Solution structure of clostridial collagenase H and its calcium-dependent global conformation change

Optimization and mechanisms of proteolytic enzyme immobilization onto large-pore mesoporous silica nanoparticles: Enhanced tumor penetration

Immobilization of proteolytic enzymes onto nanocarriers is effective to improve drug diffusion in tumors through degrading the dense extracellular matrix (ECM). Herein, immobilization and release behaviors of hyaluronidase, bromelain, and collagenase (Coll) on mesoporous silica nanoparticles (MSNs) were explored. A series of cationic MSNs (CMSNs) with large and adjustable pore sizes were synthesized, and investigated together with two anionic MSNs of different pore sizes. CMSNs4.0 exhibited the highest enzyme loading capacity for hyaluronidase and bromelain, and CMSNs4.5 was the best for Coll. High electrostatic interaction, matched pore size, and large pore volume and surface area favor the immobilization. Changes of the enzyme conformations and surface charges with pH, existence of a space around the immobilized enzymes, and the depth of the pore structures, affect the release ratio and tunability. The optimal CMSNs-enzyme complexes exhibited deep and homogeneous penetration into pancreatic tumors, a tumor model with the densest ECM, with CMSNs4.5-Coll as the best. Upon loading with doxorubicin (DOX), the CMSNs-enzyme complexes induced high anti-tumor efficiencies. Conceivably, the DOX/CMSNs4.5-NH2-Coll nanodrug exhibited the most effective tumor therapy, with a tumor growth inhibition ratio of 86.1 %. The study provides excellent nanocarrier-enzyme complexes, and offers instructive theories for enhanced tumor penetration and therapy.

A conserved strategy to attack collagen: The activator domain in bacterial collagenases unwinds triple-helical collagen

Bacterial collagenases are important virulence factors, secreted by several pathogenic Clostridium, Bacillus, Spirochaetes, and Vibrio species. Yet, the mechanism by which these enzymes cleave collagen is not well understood. Based on biochemical and mutational studies we reveal that collagenase G (ColG) from Hathewaya histolytica recognizes and processes collagen substrates differently depending on their nature (fibrillar vs. soluble collagen); distinct dynamic interactions between the activator and peptidase domain are required based on the substrate type. Using biochemical and circular dichroism studies, we identify the presumed noncatalytic activator domain as the single-domain triple helicase that unwinds collagen locally, transiently, and reversibly.

Extracellular collagenase isolated from Streptomyces antibioticus UFPEDA 3421: purification and biochemical characterization

Collagenases are proteases able to degrade native and denatured collagen, with broad applications such as leather, food, and pharmaceutical industries. The aim of this research was to purify and characterize a collagenase from Streptomyces antibioticus. In the present work, the coffee ground substrate provided conditions to obtaining high collagenase activity (377.5 U/mL) using anion-exchange DEAE-Sephadex G50 chromatographic protocol. SDS-PAGE revealed the metallo-collagenase with a single band of 41.28 kDa and was able to hydrolyzed type I and type V collagen producing bioactive peptides that delayed the coagulation time. The enzyme activity showed stability across a range of pH (6.0-11) and temperature (30-55 °C) with optima at pH 7.0 and 60 °C, respectively. Activators include Mg+2, Ca+2, Na+, K+, while full inhibition was given by other tested metalloproteinase inhibitors. Kinetic parameters (Km of 27.14 mg/mol, Vmax of 714.29 mg/mol/min, Kcat of 79.9 s-1 and Kcat/Km of 2.95 mL/mg/s) and thermodynamic parameters (Ea of 65.224 kJ/mol, ΔH of 62.75 kJ/mol, ΔS of 1.96 J/mol, ΔG of 62.16 kJ/mol, ΔGE-S of 8.18 kJ/mol and ΔGE-T of -2.64 kJ/mol) were also defined. Coffee grounds showed to be an interesting source to obtaining a collagenase able to produce bioactive peptides with anticoagulant activity.

