1. Characterization of Mca-Lys-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2, a fluorogenic substrate with increased specificity constants for collagenases and tumor necrosis factor converting enzyme
Ulf Neumann, Hisashi Kubota, Karl Frei, Vishwas Ganu, David Leppert Anal Biochem. 2004 May 15;328(2):166-73. doi: 10.1016/j.ab.2003.12.035.
Matrix metalloproteinases (MMPs) and the related tumor necrosis factor converting enzyme (TACE) are involved in tissue remodeling, cell migration, and processing of signaling molecules, such as cytokines and adhesion molecules. Fluorescence-quenched peptide substrates have been widely used to quantitate the actual enzymatic activity of MMPs. However, the various MMPs have very different specific activities toward these substrates. This restricts their value for the determination of composite proteolytic activity of mixtures of metalloproteinases in biological fluids. The N-terminal elongation of the most widely used MMP substrate (FS-1) with a Lys to the sequence Mca-Lys-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH(2) (FS-6) yields a fluorogenic peptide with improved substrate properties. As compared to FS-1, the specificity constant (kcat/Km) of FS-6 for collagenases (MMP-1, MMP-8, MMP-13) and MT1-MMP (MMP-14) is increased two- to ninefold and threefold, respectively, while those for gelatinases and matrilysin remain equally high. Using high-performance liquid chromatography-fluorescence detection, MMP activity can be quantitated in the picomolar range. FS-6 shows up to twofold higher specificity constants (kcat/Km of 0.8x10(6)M(-1)s(-1)) for TACE, as compared to standard substrates Mca-PLAQAV-Dpa-RSSSAR-NH(2) and Dabcyl-LAQAVRSSSAR-EDANS. FS-6 is fully water soluble and thus allows measurement of metalloproteinase activity in tissue culture conditions, e.g., on the surface of viable cells in situ.
2. Substrate specificity and novel selective inhibitors of TNF-alpha converting enzyme (TACE) from two-dimensional substrate mapping
Millard H Lambert, et al. Comb Chem High Throughput Screen. 2005 Jun;8(4):327-39. doi: 10.2174/1386207054020840.
We report a systematic analysis of the P1' and P2' substrate specificity of TNF-alpha converting enzyme (TACE) using a peptide library and a novel analytical method, and we use the substrate specificity information to design novel reverse hydroxamate inhibitors. Initial truncation studies, using the amino acid sequence around the cleavage site in precursor-TNF-alpha, showed that good turnover was obtained with the peptide DNP-LAQAVRSS-NH2. Based on this result, 1000 different peptide substrates of the form Biotin-LAQA-P1'-P2'-SSK(DNP)-NH2 were prepared, with 50 different natural and unnatural amino acids at P1' in combination with 20 different amino acids at P2'. The peptides were pooled, treated with purified microsomal TACE, and the reaction mixtures were passed over a streptavidin affinity column to remove unreacted substrate and the N-terminal biotinylated product. C-terminal cleavage products not binding to streptavidin were subjected to liquid chromatography/mass spectrometry analysis where individual products were identified and semiquantitated. 25 of the substrates were resynthesized as discrete peptides and assayed with recombinant TACE. The experiments show that recombinant TACE prefers lipophilic amino acids at the P1' position, such as phenylglycine, homophenylalanine, leucine and valine. At the P2' position, TACE can accommodate basic amino acids, such as arginine and lysine, as well as certain non-basic amino acids such as citrulline, methionine sulfoxide and threonine. These substrate preferences were used in the design of novel reverse hydroxamate TACE inhibitors with phenethyl and 5-methyl-thiophene-methyl side-chains at P1', and threonine and nitro-arginine at P2'.
3. New fluorogenic substrates for N-arginine dibasic convertase
E Csuhai, M A Juliano, J S Pyrek, A C Harms, L Juliano, L B Hersh Anal Biochem. 1999 Apr 10;269(1):149-54. doi: 10.1006/abio.1999.4033.
N-Arginine dibasic (NRD) convertase is a recently described peptidase capable of selectively cleaving peptides between paired basic residues. The characterization of this unique peptidase has been hindered by the fact that no facile assay procedure has been available. Here we report the development of a rapid and sensitive assay for NRD convertase, based on the utilization of two new internally quenched fluorogenic peptides: Abz-GGFLRRVGQ-EDDnp and Abz-GGFLRRIQ-EDDnp. These peptides contain the fluorescent 2-aminobenzoyl moiety that is quenched in the intact peptide by a 2, 4-dinitrophenyl moiety. Cleavage by NRD convertase at the Arg-Arg sequence results in an increase of fluorescence. NRD convertase cleaves these peptides efficiently and with high specificity as observed by both HPLC and fluorescence spectroscopy. The rate of hydrolysis of the fluorogenic substrates is proportional to enzyme concentration, and obeys Michaelis-Menten kinetics. The kinetic parameters for the fluorescent peptides (Km values of approximately 1.0 microM, and Vmax values of approximately 1 microM/(min. mg) are similar to those obtained with peptide hormones as substrates.
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