Amino acids domain recognition

The production of chimeric cDNA molecules is typically used to localize an amino acid domain in a protein that gives rise to a specific property that is absent in a homologous protein. For example, this property could be the recognition of a specific drug, interaction with a specific protein, or localization to a specific cellular location. Chimeras are often a necessary first step in the path of identifying individual... 

Domain, sequence of amino acids in a protein that can be identified as controlling a specific function, that is, recognition of ligands. 

Since the modification that causes loss of activity in the enzyme H- K 234 does not interfere with the formation of the PG-PGIP complex, the site re onable for PGIP recognition may redde in a domain different fiom the active e. Studies are now under way to establish wdiich e(s) and amino acid residues of the e/uiiopolygalacturonase are critical for interaction with PGIP. 

Fig. 4.1 Topological organization of the vanilloid receptor TRP VI. Highlighted are the molecular determinants of TRPVl regulation, such as recognition (binding) domains for capsaicin and acids, and phosphorylation sites for protein kinases. Numbers designate the key amino acid residues deduced from the rTRPVl primary sequence. Adapted from Ferrer-Montaniel, A. et al. (2004) Fur. J. Biochem. 271, 1820—1826.

Surratt CK, Johnson PS, Moriwaki A et al. p opiate receptor Charged transmembrane domain amino acids are critical for agonist recognition and intrinsic activity. J Biol Chem 1994 269 20548-20553. 

The Ras superfamily of GTP-binding proteins is composed of several subfamilies [7] which all contain the Ras-like domain of approximately 160 amino acids and 5 consensus sequences. Two of these highly conserved motifs are responsible for specific recognition of the guanosine nucleotide, and three are necessary for binding of the phosphate groups and complexation of a Mg++ ion, which is found in all Ras-like proteins. 

The precise chemical interactions between an adhesin and its receptor are also important. For example, direct- and water-mediated hydrogen bonds are the most important interactions within the carbohydrate-recognition domain in carbohydrate-binding adhesins on the host cell surface (Weis and Drickamer, 1996). Nonpolar van der Waals interactions and hydrophobic "stacking of the receptor oligosaccharide rings with aromatic amino acid side chains of the bacterial adhesin protein also contribute to oligosaccharide-protein interactions. X-ray structural... 

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