A synergy between the catalytic and structural Zn(II) ions and the enzyme and substrate dynamics underlies the structure-function relationships of matrix metalloproteinase collagenolysis

Abstract

Matrix metalloproteinases (MMPs) are Zn(II) dependent endopeptidases involved in the degradation of collagen. Unbalanced collagen breakdown results in numerous pathological conditions, including cardiovascular and neurodegenerative diseases and tumor growth and invasion. Matrix metalloproteinase-1 (MMP-1) is a member of the MMPs family. The enzyme contains catalytic and structural Zn(II) ions. Despite many studies on the enzyme, there is little known about the synergy between the two Zn(II) metal ions and the enzyme and substrate dynamics in MMP-1 structure-function relationships. We performed a computational study of the MMP-1•triple-helical peptide (THP) enzyme•substrate complex to provide this missing insight. Our results revealed Zn(II) ions' importance in modulating the long-range correlated motions in the MMP-1•THP complex. Overall, our results reveal the importance of the catalytic Zn(II) and the role of the structural Zn(II) ion in preserving the integrity of the enzyme active site and the overall enzyme-substrate complex synergy with the dynamics of the enzyme and the substrate. Notably, both Zn(II) sites participate in diverse networks of long-range correlated motions that involve the CAT and HPX domains and the THP substrate, thus exercising a complex role in the stability and functionality of the MMP-1•THP complex. Both the Zn(II) ions have a distinct impact on the structural stability and dynamics of the MMP-1•THP complex. The study shifts the paradigm from the "local role" of the Zn(II) ions with knowledge about their essential role in the long-range dynamics and stability of the overall enzyme•substrate (ES) complex.

Keywords: Catalytic and structural zinc centers; Computational modeling; Matrix metalloproteinase-1; Molecular dynamics; Zinc dependent enzymes.

Fig. 1

a) MMP-1•triple-helical peptide (THP) complex. b) Catalytic site with Zn(II) coordinated to H199, H203, and H209. c) Structural site with Zn(II) coordinated to H149, D151, H164, H177.

Fig. 2

Structure of MMP-1 CAT domain. The secondary structure elements (β-strands (orange) and α helices (light sea green)), the Zn(II) ions (Zn₁ & Zn₂ (grey)), Ca(II) ions (forest green), S-loop (blue), V-B loop (green), Ω-loop (purple) which includes the S₁’ specificity loop (red) and Met-turn (yellow) are depicted.

Fig. 3

Comparison of the overall MD properties of the simulated systems. a) RMSD, b) distance between the center of mass of catalytic Zn(II) and structural Zn(II) coordinated residues, c) distance between the center of mass of CAT and HPX domains, and d) distance between the center of mass of the catalytic site and the scissile bond. The simulated systems were MMP-1•THP complex with both the catalytic and structural Zn(II) present (MMP1 Zn₁ Zn₂) (black), without structural Zn(II) (MMP1 Zn₁) (green), without catalytic Zn(II) (MMP1 Zn₂) (red), and without both Zn(II) ions (MMP1 no Zn) (blue).

Fig. 4

The superimposed (a) catalytic site, (b) structural site, (c) S-loop, and (d) V-B loop of (MMP1 Zn₁ Zn₂) (red), (MMP1 Zn₁) (blue), (MMP1 Zn₂) (yellow), and (MMP1 no Zn) (green).

Fig. 5

a) Superimposed distances (in Angstroms) between donor nitrogen (NE) of R195 with acceptor oxygen (O) of Y221 in (MMP1 Zn₁ Zn₂) (red), (MMP1 Zn₁) (blue), (MMP1 Zn₂) (yellow), and (MMP1 no Zn) (green). The R195 – Y221 hydrogen bond is lost when the Zn(II) ion is removed from the structural site. b) Distance between donor nitrogen (NH2) of R195 with acceptor oxygen (O) of S220 in (MMP1 Zn₁ Zn₂) (red), (MMP1 Zn₁) (blue), (MMP1 Zn₂) (yellow), and (MMP1 no Zn) (green).

Fig. 6

Superimposed distances (in Angstroms) between the acceptor oxygen (O) of M217 and donor nitrogen (ND1) of catalytic site residue H209 in (MMP1 Zn₁ Zn₂) (red), (MMP1 Zn₁) (blue), (MMP1 Zn₂) (yellow), and (MMP1 no Zn) (green). Hydrogen bond formation takes place when both of the Zn(II) ions are removed from the system, which may alter the structural orientation of the catalytic site.

Fig. 7

Dynamic Cross-Correlation Analysis of MMP-1•THP. a) (MMP1 Zn₁ Zn₂), b) (MMP1 Zn₁), c) (MMP1 Zn₂), and d) (MMP1 no Zn). The positive correlations (from 0 to 1.0) between residues are shown in cyan color and negative correlations (from 0 to −1.0) are represented in pink color. The boxes in the figure show the following important motions: Correlated motion between the S₁' specificity loop and blade 1 residues (black), anticorrelated motion between the blade 2 residues and the CAT domain involving S-loop and V-B loop residues (blue), correlated motion between blade 4 residues and the CAT domain involving S-loop and V-B loop residues (red). Residues 1-162 (crystal structure numbers 81-242) denote the CAT domain, 179-367 (crystal structure numbers 259-447) denote the HPX domain, and 372-472 (crystal structure numbers 963-995) denotes the THP substrate.

Fig. 8

Principal Component Analysis (PC1) of MMP-1•THP. a) (MMP1 Zn₁ Zn₂), b) (MMP1 Zn₁), c) (MMP1 Zn₂), and d) (MMP1 no Zn). Yellow to blue is the direction of motion of the protein.