Secondary structure The

The shape of a large protein is influenced by many factors including of course Its primary and secondary structure The disulfide bond shown m Figure 27 18 links Cys 138 of carboxypeptidase A to Cys 161 and contributes to the tertiary structure Car boxypeptidase A contains a Zn " ion which is essential to the catalytic activity of the enzyme and its presence influences the tertiary structure The Zn ion lies near the cen ter of the enzyme where it is coordinated to the imidazole nitrogens of two histidine residues (His 69 His 196) and to the carboxylate side chain of Glu 72... 

Primary and Secondary Structure. The DNA double helix was first identified by Watson and Crick in 1953 (4). Not only was the Watson-Crick model consistent with the known physical and chemical properties of DNA, but it also suggested how genetic information could be organized and rephcated, thus providing a foundation for modem molecular biology. 

Secondary Structure. The silkworm cocoon and spider dragline silks are characterized as an antiparaHel P-pleated sheet wherein the polymer chain axis is parallel to the fiber axis. Other silks are known to form a-hehcal (bees, wasps, ants) or cross- P-sheet (many insects) stmctures. The cross-P-sheets are characterized by a polymer chain axis perpendicular to the fiber axis and a higher serine content. Most silks assume a range of different secondary stmctures during processing from soluble protein in the glands to insoluble spun fibers. 

The secondary structure - the regular, recuiring, arrangements in space of adjacent amino acid residues in the protein chain, e.g. a-helix, /S-sheet, etc. 

Regions of ordered secondary structure arise when a series of aminoacyl residues adopt similar phi and psi angles. Extended segments of polypeptide (eg, loops) can possess a variety of such angles. The angles that define the two most common types of secondary structure, the a helix and the (5 sheet, fall within the lower and upper left-hand quadrants of a Ramachandran plot, respectively (Figure 5-1). 

Amino acid sequences of eleven homologous sea anemone polypeptides have been elucidated. All possess three disulfide bonds. The six half-cysteine residues always occur in the same positions (7,8). Initial studies concerning the toxin secondary and tertiary structures relied upon circular dichroism, laser Raman, and, to a lesser extent, fluorescence spectral measurements (15—18). The circular dichroism spectra of the four toxins so far examined are essentially superimpos-able and thus indicate a common secondary structure. The only peak observed, a negative ellipticity at 203 nm, largely results from a non-regular ("random")... 

We limit the discussion to the level of secondary structures of sea anemone toxins since the tertiary structure of no other anemone toxins is known at present. Wid-mer et al. (7), on the basis of high resolution 2D-NMR results, have provided the most detailed information about the secondary structure of the A, sulcata toxin ATX la. Gooley and Norton (4-6) have partially assigned the toxins ATX I and AP-A, and compared their secondary structures. The NMR results are consistent and show that the anemone toxins all consist of a four strand antiparallel -sheet core and have no significant helical structure. 

Figure 16.2 Lactobacillus plantarum Mn catalase (left) stereo view of the secondary structure— the di-Mn unit as red spheres and (right) the detailed geometry of the di-Mn centre. (From Barynin et al., 2001. Copyright 2001, with permission from Elsevier.)...

This discussion puts us in a position to define a set of structural and evolutionary objects the tracing of whose history via homology, as implied by sequence similarity, is the primary aim of sequence analyses. The simple view of protein folding produces a small set of structural components to consider. This is the set of regular secondary structures the amphipathic a helix, the transmembrane or hydrophobic a. helix, the... 

The secondary structure, the mesopores, is similar to the internal structure of standard HPLC particles. This secondary structure provides the surface for retention. The standard pore size is in the order of 13 nm, resulting in a specific surface area of about 300 mVg. Due to the lower ratio of retentive structure to interstitial space, the retentivity of monoliths and the preparative loadability tends to be significantly lower than the retentivity and loadability of packed beds of 10-nm particles. Since the monolithic columns described here are made from silica, they can be derivatized in the same way and with the same technology as silica-based particles. Also, the useful pH range is the same as for silica-based particles. 

Plant defensins are cystine-rich, cationic peptides ranging in size from 45 to 54 amino acids, of which eight are cysteine. They were first discovered in wheat and barley ° and were proposed to form a novel subclass of thionins, the 7-thionins. As it became clear that they closely resemble mammalian and insect defensins in primary and secondary structure, the term plant defensins was introduced to describe these peptides. It is generally assumed that all plants express plant defensins " and that they are expressed in a wide range of plant tissue, that is, leaves, floral tissue,tubers,bark, root, pods, and seeds,with seeds in particular being from where most plant defensins have been isolated. ... 

Fig. 8. Ribbon diagram of the restraint energy-minimized average structure of singlechain monellin displaying ordered secondary structure elements and relative orientation of secondary structures. The side chain atoms for residues thought to be responsible for sweetness and receptor binding are also displayed. Reprinted with permission from Biochemistry, Vol. 38, S. Y. Lee, J. H. Lee, H. J. Chang, J. M. Cho, J. W. Jung and W. Lee, 1999, p. 2340. Copyright (1999) American Chemical Society.

An important element in the three-dimensional structure of a protein is the secondary structure. The secondary structure results from the formation of hydrogen bonds between the—N—H groups and the carbonyl (C O) groups of the peptide bonds —N—H 0=C. There are two basic ways to do this. We can form a helix or we can form a sheet. The great American chemist Linus Pauling won the Nobel Prize in Chemistry in 1954 for the elucidation of these structures. 

In proteins, specific combinations of the dihedral angles c ) and / (see p. 66) are much more common than others. When several successive residues adopt one of these conformations, defined secondary structures arise, which are stabilized by hydrogen bonds either within the peptide chain or between neighboring chains. When a large part of a protein takes on a defined secondary structure, the protein often forms mechanically stable filaments or fibers. Structural proteins of this type (see p. 70) usually have characteristic amino acid compositions. 

The primary and secondary structures greatly influence possible processing scenarios. Here, the secondary structure is generally the same as the physical structure and the primary structure is generally the same as the chemical structure. The end properties and uses are governed by intrinsic properties that in turn are related to the primary and secondary structures—the chemical and physical structures. 

The predicted secondary structures for DIMS9059 (an effective IFN inducer) and for DIMS9011 (functionally inactive negative control), both characterized by positive AG value of formation, suggest that in standard conditions these DIMS most probably will have a random secondary structure. The possible explanation of functional difference for these two compounds could be found on the tertiary structure level as well (see Note 15). 

Figure 2-2. Structures of a-helix and P-sheet Dashed lines indicate hydrogen bonds that stabilize these types of secondary structure. The hydrogen bonds of the a-helix are intrastrand, ie, formed between the backbone carbonyl oxygen and the amide hydrogen four amino acids up the helix. R groups represent the side chains in the a-helix. Side chains that would project above and below the plane of the page in the P-sheet structures have been omitted for clarity. Hydrogen bonds stabilizing the p-sheet are interstrand, ie, formed between groups on neighboring strands.

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