Macromolecular Substrates Research Articles

In vitro cleavage of bioactive peptides by peptidases from Bothrops jararaca venom and its neutralization by bothropic antivenom produced by Butantan Institute: Major contribution of serine peptidases

In Brazil, envenomation by Bothrops pitvipers is responsible for over 73% of snakebites, and their venom is a rich source of proteolytic enzymes. Most studies have demonstrated that Bothrops jararaca venom acts on macromolecular substrates, causing an imbalance in the victim's hemostatic system. In contrast, fewer studies have examined the proteolytic activity on small molecules such as peptides. In this study, we used a set of bioactive peptides (insulin B chain, Met-enkephalin, Leu-enkephalin, neuropeptide Y, peptide YY, pancreatic polypeptide, substance P and somatostatin) to identify new peptide substrates for the metallopeptidases and serine peptidases from the B. jararaca venom. The majority of these peptides were substrates for the venom, but neuropeptide Y and pancreatic polypeptide presented higher hydrolyses rates. Although most of the peptides were simultaneously substrates for both classes of proteases, serine peptidases were the most active. Substance P was an exclusive substrate for metallopeptidases, while somatostatin was a selective substrate for serine peptidases. The neutralizing efficacy of the bothropic antivenom produced by the Butantan Institute was also assessed and found to totally prevent substance P hydrolysis, whereas somatostatin cleavage was not inhibited. Thus, the antivenom effectively inhibited metallopeptidase activity, but did not neutralize some of the serine peptidases. These results indicate that, in addition to cleaving proteins, the proteolytic enzymes from this venom also hydrolyze bioactive peptides, and this peptidase activity could effectively contribute to some of the many dire manifestations of envenomation.

Generation and characterization of aptamers targeting factor XIa

BackgroundThe plasma protease factor XIa (FXIa) has become a target of interest for therapeutics designed to prevent or treat thrombotic disorders. MethodsWe used a solution-based, directed evolution approach called systematic evolution of ligands by exponential enrichment (SELEX) to isolate RNA aptamers that target the FXIa catalytic domain. ResultsTwo aptamers, designated 11.16 and 12.7, were identified that bound to previously identified anion binding and serpin bindings sites on the FXIa catalytic domain. The aptamers were non-competitive inhibitors of FXIa cleavage of a tripeptide chromogenic substrate and of FXIa activation of factor IX. In normal human plasma, aptamer 12.7 significantly prolonged the aPTT clotting time. ConclusionsThe results show that novel inhibitors of FXIa can be prepared using SELEX techniques. RNA aptamers can bind to distinct sites on the FXIa catalytic domain and noncompetitively inhibit FXIa activity toward its primary macromolecular substrate factor IX with different levels of potency. Such compounds can be developed for use as therapeutic inhibitors.

How the Loss of a Single Hydroxyl Group Affects the Proteolytic Activity of the Model Serine Protease, Trypsin

