Peptide substrate conformation, importance

This evidence demonstrates that the conformation of the peptide substrate is important for its recognition by the glycosyltransferase and that the acceptor peptides prefer the Asx-tum conformation. However, the solution conformation of a peptide may not reflect the conformation in which it actually binds to the enzyme. One approach to determining the bound conformation is to impose conformational constraints upon the peptide substrates, restricting them to a limited number of conformations or perhaps even a single conformation. 

The X-ray structures of CDKs with bound peptide substrates have revealed that the substrates bind in an extended form across the catalytic site. The conformational change of the T loop observed upon phosphorylation of Thrl 60 is critically important to substrate binding. 

S. A. Bizzozero and B. O. Zweifel (1975), The importance of the conformation of the tetrahedral intermediate for the a-chymotrypsin-catalyzed hydrolysis of peptide substrates. FEBS Lett. 59, 105-108. 

This proposal demonstrates that the sequence and conformation of the peptidal substrate can both play a critical role in protein N glycosylation. These factors combine to form a unique environment, providing the specificity and reactivity required to link an oligosaccharide to an asparagine carboxyamido nitrogen. Similar factors may play an important role in other protein processing reactions. 

Proline is one amino acid which would be expected to profoundly influence the reactivity of a peptide substrate. Proline restricts the possible conformations of a peptide chain and in addition is unable to act as a hydrogen bond donor. Both of these factors could affect peptide bond cleavage by hindering substrate binding or by preventing proper catalysis. Alternately, favorable interaction could take place between the enzyme and a prolyl residue, due either to a favorable hydrophobic interaction with the prolyl side chain or because proline restricts the peptide conformation to one which is favorable. That these effects are important is accentuated by the fact that at every subsite the cleavage probability of a substrate with a proline residue is significantly different from the mean (0.148). This is true for no other amino acid residue. Proline is favorable at P4 and P3 and unfavorable at all other subsites (P2 P3) ... 

Mimicking the secondary structure of peptides has become one of the most important tools for rational drug design (44-47). These methods induce the synthetic analog to adopt a set of target conformations, which are designed to mimic the bioactive conformation predicted in the native substrate from biophysical techniques. Molecular surrogates... 

Examination of the action of proteolytic enzymes on native proteins (or biologically active peptides) can yield two important types of information. First, determination of the susceptibility of particular bonds in a protein substrate offers a means for evaluation of certain features of the conformation of the protein (Linderstr0m-Lang, 1952 Mihalyi and Harrington, 1959). Second, proteolysis can serve as an important method for modification of the covalent structure of biologically active proteins (Anfinsen and Redfield, 1956). 

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