobin, a globular protein with extensive helical regions that are shown as coiled ribbons in this representation. 

Polyacrylamide gel electrophoresis results suggest that p-LG undergoes a greater conformational loss as a fimction of extrusion temperature than a-LA, presumably due to intermolecular disulfide bond formation. Atomic force microscopy indicates that texturization results in a loss of secondary structure of aroimd 15%, total loss of globular structure at 78 °C, and conversion to a random coil at 100 °C (Qi and Onwulata, 2011). Moisture has a small effect on whey protein texturization, whereas temperature has the largest effect. Extrusion at or above 75 °C leads to a uniform densely packed polymeric product with no secondary structural elements (mostly a-helix) remaining (Qi and Onwulata, 2011). 

Lefczynski, J. F. and Rose, G. D., Loops in globular proteins a novel category of secondary structure, Science, 234, 849, 1986. 

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