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In silico substrate binding profiling for SARS-COV-2 main protease (mpro) using hexapeptide substrates

  • Authors: Zabo, Sophakama
  • Date: 2022-10-14
  • Subjects: COVID-19 (Disease) , Peptides , Chymotrypsin like , Chymotrypsin , Proteases , Proteolytic enzymes
  • Language: English
  • Type: Academic theses , Master's theses , text
  • Identifier: http://hdl.handle.net/10962/365566 , vital:65760
  • Description: COVID-19, as a disease resulting from SARS-CoV-2 infection, and a pandemic has had a devastating effect on the world. There are limited effective measures that control the spread and treatment of COVID-19 illness. The homodimeric cysteine main protease (Mpro) is crucial to the life cycle of the virus, as it cleaves the large polyproteins 1a and 1ab into matured, functional non-structural proteins. The Mpro exhibits high degrees of conservation in sequence, structure and specificity across coronavirus species, making it an ideal drug target. The Mpro substrate-binding profiles remain, despite the resolution of its recognition sequence and cleavage points (Leu-Gln↓(Ser/Ala/Gly)). In this study, a series of hexapeptide sequences containing the appropriate recognition sequence and cleavage points were generated and screened against the Mpro to study these binding profiles, and to further be the basis for efficiency-driven drug design. A multi-conformer hexapeptide substrate library comprising optimised 81000 models of 810 unique sequences was generated using RDKit within the context of python. Terminal capping with ACE and NMe was effected using SMILES and SMARTS matching. Multiple hexapeptides were complexed with chain B of crystallographic Mpro (PDS ID: 6XHM), following the validation of chain B for this purpose using AutoDock Vina at high levels of exhaustiveness (480). The resulting Vina scores ranged between -8.7 and -7.0 kcal.mol-1, and the reproducibility of best poses was validated through redocking. Ligand efficiency indices were calculated to identify substrate residues with high binding efficiency at their respective positions, revealing Val (P3), Ala (P1′); and Gly and Ala (P2′ and P3′) as leading efficient binders. Binding efficiencies were lowered by molecular weight. Substrate recognition was assessed by mapping of binding subsites, and Mpro specificity was evaluated through the resolution of intermolecular interaction at the binding interface. Molecular dynamics simulations for 20 ns were performed to assess the stability and behaviour of 132 Mpro systems complexed with KLQ*** substrates. Principal component analysis (PCA), was performed to assess II protein motions and conformational changes during the simulations. A strategy was formulated to classify and evaluate relations in the Mpro PCA motions, revealing four main clades of similarity. Similarity within a clade (Group 2) and dissimilarity between clades were confirmed. Trajectory visualisation revealed complex stability, substrate unbinding and dimer dissociation for various Mpro systems. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
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  • Date Issued: 2022-10-14

Bioconversion of chicken feather into amino acids and keratinase production by mesophilic Chryseobacterium proteolyticum and Pseudomonas aeruginosa isolated from municipal waste dumpsites