A novel computationally engineered collagenase reduces the force required for tooth extraction in an ex-situ porcine jaw model

The currently employed tooth extraction methods in dentistry involve mechanical disruption of the periodontal ligament fibers, leading to inevitable trauma to the bundle bone comprising the socket walls. In our previous work, we have shown that a recombinantly expressed truncated version of clostridial collagenase G (ColG) purified from Escherichia coli efficiently reduced the force needed for tooth extraction in an ex-situ porcine jaw model, when injected into the periodontal ligament. Considering that enhanced thermostability often leads to higher enzymatic activity and to set the basis for additional rounds of optimization, we used a computational protein design approach to generate an enzyme to be more thermostable while conserving the key catalytic residues. This process generated a novel collagenase (ColG-variant) harboring sixteen mutations compared to ColG, with a nearly 4℃ increase in melting temperature. Herein, we explored the potential of ColG-variant to further decrease the physical effort required for tooth delivery using our established ex-situ porcine jaw model. An average reduction of 11% was recorded in the force applied to extract roots of mandibular split first and second premolar teeth treated with ColG-variant, relative to those treated with ColG. Our results show for the first time the potential of engineering enzyme properties for dental medicine and further contribute to minimally invasive tooth extraction.

Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen

Collagenase from the gram-negative bacterium Grimontia hollisae strain 1706B (Ghcol) degrades collagen more efficiently even than clostridial collagenase, the most widely used industrial collagenase. However, the structural determinants facilitating this efficiency are unclear. Here, we report the crystal structures of ligand-free and Gly-Pro-hydroxyproline (Hyp)-complexed Ghcol at 2.2 and 2.4 Å resolution, respectively. These structures revealed that the activator and peptidase domains in Ghcol form a saddle-shaped structure with one zinc ion and four calcium ions. In addition, the activator domain comprises two homologous subdomains, whereas zinc-bound water was observed in the ligand-free Ghcol. In the ligand-complexed Ghcol, we found two Gly-Pro-Hyp molecules, each bind at the active site and at two surfaces on the duplicate subdomains of the activator domain facing the active site, and the nucleophilic water is replaced by the carboxyl oxygen of Hyp at the P1 position. Furthermore, all Gly-Pro-Hyp molecules bound to Ghcol have almost the same conformation as Pro-Pro-Gly motif in model collagen (Pro-Pro-Gly)₁₀, suggesting these three sites contribute to the unwinding of the collagen triple helix. A comparison of activities revealed that Ghcol exhibits broader substrate specificity than clostridial collagenase at the P2 and P2′ positions, which may be attributed to the larger space available for substrate binding at the S2 and S2′ sites in Ghcol. Analysis of variants of three active-site Tyr residues revealed that mutation of Tyr564 affected catalysis, whereas mutation of Tyr476 or Tyr555 affected substrate recognition. These results provide insights into the substrate specificity and mechanism of G. hollisae collagenase.

Structure of Vibrio collagenase VhaC provides insight into the mechanism of bacterial collagenolysis

The collagenases of Vibrio species, many of which are pathogens, have been regarded as an important virulence factor. However, there is little information on the structure and collagenolytic mechanism of Vibrio collagenase. Here, we report the crystal structure of the collagenase module (CM) of Vibrio collagenase VhaC and the conformation of VhaC in solution. Structural and biochemical analyses and molecular dynamics studies reveal that triple-helical collagen is initially recognized by the activator domain, followed by subsequent cleavage by the peptidase domain along with the closing movement of CM. This is different from the peptidolytic mode or the proposed collagenolysis of Clostridium collagenase. We propose a model for the integrated collagenolytic mechanism of VhaC, integrating the functions of VhaC accessory domains and its collagen degradation pattern. This study provides insight into the mechanism of bacterial collagenolysis and helps in structure-based drug design targeting of the Vibrio collagenase.

The collagenolytic mechanism of Vibrio collagenase, a virulence factor, remains unclear. Here, the authors report the structure of Vibrio collagenase VhaC and propose the mechanism for collagen recognition and degradation, providing new insight into bacterial collagenolysis.

Evaluation of alternative diluents for clinical use of collagenase clostridium histolyticum (CCH-aaes)

Background

Collagenase clostridium histolyticum (CCH‐aesthetic formulation [CCH‐aaes]; QWO™ [Endo Aesthetics, Malvern PA, USA] is approved as a subcutaneous injection for treatment of cellulite. In the aesthetic practice, dilution of marketed products is commonly employed to tailor treatments to individual patients or off‐label locations. Dilution beyond the 0.23 mg/ml achievable with the proprietary diluent supplied with the CCH‐aaes lyophilized powder requires diluents readily available in clinic.

Aim

To characterize the functionality and stability of CCH‐aaes when reconstituted and/or diluted with alternative diluents, including normal saline, bacteriostatic saline, and/or proprietary diluent.

