Fig 1: Residue contribution to ΔEb from MM-PBSA calculations for peptides and MMP-2 complexes obtained from the 500 ns trajectories MD simulations.(A) Ctx – MMP-2; (B) P75 – MMP-2; (C) P76 – MMP-2; (D) P77 – MMP-2; (E) P78 – MMP-2. Top panel contains residues from MMP-2, bottom panel contains residues from peptides. ΔEcont is the contribution to binding energy for each residue.
Fig 2: Representative structures of the largest clusters of 500 ns trajectories of peptide – MMP-2 complexes obtained with the AF2 method.Protein ligand regions identified as follows: random coil, cyan; alpha helix, blue; beta sheet, red; beta turn, green. Disulfide bridges are shown in sticks. For MMP-2 receptor: collagenase-1 region, orange; collagenase-2 region, purple; remainder of protein, gray. Abbreviation for MMP-2 domains are from Table 1.
Fig 3: Binding of the peptides to MMP-2 determined by DSF.Melting curve of the MMP-2 without (black) and with peptide (red). (A) Ctx; (B) P75; (C) P76.
Fig 4: Residue-residue decomposition of ΔEb from MM-PBSA calculations of peptides – MMP-2 complexes obtained with the AF2 method.(A) Ctx – MMP-2; (B) P75 – MMP-2; (C) P76 – MMP-2; (D) P77 – MMP-2; (E) P78 – MMP-2. Top values contain residues from MMP-2, bottom values contain residues from peptides. ΔEcont is the contribution to binding energy for each residue.
Fig 5: Residue-residue decomposition of ΔEb from MMP-BSA calculations of peptides and MMP-2 complexes obtained with the HADDOCK method.(A) Ctx – MMP-2; (B) P75 – MMP-2; (C) P76 – MMP-2; (D) P77 – MMP-2; (E) P78 – MMP-2. Top values contain residues from MMP-2, bottom values contain residues from peptides. For Ctx, P75, P77, and P78, there were no contributions from MMP-2 residues. ΔEcont is the contribution to binding energy for each residue.
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