  • Authors: Giwu, Nonkonzo https://orcid.org/0000-0001-9416-7896
  • Date: 2021-02
  • Subjects: Poultry -- Processing , Proteolytic enzymes
  • Language: English
  • Type: Master's theses , text
  • Identifier: http://hdl.handle.net/10353/22732 , vital:52720
  • Description: Chicken feathers are by-products of poultry processing which are generated in large amount because of the global growing demand for poultry meats. They have high contents of crude proteins in the form of keratin which could be valorized into digestible products. Keratinases are classified as a specific collection of proteolytic enzymes that have the ability for the degradation of recalcitrant keratinous substrates. Isolation and characterization of these enzymes from various microbial producers are gaining prominence in recent years due to their industrial and biotechnological application potentials. For this research, the collection of soil samples was done as well as the isolation of bacteria and the screening for keratinolytic activity. 16S rDNA sequencing and phylogenetic analysis were used to identify the isolates with efficient chicken feathers degrading capacity. Optimum conditions for the fermentation prcocess was enhanced for the production of keratinase. The fermentation broth was also analysed for various amino acids of protein, and the biochemical properties of the enzymes were likewise determined. Twenty two (22) bacteria were isolated from the soil samples, and 18 out of the 22 isolates showed proteolytic activity on solid media with diameters of halo zone that ranged from 5 ± 0.71 mm for isolate coded as PSS-03 to 25 ± 1.41 mm for isolate coded as PSS-06. Intact chicken feathers were degraded by proteolytic bacterial isolates in variable degree that ranged from 24percent for PSS-10 and 81percent for DSS-02. Extracellular keratinase production recorded for the isolates ranged from 63.63 ± 4.14 U/mL for PSS-10 to 693.63 ± 62.99 U/mL for DSS-02. Based on 16S rDNA sequence and phylogenetic analysis, the 2 isolates with remarkable keratinolytic activity coded as DSS-02 and PSS-14 were identified as Chryseobacterium proteolyticum FGNn and Pseudomonas aeruginosa GNFx. C. proteolyticum showed the maximum keratinase production of 756.36 U/mL after 72 h of incubation at optimized fermentation conditions which involved initial medium pH (4), incubation temperature (30 oC), inoculum size (2percent; v/v), and chicken feathers (1.5percent; w/v). Similarly, P. aeruginosa optimally produced keratinase (1055.45 U/mL) after 96 h of incubation at optimized fermentation conditions that involved initial medium pH (7-8), incubation temperature (30 oC), inoculum size (5percent; v/v), and chicken feathers (2.5percent; w/v). Furthermore, feather hydrolysate from C. proteolyticum FGNn had relatively higher abundance (>1.5g/100g sample) of arginine (1.85), serine (1.63), glycine (1.9) and lysine (1.62); while P. aeruginosa GNFx feather hydrolysate showed high abundance of arginine, serine, aspartic acid, glutamic acid, glycine, alanine, valine, and leucine with respective concentration of 2.06, 1.67, 2.39, 3.05, 1.87, 1.73, 1.56 and 1.65 (g/100g sample). The results showed that keratinases from the two bacterial isolates were optimally active at pH 8, and temperature of 50 oC for FGNn keratinase and 50-60 oC for GNFx keratinase. The enzymes displayed remarkable pH stability. Keratinase from C. proteolyticum was catalytically inhibited by EDTA and 1,10-phenanthroline but not affected by PMSF; while P. aeruginosa keratinase was not significantly affected by those class of protease inhibitors. Adiitionally, FGNn keratinase demonstrated high residual activity of 90percent, 103percent, 101percent, 110percent, 130, and 105percent in the presence of DTT, hydrogen peroxides, acetonitrile, triton X-100, tween-80 and SDS, respectively. Similarly, catalytic efficiency of GNFx keratinase was promoted in the presence of hydrogen peroxides (119percent), triton X-100 (140percent), tween-80 (150percent) and SDS (147percent) compared to the control. Furthermore, the keratinases from the both bacterial isolates exhibited catalytic efficiency enhancement and remarkable structural stability in the presence of laundry detergents tested. The findings from the study suggest the application potentials of the isolates for the bioconversion of recalcitrant keratinous wastes into digestible and quality protein hydrolysates. The properties of these microbial keratinases indicate that they may be exploited for various biotechnological and industrial processes especially in the formulation of detergents. , Thesis (MSc) -- Faculty of Science and Agriculture, 2021
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  • Date Issued: 2021-02

Valorization of chicken feather through dekeratinization by keratinolytic Bacillus species to amino acid