Trypsin is used as a model for the study of serine proteases, for its fold is commonly observed in this family of enzymes. The overall aim of this study is to discern whether the Y39F trypsin variant will act on a macromolecular substrate similar to the way it interacts with macromolecular inhibitors, specifically focusing on the S prime (S') side. In wild‐type trypsin, the hydroxyl group in tyrosine at position 39 serves to stabilize the interaction with macromolecular inhibitors via the formation of hydrogen bonds at the P prime (P') subsites. A Y39F substitution was made to reduce the affinity between the enzyme variant and inhibitor. A phenylalanine was used in place of the tyrosine because the two amino acid residues are chemically similar with the exception of the hydroxyl functional group missing from the phenylalanine. The absence of the hydroxyl functional group serves to prevent the formation of hydrogen bonds between macromolecular substrates that interact with the S' site of the enzyme, presumably weakening of the enzyme‐inhibitor interaction. However, previous research from our group demonstrated that the Y39F trypsin variant was more sensitive to inhibition from both bovine pancreatic trypsin inhibitor (BPTI) and ecotin compared to wild‐type trypsin. Molecular modeling suggests that the tighter binding is a consequence of the formation of a hydrogen bond between the P2′ site and the histidine side chain at position 40 not seen in wild type trypsin. The presence of the newly formed hydrogen bond in the Y39F trypsin variant helps stabilize the enzyme‐inhibitor complex. Still, Y39F trypsin retained similar catalytic activity against N‐α‐benzyloxycarbonyl‐glycylprolylarginine p‐nitroanilide (Z‐GPR‐pNA). However, Z‐GPR‐pNA physically cannot interact with the modified S' subsites as the macromolecular inhibitors, and likely macromolecular substrates, do. Therefore, the activity observed with Z‐GPR‐pNA may not accurately reflect the activity of the Y39F variant towards macromolecular substrates. In this study, we used sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE) and gel imaging to monitor and compare the progression of macromolecular substrate hydrolysis of Y39F and wild‐type trypsin. Based on the observations made with BPTI and ecotin, we would expect that the Y39F variant would bind more tightly to a macromolecular substrate as well, likely increasing the efficiency of cleavage relative to wild‐type.Support or Funding InformationNSF Award MCB‐0643988‐02

Protein crystallization: Eluding the bottleneck of X-ray crystallography.

To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins.

Biomarkers in Lysosomal Storage Diseases.

A biomarker is generally an analyte that indicates the presence and/or extent of a biological process, which is in itself usually directly linked to the clinical manifestations and outcome of a particular disease. The biomarkers in the field of lysosomal storage diseases (LSDs) have particular relevance where spectacular therapeutic initiatives have been achieved, most notably with the introduction of enzyme replacement therapy (ERT). There are two main types of biomarkers. The first group is comprised of those molecules whose accumulation is directly enhanced as a result of defective lysosomal function. These molecules represent the storage of the principal macro-molecular substrate(s) of a specific enzyme or protein, whose function is deficient in the given disease. In the second group of biomarkers, the relationship between the lysosomal defect and the biomarker is indirect. In this group, the biomarker reflects the effects of the primary lysosomal defect on cell, tissue, or organ functions. There is no “gold standard” among biomarkers used to diagnosis and/or monitor LSDs, but there are a number that exist that can be used to reasonably assess and monitor the state of certain organs or functions. A number of biomarkers have been proposed for the analysis of the most important LSDs. In this review, we will summarize the most promising biomarkers in major LSDs and discuss why these are the most promising candidates for screening systems.

Proteinase K activity determination with β-galactosidase as sensitive macromolecular substrate

Proteinase K from Engyodontium album (proK) is a relatively unspecific serine endopeptidase which is known to attack proteins yet in their native states. If the attacked protein is an enzyme, even a partial hydrolysis by proK may lead to an inactivation of the enzyme, which can be monitored by measuring the loss of catalytic activity of the attacked enzyme. E. coli β-galactosidase (β-Gal) was used in this work as such enzyme. It was found to be a convenient and sensitive macromolecular model substrate for comparing the “native protein-attacking ability” of free and immobilized proK at pH = 7.0 and 23 °C. The β-Gal activity was measured spectrophotometrically with o-nitrophenyl-β-galactopyranoside. Reproducible proK determinations were possible for as little as 4.3 ng proK by using a proK analyte solution of 10 nM. Compared to free proK, immobilized proK was much less efficient in inactivating β-Gal, most likely due to a decreased mobility of immobilized proK and a restricted accessibility of β-Gal to the active site of proK. Worth noting is, that under conditions at which β-Gal was completely inactivated by proK, the activity of hen egg lysozyme, horseradish peroxidase, or Aspergillus sp. glucose oxidase remained unaltered.