Patients/Methods

Each dilution was assessed for purity using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE), activity using collagenase (AUX‐I) and gelatinase (AUX‐II) assays, and aggregation using size‐exclusion chromatography.

Results

When reconstituted with either saline or proprietary diluent, and diluted with proprietary diluent or saline, purity, activity, and stability of CCH‐aaes is maintained for up to 24 h at 5°C or 25°C. In contrast, use of bacteriostatic saline to reconstitute and/or dilute CCH‐aaes results in up to a 40% decrease in activity and aggregation of 5.3% of CCH‐aaes protein. Importantly, inclusion of 2% lidocaine and 1:200 000 epinephrine does not negatively impact CCH‐aaes purity, concentration, or activity for up to 24 h at 5°C or 25°C.

Conclusions

From an efficacy and safety perspective, CCH‐aaes must not be/should not be reconstituted and/or diluted with bacteriostatic saline to avoid injection of protein aggregates. Ideally, CCH‐aaes should be reconstituted in proprietary diluent: further dilution with normal saline and addition of lidocaine and epinephrine is acceptable.

Combinatorial approach for screening and assessment of multiple therapeutic enzymes from marine isolate Pseudomonas aeruginosa AR01

Industrialization and modernization have led to humans being more susceptible to diseases. Therapeutic enzymes from traditional earthbound bacterial origin result have less therapeutic value. Hence, the hunt for a novel source of enzymes is indispensable. Twenty different marine bacterial strains were isolated from mangrove soil around S. P. Pattinum, Tamilnadu, India. From repeated qualitative and quantitative experiments, the study results were that, out of twenty bacterial isolates, only one Gram-negative bacterium was positive for multiple therapeutic enzymes such as asparaginase, glutaminase, uricase and collagenase. Based on its 99% 16S rRNA sequence similarity with Pseudomonas aeruginosa, the isolate was designated as Pseudomonas aeruginosa AR01. Modified minimal medium amended with asparagine results in a simple and cost-effective, one-pot production medium for enhanced production and easy purification of all therapeutic enzymes. The biochemical studies imply that the therapeutic enzymes from P. aeruginosa AR01 may find a significant role in medical applications. The in vitro cytotoxic study reveals that the anticancer enzyme from P. aeruginosa is considerably effective with an IC50 value of 12 μg mL-1 against K-562 cell line. Colony PCR was performed for the detection of specific therapeutic enzyme-coding genes in the genome of P. aeruginosa AR01. PCR results confirm that P. aeruginosa AR01 possesses nucleotide regions for corresponding therapeutic enzymes in its gene cluster. BLASTN and BLASTX analyses of the partial nucleotide sequences of therapeutic enzymes were deposited in GenBank. The results appear so promising that Pseudomonas aeruginosa AR01 may be a potent candidate for medical biotechnology.

Strategy towards tailored donor tissue-specific pancreatic islet isolation

BACKGROUND

Optimizing the collagenase G (ColG):collagenase H (ColH) ratio is a key strategy for achieving tailored donor-tissue specific islet isolation. Collagen V (Col V) and collagen III (Col III) are crucial target matrices of ColG and ColH, respectively. We herein investigated the relevance between the expression of target matrices in pancreatic tissues and influence of ColG:ColH ratio on islet isolation outcome.

METHODS

Islet isolation was performed in Lewis and SD rats using different ColG:ColH ratios (5:1, 1:1 and 1:5; n = 7/group). The composition of Col III and Col V was examined using immunohistochemical staining, real-time polymerase chain reaction (PCR), Western blotting and mass spectrometry. Chain types in collagen I (Col I) were also assessed using mass spectrometry.

RESULTS

No beneficial effects were observed by increasing the ColG amount, irrespective of the rat strain. In contrast, the islet yield in Lewis rats was considerably increased by high amounts of ColH but decreased in SD rats, suggesting that Lewis pancreas contains more Col III than SD pancreas. Neither immunohistochemical nor real-time PCR showed correlation with isolation outcome. However, Western blotting revealed that Lewis contained considerably higher amount of Col III than SD (p = 0.10). Likewise, Col-I(α1)/Col-III(α1) and Col-I(α2)/Col-III(α1) were significantly lower in Lewis than in SD rats (p = 0.007, respectively). Furthermore, the isolation outcome was considerably correlated with the composition of homotrimeric Col I.

