Effects of the Nature of the Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies

Abstract

Matrix metalloproteinase-1 (MMP-1) is a Zn(II) dependent endopeptidase involved in the degradation of collagen, the most abundant structural protein in the extracellular matrix of connective tissues and the human body. Herein we performed a multilevel computational analysis including molecular dynamics (MD), combined quantum mechanics/molecular mechanics (QM/MM), and quantum mechanics (QM) calculations to characterize the structure and geometry of the catalytic Zn(II) within the MMP-1 protein environment in comparison to crystallographic and spectroscopic data. The substrate's removal fine-tuned impact on the conformational dynamics and geometry of the catalytic Zn(II) center was also explored. Finally, the study examined the effect of substituting catalytic Zn(II) by Co(II) on the overall structure and dynamics of the MMP-1 THP complex and specifically on the geometry of the catalytic metal center. Overall our QM/MM and QM studies were in good agreement with the MM description of the Zn(II) centers in the MD simulations.

Keywords: Matrix metalloproteinases; Molecular dynamics; QM/MM calculations; Zn(II) containing enzymes.

Figure 1.

Substrate bound MMP-1 structure (PDB ID: 4AUO). The catalytic site is highlighted in a red box and the structural site in a blue box. Ca(II) ions in the CAT and HPX domains are colored in green.

Figure 2.

a) S₁’ subsite (circled in red) and the gate-keeper residue Arg195 (white). b) 1,4 β-Met turn: Ala215 (yellow), Leu216 (red), Met217 (green), and Tyr218 (blue).

Figure 3.

Superimposed catalytic Zn(II) sites of MMP-1•THP including coordinated histidine residues (His199, His203, His209), catalytic water (Wat₁), auxiliary water (Wat₂), and conserved glutamate residue (Glu200) in the X-ray crystallographic structure (PDB ID: 4AUO) (red), MD snapshot (blue), QM/MM optimized (green), and QM-continuum solvent (yellow) models.

Figure 4.

Superimposed catalytic sites of the QM/MM optimized structures from multiple snapshots of MMP-1•THP. Snapshot 1 (used for further calculations) is represented in green, while Snapshot 2 = cyan, Snapshot 3 = yellow, Snapshot 4 = pink, and Snapshot 5 = brown.

Figure 5.

Distance plots of MMP-1•THP (black) and MMP-1•no THP (violet). a) Distance between center of mass of catalytic and structural site of MMP-1. b) Distance between center of mass of CAT and HPX domains of MMP-1.

Figure 6.

Hydrogen bonding interactions involving Arg195, Tyr221, and Ser220 for MMP-1•THP (black) and MMP-1•no THP (violet). a) Hydrogen bonding distances between the donor nitrogen (NE) of Arg195 and the acceptor oxygen (O) of Tyr221. b) Hydrogen bonding distance between donor nitrogen (NH2) of Arg195 with acceptor oxygen (O) of Ser220.

Figure 7.

Superimposed catalytic Zn(II) sites of MMP-1•THP (green) and MMP-1•no THP (orange) in QM/MM optimized structure. Zn(II) is coordinated to three histidine residues, His199, His203, and His209, a catalytic water molecule (Wat1), and an auxiliary water molecule (Wat2).

Figure 8.

The superimposed a) catalytic Zn(II) site and b) structural Zn(II) site of MMP-1•THP (red) and MMP-1 Co₁•THP (orange) from the averaged MD trajectory.

Figure 9.

The superimposed a) S-loop and b) V-B loop of MMP-1•THP (red) and MMP-1 Co₁•THP (orange) from the averaged MD trajectory.

Figure 10.

Superimposed QM/MM optimized structures of MMP-1•THP (green) and MMP-1 Co₁•THP (pink). Zn(II)/Co(II) is coordinated to three histidine residues, His199, His203, and His209, a catalytic water molecule (Wat₁), and an auxiliary water molecule (Wat₂).

Figure 11.

Superimposed QM/MM optimized structures of MMP-1 Co1•no THP (magenta) and MMP-1 Co1•no Zn2 no THP (yellow).

Figure 12.

a) New water molecules (in red and white) in the catalytic site of MMP-1 Co1•no Zn2 no THP (yellow) and MMP-1 Co1•no THP (magenta). b) Open S1’ specificity loop of MMP-1 Co1•no Zn2 no THP (yellow) and MMP-1 Co1•no THP (magenta).