Journal Article

Modeling of enzyme–substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10

McCulloch, Daniel R., Herington, Adrian C., van der Spoel, David, Manzetti, Sergio

2003

Overview

The matrix metalloproteases (MMPs) and the ADAMs (A Disintegrin And Metalloprotease domain) are proteolytic enzyme families containing a catalytic zinc ion, that are implicated in a variety of normal and pathological processes involving tissue remodeling and cancer. Synthetic MMP inhibitors have been designed for applications in pathological situations. However, a greater understanding of substrate binding and the catalytic mechanism is required so that more effective and selective inhibitors may be developed for both experimental and clinical purposes. By modeling a natural substrate spanning P4-P4' in complex with the catalytic domains, we aim to compare substrate-specificities between Stromelysin-1 (MMP-3), ADAM-9 and ADAM-10, with the aid of molecular dynamics simulations. Our results show that the substrate retains a favourable antiparallel beta-sheet conformation on the P-side in addition to the well-known orientation of the P'-region of the scissile bond, and that the primary substrate selectivity is dominated by the sidechains in the S1' pocket and the S2/S3 region. ADAM-9 has a hydrophobic residue as the central determinant in the S1' pocket, while ADAM-10 has an amphiphilic residue, which suggests a different primary specificity. The S2/S3 pocket is largely hydrophobic in all three enzymes. Inspired by our molecular dynamics calculations and supported by a large body of literature, we propose a novel, hypothetical, catalytic mechanism where the Zn-ion polarizes the oxygens from the catalytic glutamate to form a nucleophile, leading to a tetrahedral oxyanion anhydride transition state.

• Publisher: Springer Nature B.V
• Subject: ADAM Proteins / Amino Acid Sequence / Amyloid Precursor Protein Secretases / Aspartic Acid Endopeptidases / Catalytic Domain / Disintegrins - chemistry / Disintegrins - metabolism / Drug Design / Endopeptidases - chemistry / Endopeptidases - metabolism / Enzymes / Kinetics / Matrix Metalloproteinase 3 - chemistry / Matrix Metalloproteinase 3 - metabolism / Membrane Proteins - chemistry / Membrane Proteins - metabolism / Metalloendopeptidases - chemistry / Metalloendopeptidases - metabolism / Models, Molecular / Protein Conformation / Substrate Specificity / Substrates