Conformational variability of matrix metalloproteinases: Beyond a single 3D structure

Abstract

The structures of the catalytic domain of matrix metalloproteinase 12 in the presence of acetohydroxamic acid and N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid have been solved by x-ray diffraction in the crystalline state at 1.0 and 1.3-Å resolution, respectively, and compared with the previously published x-ray structure at 1.2-Å resolution of the adduct with batimastat. The structure of the N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid adduct has been solved by NMR in solution. The three x-ray structures and the solution structure are similar but not identical to one another, the differences being sizably higher in the loops. We propose that many of the loops show a dynamical behavior in solution on a variety of time scales. Different conformations of some flexible regions of the protein can be observed as ''frozen'' in different crystalline environments. The mobility in solution studied by NMR reveals conformational equilibria in accessible time scales, i.e., from 10 ؊5 s to ms and more. Averaging of some residual dipolar couplings is consistent with further motions down to 10 ؊9 s. Finally, local thermal motions of each frozen conformation in the crystalline state at 100 K correlate well with local motions on the picosecond time scale. Flexibility͞con-formational heterogeneity in crucial parts of the catalytic domain is a rule rather than an exception in matrix metalloproteinases, and its extent may be underestimated by inspection of one x-ray structure. Backbone flexibility may play a role in the difficulties encountered in the design of selective inhibitors, whereas it may be a requisite for substrate binding and broad substrate specificity. macrophage metalloelastase ͉ protein mobility ͉ solution structure ͉ x-ray structure

Towards third generation matrix metalloproteinase inhibitors for cancer therapy

“…Although, these adaptations occurred upon binding of different inhibitors, the character of the void spaces is quite similar (data not shown). (Moy et al, 2002;Bertini et al, 2005;Cuniasse et al, 2005). This can be exploited to accommodate unfavorable binding groups in MMPIs.…”

Matrix metalloproteinase 12 silencing: A therapeutic approach to treat pathological lung tissue remodeling?

“…However, inhibiting a specific MMP is a difficult goal because of the high conservation between many MMPs in terms of overall 3D-structure, topology of the catalytic domain and requirement of specific amino-acid residues in the active site [90,91]. This is why although many MMPs inhibitors have been developed, very few of them have proved to specifically target a particular MMP.…”

Matrix metalloproteases in head and neck cancer

“…88 Difficulties with the development of selective inhibitors may be a function of conformational variability at the catalytic site. 89 The MMP responsible for musculoskeletal pain has not been identified and could be MT1-MMP (based on the phenotype of MT1-MMP null mice). Furthermore, MT1-MMP null mice have defects in early postnatal development that result in dwarfism, but it is unknown whether treatment with MT1-MMP-specific inhibitors will negatively impact mature bone remodeling.…”