Snapshots of the Reaction Mechanism of Matrix Metalloproteinases

Bertini, Ivano; Calderone, V.; Fragai, Marco; Luchinat, Claudio; Maletta, M.; Yeo, Kwon Joo

doi:10.1002/ange.200603100

Cited by 29 publications

(42 citation statements)

References 32 publications

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“…To further explore whether the locally unfolded states sampled in the unfolding simulations are consistent with the MMP catalytic site, we docked representative structures from each minimum arising from the various pmfs into the crystallographic structure of the MMP catalytic site. Because there is considerable homology between the catalytic domains of different collagenases, we chose the catalytic domain from the crystallographic structure in the pdb that was solved to the highest resolution (i.e., MMP8 [PDB ID 2OY4]) 32, 33, 42…”

Section: Resultsmentioning

confidence: 99%

“…Structures arising from simulations that restrain the triple‐helical peptide to adopt a radius of gyration consistent with a local energy minimum were individually docked into the MMP8 binding site. Docking simulations were performed using a harmonic restraining potential that biased the rigid backbone of each partially unfolded structure to adopt the backbone conformation of a single stranded collagen‐like peptide found in the binding site of a related MMP 33. Docked structures that have a low rms between the collagen‐triple helix and the corresponding residues in a bound collagen‐like peptide are most complementary to the active site (see Methods section).…”

Section: Resultsmentioning

confidence: 99%

“…A cocrystal structure of a cleaved hexapeptide (electron density was seen for only five residues in the active site) corresponding to the consensus sequence of Types I and III collagen in the active site of the catalytic domain of MMP12 (PDB ID 2OXZ32, 33 solved at 1.8‐Å resolution) was used as the starting structure for the docking simulations 33. Given the structural similarity between the catalytic domains of MMP12 and MMP8 (PDB ID 2OY232, 33 solved at 1.5‐Å resolution), with a backbone RMSD of only 0.67 Å, the two structures were aligned and the two peptide fragments were positioned in the active site of MMP8. Selected residues were mutated in the peptide fragment in silico in order to obtain the corresponding amino acid sequence of the Type III collagen cleavage site.…”

Section: Methodsmentioning

confidence: 99%

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Conformational selection and collagenolysis in Type III collagen

Salsas-Escat¹,

Stultz²

2009

Proteins

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Matrix metalloproteases (MMPs) cleave native collagen at a single site despite the fact that collagen contains more than one scissile bond that can, in principle, be cleaved. For peptide bond hydrolysis to occur at one specific site, MMPs must (1) localize to a region near the unique scissile bond, (2) bind residues at the catalytic site that form the scissile bond, and (3) hydrolyze the corresponding peptide bond. Prior studies suggest that for some types of collagen, binding of noncatalytic MMP domains to amino acid sequences in the vicinity of the true cleavage site facilitates the localization of collagenases. In the present study, our goal was to determine whether binding to the catalytic site also plays a role in determining MMP specificity. To investigate this, we computed the conformational free energy landscape of Type III collagen at each potential cleavage site. The free energy profiles suggest that although all potential cleavage sites sample unfolded states at relatively low temperatures, the true cleavage site samples structures that are complementary to the catalytic site. By contrast, potential cleavage sites that are not cleaved sample states that are relatively incompatible with the MMP active site. Furthermore, our findings point to a specific role for arginine residues in modulating the structural stability of collagen near the collagenase cleavage site. These data imply that locally unfolded potential cleavage sites in Type III collagen sample distinct unfolded ensembles, and that the region about the true collagenase cleavage site samples states that are most complementary to the MMP active site.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Conformational selection and collagenolysis in Type III collagen

Salsas-Escat¹,

Stultz²

2009

Proteins

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“…X-ray crystallographic studies of MMP-12 and MMP-8 identified contacts from a single-stranded collagen-like peptide after hydrolysis (Bertini et al, 2006). The peptide fragments Pro-Gln-Gly and Ile-Ala-Gly, representing the cleavage site in the α1(I) collagen chain by collagenolytic MMPs (Fields, 2013), were held in place in the active site (Fig.…”

Section: Structural Evaluation Of Mmp Interactions With Collagenmentioning

confidence: 99%

“…(B) Ile-Ala-Gly adduct of MMP-12. Reproduced from Bertini et al (2006) by the permission of Wiley-VCH Verlag GmbH & Co. …”

Section: Figurementioning

confidence: 99%

Biophysical Studies of Matrix Metalloproteinase/Triple-Helix Complexes

Fields¹

2014

Metal-Containing Enzymes

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Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. The structures of MMPs, in solution and solid state and in the presence and absence of triple-helical collagen models, have been assessed by NMR spectroscopy, small-angle X-ray scattering, and X-ray crystallography. Structures observed in solution exhibit flexibility between the MMP catalytic (CAT) and hemopexin-like (HPX) domains, while solid-state structures are relatively compact. Evaluation of the maximum occurrence (MO) of MMP-1 conformations in solution found that, for all the high MO conformations, the CAT and HPX domains are not in tight contact, and the residues of the HPX domain reported to be responsible for the binding to the collagen triple-helix are solvent exposed. A mechanism for collagenolysis has been developed based on analysis of MMP solution structures. Information obtained from solid-state structures has proven valuable for analyzing specific contacts between MMPs and the collagen triple-helix.

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A High‐Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties

et al. 2021

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Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones.

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Snapshots of the Reaction Mechanism of Matrix Metalloproteinases

Cited by 29 publications

References 32 publications

Conformational selection and collagenolysis in Type III collagen

Conformational selection and collagenolysis in Type III collagen

Biophysical Studies of Matrix Metalloproteinase/Triple-Helix Complexes

A High‐Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties

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