Protein-binding specificity, modification

Syndecans are transmembrane proteins, which are modified by the addition of heparan sulphate glycos-aminoglycan (GAG) chains and other sugars. Syndecans bind a wide variety of different ligands via their heparan sulphate chains. Binding specificities may vary depending on cell-type specific modifications of the heparan sulphate chains. 

Of all the novel protein types found in nematodes, only two have had biochemical activites ascribed, and these both happen to be lipid-binding proteins (LBPs). This chapter will focus on these, plus those that are structurally similar to those of vertebrates but appear to have nematode-specific modifications to their structures and functions. 

By using recombinant DNA techniques, modifications in the protein backbone, such as additions, deletions and alterations of amino acids, are easily achieved. These modifications can contribute to improved pharmacokinetic properties of the construct. Additions may consist of the introduction of residues that allow covalent conjugation of drug molecules. Deletions of amino acids can employed to remove membrane-bound regions of a protein, thereby increasing its solubility. Single amino acid modifications can be used to minimize antibody responses and alter the binding specificity and/or the three-dimensional structure of a certain protein. 

A further post-translational modification of p53 is an acetylation at the C terminus, for which stimulation of specific DNA binding has been reported (Wei and Roeder, 1997). Possibly, this acetylation is mediated by the CBP/p300 proteins (see 1.4.6), with which the p53 protein can specifically interact. 

An affinity label, or active-site-directed irreversible inhibitor, is a chemically reactive compound that is designed to resemble a substrate of an enzyme, so that it binds specifically to the active site and forms covalent bonds with the protein residues.1-3 Affinity labels are very useful for identifying catalytically important residues and determining their pKa values from the pH dependence of the rate of modification. 

Structurally, each Ga subunit consists of two domains—a GTPase domain, and a a-helical domain. In between these two domains is a cleft where guanine nucleotide binds. Lipid modification of a Cys residue near the amino-terminus of the Ga subunit allows for binding to membrane [8], and the carboxyl terminus of the protein appears important for interaction with receptor. Indeed, the last five residues of Ga are believed to contribute to specificity of interaction [reviewed in 9]. However Ho and Wong [10] have demonstrated that the amino terminus of Gaz is also a critical determinant of its coupling to the delta opioid receptor. 

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