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Oyewusi HA, Adedamola Akinyede K, Wahab RA, Susanti E, Syed Yaacob SN, Huyop F. Biological and molecular approaches of the degradation or decolorization potential of the hypersaline Lake Tuz Bacillus megaterium H2 isolate. J Biomol Struct Dyn 2024; 42:6228-6244. [PMID: 37455463 DOI: 10.1080/07391102.2023.2234040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
The presence of synthetic dyes in water bodies and soil is one of the major issues affecting the global ecology, possibly impacting societal well-being adversely due to the colorants' recalcitrance and toxicity. Herein, the study spectrophotometrically monitored the ability of the Bacillus megaterium H2 azoreductase (AzrBmH2) to degrade four synthetic dyes, reactive blue 4, remazol brilliant red, thymol blue, and methyl red, followed by in-silico assessment using GROMACS. We found that the bacterium degraded as much as 60% of all four synthetic dyes at various tested concentrations. The genome analysis revealed five different azoreductase genes, which were then modeled into the AzrBmH21, AzrBmH22/3, and AzrBmH24/5 templates. The AzrBmH2-substrate complexes showed binding energies with all the dyes of between -10.6 to -6.9 kcal/mol and formed 4-6 hydrogen bonds with the predicted catalytic binding residues (His10, Glu 14, Ser 58, Met 99, Val 107, His 183, Asn184 and Gln 191). In contrast, the lowest binding energies were observed for the AzrBmH21-substrates (-10.6 to -7.9). Molecular dynamic simulations revealed that the AzrBmH21-substrate complexes were more stable (RMSD 0.2-0.25 nm, RMSF 0.05 - 0.3 nm) and implied strong bonding with the dyes. The Molecular Mechanics Poisson-Boltzmann Surface Area results also mirrored this outcome, showing the lowest azoreductase-dye binding energy in the order of AzrBmH21-RB4 (-78.18 ± 8.92 kcal/mol), AzrBmH21-RBR (-67.51 ± 7.74 kcal/mol), AzrBmH21-TB (-46.62 ± 5.23 kcal/mol) and AzrBmH21-MR (-40.78 ± 7.87 kcal/mol). In short, the study demonstrated the ability of the B. megaterium H2 to efficiently decolorize the above-said synthetic dyes, conveying the bacterium's promising use for large-scale dye remediation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Department of Science Technology, Biochemistry Unit, The Federal Polytechnic, Ado Ekiti, Nigeria
| | - Kolajo Adedamola Akinyede
- Department of Science Technology, Biochemistry Unit, The Federal Polytechnic, Ado Ekiti, Nigeria
- Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Department of Applied Science, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Malang, Indonesia
| | - Evi Susanti
- Department of Applied Science, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Malang, Indonesia
| | - Syariffah Nuratiqah Syed Yaacob
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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2
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Wahhab BH, Oyewusi HA, Wahab RA, Mohammad Hood MH, Abdul Hamid AA, Al-Nimer MS, Edbeib MF, Kaya Y, Huyop F. Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey. J Biomol Struct Dyn 2024; 42:1429-1442. [PMID: 37038649 DOI: 10.1080/07391102.2023.2199870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 04/01/2023] [Indexed: 04/12/2023]
Abstract
This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of -2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of -4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (-21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Batool Hazim Wahhab
- Department of Microbiology, Faculty of Medicine, Al-Mustansiriyah University, Iraq
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Mohammad Hakim Mohammad Hood
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Marwan Salih Al-Nimer
- Department of Pharmacology, College of Medicine, University of Diyala, Baqubah, Iraq
| | - Mohamed Faraj Edbeib
- Department of Medical Laboratories, Faculty of Medical Technology, Bani Walid University, Libya
| | - Yilmaz Kaya
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