  • Authors: Matches, Lupho
  • Date: 2021-02
  • Subjects: Proteolytic enzymes , Poultry -- Processing
  • Language: English
  • Type: Master's theses , text
  • Identifier: http://hdl.handle.net/10353/20451 , vital:45667
  • Description: The poultry meat processing sector generates chicken feathers as by-products, and they are 90percent keratin in composition. Keratin is an insoluble and structural protein that shows recalcitrance to hydrolysis by classical proteolytic enzymes, including trypsin, pepsin, and papain. Keratinases are a group of proteolytic enzymes endowed with keratin degradation into peptides and amino acids. They are recently gaining traction for their multifaceted potential application in the green industrial space. Hence, keratinolytic bacteria previously isolated from dumpsite were identified using 16S rDNA sequencing. The optimal fermentation conditions were determined for enhanced extracellular keratinase production and chicken feather degradation. Also, the amino acid analysis of the chicken feather hydrolysates was carried out. The biochemical properties of the keratinases were also determined. Based on 16S rDNA sequencing and phylogenetic analysis, the isolates coded as SSN-02 and HSN-03 showed a high percentage of sequence homology with Bacillus spp.; hence, they were identified as Bacillus sp. NFH5 and Bacillus sp. FHNM, respectively. Bacillus sp. NFH5 showed optimal keratinase production of 1149.99 ± 80.99 U/mL after 96 h of incubation time, in optimized fermentation conditions that included pH (4.0), chicken feather (1.5percent, w/v), inoculum size (3percent, v/v) and temperature (30 oC). Similarly, Bacillus sp. FHNM demonstrated the maximum keratinase production of 480 ± 41.14 U/mL 144 h post cultivation, in optimized fermentation conditions with pH (7.0), chicken feather (2.0percent, w/v), inoculum size (3percent, v/v) and temperature (30 oC). For Bacillus sp. NFH5 chicken feather hydrolysate, the amino acids in relatively higher concentration (>1.0g/100g sample) include arginine (1.8), serine (1.16), aspartic acid (1.95), glutamic acid (2.47), proline (1.16) and glycine (1.45). Bacillus sp. FHNM feather hydrolysates, contained (g/100g of sample): arginine (1.9), serine (1.4), aspartic acid (2.5), glutamic acid (2.51), glycine (1.51), proline (1.13), leucine (1.030, histidine (1.25), and lysine (1.06) (g/100g of sample) in high concentration. The keratinases were optimally active at pH 8.0. Bacillus sp. FHNM showed an optimal temperature of 100 oC; while Bacillus sp. NFH5 keratinase displayed optimal activity at 90 oC. EDTA and 1,10-phenanthroline inhibited the keratinases, and the inhibition pattern indicated that they belong to metalloprotease. Keratinase from Bacillus sp. FHNM showed considerable residual activity in the presence of Co²⁺ (93percent), Fe³⁺ (99percent), and K⁺ (94percent). Bacillus sp. NFH5 keratinase retained 92percent, 92percent, 93percent of the original activity against Ba²⁺, Na⁺ and Fe³⁺ treatment. Bacillus sp. FHNM keratinase was remarkably stable after 60 min of detergents treatment with residual activity of 89percent, 96percent, 81percent, 73percent, 96percent, 88percent, 88percent and 98percent for Omo, Surf, Ariel, Sunlight, Prowash, Freshwave, Sky, and Evaklin, respectively. Maq impacted the enzyme stability negatively, with residual activity of 48percent after 60 min of incubation. Additionally, keratinase Bacillus sp. NFH5 retained 68percent, 78percent, 80percent, 84percent, 57percent, 80percent, 98percent, 106percent and 106percent of the original activity against Omo, Surf, Ariel, Sunlight, Maq, Prowash, Freshwave, Sky and Evaklin, respectively. Therefore, these results suggest that Bacillus spp. could be ideal candidates for sustainable production of active keratinases and valorization of the abundantly generated keratinous biomass. The stability displayed by keratinases from Bacillus sp. FHNM and Bacillus sp. NFH5 suggests their promising candidacy for detergent formulation. , Thesis (MSc) -- Faculty of Science and Agriculture, 2021
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  • Date Issued: 2021-02

Production, purification, and characterisation of proteases from an ericoid mycorrhizal fungus, Oidiodendron maius

  • Authors: Manyumwa, Colleen Varaidzo
  • Date: 2018
  • Subjects: Ascomycetes , Mycorrhizal fungi , Ericaceae , Proteolytic enzymes , Silver Recycling
  • Language: English
  • Type: Master's theses , text
  • Identifier: http://hdl.handle.net/10962/62833 , vital:28298
  • Description: The aim of this study was to produce, purify and characterise proteases from the ericoid mycorrhizal fungus, Oidiodendron maius (CafRU082b/KP119480), as well as to explore their potential application in the recovery of silver from X-ray film. Firstly, the growth of the ericoid mycorrhizal fungus, Oidiodendron maius (CafRU082b), was studied, and its ability to produce proteolytic enzymes was investigated. O. maius proved to grow well in the dark, submerged in Modified Melin Norkran’s liquid medium at a pH of 5 and at 25°C. Pure cultures of the fungus were maintained on Potato Dextrose Agar (PDA). The fungus grew on PDA plates containing different substrates including haemoglobin, casein, gelatin as well as azocasein. Zones of clearance, however, were only observed on plates containing gelatin after treatment with mercuric chloride, HgCl2. Proteases were successfully produced after 14 days when gelatin was incorporated into the growth medium. After production of the proteases, purification and characterisation of the enzymes was performed. Purification of the enzymes was performed by acetone precipitation followed by ultrafiltration with 50 kDa and 30 kDa cut off membrane filters. A final purification fold of approximately 37.6 was achieved. Unusual yields of above 100% were observed after each purification step with the final yield achieved being 196% with a final specific activity of 2707 U/mg. SDS-PAGE revealed a protease band of 35 kDa which was also visible on the zymogram at approximately 36 kDa. The zymogram showed clear hydrolysis bands against a blue background after staining with Coomassie Brilliant Blue. Physico-chemical characterisation of the protease revealed its pH optimum to be pH 3.0 and its temperature optimum 68°C. Another peak was observed on the pH profile at pH 7.0. The protease exhibited high thermostability at temperatures 37°C, 80°C as well as 100°C with the enzyme retaining close to 50% of its initial activity after 4 h of exposure to all three temperatures. All ions tested for their effects on the proteases, except Ca2+, enhanced protease activity. Ca2+ did not exhibit any significant effect on the enzyme’s activity while Zn2+ had the highest effect, enhancing enzyme activity by 305%. The proteases, however, were not significantly inhibited by EDTA, a metal chelating agent and a known metalloprotease inhibitor. The enzyme was classified as an aspartic protease due to complete inhibition by 25 μM of pepstatin A, coupled to its low pH optimum of 3.0. Addition of trans-Epoxysuccinyl-L-leucylamido-(4-guanidino)butane (E-64), a cysteine protease inhibitor, and 2-mercaptoethanol increased protease activity. The proteases exhibited a narrow substrate specificity towards gelatin and no other substrate. Substrate kinetics values were plotted on a Michaelis-Menten Graph and showed that the enzyme had a Vmax of 55.25 U/ml and a Km of 2.7 mg/ml gelatin. A low Km indicated that the protease had a high affinity for gelatin. Silver recovery studies from X-ray film revealed the proteases’ capability to remove silver from X-ray film, leaving the film intact. The recovery of silver was perceived visually, by film observation, as well as by scan electron microscopy (SEM) images, where clearance of the film was observed after incubation with the enzyme. Energy dispersive X-ray spectroscopy (EDS) profiles also confirmed removal of silver from the film, with a Ag peak showing on the profile of the film before treatment with the proteases and no peak after treatment. The crude protease sample was, however, catalytically more efficient compared to the partially purified sample. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2018
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  • Date Issued: 2018

