cathepsin e substrate  (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

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: Left: Close up view of the binding cleft of MMP-9 and MMP-14 with ES001 (green) at the catalytic site. Oxygen atoms of ES001 in red, nitrogen atoms in dark blue, while hydrogen atoms connected to nitrogen or oxygen atoms are in white. The surface of the binding cleft depicted in yellow, with the P 1 ’ residue indicated. The Cα trace of the catalytic part is shown in light blue. MD frames after 161 ns of simulation with MMP-9 and after 125 ns with MMP-14 are used as representatives for the MD frames. The yellow backbone Cα trace of MMP-9 highlights the fibronectin repeats. Right: 2D illustration of the complexes with the most important ES001-enzyme interactions, where amino acids within 4 Å of the substrate are included. The percentages represent the frequency of these interactions observed in MD frames, with only those present in more than 30% of the frames included.

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

Techniques: Binding Assay, Residue