Matrix metalloproteinase 3 , CAS No.79955-99-0

CAS: 79955-99-0 Cat. No.: M1440799

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Panoramica

Matrix metalloproteinase 3 is a biochemical reagent that can be used as a biological material or organic compound for life science related research.

Specifications

Condizioni di conservazione di stoccaggio

Store at -20°C

Spedito in

Ice chest + Ice pads

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Application Protocols

Note: Specific validated protocols for this SKU are not provided in the Product Data. The following are literature‑based examples for MMP‑3.

A. Fluorogenic peptide assay (96‑well)

• Prepare assay buffer: 50 mM Tris‑HCl pH 7.5, 150 mM NaCl, 10 mM CaCl2, 0.01% Brij‑35; optionally 0.1 mg/mL BSA.
• Prepare substrate at 5× KM (e.g., 25–50 µM) in buffer; keep DMSO ≤1%.
• Dilute MMP‑3 to 0.2–2 nM in buffer; equilibrate 10 min at assay temperature (25–30°C).
• Start reaction by adding enzyme to substrate (final 1×); read fluorescence kinetically (Ex/Em per substrate; e.g., 328/393 nm for Mca) for 10–30 min.
• Controls: +EDTA (10 mM), +broad‑spectrum inhibitor, vehicle only.

B. Casein/gelatin zymography (as positive control)

• Run samples on SDS‑PAGE gels co‑polymerized with casein or gelatin.
• Renature in 2.5% Triton X‑100, then incubate overnight in 50 mM Tris‑HCl pH 7.5 with 10 mM CaCl2 and 150 mM NaCl at 37°C.
• Stain with Coomassie; clear bands indicate proteolysis.

C. Activation of pro‑MMPs

• Incubate pro‑MMP substrate with MMP‑3 at a defined molar ratio (e.g., 1:50 to 1:200) in Tris buffer with Ca2+/Zn2+ at 25–37°C for 30–120 min; quench or purify activated enzyme.

Adjust concentrations and times based on the specific construct and activity stated on the CoA (not specified for this item).

Biological Roles

General biology of MMP‑3 (literature)

• Function: Secreted zinc‑ and calcium‑dependent endopeptidase (stromelysin‑1) that cleaves a broad spectrum of extracellular matrix (ECM) proteins including proteoglycans, fibronectin, laminin, and certain collagens. It also processes non‑ECM proteins (e.g., cytokine precursors, cell‑surface molecules) in vitro.
• Activation and regulation: Produced as an inactive pro‑enzyme (pro‑MMP‑3). Activation occurs via proteolytic removal of the pro‑peptide or chemical disruption of the cysteine switch. Endogenous regulation involves tissue inhibitors of metalloproteinases (TIMPs), particularly TIMP‑1 and TIMP‑2.
• Structural determinants: Catalytic domain contains the consensus Zn2+‑binding sequence HELGHXXGXXH and a deep S1′ specificity pocket that favors hydrophobic residues at P1′. The hemopexin‑like domain modulates substrate recognition and interactions with inhibitors and activators.
• Systems context: Contributes to ECM remodeling during development, morphogenesis, and wound healing; participates in MMP activation cascades by converting latent pro‑MMPs to their active forms.
• Localization: Secreted into the extracellular space; may associate with the cell surface or ECM components.

Note

• The above information summarizes the enzyme’s biochemical roles for research context. It does not imply medical or clinical claims. Item‑specific sequence, species, and construct details are not specified for this product; refer to the CoA/Spec Sheet.

Buffer Applications

Applicability

• MMP‑3 is not a buffering reagent. However, its performance depends critically on the buffer composition used in assays and handling.

Assay buffer examples (literature; general guidance)

• Activity assay buffer (typical): 50 mM Tris‑HCl, pH 7.5–8.0; 150 mM NaCl; 5–10 mM CaCl2; 0.005–0.05% Brij‑35; 0.1 mg/mL BSA optional to reduce adsorption; add 1–5 µM ZnCl2 if required.
• Storage/dilution buffer: 25–50% glycerol (v/v) in Tris‑HCl pH 7.5 with 150 mM NaCl and 5 mM CaCl2 to support stability at −20°C; avoid EDTA (literature practice).
• Inhibition control buffer: Same as activity buffer plus 5–10 mM EDTA to confirm metal dependence (expect complete loss of activity).