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Selim MS, Mounier MM, Abdelhamid SA, Hamed AA, Abo Elsoud MM, Mohamed SS. Characterization, modeling, and anticancer activity of L.arginase production from marine Bacillus licheniformis OF2. BMC Biotechnol 2024; 24:6. [PMID: 38273334 PMCID: PMC10811824 DOI: 10.1186/s12896-024-00829-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND L-arginase, is a powerful anticancer that hydrolyzes L-arginine to L-ornithine and urea. This enzyme is widely distributed and expressed in organisms like plants, fungi, however very scarce from bacteria. Our study is based on isolating, purifying, and screening the marine bacteria that can produce arginase. RESULTS The highest arginase producing bacteria will be identified by using microbiological and molecular biology methods as Bacillus licheniformis OF2. Characterization of arginase is the objective of this study. The activity of enzyme was screened, and estimated beside partial sequencing of arginase gene was analyzed. In silico homology modeling was applied to generate the protein's 3D structure, and COACH and COFACTOR were applied to determine the protein's binding sites and biological annotations based on the I-TASSER structure prediction. The purified enzyme was undergone an in vitro anticancer test. CONCLUSIONS L-arginase demonstrated more strong anti-cancer cells with an IC50 of 21.4 ug/ml in a dose-dependent manner. L-arginase underwent another investigation for its impact on the caspase 7 and BCL2 family of proteins (BCL2, Bax, and Bax/Bcl2). Through cell arrest in the G1/S phase, L-arginase signals the apoptotic cascade, which is supported by a flow cytometry analysis of cell cycle phases.
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Affiliation(s)
- Manal S Selim
- Microbial Biotechnology Department, National Research Centre, Cairo, Egypt
| | - Marwa M Mounier
- Pharmacognosy Department, National Research Centre, Cairo, Egypt
| | | | | | | | - Sahar S Mohamed
- Microbial Biotechnology Department, National Research Centre, Cairo, Egypt
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4
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Khedr M, Khalil KMA, Kabary HA, Hamed AA, Badawy MSEM, Abu-Elghait M. Molecular docking and nucleotide sequencing of successive expressed recombinant fungal peroxidase gene in E.coli. J Genet Eng Biotechnol 2022; 20:94. [PMID: 35776246 PMCID: PMC9249955 DOI: 10.1186/s43141-022-00377-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022]
Abstract
Background Fungal peroxidases are oxidoreductases that utilize hydrogen peroxide to catalyze lignin biodegradation. Results PER-K (peroxidase synthesis codon gene) was transformed from Aspergillus niger strain AN512 deposited in the National Center for Biotechnology Information with the accession number OK323140 to Escherichia coli strain (BL21-T7 with YEp356R recombinant plasmid) via calcium chloride heat-shock method. The impact of four parameters (CaCl2 concentrations, centrifugation time, shaking speed, growth intensity) on the efficacy of the transformation process was evaluated. Furthermore, peroxidase production after optimization was assessed both qualitatively and quantitatively, as well as SDS-PAGE analysis. The optimum conditions for a successful transformation process were as follows: CaCl2 concentrations (50 mM), centrifugation time (20 min), shaking speed (200 rpm), and growth optical density (0.45). PCR and gel electrophoresis detect DNA bands with lengths 175, 179, and 211 bps corresponding to UA3, AmpR, and PER-K genes respectively besides partially sequencing the PER-K gene. Pyrogallol/hydrogen peroxide assay confirmed peroxidase production, and the activity of the enzyme was determined to be 3924 U/L. SDS-PAGE analysis also confirms peroxidase production illustrated by the appearance of a single peroxidase protein band after staining with Coomassie blue R-250. Conclusion A successful peroxidase-gene (PER-K) transformation from fungi to bacteria was performed correctly. The enzyme activity was screened, and partial sequencing of PER-K gene was analyzed successively. The protein 3D structure was generated via in silico homology modeling, and determination of binding sites and biological annotations of the constructed protein were carried out via COACH and COFACTOR based on the I-TASSER structure prediction. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00377-6.
