Structural domains, table

The MMPs are a family of zinc-dependent neutral endopep-tidases that share structural domains but differ in substrate specificity, cellular sources, and inductivity (Table I). All the MMPs are important for remodeling of the extra cellular matrix and share the following functional features (/) they degrade extracellular matrix components, including fibronectin, collagen, elastin, proteoglycans, and laminin, (//) they are secreted in a latent proform and require activation for proteolytic activity, (///) they contain zinc at their active site and need calcium for stability, (/V) they function at neutral pH, and (v) they are inhibited by specific tissue inhibitors of metalloproteinases (TIMPs). 

The thin filaments of muscle 367 Table 7-3 A Few Well-Known Structural Domains... 

The apoproteins are distinct physically, chemically, and immunochemically and have important roles in lipid transport and metabolism (Table 20-1). In keeping with their individual metabolic functions, they have specific structural domains. Amino acid substitutions or deletions in critical domains result in functional abnormalities. The apoproteins share a common structure in the form of an amphipathic helix, in which the amino acid residues have hydrophobic side chains on one face of the helix and hydrophilic polar residues on the other. The hydrophilic face is believed to interact with the polar head groups of the phospholipids, while the hydrophobic residues interact with their fatty acid portions. 

Many proteins share structural similarities due to the evolutionary process involving substitutions, insertions and deletions in amino add sequences. Consequently protein structures can be characterized according to their connnon substructures (supersecondary structures, e.g. motifs, domains). For proteins with conserved functions, the structural environments of critical active site residues are also conserved. In an attempt to better understand seqnence-structuie relationships and the underlying evolutionary processes that give rise to different fold famihes, a variety of structure classification schemes have been established. Analyses of the 3D structures archived in PDB generate various databases for the specification/search of characteristic substructures and protein structure classifications (Table 16.6). 

A family of protein polymers, ProLastins, were produced consisting of silklike (S) and elastinlike (E) peptide blocks in various block lengths and compositional ratios (Ferrari et al, 1986, and Cappello et al, 1990). The elastinlike block consists of the five amino add sequence, GVG T (Urn 1984, Urry et al., 1976, and Uriy 1988). As a family, silk-elastinlike copolymers (SELP s) consist of exact periodic alternation of silk and elastinlike domains. Individual members of the family vary in the number of silk or elastin blocks within the repeating domains. Table 2 displays the compositional structures of some ProLastin monomers. 

Structures of various ThDP-dependent enzymes have been reported. In 2006, Duggleby proposed classifying ThDP-dependent enzymes into five broad families, based on their structural (domain) relationships and possible evolutionary routes (Table 4.1) (Duggleby 2006). 

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