The preparation and study of the properties of macroporous monolith-based continuous flow bioreactors

The surfaces of macroporous monolithic disks were modified with hydrolytic enzymes, viz., α-chymotrypsin and ribonuclease A. The effect of the enzyme-immobilization approach and the amount of the aldehyde groups in the polymer spacer, as well as the flow rate of the substrate solution on the efficiency of the heterogeneous biocatalysis was explored using the reactions of hydrolysis of both low and macromolecular substrates as examples.

Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms.

We investigated bacterial carbon assimilation from stable isotope-labelled macromolecular substrates (proteins; lipids; and two types of polysaccharides, starch and cellobiose) while attached to killed diatom detrital particles during laboratory microcosms incubated for 17 days. Using Chip-SIP (secondary ion mass spectrometry analysis of RNA microarrays), we identified generalist operational taxonomic units (OTUs) from the Gammaproteobacteria, belonging to the genera Colwellia, Glaciecola, Pseudoalteromonas and Rheinheimera, and from the Bacteroidetes, genera Owenweeksia and Maribacter, that incorporated the four tested substrates throughout the incubation period. Many of these OTUs exhibited the highest isotope incorporation relative to the others, indicating that they were likely the most active. Additional OTUs from the Gammaproteobacteria, Bacteroidetes and Alphaproteobacteria exhibited generally (but not always) lower activity and did not incorporate all tested substrates at all times, showing species succession in organic carbon incorporation. We also found evidence to suggest that both generalist and specialist OTUs changed their relative substrate incorporation over time, presumably in response to changing substrate availability as the particles aged. This pattern was demonstrated by temporal succession from relatively higher starch incorporation early in the incubations, eventually switching to higher cellobiose incorporation after 2 weeks.

Macromolecular cross-linked enzyme aggregates (M-CLEAs) of α-amylase

Macromolecular cross-linked enzyme aggregates (M-CLEAs) of α-amylase were prepared by precipitation and subsequent cross-linking. The non-toxic, biodegradable, biocompatible, renewable polysaccharide based macromolecular cross-linkers viz. agar, chitosan, dextran, and gum arabic were used as a substitute for traditional glutaraldehyde to augment activity recovery toward macromolecular substrate. Macromolecular cross-linkers were prepared by periodate mediated controlled oxidation of polysaccharides. The effects of precipitating agent, concentration and different cross-linkers on activity recovery of α-amylase CLEAs were investigated. α-Amylase aggregated with ammonium sulphate and cross-linked by dextran showed 91% activity recovery, whereas glutaraldehyde CLEAs (G-CLEAs) exhibited 42% activity recovery. M-CLEAs exhibited higher thermal stability in correlation with α-amylase and G-CLEAs. Moreover, dextran and chitosan M-CLEAs showed same affinity for starch hydrolysis as of free α-amylase. The changes in secondary structures revealed the enhancements in structural and conformational rigidity attributed by cross-linkers. Finally, after five consecutive cycles dextran M-CLEAs retained 1.25 times higher initial activity than G-CLEAs.

Hydrolysis of casein and β-lactoglobulin by immobilized papain after pre-treatment with immobilized trypsin

Protein hydrolysis using immobilized proteases may present problems, which are mainly caused by the diffusion of macromolecular substrate. Pre-hydrolysed substrate could be a viable alternative in this process. The aim of this work was to test the casein and β-lactoglobulin hydrolysis using immobilized papain on glyoxyl-agarose, following substrate pre-treatment with immobilized trypsin. Although immobilized papain showed difficulties to degrade the milk proteins, after 10 min of trypsin pre-hydrolysis, the immobilized papain was able to achieve the maximum degree of hydrolysis in shorter time. For pre-hydrolysate casein, the immobilized papain reached 98.9% at 60 min total reaction (including the 10 min pre-digestion). As for β-lactoglobulin, immobilized papain was capable of achieving maximum levels after just 60 min of reaction, where the free enzyme only achieved 60% of its maximum. Pre-hydrolysis with trypsin appears to have worked well as a pre-treatment method to increase the proteolytic action of immobilized papain.

