fluorogenic peptide substrate mca rppgfsafk dnp oh  (R&D Systems)

Journal: PLOS One

Article Title: Interactions of substrates and phosphinyl containing inhibitors with bacterial and human zinc proteases

doi: 10.1371/journal.pone.0329362

Figure Lengend Snippet: Two dimensional (2D) illustrations of the substrate probe from the X-ray crystallographic complex with MMP-9 (PDB ID: 4JIJ ), as well as the substrates Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH 2 (ES001) and Mca-Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys(Dnp)-OH (ES005). ES001 was used in enzyme inhibition studies with MMP-9 and MMP-14, while ES005 was used in studies with TLN, PLN, and ALN. The P 1 and P 1 ’ residues in MD simulations of ES001 with MMP-9 and MMP-14, and of ES005 with TLN, are indicated in the figure.

Article Snippet: ES001 and ES005 were from R&D Systems (Minneapolis, MN, USA).

Techniques: Enzyme Inhibition Assay

Journal: PLOS One

Article Title: Interactions of substrates and phosphinyl containing inhibitors with bacterial and human zinc proteases

doi: 10.1371/journal.pone.0329362

Figure Lengend Snippet: MS spectra obtained after 0 and 5 minutes incubation of 50 µM (Mca-Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys(Dnp)-OH) ES005 with 10 nM thermolysin (TLN). The m/z values marked in green, blue and red represents N-terminal cleavage products of ES005 obtained after Ala-Phe, Ser-Ala, and Gly-Phe cleavage, respectively.

Article Snippet: ES001 and ES005 were from R&D Systems (Minneapolis, MN, USA).

Techniques: Incubation

Journal: PLOS One

Article Title: Interactions of substrates and phosphinyl containing inhibitors with bacterial and human zinc proteases

doi: 10.1371/journal.pone.0329362

Figure Lengend Snippet: Relative intensities in percent of substrate Mca-Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys(Dnp)-OH (ES005) and cleavage products at 1, 3, 5, 10, 20 and 60 minutes of incubation of 50 µM ES005 with 5 and 10 nM thermolysin (TLN). The m/z value of 1388 represents the substrate ES005, whereas the m/z values of 947, 876 and 642 represent the N-terminal cleavage products after Ala-Phe, Ser-Ala, and Gly-Phe cleavage, respectively.

Article Snippet: ES001 and ES005 were from R&D Systems (Minneapolis, MN, USA).

Techniques: Incubation

Journal: PLOS One

Article Title: Interactions of substrates and phosphinyl containing inhibitors with bacterial and human zinc proteases

doi: 10.1371/journal.pone.0329362

Figure Lengend Snippet: Left: Close ups of the TLN binding cleft surface (yellow) during the three MD simulations: TLN/ES005-GF, TLN/ES005-AF and TLN/ES005-SA. The Cα-trace of TLN is shown in light blue. ES005 atoms are colour coded: carbon in green, oxygen in red, and nitrogen in dark blue. The representative coordinate sets were selected at 137 ns, 160 ns, and 200 ns for the TLN/ES005-GF, TLN/ES005-AF, and TLN/ES005-SA simulations, respectively. Right: 2D illustration of the TLN/ES005 complexes, highlighting the most significant interactions. Amino acids within 4 Å of the substrate are included, with interaction frequencies indicated as percentage of MD frames. Only interaction present in more than 30% of the frames are included.

Article Snippet: ES001 and ES005 were from R&D Systems (Minneapolis, MN, USA).

Techniques: Binding Assay