Helical structure, of proteins

In contrast with the right-handed a-helical structure of proteins a similar left-handed folding is theoretically possible in which the dihedral angles would be approximately VF = 50° and = 90°. Because of the substituent... 

In the 1930s, Linus Pauling published his results on the nature of the covalent bond. Pauling electronegativity is named after him. In the 1950s, Pauling determined the a-helical structure of proteins. 

The CD Spectra of P-sheet and random-coil conformations are isodichroic (identical elUp-ticity values) at 208 nm with an average effipticity of OOOdegcm dmor. The observed ellipticity at 208 nm for a-helix is -32600 4000deg cm dmoC. Thus the a-helical content (fraction of a-helical structure, of proteins can be estimated according to... 

Indicate whether each statement is true or false (a) In the alpha helical structure of proteins, hydrogen bonding occurs between the side chains (R groups), (b) Dispersion forces, not hydrogen bonding, holds beta sheet structures together. 

Within months of the appearance of the article by the Dutch crystallographers Bijvoet, Peerdeman, and von Bommel on the absolute structure of (+ )-tartrate, Linus Pauling (Biographic Photo 2.5), Robert Corey, and Herman Branson published a milestone article on the helical structure of proteins [8]. Fischer had actually shown 50 years earlier that proteins were a linear chain of amino acids, but the overall three-dimensional structure of proteins was unknown. We introduced L-amino acids in Chapter 1 in our discussion of nomenclature, and we draw a... 

The cylinder model is used to characterize the helices in the secondary structure of proteins (see the helices in Figure 2-124c),... 

By analogy to the levels of structure of proteins the primary structure of DNA IS the sequence of bases along the polynucleotide chain and the A DNA B DNA and Z DNA helices are varieties of secondary structures... 

Chofhia, C., Levitt, M., Richardson, D. Structure of proteins packing of a-helices and pleated sheets. 

Pauling, L., Corey, R.B., Branson, H.R. The structure of proteins two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sd. USA 37 205-211, 1951. 

FIGURE 5.8 Two structural motifs that arrange the primary structure of proteins into a higher level of organization predominate in proteins the a-helix and the /3-pleated strand. Atomic representations of these secondary structures are shown here, along with the symbols used by structural chemists to represent them the flat, helical ribbon for the a-helix and the flat, wide arrow for /3-structures. Both of these structures owe their stability to the formation of hydrogen bonds between N—H and 0=C functions along the polypeptide backbone (see Chapter 6). 

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. 

Figure 3-4. Dimensions of a fully extended polypeptide chain. The four atoms of the peptide bond (colored blue) are coplanar. The unshaded atoms are the a-carbon atom, the a-hydrogen atom, and the a-R group of the particular amino acid. Free rotation can occur about the bonds that connect the a-carbon with the a-nitrogen and with the a-carbonyl carbon (blue arrows). The extended polypeptide chain is thus a semirigid structure with two-thirds of the atoms of the backbone held in a fixed planar relationship one to another. The distance between adjacent a-carbon atoms is 0.36 nm (3.6 A). The interatomic distances and bond angles, which are not equivalent, are also shown. (Redrawn and reproduced, with permission, from Pauling L, Corey LP, Branson PIR The structure of proteins Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 1951 37 205.)...

Figure 5-6. Examples of tertiary structure of proteins. Top The enzyme triose phosphate isomerase. Note the elegant and symmetrical arrangement of alternating p sheets and a helices. (Courtesy of J Richardson.) Bottom Two-domain structure of the subunit of a homodimeric enzyme, a bacterial class II HMG-CoA reductase. As indicated by the numbered residues, the single polypeptide begins in the large domain, enters the small domain, and ends in the large domain. (Courtesy ofC Lawrence, V Rod well, and C Stauffacher, Purdue University.)...

From the atomic to the macroscopic level chirality is a characteristic feature of biological systems and plays an important role in the interplay of structure and function. Originating from small chiral precursors complex macromolecules such as proteins or DNA have developed during evolution. On a supramolecular level chirality is expressed in molecular organization, e.g. in the secondary and tertiary structure of proteins, in membranes, cells or tissues. On a macroscopic level, it appears in the chirality of our hands or in the asymmetric arrangement of our organs, or in the helicity of snail shells. Nature usually displays a preference for one sense of chirality over the other. This leads to specific interactions called chiral recognition. 

The discovery of the base-paired, double-helical structure of deoxyribonucleic acid (DNA) provides the theoretic framework for determining how the information coded into DNA sequences is replicated and how these sequences direct the synthesis of ribonucleic acid (RNA) and proteins. Already clinical medicine has taken advantage of many of these discoveries, and the future promises much more. For example, the biochemistry of the nucleic acids is central to an understanding of virus-induced diseases, the immune re-sponse, the mechanism of action of drugs and antibiotics, and the spectrum of inherited diseases. 

In proteins in particular the peptide bonds contribute to the CD-spectra of the macromolecule. Here, CD-spectra reflect the secondary structure of proteins, which are derived from CD-spectra of model macromolecules with only one defined secondary structure (like poly-L-lysine at given pH values) or based on spectra of proteins with known structures (e.g.,from X-ray crystallography). The amount of a-helices or -sheets in the unknown structure is calculated by linear combination of the reference spectra [150,151]. 

Figure 11.2 The secondary structure of proteins. The simplest spatial arrangement of amino acids in a polypeptide chain is as a fully extended chain (a) which has a regular backbone structure due to the bond angles involved and from which the additional atoms, H and O, and the amino acid residues, R, project at varying angles. The helical form (b) is stabilized by hydrogen bonds between the —NH group of one peptide bond and the —CO group of another peptide bond. The amino acid residues project from the helix rather than internally into the helix.

These model experiments involving e.e. amplification of amino adds during polymerization admittedly need prebiotically unrealistic substrates as well as carefully contrived experimental conditions. Nevertheless, it is noteworthy that both secondary structures of proteins, a-helices, and P-sheets have been found capable of acting stereoselectively to provide e.e. enhancements during these model polymerizations. 

The influence of secondary structure on reactions of deamidation has been confirmed in a number of studies. Thus, deamidation was inversely proportional to the extent of a-helicity in model peptides [120], Similarly, a-hel-ices and /3-turns were found to stabilize asparagine residues against deamidation, whereas the effect of /3-sheets was unclear [114], The tertiary structure of proteins is also a major determinant of chemical stability, in particular against deamidation [121], on the basis of several factors such as the stabilization of elements of secondary structure and restrictions to local flexibility, as also discussed for the reactivity of aspartic acid residues (Sect. 6.3.3). Furthermore, deamidation is markedly decreased in regions of low polarity in the interior of proteins because the formation of cyclic imides (Fig. 6.29, Pathway e) is favored by deprotonation of the nucleophilic backbone N-atom, which is markedly reduced in solvents of low polarity [100][112],... 

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