Turn, Protein Secondary Structures

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. 

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). 

The above description is a considerable simplification of protein secondary structure possibilities. Thus a number of helix types are possible in addition to the a-helix. Further, particular structured 3-turns exist that are stabilized by hydrogen bonding and link other secondary structure elements. Relatively unstructured coils, loops and random coils can also link a-helical and 3-strand elements. 

Table 10.1 summarizes neural network applications for protein structure prediction. Protein secondary structure prediction is often used as the first step toward understanding and predicting tertiary structure because secondary structure elements constitute the building blocks of the folding units. An estimated 90% or so of the residues in most proteins are involved in three classes of secondary structures, the a-helices, p-strands or reverse turns. Related to the secondary structure prediction are also the prediction of solvent accessibility, transmembrane helices, and secondary structure content (10.2). Neural networks have also been applied to protein tertiary structure prediction, such as the prediction of the backbones or side-chain packing, and to structural class prediction (10.3). 

Figure 4. Protein secondary structural elements (a) right-handed a-helix showing intrachain hydrogen bonds as dotted lines (crR 0 = —60°, 0 = —60°) (b) antiparallel /S-pleated sheet showing interchain hydrogen bonds as dashed lines WA 0 = —120°, 0 = 120°) (c) /3-turns of types I and II, differing in the orientation of the central peptide group. [Part (a) is adapted from A. L. Lehninger, Biochemistry (Worth Publishers, Inc., New York, 1975) (b) from Ref. 81 and (c) from Ref. 53.J...

The a helix, 3 strand and sheet, and turn are the most prevalent elements of protein secondary structure, which is stabilized by hydrogen bonds between atoms of the peptide backbone. 

See also Fibrous Proteins, Secondary Structure (General), a-Helix, / -Sheets, / -Turns... 

The best method to use for the estimation of protein secondary structure involves band-fitting the amide I band. The parameters required, and the number of component bands and their positions are obtained from the resolution-enhanced spectra. The fractional areas of the fitted component bands are directly proportional to the relative amounts of structure that they represent. The percentages of helices, -structures and turns are estimated by addition of the areas of all of the component bands assigned to each of these structures and then expressing the sum as a fraction of the total amide I area. The... 

Turn, a secondary structure element of nonperiodic nature. Turns are found in proteins and peptides. They are classified by the number of amino acids (n) involved, and the dihedral angles ip and tp of the n-2 middle amino acids, y-Turns are formed by three amino acids, /i-turns by four amino acids, and a-tums by five amino acid residues. Turns are often stabilized by a hydrogen bond between the amino group of the C-terminal amino acid and the carboxy group of the N-terminal amino acid. 

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 ... 

Protein Secondary structure (%) a Helix jS Sheet Turn Random Method... 

There are four structural arenas covered by secondary structure prediction methodologies from the amino acid sequence alone (1) typical protein secondary structures as helices, j0-strands, turns and coil (c.f., 60-62) (li) transmembrane helices (iii) signal and target sequences and (Iv) antigenic sites. The prediction area is usually in a constant state of review. It is intended here to give only a summary of the techniques and their usefulness and to discuss some of the more recent developments. Recent reviews will be given. 

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