Comparative study of clan CA cysteine proteases: an insight into the protozoan parasites

  • Authors: Moyo, Sipho Dugunye
  • Date: 2015
  • Subjects: Cysteine proteinases , Proteolytic enzymes , Protozoan diseases , Parasites , Protozoan diseases -- Chemotherapy , Bioinformatics , Plasmodium , Antiprotozoal agents
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4165 , http://hdl.handle.net/10962/d1020309
  • Description: Protozoan infections such as Malaria, Leishmaniasis, Toxoplasmosis, Chaga’s disease and African trypanosomiasis caused by the Plasmodium, Leishmania, Toxoplasma and Trypanosoma genuses respectively; inflict a huge economic, health and social impact in endemic regions particularly tropical and sub-tropical regions. The combined infections are estimated at over a billion annually and approximately 1.1 million deaths annually. The global burden of the protozoan infections is worsened by the increased drug resistance, toxicity and the relatively high cost of treatment and prophylaxis. Therefore there has been a high demand for new drugs and drug targets that play a role in parasite virulence. Cysteine proteases have been validated as viable drug targets due to their role in the infectivity stage of the parasites within the human host. There is a variety of cysteine proteases hence they are subdivided into families and in this study we focus on the clan CA, papain family C1 proteases. The current inhibitors for the protozoan cysteine proteases lack selectivity and specificity which contributes to drug toxicity. Therefore there is a need to identify the differences and similarities between the host, vector and protozoan proteases. This study uses a variety of bioinformatics tools to assess these differences and similarities. The Plasmodium cysteine protease FP-2 is the most characterized protease hence it was used as a reference to all the other proteases and its homologs were retrieved, aligned and the evolutionary relationships established. The homologs were also analysed for common motifs and the physicochemical properties determined which were validated using the Kruskal-Wallis test. These analyses revealed that the host and vector cathepsins share similar properties while the parasite cathepsins differ. At sub-site level sub-site 2 showed greater variations suggesting diverse ligand specificity within the proteases, a revelation that is vital in the design of antiprotozoan inhibitors.
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  • Date Issued: 2015