Practical tips

• pH window: Most MMPs, including MMP‑3, show optimal activity near neutral to slightly basic pH; verify for your construct.
• Ionic strength: 100–200 mM NaCl reduces nonspecific interactions and improves assay robustness.
• Additives: Nonionic detergents minimize surface adsorption; carrier proteins can stabilize dilute enzyme solutions but may interfere with low‑background fluorescence assays—evaluate empirically.

Item note

• Exact buffer composition for this SKU is not specified; consult the CoA for formulation and any stabilizers present.

Green Alternatives

Context

• As a protein enzyme, MMP‑3 work is inherently aqueous. Greener practice focuses on buffer selection, minimizing hazardous additives, and designing low‑waste assays.

Greener choices (literature/best practice)

• Buffer systems: Prefer HEPES or MOPS over Tris if temperature excursions are likely; these Good’s buffers are zwitterionic with low biological toxicity and minimal metal chelation at working concentrations.
• Detergents: Use readily biodegradable nonionic surfactants at the lowest effective concentration (e.g., ≤0.02% Brij‑35). Avoid SDS and cationic surfactants that denature proteins.
• Cosolvents: Limit DMSO to ≤1% v/v; avoid DMF/MeCN in routine assays. Where possible, dissolve inhibitors in concentrated DMSO stocks and dilute into aqueous buffer immediately before use.
• Assay miniaturization: Move to 384‑ or 1536‑well plates to reduce reagent consumption and plastic waste; validate linearity and edge effects.
• Reusability: Adopt low protein binding, recyclable plastics where compatible; collect liquid waste streams separately for appropriate treatment.

Comparison table (literature)

• Tris‑HCl vs. HEPES: Tris is effective but temperature‑sensitive and can interact weakly with metals; HEPES offers better thermal stability and lower metal interaction—often preferred for metal‑dependent enzymes like MMP‑3.

Note

• Specific excipients and formulation for this item are not specified; ensure greener substitutions maintain enzyme activity.

Pharmaceutical Uses

Scope and limitations

• This product is supplied strictly for research use only. No clinical or therapeutic use is intended or implied.

Relevant non‑clinical/industrial contexts (literature)

• Screening and characterization: Widely used as a biochemical target for discovery and profiling of metalloproteinase inhibitors, including benchmarking compound selectivity across MMP family members.
• QC reference material: Serves as a positive control enzyme in lot release tests for fluorogenic substrate assays and for validating zymography gels in development laboratories.
• Formulation research tools: Utilized to study enzyme–inhibitor binding kinetics (SPR, ITC) and to evaluate excipient effects on metalloproteinase stability and activity.
• Bioprocess R&D: May be used to assess protease carryover resistance in protein formulations or to intentionally process ECM‑mimetic scaffolds in materials research.

Item-specific note

• Any pharmacopeial status, GMP grade, or endotoxin specification for this SKU is not specified; consult the CoA/Spec Sheet if your workflow requires defined quality attributes.

Physical Properties

Item-specific physical properties

• Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight (as supplied): Not specified for this item; refer to CoA/Spec Sheet.

General/literature values and behavior (for MMP‑3 proteins)

• Typical sizes: Pro‑MMP‑3 (zymogen) ~50–57 kDa; mature catalytic forms commonly ~45 kDa depending on activation/processing (literature; isoform and tag dependent).
• Isoelectric point (pI): Reported in literature in the acidic range for human stromelysin‑1; exact value depends on sequence, glycosylation, and tags.
• Solubility: Readily soluble in physiological aqueous buffers; activity depends on the presence of Ca2+ and Zn2+. Avoid strong chelators (EDTA, EGTA) that abrogate activity (literature).
• Stability: Sensitive to repeated freeze–thaw; activity maintained by storage at ≤−20°C to −80°C, aliquoting, and inclusion of carrier protein or glycerol (literature guidance).
• Extinction coefficient: Sequence‑dependent; if needed, calculate from the exact sequence on the CoA using Tyr/Trp/Cys content (literature practice).
• Cofactor dependence: Catalytic activity requires Zn2+ and is stabilized by Ca2+ (literature).

