Kinetic and Computational Investigations into the Origin of Metal‐Ion Specificity in Matrix Metalloproteinase‐1

• Published in: The FASEB Journal
• Main Authors: Grove, Laurie E., Palladini, Jacob
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2020
• Subjects: Orca
• Online Access: http://dx.doi.org/10.1096/fasebj.2020.34.s1.00585

Matrix Metalloproteinases (MMPs) are a family of Zn‐dependent proteases responsible for cleaving peptide bonds. MMPs have essential roles in cell proliferation, differentiation, immune responses, among many others. Human MMPs have been implicated in a number of diseases including cancer and arthritis and as such have been the focus of studies related to their roles. We are interested in exploring the high specificity for the Zn 2+ ion by MMP‐1 using kinetic assays and computational modeling. Human MMP‐1 contains a classical HEXXHXXGXXH Zn‐binding domain. Both the Zn 2+ and second sphere Glu219 residue are involved in the first step of catalysis – deprotonating a Zn‐coordinated water. Interestingly, the Volvox species has a proteinase (VMP3) with a modified QEXXHXXGXXH metal‐binding domain that displays enhanced activity with Cu 2+ and is much less active with Zn 2+ . In our study, a variety of metal‐substituted samples of MMP‐1 were prepared using dialysis to remove the Zn 2+ ion. Kinetic assays using a FRET substrate demonstrate less than 5% activity in all cases when Cu 2+ is substituted for Zn 2+ . To further explore these results, we developed a series of computational models of the MMP‐1 active site substituting either Zn 2+ or Cu 2+ into the active site. Density Functional Theory (DFT) as implemented in the ORCA program was used to develop these models, simulating the protein environment using either solvation models or by directly including second sphere residues as part of the quantum mechanics (QM) calculation. Models were validated by comparison to experimental results, including the kinetic data and spectroscopy data in the case of the Cu 2+ models. Our work shows two effects at play. First, the first sphere geometry in MMP‐1 is primed to support a tetrahedral coordination environment, which is preferred by Zn 2+ whereas Cu 2+ prefers a square planar coordination environment. Second, the positioning of the Zn 2+ ‐OH 2 unit in the active site positions the water for deprotonation by Glu219. In the Cu ...