Protein structure hierarchy

Condensation between the -NFI3 and the -COO groups of two amino acids generates a peptide bond and results in the formation of a dipeptide. 

Nonpolar glycine (G) , alanine (A), valine (V), leucine (L), isoleucine (I), proline (P), methionine (M), phenylalanine (F), tryptophan (W) 

Polar serine (S), threonine (T), asparagine (N), glutamine (Q), cysteine (C), tyrosine (Y) 

Acidic (polar) aspartic acid (D), glutamic acid (E) 

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A description of the protein-structure hierarchy is incomplete without a discussion of structural motifs, which are critical to an understanding of protein structure [17]. Identification of recurring motifs in protein structures has refined our knowledge of the protein-structure hierarchy these motifs occur at all levels from primary to tertiary. The Phe-Asp-Thr-Gly-Ser sequence found in the active site of all aspartic acid proteinases, and the Gly-Gly-X-Leu sequence (where X represents any amino acid residue) that predicts a 3-strand for the last two residues [17], are examples of sequence motifs a-helices, P-strands, and turns are examples of secondary-structural motifs PaP and PxP units, P-hairpins, and Greek keys are examples of supersecondary-structural motifs and four-a-helix bundles and TIM barrels are examples of tertiary-structural motifs. The tertiary fold of a protein is characterized by its tertiary-structural motif. 

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. 

The complex hierarchy of native protein structure may be disrupted by multiple possible destabilizing mechanisms. As has been described in the foregoing, these processes may disrupt noncovalent forces of interaction or may involve covalent bond breakage or formation. A summary of the processes involved in the irreversible inactivation of proteins is illustrated in Fig. 3 and described briefly in the following section. Detailed discussions of mechanisms of protein desta-... 

Figure 1.3 Folding of a polypeptide chain illustrating the hierarchy of protein structure from primary structure through secondary structure and tertiary structure.

The hierarchy of protein structure is illustrated in hgure 11.4. Here too we have a wealth of structural information. The quaternary structures for many proteins are now known and generally available in databases. As complex as these are, this is not the end of the story. We have atom-by-atom structures for entities as complex as viruses and the ribosome, an intracellular RNA-protein complex and the site of protein synthesis. Modem structural biology continues to provide detailed insights into some of the most complex constracts of nature. We are better off for having these insights. 

Figure 11.4 The structural hierarchy in proteins, (a) A segment of primary structure (b) secondary structure illustrated as a segment of alpha helix (c) tertiary structure in which helices are interspersed with coils, and (d) quaternary structure. (Illustration, Irving Geis/Geis Archive Trust. Copyright Howard Hughes Medical Institute. Reproduced with permission.)...

The Structure of the a-Keratins Was Determined with the Help of Molecular Models The fi-Keratins Form Sheetlike Structures with Extended Polypeptide Chains Collagen Forms a Unique Triple-Stranded Structure Globular Protein Structures Are Extremely Varied and Require a More Sophisticated Form of Analysis Folding of Globular Proteins Reveals a Hierarchy of Structural Organization... 

Hierarchies of protein structures. (Illustration for part c copyright by Irving Geis. Reprinted by permission.)... 

Although helical structures dominate the structural hierarchies found in proteins, random chain structures similar to those found in natural rubber also are found in tissues. The most-studied random chain polymer found in vertebrate tissues is elastin. 

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