Substrate peptide sequence selection

Tethering with extenders was also used to identify inhibitors to the antiinflammatory target caspase-1 [28, 29]. In this case, one of the same extenders previously designed for caspase-3 selected an entirely different set of fragments. This is consistent with different substrate peptide sequence preferences WEHD for caspase-1 vs DEVD for caspase-3 [30]. 

MAO A and B differ in primary structure and in substrate specificity [5,7]. The two isozymes, located on the mitochondrial outer membranes, have 70% homology in peptide sequence and share common mechanistic details. It is now recognized that these are different proteins encoded by different genes, but probably derived from a common ancestral gene. Crystal structures for both MAO A and B complexes with inhibitors have recently been reported [8]. Serotonin is selectively oxidized by MAO A, whereas benzylamine and 2-phenylethylamine are selective substrates for MAO B. Dopamine, norepinephrine, epinephrine, trypt-amine, and tyramine are oxidized by both MAO A and B in most species [9]. In addition, MAO A is more sensitive to inhibition by clorgyline (1), whereas MAO B is inhibited by low concentrations of L-deprenyl ((f )-( )-deprenyl) (2) [5,6cj. Development of inhibitors that are selective for each isozyme has been an extremely active area of medicinal chemistry [8]. 

Well-defined peptides of known sequence have been used to shed light on the mechanism of catalysis in the epoxidation of enones with hydrogen peroxide [91, 93-95]. The peptide sequences of the catalysts have been systematically varied and correlated with catalytic activity and selectivity. From the many variations investigated it was concluded (i) that the N-terminal region of the peptides harbors the catalytically active site, and that (ii) a helical conformation is required for the peptide catalysts to be active. The latter conclusion is supported both by the dependence of catalytic activity on chain-length and by IR investigations [91, 94]. NMR data that might aid further elucidation of catalyst structure, interaction with the substrate enones, etc., are, unfortunately, not yet available. 

Hougland, J.L., Hicks, K.A., Hartman, H.L., Kelly, R.A., Watt, T.J., and Fierke, C.A. (2010). Identification of novel peptide substrates for protein farnesyltransferase reveals two substrate classes with distinct sequence selectivities. J Mol Biol 395 176-190. 

Studies by many workers have revealed two peptide sequences which are very selective for thrombin -Phe-Val-Arg- and -X-Pro-Arg- (C5, S24, S26). As can be seen in Table 3, these two sequences have been widely used to design the various synthetic substrates to detect thrombin. This measurement can be done directly by incubating this enzyme with the appropriate substrate. Latallo has recommended adding an agent like aprotinin or soybean trypsin inhibitor to prevent attack by kallikrein, Factor Xa, or plasmin on these thrombin substrates (L5). The use of the original substrate, S-2160, has sharply declined due to its lower sensitivity, specificity, and solubility when compared to substrates like S-2238 and Chromozyn TH. Today,... 

This asparagine-selective peptide cleavage was of wide substrate generality (20 examples), including an unnatural peptide sequence comprising o-amino acids and chemically modified (oxidized) amino acids that were not cleaved by peptidases. 

The above studies established (1) that broad peptide sequence space can furnish catalysts that are effective across both a wide array of substrates and for several chemical transformations and (2) that nucleophilic peptide catalysis was effective at modulating barriers to reaction in the context of enantioselective reactions and site-selective reactions such that inherent preferences could be enhanced, e.g., inositols (Fig. 2c), or inverted (Fig. 2c) in a catalyst-controlled manner. At this time it became clear that the stage was set to explore beyond model systems and to begin treating large, complex natural products as substrates themselves. 

The thermodynamic stability, the aggregation state, and the relative orientation of the helical strands in such peptides were shown to depend largely on the identity of the amino acid residues at positions a, d, e, and g. The use of leucine and valine at the hydrophobic core (positions a and glutamic acid and lysine at the e and g positions were shown to control equilibrium between dimeric and trimeric coiled-coil aggregation states." Peptide sequences that allow interconversion between dimeric and trimeric parallel coiled coils were found as productive templates to enhance substrate selectivity, catalytic efficiency, and turnover and were commonly used in peptide-replicating systems. 

A derivatization can be performed to induce a selective attachment of target cells either on new polymers designed to control non specific cell attachment (Sect. 3) or on any other substrate intended for biomaterial applications. Photoimmobilization of peptidic sequences was performed on newly synthesized PCPUR con-... 

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