Differential MMP-14 targeting by Biglycan (BGN), Decorin (DCN), Fibromodulin (FMOD), and Lumican (LUM) unraveled by In Silico Approach - Archive ouverte HAL Access content directly
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Differential MMP-14 targeting by Biglycan (BGN), Decorin (DCN), Fibromodulin (FMOD), and Lumican (LUM) unraveled by In Silico Approach

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Abstract

Schematic comparison of the LRR sequences of BGN, DCN, FMOD and LUM from LRR1 to LRR12 and positions of their O-and N-glycosylation sites. The locations of the LRR and glycosylation sites were extracted from the uniprot server using the sequence references specified on the right of the panel. Signal peptide and propeptide are depicted. (B) Structural alignment of the four SLRP structures. (C) Dual presentation of the sequence and the local secondary structure alignment. Sequence conservation is highlighted by colored letters: pink (identity for two out of four sequences), dark red (identity for all four sequences). Elements of the local secondary structure are depicted using blue arrows (β-sheets) and red cylinders (α-helices). LRR positions are indicated as rectangular boxes. I. Comparisons of the human BGN, DCN, FMOD, and LUM core protein structures and post-translational modification positions II. Secondary structures and N-glycosylation positions on human BGN, DCN, FMOD and LUM V. Impact of the carbohydrate shielding of lumican on LRR accessibility (A) Front view showing the solvent-unaccessible as well as solvent accessible LRRs. The C-terminal LRRs (LRR-7 to LRR-11) are labelled adjacent to the respective β-strands. (B) Solvent accessible surface areas (AccAr) and relative accessibility (RelAcc) of selected lumican residues that are part of LRR7, LRR9 and LRR11. A residue is considered buried when its RelAcc is < 20 and it is considered accessible when its RelAcc is > 20. >> improved accessibilities upon glycosylation III. MMP-14 catalytic domain complexes formed with human SLRPs IV. MMP-14 activity regulated by SLRPs (A) Top-view showing the N-terminal half of lumican with the residues of cleavage sites 1 and 2 represented as Van der Waals (VdW) spheres. (B) Bottom-view showing the C-terminal half of lumican with the residues of cleavage sites 3 and 4 represented as VdW spheres. Protein is represented as cartoon, coloured in blue-white-red scheme (N-terminal to C-terminal), and carbohydrate residues are represented as sticks and coloured according to the SNFG scheme [Varki, Proteomics 2009]. The cleavage sites were taken from the experimental studies on lumican proteolysis by MMP-14 [Li, Cancer Research 2004]. (C) Solvent accessible surface areas (AccAr) and relative accessibility (RelAcc) of lumican residues situated in the cleavage sites. A residue is considered buried when its RelAcc is < 20, and it is considered accessible when its RelAcc is > 20. >> decreased accessibilities upon glycosylation VI. Impact of the carbohydrate shielding of lumican on MMP-14 cleavage sites accessibility PURPOSE: Small leucine-rich proteoglycans (SLRPs) are major regulators of extracellular matrix assembly and cell signaling. Lumican, a member of the SLRPs family, and its derived peptides were shown to possess anti-tumor activity by interacting directly with the catalytic domain of MMP-14 leading to the inhibition of its activity. The aim of the present report was to characterize by in silico 3D modeling the structure and the dynamics of four SLRPs (Biglycan (BGN), Decorin (DCN), Fibromodulin (FMOD), Lumican (LUM)) including their core protein and their specific polysaccharide chains to assess their capacity to bind to MMP-14 and to regulate its activity. METHODS: Molecular docking experiments were performed to identify the specific amino acids of MMP-14 interacting with each of the four SLRPs using the Hex software. The inhibition of each SLRP (100nM) on MMP-14 activity was measured and the constants of inhibition (K i) were evaluated. The impact of the glycan chain number, structures and dynamics of lumican on the interaction with MMP-14 was assessed in silico by molecular dynamics simulations using GROMACS software. RESULTS: Molecular docking analysis showed that all SLRPs bind to MMP-14 through their concave face, but in different regions of the catalytic domain of MMP-14. Each SLRPs inhibited significantly the MMP-14 activity (BGN: 92%, K i : 19nM; DCN: 76%, K i : 30.9nM; FMOD: 83%, K i : 27.1nM; LUM: 86%, K i : 29.3nM). Finally, molecular dynamics showed the role of glycan chains in interaction with MMP-14 and shielding effect of SLRPs. DISCUSSION: Altogether, the results demonstrated that each SLRP exhibited inhibition of MMP-14 activity. However, the differential targeting of MMP-14 by the SLRPs was shown to be related not only to the core protein conformation but also to the glycan chain structures and dynamics. CONCLUSION: These results might explain, at least in part, the differential effects of SLRPs in tumor progression due to the differential regulation of SLRPs on MMP-14 activity.
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hal-03926581 , version 1 (06-01-2023)

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  • HAL Id : hal-03926581 , version 1

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R Rivet, R Mallenahalli Rao, P Nizet, N Belloy, L Huber, et al.. Differential MMP-14 targeting by Biglycan (BGN), Decorin (DCN), Fibromodulin (FMOD), and Lumican (LUM) unraveled by In Silico Approach. Matrix Biology Europe (MBE) Florence, Sep 2022, FLORENCE, Italy. ⟨hal-03926581⟩
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