Notes

• Exact buffer composition, concentration, excipients, and any tags/additives are not specified for this item; consult the CoA/Spec Sheet for definitive physical data.

Quality and Grades

Item-specific quality information

• Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.

How to interpret grades for MMP‑3 products (general guidance)

• Recombinant vs. native: Recombinant human or animal MMP‑3 is often supplied as pro‑enzyme or activated enzyme. The CoA should state source (species, expression host), construct (full length, catalytic domain only), and any affinity tags.
• Purity metrics: SDS‑PAGE purity (e.g., ≥90–95%), LC‑MS intact mass, and endotoxin levels (EU/µg) are common. Activity is typically reported in units per mg against a standard fluorogenic peptide substrate; zymography or kinetic constants (kcat, KM) may also be provided. For this catalog item, these values are not specified—consult the CoA.
• Inhibitor sensitivity: Active MMP‑3 should be fully inhibited by broad‑spectrum inhibitors (e.g., batimastat, marimastat) and by TIMPs (e.g., TIMP‑1). Such controls are frequently included in quality release testing (literature practice).
• Stabilizers/excipients: Proteins may be formulated with salts, calcium, zinc, glycerol, sugars, or carrier proteins (e.g., BSA). This item’s excipients are not specified—refer to the Spec Sheet.
• Documentation: For regulated workflows (QC, platform assays), ensure batch‑specific CoA provides lot number, concentration determination method (A280, BCA), storage buffer, and recommended handling.

Reaction and Applications

Research applications (literature; expand beyond catalog header)

• Proteolysis of ECM components: Degrades proteoglycans, fibronectin, laminin, and non‑fibrillar collagens; widely used to model extracellular matrix remodeling in vitro.
• Activation of other MMP zymogens: Efficiently activates pro‑MMP‑1, pro‑MMP‑7, and pro‑MMP‑9, enabling cascade studies and preparation of active MMPs from pro‑forms.
• Inhibitor screening and kinetics: Gold‑standard enzyme for evaluating small‑molecule and biological MMP inhibitors; kinetic assays with fluorogenic peptides provide kcat/KM, IC50, and Ki estimations.
• Zymography and substrate profiling: Serves as a positive control in casein/gelatin zymography; used in proteomic substrate discovery (PICS, TAILS) to map cleavage preferences.
• Protease engineering and mechanistic studies: Model system for metzincin catalytic mechanisms, metal dependence, and exosite contributions from the hemopexin domain.

Practical tips (literature)

• Activation state: Confirm whether the supplied enzyme is pro‑ or active. For pro‑MMP‑3, activation can be achieved chemically (e.g., APMA) or proteolytically; optimize to avoid over‑processing.
• Controls: Include EDTA control (complete inhibition) and a broad‑spectrum hydroxamate inhibitor to demonstrate assay window.
• Substrates: Well‑characterized FRET peptides (e.g., Mca‑/Dnp or Dnp‑quenched sequences with a Leu↓Gly scissile bond) yield high signal‑to‑noise.
• Surface loss: Minimize adsorption by adding 0.01–0.05% nonionic detergent and low protein binding plastics.

Reaction Conditions

General assay conditions (literature guidance; not item‑specific specifications)

• Buffer: 50 mM Tris‑HCl, pH 7.5–8.0; 150 mM NaCl; 5–10 mM CaCl2; 0.005–0.05% Brij‑35; optional 0.1 mg/mL BSA; add 1–5 µM ZnCl2 if needed.
• Temperature: 25–37°C depending on assay format. Many kinetic screens are run at 25–30°C to reduce evaporation and maintain linearity.
• Enzyme concentration: Common working range 0.1–10 nM for fluorogenic substrates; adjust to keep initial velocity linear and substrate turnover <10% during measurement.
• Substrates: FRET peptides bearing a hydrophobic residue at P1′ (e.g., Leu) such as Mca‑PLGL‑Dpa‑AR‑NH2 are frequently used; tune substrate concentration around KM (often low‑ to mid‑µM, substrate‑dependent).
• Controls: Include vehicle control (e.g., 1% DMSO), EDTA (5–10 mM, full inhibition), and a broad‑spectrum hydroxamate inhibitor for assay window verification.
• Activation: If supplied as pro‑MMP‑3, chemical activation with APMA (e.g., 1 mM, 1–2 h, 37°C) or proteolytic activation by trypsin or other MMPs can be employed, followed by removal/inactivation of the activator (optimize to minimize autolysis).
• Data quality: Monitor inner‑filter effects at high substrate/product absorbance; validate linear range and pathlength in microplates.

