The Interface between Catalytic and Hemopexin Domains in Matrix Metalloproteinase-1 Conceals a Collagen Binding Exosite

Arnold, Laurence H.; Butt, Louise E.; Prior, Stephen H.; Read, Christopher M.; Fields, Gregg B.; Pickford, Andrew R.

doi:10.1074/jbc.m111.285213

Cited by 53 publications

(78 citation statements)

References 61 publications

(78 reference statements)

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“…Similar R g values were also obtained for the highest MO structures without inclusion of the SAXS restraints in the calculations. This range of R g is in better agreement with the experimentally determined values from the SAXS data alone (28.5-29.0 Å) (8,15), indicating that x-ray structures were more compact than the average solution conformation. Furthermore, the relative orientations of HPX and CAT domains in the structures with the highest MO were different from those in the x-ray crystallographic structures.…”

Section: Volume 288 • Number 42 • October 18 2013supporting

confidence: 78%

“…Different generalized order parameters as well as different scaling factors of the components of the anisotropy tensor indicated that the HPX domain motion caused different motional averaging for the different metals, because of the different rhombicity and directions of the principal axes of the anisotropy tensors. SAXS data, previously measured for MMP-1 in solution under the same experimental conditions as utilized here (8,15), also indicated that the structure of the protein cannot be described by the crystallographic conformation alone, but that ensembles with closed and more extended conformations must be considered, further indicating that the protein experiences noticeable flexibility.…”

Section: Resultsmentioning

confidence: 99%

“…A range of solution and crystal state conformations has been described for full-length MMP-1 (Fig. 1B) (8,9,(12)(13)(14)(15)(16). MMP-1 has been experimentally found to interact with the collagen triple-helix through specific residues in blades I and II of the HPX domain (Fig.…”

Section: Matrix Metalloproteinases (Mmps)mentioning

confidence: 99%

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Examination of Matrix Metalloproteinase-1 in Solution

Cerofolini¹,

Fields

Fragai

et al. 2013

Journal of Biological Chemistry

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Background: Matrix metalloproteinase-1 (MMP-1) collagenolysis relies on interdomain flexibility. Results: In all high maximum occurrence conformations, the MMP-1 hemopexin-like domain residues reported responsible for binding to the collagen triple-helix are solvent exposed. Conclusion: MMP-1 in solution is poised to interact with collagen and proceed along the steps of collagenolysis. Significance: The maximum occurrence approach can evaluate the predominant domain conformations for numerous multidomain enzymes.

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Section: Volume 288 • Number 42 • October 18 2013supporting

confidence: 78%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Examination of Matrix Metalloproteinase-1 in Solution

Cerofolini¹,

Fields

Fragai

et al. 2013

Journal of Biological Chemistry

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“…Comparison of the crystal structure of proMMP-1 (29) with the structure of the activated form of MMP-1(E200A) (6,7) suggested that the Cat-Hpx linker region confers interdomain flexibility. Such flexing was further demonstrated for MMP-1 by NMR and small angle X-ray scattering studies (40,41) and seems to be a common property of MMPs (42,43). Our crystal structure of MMP-1 bound to collagen has a more closed conformation than free MMP-1 (SI Appendix, Fig.…”

Section: Discussionmentioning

confidence: 85%

Structural insights into triple-helical collagen cleavage by matrix metalloproteinase 1

Manka

Carafoli

Visse

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

187

307

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Collagenases of the matrix metalloproteinase (MMP) family play major roles in morphogenesis, tissue repair, and human diseases, but how they recognize and cleave the collagen triple helix is not fully understood. Here, we report temperature-dependent binding of a catalytically inactive MMP-1 mutant (E200A) to collagen through the cooperative action of its catalytic and hemopexin domains. Contact between the two molecules was mapped by screening the Collagen Toolkit peptide library and by hydrogen/deuterium exchange. The crystal structure of MMP-1(E200A) bound to a triplehelical collagen peptide revealed extensive interactions of the 115-Å-long triple helix with both MMP-1 domains. An exosite in the hemopexin domain, which binds the leucine 10 residues C-terminal to the scissile bond, is critical for collagenolysis and represents a unique target for inhibitor development. The scissile bond is not correctly positioned for hydrolysis in the crystallized complex. A productive binding mode is readily modeled, without altering the MMP-1 structure or the exosite interactions, by axial rotation of the collagen homotrimer. Interdomain flexing of the enzyme and a localized excursion of the collagen chain closest to the active site, facilitated by thermal loosening of the substrate, may lead to the first transition state of collagenolysis. extracellular matrix | X-ray crystallography | protease T he interstitial collagens I, II, and III are the major structural proteins in connective tissues such as skin, bone, cartilage, tendon, and blood vessels (1). They consist of three α chains with repeating Gly-X-Y triplets (X and Y are often proline and hydroxyproline, respectively) that intertwine each other to form a triple helix of ∼300 nm in length (2). Interstitial collagens are resistant to most proteolytic enzymes, but vertebrate collagenases cleave them at a single site approximately three-quarters of the way from the N terminus of the triple helix, thus initiating collagenolysis (3). Owing to this unique activity, collagenases play important roles in embryo development, morphogenesis, tissue remodeling, wound healing, and human diseases, such as arthritis, cancer, and atherosclerosis (4, 5).Matrix metalloproteinase 1 (MMP-1) is a typical vertebrate collagenase (3). It consists of an N-terminal catalytic (Cat) domain containing an active-site zinc ion and a C-terminal hemopexin (Hpx) domain comprised of a four-bladed β-propeller, which are connected by a linker region (6, 7). Although the Cat domain can cleave a number of noncollagenous proteins including heat-denatured collagen (gelatin), its activity on native triplehelical collagen is negligible. The combination of the Cat and Hpx domains is required for MMP-1 to be able to degrade native collagen, and the same is true for all other collagenolytic MMPs, namely MMP-2, MMP-8, MMP-13, and MMP-14 (3). How collagenases interact with collagen and how the Hpx domain endows these enzymes with collagenolytic activity is not clearly understood. Another enigma of collagenolysis bec...