CONCLUSIONS

The Col III expression and the composition of homotrimeric Col I in pancreatic tissues determined using mass analyses appeared useful for optimizing the ColG:ColH ratio in islet isolation.

Ca2+ -induced orientation of tandem collagen binding domains from clostridial collagenase ColG permits two opposing functions of collagen fibril formation and retardation

To penetrate host tissues, histotoxic clostridia secrete virulence factors including enzymes to hydrolyze extracellular matrix. Clostridium histolyticum, recently renamed as Hathewaya histolytica, produces two classes of collagenase (ColG and ColH). The high-speed AFM study showed that ColG collagenase moves unidirectionally to plane collagen fibril and rebundles fibril when stalled . The structural explanation of the roles for the tandem collagen-binding segment (CBDs) is illuminated by its calcium-bound crystal structure at 1.9 Å resolution (R_work = 15.0%; R_free = 19.6%). Activation may involve calcium-dependent domain rearrangement supported by both small-angle X-ray scattering and size exclusion chromatography. At pCa ≥ 5 (pCa = -log[Ca²⁺ ]), the tandem CBD adopts an extended conformation that may facilitate secretion from the bacterium. At pCa ≤ 4, the compact structure seen in the crystal structure is adopted. This arrangement positions the two binding surfaces ~ 55 Å apart, and possibly ushers ColG along tropocollagen molecules that allow for unidirectional movement. A sequential binding mode where tighter binding CBD2 binds first could aid in processivity as well. Switch from processive collagenolysis to fibril rearrangement could be concentration dependent. Collagen fibril formation is retarded at 1 : 1 molar ratio of tandem CBD to collagen. Tandem CBD may help isolate a tropocollagen molecule from a fibril at this ratio. At 0.1 : 1 to 0.5 : 1 molar ratios fibril self-assembly was accelerated. Gain of function as a result of gene duplication of CBD for the M9B enzymes is speculated. The binding and activation modes described here will aid in drug delivery design.

ACCESSION CODES

The full atomic coordinates of the tandem CBD and its corresponding structure factor amplitudes have been deposited in the Protein Data Bank (PDB accession code 5IKU). Small-angle X-ray scattering data and corresponding ab initio models have been submitted to the Small Angle Scattering Biological Data Bank (SASBDB). Accession codes CL2, collagenase module 2, CN2, CP2 are assigned to envelopes for tandem CBD at -log[Ca²⁺ ] (pCa) 3, 4, 5, and 6, respectively. Accession code DC64 was assigned to the complex of polycystic kidney disease-CBD1-CBD2 with mini-collagen.

Cyclic Polymer Grafts That Lubricate and Protect Damaged Cartilage

Tissue-reactive graft copolymers were designed to protect the cartilage against enzymatic degradation and restore its lubrication properties during the early stages of osteoarthritis (OA). The copolymers feature a poly(glutamic acid) (PGA) backbone bearing hydroxybenzaldehyde (HBA) functions and cyclic poly(2-methyl-2-oxazoline) (PMOXA) side chains. PGA-PMOXA-HBA species chemisorb on the degraded tissue via Schiff bases and expose the biopassive and lubricious PMOXA cyclic grafts at the interface. The smaller hydrodynamic radius by cyclic PMOXA side chains coupled to the intrinsic absence of chain ends generate denser and more lubricious films on cartilage when compared to those produced by copolymers bearing linear PMOXA. Topology effects demonstrate how the introduction of cyclic polymers within tissue-reactive copolymers substantially improve their tribological and biopassive properties, suggesting a plethora of possible applications for cyclic macromolecules in biomaterials formulations.

Microbial collagenases: challenges and prospects in production and potential applications in food and nutrition

Microbial collagenases are promising enzymes in view of their extensive industrial and biological applications.

Collagen V Is a Potential Substrate for Clostridial Collagenase G in Pancreatic Islet Isolation

The clostridial collagenases, H and G, play key roles in pancreatic islet isolation. Collagenases digest the peptide bond between Yaa and the subsequent Gly in Gly-Xaa-Yaa repeats. To fully understand the pancreatic islet isolation process, identification of the collagenase substrates in the tissue is very important. Although collagen types I and III were reported as possible substrates for collagenase H, the substrate for collagenase G remains unknown. In this study, collagen type V was focused upon as the target for collagenases. In vitro digestion experiments for collagen type V were performed and analyzed by SDS-PAGE and mass spectrometry. Porcine pancreatic tissues were digested in vitro under three conditions and observed during digestion. The results revealed that collagen type V was only digested by collagenase G and that the digestion was initiated from the N-terminal part. Tissue degradation during porcine islet isolation was only observed in the presence of both collagenases H and G. These findings suggest that collagen type V is one of the substrates for collagenase G. The enzymatic activity of collagenase G appears to be more important for pancreatic islet isolation in large mammals such as pigs and humans.

Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH

The surface properties and dynamics of PKD-like domains from ColG and ColH differ.

Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca²⁺-triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca²⁺-bound holo s2b (1.4 Å resolution, R = 15.0%, R_free = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, R_free = 20.7%), as well as of Ca²⁺-free apo s2a (1.8 Å resolution, R = 20.7%, R_free = 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, R_free = 21.2%; 1.6 Å resolution, R = 16.2%, R_free = 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca²⁺ pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3. B-factor analyses suggest that in the presence of Ca²⁺ the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca²⁺ binding. Conserved residues not only interact with Ca²⁺, but also position the Ca²⁺-interacting water molecule. Ca²⁺ aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca²⁺ binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

Weak protein-ligand interactions studied by small-angle X-ray scattering

Small-angle X-ray scattering (SAXS) is a powerful technique for studying weak interactions between proteins and their ligands (other proteins, DNA/RNA or small molecules) in solution. SAXS provides knowledge about the equilibrium state, the stoichiometry of binding and association-dissociation processes. The measurements are conducted in a solution environment that allows easy monitoring of modifications in protein-ligand association state upon environmental changes. Model-free parameters such as the molecular mass of a system and the radius of gyration can be obtained directly from the SAXS data and give indications about the association state. SAXS is also widely employed to build models of biological assemblies at a resolution of approximately 10-20 Å. Low-resolution shapes can be generated ab initio, although more detailed and biologically interpretable information can be obtained by hybrid modelling. In the latter approach, composite structures of protein-ligand complexes are constructed using atomic models of individual molecules. These may be predicted homology models or experimental structures from X-ray crystallography or NMR. This review focuses on using SAXS data to model structures of protein-ligand complexes and to study their dynamics. The combination of SAXS with other methods such as size exclusion chromatography and dynamic light scattering is discussed.

Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen

Clostridial collagenases are among the most efficient degraders of collagen. Most clostridia are saprophytes and secrete proteases to utilize proteins in their environment as carbon sources; during anaerobic infections, collagenases play a crucial role in host colonization. Several medical and biotechnological applications have emerged utilizing their high collagenolytic efficiency. However, the contribution of the functionally most important peptidase domain to substrate specificity remains unresolved. We investigated the active site sequence specificity of the peptidase domains of collagenase G and H from Clostridium histolyticum and collagenase T from Clostridium tetani. Both prime and non-prime cleavage site specificity were simultaneously profiled using Proteomic Identification of protease Cleavage Sites (PICS), a mass spectrometry-based method utilizing database searchable proteome-derived peptide libraries. For each enzyme we identified > 100 unique-cleaved peptides, resulting in robust cleavage logos revealing collagen-like specificity patterns: a strong preference for glycine in P3 and P1′, proline at P2 and P2′, and a slightly looser specificity at P1, which in collagen is typically occupied by hydroxyproline. This specificity for the classic collagen motifs Gly-Pro-X and Gly-X-Hyp represents a remarkable adaptation considering the complex requirements for substrate unfolding and presentation that need to be fulfilled before a single collagen strand becomes accessible for cleavage.

Biological significance

We demonstrate the striking sequence specificity of a family of clostridial collagenases using proteome derived peptide libraries and PICS, Proteomic Identification of protease Cleavage Sites. In combination with the previously published crystal structures of these proteases, our results represent an important piece of the puzzle in understanding the complex mechanism underlying collagen hydrolysis, and pave the way for the rational design of specific test substrates and selective inhibitors.

This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?

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Active site specificity profiling of 3 clostridial collagenases—ColG and H from C. histolyticum, and ColT from C. tetani.

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Their high sequence specificity to collagen-like sequence points towards a co-evolution with the mammalian substrate.

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Significant differences to MMPs and a more promiscuous cleavage mechanism facilitating rapid collagenolysis were revealed.

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Human proteome-derived peptide libraries & PICS are suitable for active site specificity profiling of pathogenic proteases.

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Results pave the way for rational design of test substrates and selective inhibitors.