Malarial drug targets cysteine proteases as hemoglobinases

  • Authors: Mokoena, Fortunate
  • Date: 2012
  • Subjects: Malaria -- Chemotherapy , Antimalarials , Hemoglobin , Proteolytic enzymes , Cysteine proteinases , Plasmodium falciparum , Plasmodium vivax , Papain
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4005 , http://hdl.handle.net/10962/d1004065 , Malaria -- Chemotherapy , Antimalarials , Hemoglobin , Proteolytic enzymes , Cysteine proteinases , Plasmodium falciparum , Plasmodium vivax , Papain
  • Description: Malaria has consistently been rated as the worst parasitic disease in the world. This disease affects an estimated 5 billion households annually. Malaria has a high mortality rate leading to distorted socio-economic development of the world at large. The major challenge pertaining to malaria is its continuous and rapid spread together with the emergence of drug resistance in Plasmodium species (vector agent of the disease). For this reason, researchers throughout the world are following new leads for possible drug targets and therefore, investigating ways of curbing the spread of the disease. Cysteine proteases have emerged as potential antimalarial chemotherapeutic targets. These particular proteases are found in all living organisms, Plasmodium cysteine proteases are known to degrade host hemoglobin during the life cycle of the parasite within the human host. The main objective of this study was to use various in silico methods to analyze the hemoglobinase function of cysteine proteases in P. falciparum and P. vivax. Falcipain-2 (FP2) of P. falciparum is the best characterized of these enzymes, it is a validated drug target. Both the three-dimensional structures of FP2 and its close homologue falcipain-3 (FP3) have been solved by the experimental technique X-ray crystallography. However, the homologue falcipain-2 (FP2’)’ and orthologues from P.vivax vivapain-2 (VP2) and vivapain-3 (VP3) have yet to be elucidated by experimental techniques. In an effort to achieve the principal goal of the study, homology models of the protein structures not already elucidated by experimental methods (FP2’, VP2 and VP3) were calculated using the well known spatial restraint program MODELLER. The derived models, FP2 and FP3 were docked to hemoglobin (their natural substrate). The protein-protein docking was done using the unbound docking program ZDOCK. The substrate-enzyme interactions were analyzed and amino acids involved in binding were observed. It is anticipated that the results obtained from the study will help focus inhibitor design for potential drugs against malaria. The residues found in both the P. falciparum and P. vivax cysteine proteases involved in hemoglobin binding have been identified and some of these are proposed to be the main focus for the design of a peptidomimetric inhibitor.
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  • Date Issued: 2012

Structural analysis of prodomain inhibition of cysteine proteases in plasmodium species

  • Authors: Njuguna, Joyce Njoki
  • Date: 2012
  • Subjects: Plasmodium , Cysteine proteinases , Proteolytic enzymes , Malaria -- Chemotherapy , Antimalarials , Plasmodium falciparum
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4021 , http://hdl.handle.net/10962/d1004081 , Plasmodium , Cysteine proteinases , Proteolytic enzymes , Malaria -- Chemotherapy , Antimalarials , Plasmodium falciparum
  • Description: Plasmodium is a genus of parasites causing malaria, a virulent protozoan infection in humans resulting in over a million deaths annually. Treatment of malaria is increasingly limited by parasite resistance to available drugs. Hence, there is a need to identify new drug targets and authenticate antimalarial compounds that act on these targets. A relatively new therapeutic approach targets proteolytic enzymes responsible for parasite‟s invasion, rupture and hemoglobin degradation at the erythrocytic stage of infection. Cysteine proteases (CPs) are essential for these crucial roles in the intraerythrocytic parasite. CPs are a diverse group of enzymes subdivided into clans and further subdivided into families. Our interest is in Clan CA, papain family C1 proteases, whose members play numerous roles in human and parasitic metabolism. These proteases are produced as zymogens having an N-terminal extension known as the prodomain which regulates the protease activity by selectively inhibiting its active site, preventing substrate access. A Clan CA protease Falcipain-2 (FP-2) of Plasmodium falciparum is a validated drug target but little is known of its orthologs in other malarial Plasmodium species. This study uses various structural bioinformatics approaches to characterise the prodomain‟s regulatory effect in FP-2 and its orthologs in Plasmodium species (P. vivax, P. berghei, P. knowlesi, P. ovale, P. chabaudi and P. yoelii). This was in an effort to discover short peptides with essential residues to mimic the prodomain‟s inhibition of these proteases, as potential peptidomimetic therapeutic agents. Residues in the prodomain region that spans over the active site are most likely to interact with the subsite residues inhibiting the protease. Sequence analysis revealed conservation of residues in this region of Plasmodium proteases that differed significantly in human proteases. Further prediction of the 3D structure of these proteases by homology modelling allowed visualisation of these interactions revealing differences between parasite and human proteases which will lead to significant contribution in structure based malarial inhibitor design.
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  • Date Issued: 2012

SphereZyme (TM) technology for enhanced enzyme immobilisation application in biosensors

