High-Throughput Multiplexed Peptide-Centric Profiling Illustrates Both Substrate Cleavage Redundancy and Specificity in the MMP Family

Kukreja, Muskan; Shiryaev, Sergey A.; Cieplak, Piotr; Muranaka, Norihito; Routenberg, David A.; Chernov, Andrei V.; Kumar, Sonu; Remacle, Albert G.; Smith, Jeffrey W.; Kozlov, I. A.; Strongin, Alex Y.

doi:10.1016/j.chembiol.2015.07.008

Cited by 27 publications

(40 citation statements)

References 59 publications

(77 reference statements)

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“…The cross-validation tests involving the hundreds of the MMP cleavage sequences identified by others (17,(21)(22)(23)(24)(25) validated the accuracy of our cleavage prediction software. Specifically, false prediction rate, accuracy, and specificity were 2-3, 94 -96, and 97-98%, respectively, for MMP-9, suggesting that, in addition to the previously known cleavage targets, we can now identify novel, previously unrecognized substrates of this proteinase (17,20).…”

Section: Resultsmentioning

confidence: 95%

“…Here, we employed a high throughput multiplexed peptide-centric profiling technology involving the cleavage of 18,583 peptides by the 18 individual proteinases from the main subgroups of the MMP family (20). Volumes of the experimental data we acquired, merged with advanced bioinformatics, enabled comparison of the MMP cleavage preferences on a global scale and led to the previously unprecedented level of knowledge in MMP biology.…”

Section: Resultsmentioning

confidence: 99%

“…MMP-9 activity is stimulated by a limited set of conditions that are prevalent in inflammation, including peripheral nerve injury, and also in neurogenesis (27,28). Because our software correctly predicts a vast majority of MMP-9 substrates (17,20) and because the R907Q missense mutation reduced the presentation of the mutant protein at the plasma membrane, we hypothesized that the mutation enhanced the susceptibility of the membrane Nav1.7 to MMP-9 proteolysis, leading to the fragmented channel incapable of assembling a functional pore at the plasma membrane.…”

Section: Resultsmentioning

confidence: 99%

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Matrix Metalloproteinase (MMP) Proteolysis of the Extracellular Loop of Voltage-gated Sodium Channels and Potential Alterations in Pain Signaling

Remacle

Kumar

Motamedchaboki

et al. 2015

Journal of Biological Chemistry

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Background:Mutations in the voltage-gated sodium channel Nav1.7 cause congenital insensitivity to pain (CIP) in humans. Results: Missense mutation R907Q in the extracellular disordered loop of Nav1.7 may also cause CIP because of the enhanced MMP-9 proteolysis of the mutant. Conclusion: Accelerated cleavage of Nav1.7 by MMP-9 explains insensitivity to pain. Significance: MMP proteolysis of sodium channels is a novel biochemical phenomenon.

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Section: Resultsmentioning

confidence: 95%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Matrix Metalloproteinase (MMP) Proteolysis of the Extracellular Loop of Voltage-gated Sodium Channels and Potential Alterations in Pain Signaling

Remacle

Kumar

Motamedchaboki

et al. 2015

Journal of Biological Chemistry

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“…These results suggest that MMP-12 can act as a "true collagenase," preferentially cleaving a specific sequence in triple-helical conformation while having little or no activity toward the sequence in a nontriple-helical context. Indeed, recent analysis of hydrolysis among thousands of linear peptide sequences indicates that the single strand of collagen V residues 436 -450, apart from Val at P 1 Ј, lacks cleavage motifs favored by MMP-12 (56,57).…”