Magnetic macromolecular cross linked enzyme aggregates (CLEAs) of glucoamylase

This work illustrates the preparation of magnetic macromolecular glucoamylase CLEAs using dialdehydic pectin, as a cross linker instead of traditional glutaraldehyde. The effect of precipitators type and amount, cross linker concentration, cross linking time and amount of amino functionalized magnetic nanoparticles (AFMNs) on glucoamylase activity was studied. Glucoamylase magnetic macromolecular CLEAs prepared by precipitation in presence of AFMNs by ammonium sulfate were subsequently cross linked by dialdehydic pectin. After cross-linked by pectin, 95.4% activity recovery was achieved in magnetic macromolecular CLEAs, whereas in case of glutaraldehyde cross linker, 85.3% activity recovery was achieved. Magnetic macromolecular CLEAs showed 2.91 and 1.27 folds higher thermal stability as compared to free and magnetic glutaraldehyde CLEAs. In kinetics study, magnetic macromolecular CLEAs retained same Km values, whereas magnetic glutaraldehyde CLEAs showed higher Km value than free enzyme. The porous structure of magnetic macromolecular CLEAs was not only enhanced mass transfer toward macromolecular substrates, but also showed compression resistance for 5 consecutive cycles which was checked in terms of effectiveness factor. At the end, in reusability study; magnetic macromolecular CLEAs were retained 84% activity after 10th cycle without leaching of enzyme which is 22% higher than traditional magnetic CLEAs.

Enzymatic Transesterification of Kraft Lignin with Long Acyl Chains in Ionic Liquids.

Valorization of lignin is essential for the economic viability of the biorefinery concept. For example, the enhancement of lignin hydrophobicity by chemical esterification is known to improve its miscibility in apolar polyolefin matrices, thereby helping the production of bio-based composites. To this end and due to its many reactive hydroxyl groups, lignin is a challenging macromolecular substrate for biocatalyzed esterification in non-conventional media. The present work describes for the first time the lipase-catalyzed transesterification of Kraft lignin in ionic liquids (ILs). Three lipases, three 1-butyl-3-methylimidazolium based ILs and ethyl oleate as long chain acyl donor were selected. Best results were obtained with a hydrophilic/hydrophobic binary IL system (1-butyl-3-methylimidazolium trifluoromethanesulfonate/1-butyl-3-methylimidazolium hexafluoro- phosphate, 1/1 v/v) and the immobilized lipase B from Candida antarctica (CALB) that afforded a promising transesterification yield (ca. 30%). Similar performances were achieved by using 1-butyl-3-methylimidazolium hexafluorophosphate as a coating agent for CALB rather than as a co-solvent in 1-butyl-3-methylimidazolium trifluoromethane-sulfonate thus limiting the use of hydrophobic IL. Structural characterization of lignin oleate was performed by spectroscopic studies (FTIR and 1H-NMR). The synthesized lignin oleate exhibited interesting thermal and textural properties, different from those of the original Kraft lignin.

Single-Molecule Imaging at High Fluorophore Concentrations by Local Activation of Dye

Single-molecule fluorescence microscopy is a powerful tool for observing biomolecular interactions with high spatial and temporal resolution. Detecting fluorescent signals from individual labeled proteins above high levels of background fluorescence remains challenging, however. For this reason, the concentrations of labeled proteins in in vitro assays are often kept low compared to their in vivo concentrations. Here, we present a new fluorescence imaging technique by which single fluorescent molecules can be observed in real time at high, physiologically relevant concentrations. The technique requires a protein and its macromolecular substrate to be labeled each with a different fluorophore. Making use of short-distance energy-transfer mechanisms, only the fluorescence from those proteins that bind to their substrate is activated. This approach is demonstrated by labeling a DNA substrate with an intercalating stain, exciting the stain, and using energy transfer from the stain to activate the fluorescence of only those labeled DNA-binding proteins bound to the DNA. Such an experimental design allowed us to observe the sequence-independent interaction of Cy5-labeled interferon-inducible protein 16 with DNA and the sliding via one-dimensional diffusion of Cy5-labeled adenovirus protease on DNA in the presence of a background of hundreds of nanomolar Cy5 fluorophore.