  • Authors: Molawa, Letshego Gloria
  • Date: 2011
  • Subjects: Immobilized enzymes , Hydrolases , Hydrolysis , SphereZyme , Biosensors , Proteolytic enzymes
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:3989 , http://hdl.handle.net/10962/d1004048 , Immobilized enzymes , Hydrolases , Hydrolysis , SphereZyme , Biosensors , Proteolytic enzymes
  • Description: Self-immobilisation enzyme technologies, such as SphereZyme™, suffer from the lack of applicability to hydrolyse large substrates. Solid support immobilisation is usually a method of choice, to produce a stable biocatalyst for large substrates hydrolysis in the industry. In order to investigate this limitation, a commercial protease called Alcalase® was chosen as a model enzyme due to its natural activity (hydrolysis of large substrates-proteins). Prior to immobilising through the SphereZyme™ technology, Alcalase® was partially purified through dialysis followed by CM Sepharose™ FF cation exchanger. Sample contaminants, such as salts and stabilisers can inhibit protein crosslinking by reacting with glutaraldehyde. Alcalase® was successfully separated into 3 proteases with the major peak correlating to a positive control run on native PAGE, indicating that it was likely subtilisin Carlsberg. A 16% alkaline protease activity for azo-casein hydrolysis was retained when 5% v/v PEI: 25% v/v glutaraldehyde solution was used as a crosslinking agent in Alcalase® SphereZyme™ production. An increase in activity was also observed for monomeric substrates (PNPA) where the highest was 55%. The highest % activities maintained when 0.33 M EDA: 25% v/v glutaraldehyde solution was initially used as crosslinking agent were 4.5% and 1.6% for monomeric and polymeric substrates, respectively. PEI is a hydrophilic branched polymer with an abundance of amine groups compared to EDA. A comparison study of immobilisation efficiencies of SphereZyme™, Eupergit® and Dendrispheres was also performed for large substrate biocatalysis. The two latter technologies are solid-support immobilisation methods. Dendrispheres reached its maximum loading capacity in the first 5 minute of the one hour binding time. Twenty minutes was chosen as a maximum binding time since there was constant protein maintained on the solid support and no enzyme loss was observed during the 1 hour binding time. PEI at pH 11.5, its native pH, gave the highest immobilisation yield and specific activity over the PEI pH range of 11.5 to 7. SphereZyme™ had the highest ratio for azocasein hydrolysis followed by Dendrispheres and Eupergit®. The SphereZyme™ was also shown to be applicable to biosensors for phenol detection. Different modifications of glassy carbon electrode (GCE) were evaluated as a benchmark for the fabrication of SphereZyme™ modified phenol biosensor. GCE modified with laccase SphereZyme™ entrapped in cellulose membrane was the best modification due to the broad catechol range (<0.950 mM), high correlation coefficient (R2, 0.995) and relative high sensitivity factor (0.305 μA.mM-1). This type of biosensor was also shown to be electroactive at pH 7.0 for which its control, free laccase, lacked electroactivity. From the catalytic constants calculated, GCE modified with laccase SphereZyme™ entrapped in cellulose membrane also gave the highest effectiveness factor (Imax/Km app) of 1.84 μA.mM-1. The modified GCE with Alcalase® SphereZyme™ was relatively more sensitive than GCE modified with free Alcalase®.
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  • Date Issued: 2011

Purification and partial characterisation of cathepsin D from ostrich skeletal muscle, and its activity during meat maturation

  • Authors: Krause, Jason
  • Date: 2009
  • Subjects: Proteolytic enzymes , Ostrich products industry
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10313 , http://hdl.handle.net/10948/1461 , Proteolytic enzymes , Ostrich products industry
  • Description: Cathepsin D, a muscle proteinase, participates in lysosomally mediated protein degradation in vivo. This enzyme has been proposed to play a significant role in the postmortem proteolysis process apparently associated with tenderisation. The lack of data on the postmortem characteristics of ostrich meat, especially on the ageing process and its influence on meat tenderness, called for an investigation into this process. There is no data available for purified ostrich cathepsin D, and the aim of this study was, therefore, to isolate, purify and characterise cathepsin D from ostrich skeletal muscle and subsequently investigate the possible role that it may have in the tenderisation process of meat. Cathepsin D was successfully isolated and purified from ostrich skeletal muscle using pepstatin A-agarose chromatography. The purified enzyme was composed of two subunits (14 and 29kDa). The amino acid composition as well as the N-terminal amino acid sequence of both subunits were determined. Kinetic parameters (Km and Vm), thermodynamic parameters (Ea, ∆H, ∆S and ∆G) and functional characteristics (effect of pH, temperature and various inhibitors on cathepsin D activity) were determined and are reported in this study. Ostrich muscle cathepsin D showed a pH optimum of 4 and a temperature optimum of 45°C. The activity of cathepsin D was strongly inhibited by pepstatin A and DTT. Purified ostrich cathepsin D displayed kinetic and functional properties similar to previously reported values from various species. The effect of storage on the activity of cathepsin D was investigated over a 30 day period. It was established that substantial postmortem cathepsin D activity remained throughout the storage period, to implicate cathepsin D, fulfilling a possible role in meat maturation.
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  • Date Issued: 2009

