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Kinetic and Computational Investigations into the Origin of Metal‐Ion Specificity in Matrix Metalloproteinase‐1
Author(s) -
Grove Laurie E.,
Palladini Jacob
Publication year - 2020
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2020.34.s1.00585
Subject(s) - matrix metalloproteinase , chemistry , metal , coordination sphere , density functional theory , active site , metal ions in aqueous solution , solvation , enzyme , ion , computational chemistry , biochemistry , organic chemistry
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 2+ models, the distortion of the Cu 2+ ‐OH 2 unit due to the less stable coordination species increases the energy associated with proton transfer. This work provides a clear example of how first and second sphere active site residues are finely tuned to maximize enzyme activity. Support or Funding Information Wentworth Institute of Technology