Insight into the substrate specificity of keratinase KerSMD from Stenotrophomonas maltophilia by site-directed mutagenesis studies in the S1 pocket

Mutagenesis at position 215 could shift the catalytic ability of keratinase KerSMD to hydrolyze synthetic peptides and macromolecular substrates. We improved keratinolytic activity of five mutants and obtained two thermophilic keratinases.

Snake venom serine proteinases specificity mapping by proteomic identification of cleavage sites.

Proteolysis is key to various pathological effects observed upon envenomation by viperid snakes. The use of the Proteomic Identification of protease Cleavage Sites (PICS) approach for the easy mapping of proteinase subsite preferences at both the prime- and non-prime sides concurrently gives rise to a fresh understanding of the interaction of the snake venom serine proteinases with peptide and macromolecular substrates and indicates that their hydrolytic activity is influenced by the amino acid sequences adjacent to the scissile bond.

Entrapment of α-Amylase in Agar Beads for Biocatalysis of Macromolecular Substrate.

Attempts have been made to optimize immobilization parameters, catalytic property, and stability of immobilized α-amylase in agar. The work compares natural entrapment efficiency of agar with the ionotropically cross-linked agar hydrogel, with the advantage of easy scale-up and cost and time effectiveness. Beads prepared with 3% (w/v) agar and 75 mM calcium chloride and hardened for 20 minutes were selected for further studies on the basis of entrapment efficiency (80%) and physical stability. Following entrapment, pH and temperature optima of enzyme were shifted from 6 to 6.5 and 50 to 55°C, respectively. Michaelis constant (K m) for both free and entrapped enzymes remained the same (0.83%) suggesting no change in substrate affinity. However, V max⁡ of entrapped enzyme decreased ~37.5-fold. The midpoint of thermal inactivation for entrapped enzyme increased by 8 ± 1°C implying its higher thermal stability. The entrapped enzyme in calcium agar bead had an Ea value of 27.49 kcal/mol compared to 17.6 kcal/mol for free enzyme indicating increased stability on entrapment. Half-life of enzyme increased ~2.2 times after entrapment in calcium agar at 60°C indicating stabilization of enzyme. The reusability of beads was size dependent. Beads with diameter <710 μm were stable and could be reused for 6 cycles with ~22% loss in activity.

Removal of Metal Ions from Aqueous Solutions by Complexation –Ultrafiltration Hybrid Process: A Bibliographical Overview

Water pollution by metal ions contaminants is a worldwide alarming problem. Clean and safe water is becoming in the same time an increasing scare resource. Thus, to keep this fundamental resource available and suitable for use, water treatment methods are investigated by means of numerous research studies since the purification of water and its re-use and, in a larger scale, the environmental protection will be essential henceforth in any strategy of development. Membrane processes, in general, and ultrafiltration, in particular, develop, without stopping, since the beginning of the sixties to meet the vital need for environmental safety which justifies the policies of durable development adopted today all over the world. Thanks to its growing, ultrafiltration becomes an irreplaceable weapon in the control of pollution. It is classified as a soft and clean technology since it needs low energy consumption and ensures a notable reduction in pollution production during the treatment step. Ultrafiltration is a pressure driven membrane process with the ability to separate molecules in solution on the basis of size. A microporous ultfafiltration membrane retains species with molecular weight higher than its cut off, while small molecules as solvents and microsolutes can pass freely through it. Thus, metal ions aren’t rejected by ultrafiters. However, ultrafiltration can be used to remove metal ions from aqueous solutions by coupling the process with complexation. Indeed, the complexation of metal ions using water soluble polymers as substrates is able to expand artificially the size of the metallic species so as to make possible their rejection by the microporous ultrafilters. The complexation –ultrafiltration hybrid process was first suggested at the end of the sixties by A. S. Michaels. Since then, many studies have shown its effectiveness in the treatment of aqueous solutions containing metal ions. This paper gives an overview of academic studies that illustrate and demonstrate the efficiency and the promising of the hybrid process in the purification of water from metal ions contaminants beforehand sequestered by adequate water –soluble macromolecular substrates.