Purification and partial characterization of a Myofibril-Bound Serine Protease and its endogenous inhibitor from skeletal muscle of the ostrich

  • Authors: Tshidino, Shonisani Cathphonia
  • Date: 2008
  • Subjects: Proteolytic enzymes , Ostrich products industry
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:10330 , http://hdl.handle.net/10948/703 , Proteolytic enzymes , Ostrich products industry
  • Description: The ostrich is becoming an important source of meat for humans in developed and developing countries. This study was conducted to purify and characterize myofibrilbound serine protease (MBSP) and its endogenous inhibitor (MBSPI) from skeletal muscle of the ostrich. It is well documented that MBSP is tightly bound to myofibrils and its endogenous inhibitor has been purified from the same tissue of other studied mammalian species. Literature supports an association of MBSP and its endogenous inhibitor with the degradation of myofribrillar proteins, resulting in the softening of muscle that lead to the conversion of muscle into meat with the control of the inhibitor. MBSP was successfully dissociated from washed myofibrils by 40 percent ethylene glycol at pH 8.5. Following centrifugation, MBSP was partially purified in two chromatographic steps, namely Toyopearl Super Q 650S and p-aminobenzamidine-Agarose. On the other hand, MBSPI was fractionated from the sarcoplasmic fraction using 75 percent ammonium sulfate saturation, followed by centrifugation and partially purified by three chromatographic steps, namely Toyopearl Super Q 650S, Superdex 200 and HiTrap SP HR. Ostrich MBSP was physicochemically and kinetically characterized, while MBSPI was only physicochemically characterized. Ostrich MBSP revealed an Mr of 21 kDa, cleaving synthetic fluorogenic substrates specifically at the carboxyl side of arginine residues. Optimum pH and temperature of ostrich MBSP were 8.0 and 40˚C, respectively. Kinetic parameters (Km and Vmax values) were calculated from Lineweaver-Burk plots. The characteristics of ostrich MBSP were compared to the values obtained for commercial bovine trypsin in this study, as well as that obtained for MBSP from various fish species and mouse. The results suggest that ostrich MBSP is a trypsin-like serine protease, thereby confirming the existence of MBSP in ostrich skeletal muscle. Partially purified ostrich MBSPI (Mr 17 kDa) (one form) shares 100 percent identity to myoglobin from the same species, while 2 other forms of MBSPI (Mr values of 35 and 36 kDa) exhibited high sequence identity to glyceraldehyde 3- phosphate dehydrogenase (GAPDH) (76 percent) from human and rat.
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  • Date Issued: 2008

Studies directed towards the synthesis of chromone carbaldehyde-derived HIV-1 protease inhibitors

  • Authors: Molefe, Duduzile Mabel
  • Date: 2008
  • Subjects: Protease Inhibitors , HIV infections , HIV (Viruses) , AIDS (Disease) , Proteolytic enzymes , Heterocyclic compounds -- Derivatives , Chemical kinetics , Nuclear magnetic resonance spectroscopy
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:4526 , http://hdl.handle.net/10962/d1015542
  • Description: A series of chromone-3-carbaldehydes have been prepared using Vilsmeier-Haack methodology while a corresponding series of chromone-2-carbaldeydes have been synthesized via the Kostanecki-Robinson reaction. Baylis-Hillman reactions have been conducted on both series of chromone carbaldehydes using three different catalysts, viz., 1,4-diazabicyclo(2.2.2]octane (DABCO), 1,8-diazabicyclo[5.4.0]undec- 7-ene (DBU) and 3-hydroxyquinuclidine (3HQ), and acrylonitrile, methyl acrylate and methyl vinyl ketone as the activated alkenes. These reactions have typically (but not always!) afforded both normal Baylis-Hillman and dimeric products. Attention has also been given to the use of 1-methyl-2-pyrrolidine (1-NMP), an ionic liquid, to replace normal organic solvents, and it has been found that, in the presence of DABCO, chromone-3-carbaldehydes afford the dimeric products alone. Reactions of chromone-3-carbaldehydes with methyl vinyl ketone have yielded unexpected, novel adducts, which appear to arise from preferential attack at C(2) in the chromone nucleus. Research on chromone-2-carbaldeydes under Baylis-Hillman conditions has also resulted in the formation of some interesting products instead of the expected Baylis-Hillman adducts. The Baylis-Hillman products have been explored as substrates for aza-Michael reactions using various amino derivatives including protected amino acids in the presence of the tetrabutylammonium bromide (TBAB) and the ionic liquid, 3-butyl-1- methylimidazoleboranetetrafluoride (BmimBF₄), as catalysts. The aza-Michael products have been targeted as truncated ritonavir analogues for investigation as potential HIV -1 protease inhibitors, and representative compounds have been subjected to enzyme inhibition assays to explore the extent and type of inhibition. Lineweaver-Burk and Dixon plots have indicated competitive inhibition in one case as well as non-competitive inhibition in another, and the inhibition constants (Ki) have been compared with that of the ritonavir. Computer modelling studies have also been conducted on selected chromonecontaining derivatives, using the ACCELRYS Cerius² platform. Interactive docking of the chromone-containing ligands into the HIV -1 protease receptor site, using the Ligandfit module, has indicated the importance of hydrogen-bonding interactions mediated by bridging water molecules situated in the receptor cavity. NMR spectroscopy has been used to elucidate complex and competing mechanistic pathways involved in the Baylis-Hillman reactions of selected 2-nitrobenzaldehydes with MVK in the presence of DABCO - reactions which afford the normal BaylisHillman product, the MVK dimer and syn- and anti-Baylis-Hillman type diadducts. The kinetic data confirm the concomitant operation of two pathways and reveal that, in the initial stage of the reaction, the product distribution is kinetically controlled, whereas in the latter stage, thermodynamic control results in the consumption of the normal Baylis-Hillman product and predominance of the anti-diadduct.
  • Full Text:
  • Date Issued: 2008

