Protein structure, common characteristics

Many proteins consist of two or more interacting polypeptide chains of characteristic tertiary structure, each of which is commonly referred to as a subunit of the protein. Subunit organization constitutes another level in the hierarchy of protein structure, defined as the protein s quaternary (4°) structure (Figure 5.10). Questions of quaternary structure address the various kinds of subunits within a protein molecule, the number of each, and the ways in which they interact with one another. 

Other examples of basic binding blocks include (1) ATP binding cassette transporter with a characteristic nucleotidebinding domain signature, (2) cyclic AMP or cyclic GMP receptor proteins, and (3) BH domain signature found in Bcl-fami-lies. A more complete description of these proteins with common structural and functional domains is listed in Table 16.5. The... 

From the viewpoint of zootaxa, the silkworm and the spider belong to insect and arachnid of arthropod, respectively. Their silk proteins (fibroin for silkworm silk and spidroin for spider major ampullate silk) do not have any genetic heritage in common and their amino acids sequence compositions are different too. However, the silkworm and spider employ a similar spinning process to produce silk. Furthermore, the silkworm silk and the major ampullate silk have a number of similar structural characteristics, both at the level of the secondary protein structure and the condensed silk morphology. Therefore, for the sake of convenience, they are discussed together in some parts of this text. 

Enzymatic cofactors, such as nicotinamide adenine dinucleotide (NADH), nicotinamide adenine dinucleotide phosphate (NADPH), flavin adenine dinucleotide (EAD), flavin mononucleotide (EMN), and pyridoxal phosphate, are fluorescent and commonly found associated with various proteins where they are responsible for electron transport (see Fig. lb and Table 1). NADH and NADPH in the oxidized form are nonfluorescent, whereas conversely the flavins, FAD and EMN, are fluorescent only in the oxidized form. Both NADH and FAD fluorescence is quenched by the adenine found within their cofactor structures, whereas NADH-based cofactors generally remain fluorescent when interacting with protein structures. The fluorescence of these cofactors is often used to study the cofactors interaction with proteins as well as with related enzymatic kinetics (1, 9-12). However, their complex fluorescent characteristics have not led to widespread applications beyond their own intrinsic function. 

As described earlier, the ability to site specifically replace one amino acid with another genetically encoded residue provides extraordinary access to analyze protein structure and function. An area where it is often applied is in the assessment of the role of phosphorylation of side chains. Typically, two classes of mutants are made those that prevent modification (nonphosphorylatable) and those that are constitutive (nonhydrolyzable) phosphorylated mimics. For the former, the phosphorylatable residues Ser and Thr are replaced with Ala, and Tyr with Phe (Fig. 7.2-3). These are reasonably successful in many cases, although they can be misleading because they lack the hydrogen-bonding and polarity characteristics of the authentic residues [19]. More difficult is the substitution of a phosphoamino acid with one of the 20 encoded residues. Phosphoserine/threonine is commonly replaced with Asp or Glu residues (Fig. 7.2-4). However, Asp and Glu are deficient in several respects. First,... 

The CRP - DNA Complex - The structure of the CRP-cAMP-DNA complex, as revealed by x-ray crystallography, shows how the protein binds to DNA. Each CRP subunit contains a characteristic pair of 01 helices, called a helix-turn-helix structural motif (see Figure 28.23). It is found in several DNA-binding regulatory proteins, suggesting common evolutionary origins for this family of proteins. 

There are many different three-dimensionai shapes that proteins adopt to perform important functions in the body. A common characteristic found in many transcription factors and regulatory proteins is zinc fingers, where a zinc atom plays an important role in the structure and function of the protein. Por this reason, different forms of zinc are often found in commercial vitamin supplements, including zinc sulfate. Ifthe solubility of ZnS04 is... 

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