Expected outcomes

• Under the above conditions, robust increases in fluorescence over time with signal abolished by EDTA indicate active, metal‑dependent catalysis (qualitative benchmark). Quantitative rates are substrate‑ and batch‑dependent.

Safety and Handling

Item-specific safety data

• GHS classification, signal word, pictograms, H‑statements: Not specified for this item; refer to the SDS.

General guidance for handling recombinant/isolated proteases (literature/best practice)

• Hazards: Proteolytic enzyme; may cause allergic sensitization upon inhalation or skin contact. Avoid aerosol generation. Treat as a proteinaceous laboratory reagent of unknown toxicity; for research use only.
• PPE: Laboratory coat, safety glasses, and appropriate disposable gloves (nitrile). Use a certified biosafety cabinet when handling powders/lyophilizates or when preparing stocks that may aerosolize.
• Engineering controls: Work in well‑ventilated area or BSC; keep containers closed.
• Incompatibilities: Avoid buffers containing strong metal chelators (EDTA/EGTA) if activity must be preserved. Avoid prolonged exposure to extremes of pH, oxidants, or high temperature that denature proteins.
• First aid (overview; defer to SDS):
  • Inhalation: Move to fresh air; seek medical attention if symptoms occur.
  • Skin/eye contact: Rinse with water for at least 15 minutes; remove contaminated clothing.
  • Ingestion: Rinse mouth; seek medical advice.
• Spill response: Avoid dust; gently dampen and collect with absorbent. Decontaminate surfaces with protein‑denaturing agents (e.g., dilute bleach) followed by water.
• Waste: Dispose according to institutional and local regulations for biological/biochemical waste.
• Transport/storage risks: Maintain cold chain; repeated freeze–thaw cycles reduce activity.

Solvent Selection

Applicability

• MMP‑3 is a water‑soluble protein enzyme; solvent selection centers on aqueous buffer systems rather than organic solvents.

General/literature guidance for buffers and cosolvents

• Preferred medium: Neutral to slightly basic aqueous buffers (e.g., 25–50 mM Tris‑HCl, pH 7.5–8.0) supplemented with 100–200 mM NaCl, 5–10 mM CaCl2, and trace Zn2+ to maintain activity and stability.
• Detergents: 0.01–0.05% nonionic surfactants (e.g., Brij‑35, Tween‑20) can minimize adsorption and improve kinetic reproducibility in fluorogenic assays (literature).
• Organic cosolvents: Keep DMSO ≤1–2% v/v during inhibitor screening to maintain enzyme integrity; pre‑equilibrate enzyme in assay buffer before introducing DMSO (literature recommendation).
• Chelators: Avoid EDTA/EGTA or phosphate concentrations that chelate/compete with metal binding when activity must be preserved.
• Redox environment: Reducing agents (e.g., 1–2 mM DTT) are generally avoided for long incubations because they may perturb the cysteine switch and metal coordination; if used, validate activity empirically.

Comparison (literature)

• Tris‑HCl vs. HEPES: Tris provides robust buffering at pH 7.5–8.5 and is commonly used for MMP assays; HEPES (pKa ~7.5) offers better temperature stability and minimal metal chelation. Both are acceptable when supplemented with Ca2+/Zn2+.

Storage and Reconstitution

Item-specific storage and shipping

• Storage: Store at −20°C (per Product Data). Avoid repeated freeze–thaw.
• Shipping: Shipped in an ice chest with ice pads to maintain the cold chain.

