Question

Compare and contrast how non-specific and specific interactions contribute to the binding of target molecules, using serine proteases and bZip proteins as examples. Illustrate your answer with structures and diagrams? (2 page Min)

Answer 1

are also termed 3C proteases (from their expression in picornaviruses) or chymotrypsin-like proteases. Most have a catalytic triad of amino acids (His, Asp, Ser) but in some, the Ser is replaced by Cys; as the latter have the same overall structure as serine proteases they are termed “serine-like” proteases. The serine residue is unusually active and acts as a nucleophile during catalysis by donating an electron to the carbonyl carbon of the peptide bond to be hydrolyzed. An acyl serine is formed and a proton donated to the departing amyl group by the active-site histidine residue. The acyl enzyme is then hydrolyzed, the carboxylic acid product is released, and the active site is regenerated. Serine proteases cleave primarily at Gln–Gly, Gln–Ser, Gln–Ala, and Gln–Asn (reviewed by Palmenberg, 1990)The Basic Leucine Zipper Domain (bZIP domain) is found in many DNA binding eukaryotic proteins. One part of the domain contains a region that mediates sequence specific DNA binding properties and the leucine zipper that is required to hold together (dimerize) two DNA binding regions. The DNA binding region comprises a number of basic amino acids such as arginine and lysine. Proteins containing this domain are transcription factors.