Purification and characterisation of 20S proteasome from ostrich skeletal muscle and its role in meat tenderisation

  • Authors: Thomas, Adele René
  • Date: 2004
  • Subjects: Proteolytic enzymes , Ostrich products industry
  • Language: English
  • Type: Thesis , Doctoral , DPhil
  • Identifier: vital:11081 , http://hdl.handle.net/10948/320 , Proteolytic enzymes , Ostrich products industry
  • Description: The proteasome is renowned for its high molecular weight, multisubunit and mulicatalytic nature. One of its many suggested roles is the degradation of myofibrillar proteins, and therefore it has been proposed to play a role in the meat tenderisation process. The aim of this study was therefore to isolate, purify and characterise the 20S proteasome from ostrich skeletal muscle, with a view to ultimately investigating its role in the tenderisation process of ostrich meat. The 20S proteasome was successfully isolated and purified from ostrich skeletal muscle using Toyopearl Super Q-650S, Sephacryl S-300, hydroxylapatite and Mono Q chromatographies. The intact molecule showed a molecular weight of 725 K and a pI of 6.67. The subunits showed a molecular weight range of 22.2-33.5 K and a pI range of 3-9. 2D-PAGE revealed at least 14 polypeptides. The amino acid composition of the intact enzyme and of each of the eight subunits separating on SDSPAGE, as well as the N-terminal sequences of five of the eight subunits, were determined. The trypsinlike (Tr-L), chymotrypsin-like (ChT-L), peptidylglutamyl peptide hydrolase (PGPH) and caseinolytic activities showed pH optima of 11, 9, 7-8 and 10.3, and temperature optima of 40, 60, 70 and 60oC, respectively. The pH stability range for all four activities was 5-12. The ChT-L and PGPH activities showed thermostabilities up to 60oC, whereas the Tr-L and caseinolytic activities were stable up to 40o C. The enzyme showed complex kinetics. It was inhibited by the peptide aldehyde Z-LLL-CHO and cysteine protease inhibitors. Cations had negligible effects on the enzyme, excepting for Ca2+ and Mg2+. Of the detergents tested, SDS had the most potent stimulatory effect, particularly on the PGPH and caseinolytic activities. The fatty acid studies showed that unsaturation enhanced the ChT-L and the caseinolytic activities, while it completely suppressed the Tr-L activity. Heating at 60oC for 1-2 min stimulated the caseinolytic and PGPH activities. The studies on the role of ostrich skeletal muscle 20S proteasome in ostrich meat tenderisation suggested a definite but minor role of this enzyme, based on the fact that it remained active throughout the 12 days of storage of ostrich M. iliofibularis meat at 4oC and that it participated in myofibril degradation of post-mortem muscle, but to a small degree. These results support the proposal that the proteasome comes into play after the calpains have initiated degradation. However, there was a lack of improvement in tenderness values and minimal myofibrillar degradation over the 12-day storage period of the ostrich M. iliofibularis meat, leading to the conclusion that the tenderisation of this meat was incomplete after 12 days.
  • Full Text:
  • Date Issued: 2004
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