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