Section: Resultsmentioning

confidence: 99%

Path to Collagenolysis

Prior

Byrne

Tokmina‐Roszyk

et al. 2016

Journal of Biological Chemistry

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Collagenolysis is essential in extracellular matrix homeostasis, but its structural basis has long been shrouded in mystery. We have developed a novel docking strategy guided by paramagnetic NMR that positions a triple-helical collagen V mimic (synthesized with nitroxide spin labels) in the active site of the catalytic domain of matrix metalloproteinase-12 (MMP-12 or macrophage metalloelastase) primed for catalysis. The collagenolytically productive complex forms by utilizing seven distinct subsites that traverse the entire length of the active site. These subsites bury ϳ1,080 Å 2 of surface area, over half of which is contributed by the trailing strand of the synthetic collagen V mimic, which also appears to ligate the catalytic zinc through the glycine carbonyl oxygen of its scissile GϳVV triplet. Notably, the middle strand also occupies the full length of the active site where it contributes extensive interfacial contacts with five subsites. This work identifies, for the first time, the productive and specific interactions of a collagen triple helix with an MMP catalytic site. The results uniquely demonstrate that the active site of the MMPs is wide enough to accommodate two strands from collagen triple helices. Paramagnetic relaxation enhancements also reveal an extensive array of encounter complexes that form over a large part of the catalytic domain. These transient complexes could possibly facilitate the formation of collagenolytically active complexes via directional Brownian tumbling.Collagens comprise around 30% of the protein mass of the body (1) and resist general proteolysis. Matrix metalloproteinases (MMPs) 2 degrade collagen during cancer cell migration (2), angiogenesis (3, 4), destabilization of atherosclerotic plaques (5), and arthritis (6) and after myocardial infarction (7). For instance, plaques contain a collagen-rich cap and are sensitive to MMP-12 secreted by macrophages that makes them more vulnerable to rupture, precipitating myocardial infarction, or stroke (8).Collagen fibrils are bundles of staggered triple helices. Each triple helix comprises three extended strands twisted into a right-handed superhelix with hydrogen bonding between chains (9). Each collagen chain is a long series of GXY triplets in which the glycine is in the interior, X is often proline, and Y is often a stabilizing 4-hydroxyproline (Hyp). Because each chain is offset by one residue, the chains have been named leading, middle, and trailing (10). Lack of Pro and Hyp in four GXY triplets on the C-terminal side of the MMP scissile bond in interstitial collagens (types I, II, and III) was proposed to loosen the triple helix (1); this was later observed as 10-fold symmetry (11).Protease substrates are labeled by increasing distance from the scissile peptide bond with a prime indicating the C-terminal side: P 4 -P 3 -P-P 1 ϳP 1 Ј-P 2 Ј-P 3 Ј-P 4 Ј where ϳ denotes the scissile peptide bond. We refer to the residues on the N-terminal side of the scissile bond as "unprimed" and those on the C-terminal side as "primed." The...

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“…In combination with in vitro translation, nucleic acid sequencing has been used to determine protease cleavage sites (17). Such a setup has recently enabled the family-wide portrayal of matrix metalloprotease (MMP) specificity determinants (18). Cysteine cathepsin specificity has also been investigated by a nonpeptide approach termed fast profiling of protease specificity (19).…”

mentioning

confidence: 99%

Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics

Biniossek

Niemer

Maksimchuk

et al. 2016

Molecular & Cellular Proteomics

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We present protease specificity profiling based on quantitative proteomics in combination with proteome-derived peptide libraries. Peptide libraries are generated by endoproteolytic digestion of proteomes without chemical modification of primary amines before exposure to a protease under investigation. After incubation with a test protease, treated and control libraries are differentially isotope-labeled using cost-effective reductive dimethylation. Upon analysis by liquid chromatography-tandem mass spectrometry, cleavage products of the test protease appear as semi-specific peptides that are enriched for the corresponding isotope label. We validate our workflow with two proteases with well-characterized specificity profiles: trypsin and caspase-3. We provide the first specificity profile of a protease encoded by a human endogenous retrovirus and for chlamydial protease-like activity factor (CPAF). For CPAF, we also highlight the structural basis of negative subsite cooperativity between subsites S1 and S2. For A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) -4, -5, and -15, we show a canonical preference profile, including glutamate in P1 and glycine in P3. In total, we report nearly 4000 cleavage sites for seven proteases. Our protocol is fast, avoids enrichment or synthesis steps, and enables probing for lysine selectivity as well as subsite cooperativity. Due to its simplicity, we anticipate usability by most proteomic laboratories. Molecular & Cellular

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High-Throughput Multiplexed Peptide-Centric Profiling Illustrates Both Substrate Cleavage Redundancy and Specificity in the MMP Family

Cited by 27 publications

References 59 publications

Matrix Metalloproteinase (MMP) Proteolysis of the Extracellular Loop of Voltage-gated Sodium Channels and Potential Alterations in Pain Signaling

Matrix Metalloproteinase (MMP) Proteolysis of the Extracellular Loop of Voltage-gated Sodium Channels and Potential Alterations in Pain Signaling

Path to Collagenolysis

Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics

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