Natural anionic polymer acts as highly efficient trypsin inhibitor based on an electrostatic interaction mechanism.

Sodium alginate (SA), acting as a trypsin inhibitor by means of electrostatic interaction, is studied. The half-maximal inhibitory concentration (IC50 = 0.05 μg mL(-1) ) of this natural anionic polymer is about 400 times lower than that of commercial soybean trypsin inhibitor (STI). Unlike the Ca(2+) -deprivation mechanisms, its inhibition may be attributed to preventing the trypsin active site (TAS) from accessing the macromolecular substrates instead of denaturing it. SA is an efficient, innocuous, and cost-effective inhibitory excipient that can be conveniently used in many peptide and protein dosage formulations.

A Distinct Metabolic Signature of Human Colorectal Cancer with Prognostic Potential

Metabolic phenotyping has provided important biomarker findings, which, unfortunately, are rarely replicated across different sample sets due to the variations from different analytical and clinical protocols used in the studies. To date, very few metabolic hallmarks in a given cancer type have been confirmed and validated by use of a metabolomic approach and other clinical modalities. Here, we report a metabolomics study to identify potential metabolite biomarkers of colorectal cancer with potential theranostic value. Gas chromatography-time-of-flight mass spectrometry (GC-TOFMS)-based metabolomics was used to analyze 376 surgical specimens, which were collected from four independent cohorts of patients with colorectal cancer at three hospitals located in China and City of Hope Comprehensive Cancer Center in the United States. Differential metabolites were identified and evaluated as potential prognostic markers. A targeted transcriptomic analysis of 29 colorectal cancer and 27 adjacent nontumor tissues was applied to analyze the gene expression levels for key enzymes associated with these shared metabolites. A panel of 15 significantly altered metabolites was identified, which demonstrates the ability to predict the rate of recurrence and survival for patients after surgery and chemotherapy. The targeted transcriptomic analysis suggests that the differential expression of these metabolites is due to robust metabolic adaptations in cancer cells to increased oxidative stress as well as demand for energy, and macromolecular substrates for cell growth and proliferation. These patients with colorectal cancer, despite their varied genetic background, mutations, pathologic stages, and geographic locations, shared a metabolic signature that is of great prognostic and therapeutic potential.

Functional transformations of bile acid transporters induced by high-affinity macromolecules

Apical sodium-dependent bile acid transporters (ASBT) are the intestinal transporters that form intermediate complexes with substrates and its conformational change drives the movement of substrates across the cell membrane. However, membrane-based intestinal transporters are confined to the transport of only small molecular substrates. Here, we propose a new strategy that uses high-affinity binding macromolecular substrates to functionally transform the membrane transporters so that they behave like receptors, ultimately allowing the apical-basal transport of bound macromolecules. Bile acid based macromolecular substrates were synthesized and allowed to interact with ASBT. ASBT/macromolecular substrate complexes were rapidly internalized in vesicles, localized in early endosomes, dissociated and escaped the vesicular transport while binding of cytoplasmic ileal bile acid binding proteins cause exocytosis of macromolecules and prevented entry into lysosomes. This newly found transformation process of ASBT suggests a new transport mechanism that could aid in further utilization of ASBT to mediate oral macromolecular drug delivery.