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“…The mechanistic relationship between cleavage of a linear sequence, as studied here, and cleavage of 3D triple helical collagen by some MMPs is not entirely clear. In almost all cases, the hemopexin domain, which is adjacent to the catalytic domain, is required for cleaving collagen (40)(41)(42), probably by providing an ancillary binding surface. Furthermore, recent work indicates that the MMP-1 collagenase is engaged in an intermittent diffusion alongside the collagen fibril, with the bias component being attributed to proteolysis of substrate (43).…”

Section: Discussionmentioning

confidence: 99%

Basis for substrate recognition and distinction by matrix metalloproteinases

Ratnikov¹,

Cieplak²,

Gramatikoff³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Genomic sequencing and structural genomics produced a vast amount of sequence and structural data, creating an opportunity for structure-function analysis in silico [Radivojac P, et al. (2013) Nat Methods 10(3):221-227]. Unfortunately, only a few large experimental datasets exist to serve as benchmarks for functionrelated predictions. Furthermore, currently there are no reliable means to predict the extent of functional similarity among proteins. Here, we quantify structure-function relationships among three phylogenetic branches of the matrix metalloproteinase (MMP) family by comparing their cleavage efficiencies toward an extended set of phage peptide substrates that were selected from ∼64 million peptide sequences (i.e., a large unbiased representation of substrate space). The observed second-order rate constants [k (obs) ] across the substrate space provide a distance measure of functional similarity among the MMPs. These functional distances directly correlate with MMP phylogenetic distance. There is also a remarkable and near-perfect correlation between the MMP substrate preference and sequence identity of 50-57 discontinuous residues surrounding the catalytic groove. We conclude that these residues represent the specificity-determining positions (SDPs) that allowed for the expansion of MMP proteolytic function during evolution. A transmutation of only a few selected SDPs proximal to the bound substrate peptide, and contributing the most to selectivity among the MMPs, is sufficient to enact a global change in the substrate preference of one MMP to that of another, indicating the potential for the rational and focused redesign of cleavage specificity in MMPs.protease | specificity-determining positions | MMPs A paramount objective of biological research is to understand how sequence encodes function. Previously, functional regions in proteins were identified using large-scale mutagenesis (e.g., alanine scanning) (1). More recently, our insights are largely gained by computational approaches aimed at comparing sequences and structures of large protein sets across multiple genomes. The vast increase in the number of available sequences makes it possible to compare homology between sequences from genome projects to proteins of known structure and function and, as a result, identify functional similarities in silico (2-4). Because the global fold of most ordered proteins can be reliably predicted (5, 6) and because the catalytic residues of most classes of enzymes are either known or can be inferred (7,8), protein sequences can now be directly used to elucidate and classify major protein functions (9-12), and are even being extended to predict enzyme substrates (13).However, such classifications fail to explain the specialization and expansion of function that is required for organismal plasticity, complexity, and adaptability, all of which are normally driven by gene duplications and subsequent divergence. Computational approaches aimed at identifying functional distinctions across protein families have pri...

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The Interface between Catalytic and Hemopexin Domains in Matrix Metalloproteinase-1 Conceals a Collagen Binding Exosite

Cited by 53 publications

References 61 publications

Examination of Matrix Metalloproteinase-1 in Solution

Examination of Matrix Metalloproteinase-1 in Solution

Structural insights into triple-helical collagen cleavage by matrix metalloproteinase 1

Basis for substrate recognition and distinction by matrix metalloproteinases

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