General reconstitution guidance (literature; verify with CoA)

• Reconstitution buffer: Use chilled buffer lacking chelators—e.g., 25–50 mM Tris‑HCl, pH 7.5–8.0; 150 mM NaCl; 5 mM CaCl2; optional 1–5 µM ZnCl2. Avoid EDTA/EGTA.
• Concentration: Reconstitute to a convenient stock (e.g., 0.1–1 mg/mL or as activity units/mL) to minimize freeze–thaw damage. Exact concentration for this item is not specified; see CoA.
• Stabilizers: 10–50% glycerol and/or 0.1 mg/mL carrier protein (e.g., BSA) can improve stability for storage at −20°C. Validate compatibility with downstream assays.
• Aliquoting: Dispense single‑use aliquots; flash‑freeze in liquid N2 or a dry‑ice/ethanol bath before storage to reduce ice damage.
• Handling: Thaw on ice; gently mix—do not vortex. Keep on ice during use. Return unused aliquots promptly to storage.
• Short‑term storage: At 2–8°C for hours to 1–2 days may be acceptable if stabilized; monitor activity.
• Long‑term storage: For maximal stability, consider −80°C. Avoid frost‑free freezers.

Documentation

• Buffer composition, excipients, protein form (pro vs. active), exact concentration, and any tags are not specified for this item; refer to the CoA/Spec Sheet for definitive instructions.

Structure and Identity

Item-specific facts (from Product Data)

• Name: Matrix metalloproteinase 3 (MMP‑3; also known as stromelysin‑1)
• CAS: 79955-99-0
• Storage: Store at −20°C (per Product Data)
• Shipped: Ice chest + ice pads
• Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
• SMILES: Not applicable to proteins; not specified for this item.
• InChIKey: Not applicable to proteins; not specified for this item.

General structural features (literature)

• Protein family: Metzincin superfamily, Matrix Metalloproteinases (MMPs).
• Domain architecture: N‑terminal signal peptide (secreted), pro‑peptide (cysteine switch), catalytic domain containing the Zn2+‑binding consensus motif (HELGHXXGXXH), flexible linker (hinge), and C‑terminal hemopexin‑like domain that mediates substrate and inhibitor interactions.
• Metal cofactors: One catalytic Zn2+ and multiple structural Ca2+ ions are typically bound in active forms (literature).
• Quaternary state: Functions as a monomer; can associate with substrates/inhibitors (e.g., TIMPs) (literature).

2D/primary structure description (literature)

• Linear polypeptide with an N‑terminal pro‑segment blocking the active site via the Cys‑Zn2+ switch; upon activation, the catalytic domain presents a deep S1′ pocket adjacent to the catalytic glutamate that polarizes a water molecule for peptide‑bond hydrolysis; the C‑terminal β‑propeller (hemopexin) domain confers substrate selectivity and protein–protein interactions.

Synthetic Utility

Applicability

• Traditional “synthetic utility” (as in small‑molecule transformations) is not directly applicable to a protein enzyme like MMP‑3.

Relevant utility in chemical biology and materials (literature)

• Biocatalytic processing of biomaterials: MMP‑3 can remodel or degrade ECM‑mimetic hydrogels and peptide‑functionalized polymers, enabling controlled release or degradation studies.
• Proteolytic mapping: Employed to generate defined protein fragments for structural proteomics and epitope exposure studies.
• Retrosynthetic design of substrates/inhibitors: Knowledge of the S1′ pocket preferences and catalytic mechanism underpins the design of FRET substrates and hydroxamate‑based inhibitors used as chemical probes.
• Cascade activation: Used to activate other pro‑MMPs in situ, furnishing active enzymes for downstream biochemical experiments without separate expression/purification.

Note

• If your goal is small‑molecule synthesis, this section is not applicable; see Reaction & Applications and Reaction Conditions for assay‑focused guidance.

Target Specificity

This section typically applies to antibodies or affinity reagents. For this product (the enzyme MMP‑3 itself), antigen/clone/isotype details are not applicable.

Item-specific note

• Target/antigen, epitope mapping, species reactivity, clone, and isotype: Not applicable to this item; not specified for this item.

Related literature context

• Endogenous inhibitors and binding partners include TIMP‑1/TIMP‑2 and engineered hydroxamate inhibitors; substrate specificity is dictated by the S1′ pocket favoring hydrophobic residues at P1′.