title: 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-A resolution, respectively, and compared with the previously published x-ray structure at 1.2-A 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. Flexibility/conformational 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.
authors.affiliation: Magnetic Resonance Center (Centro di Risonanze Magnetiche), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy. bertini@cerm.inifi.it
authors.forename: Ivano
authors.initials: I
authors.lastname: Bertini
authors.forename: Vito
authors.initials: V
authors.lastname: Calderone
authors.forename: Marta
authors.initials: M
authors.lastname: Cosenza
authors.forename: Marco
authors.initials: M
authors.lastname: Fragai
authors.forename: Yong-Min
authors.initials: YM
authors.lastname: Lee
authors.forename: Claudio
authors.initials: C
authors.lastname: Luchinat
authors.forename: Stefano
authors.initials: S
authors.lastname: Mangani
authors.forename: Beatrice
authors.initials: B
authors.lastname: Terni
authors.forename: Paola
authors.initials: P
authors.lastname: Turano
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D006877:Hydroxamic Acids / Q000737:chemistry / Q000378:metabolism; D053508:Matrix Metalloproteinase 12; D008666:Metalloendopeptidases / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D009068:Movement; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D013449:Sulfonamides / Q000737:chemistry / Q000378:metabolism; D013997:Time Factors
chemical_list: D006877:Hydroxamic Acids; C500716:N-isobutyl-N-(4-methoxyphenylsulfonyl)glycylhydroxamic acid; D013449:Sulfonamides; C006358:acetohydroxamic acid; D008666:Metalloendopeptidases; D053508:Matrix Metalloproteinase 12