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Affiliation(s)
- Mohamed Khedr
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt
| | - Kamal M A Khalil
- Genetic Engineering and Biotechnology Division, Genetics and Cytology Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Hoda A Kabary
- Agricultural Microbiology Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Ahmed A Hamed
- Microbial Chemistry Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Mona Shaban E M Badawy
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Mohammed Abu-Elghait
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt.
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Ezema BO, Omeje KO, Bill RM, Goddard AD, O Eze SO, Fernandez-Castane A. Bioinformatic characterization of a triacylglycerol lipase produced by Aspergillus flavus isolated from the decaying seed of Cucumeropsis mannii. J Biomol Struct Dyn 2022; 41:2587-2601. [PMID: 35147487 DOI: 10.1080/07391102.2022.2035821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lipases are enzymes of industrial importance responsible for the hydrolysis of ester bonds of triglycerides. A lipolytic fungus was isolated and subsequently identified based on the ITS sequence analysis as putative Aspergillus flavus with accession number LC424503. The gene coding for extracellular triacylglycerol lipase was isolated from Aspergillus flavus species, sequenced, and characterised using bioinformatics tools. An open reading frame of 420 amino acid sequence was obtained and designated as Aspergillus flavus lipase (AFL) sequence. Alignment of the amino acid sequence with other lipases revealed the presence GHSLG sequence which is the lipase consensus sequence Gly-X1-Ser-X2-Gly indicating that it a classical lipase. A catalytic active site lid domain composed of TYITDTIIDLS amino acids sequence was also revealed. This lid protects the active site, control the catalytic activity and substrate selectivity in lipases. The 3-Dimensional structural model shared 34.08% sequence identity with a lipase from Yarrowia lipolytica covering 272 amino acid residues of the template model. A search of the lipase engineering database using AFL sequence revealed that it belongs to the class GX-lipase, superfamily abH23 and homologous family abH23.02, molecular weight and isoelectric point values of 46.95 KDa and 5.7, respectively. N-glycosylation sites were predicted at residues 164, 236 and 333, with potentials of 0.7250, 0.7037 and 0.7048, respectively. O-glycosylation sites were predicted at residues 355, 358, 360 and 366. A signal sequence of 37 amino acids was revealed at the N-terminal of the polypeptide. This is a short peptide sequence that marks a protein for transport across the cell membrane and indicates that AFL is an extracellular lipase. The findings on the structural and molecular properties of Aspergillus flavus lipase in this work will be crucial in future studies aiming at engineering the enzyme for biotechnology applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Benjamin O Ezema
- The Biochemistry Unit, Department of Science Laboratory Technology, University of Nigeria, Nsukka, Nigeria.,Department of Biochemistry, University of Nigeria, Nsukka, Nigeria.,Aston Institute of Materials Research, Aston University, Birmingham, UK.,Energy and Bioproducts Research Institute, Aston University, Birmingham, UK
| | - Kingsley O Omeje
- Department of Biochemistry, University of Nigeria, Nsukka, Nigeria
| | | | | | | | - Alfred Fernandez-Castane
- Aston Institute of Materials Research, Aston University, Birmingham, UK.,Energy and Bioproducts Research Institute, Aston University, Birmingham, UK
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Lameh F, Baseer AQ, Ashiru AG. Comparative molecular docking and molecular-dynamic simulation of wild-type- and mutant carboxylesterase with BTA-hydrolase for enhanced binding to plastic. Eng Life Sci 2022; 22:13-29. [PMID: 35024024 PMCID: PMC8727734 DOI: 10.1002/elsc.202100083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/25/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
According to the literature review, microbial degradation of polyethylene terephthalate by PETases has been detected effective and eco-friendly. However, the number of microorganisms capable of such feats is limited with some undesirable bioprospecting results. BTA-hydrolase has been already reported capable of degrading polyethylene terephthalate. Therefore, mutation by in silico site-directed mutagenesis means to introduce current isomer of PETase for polyethylene terephthalate degradative capability as a better approach to resolve this issue. This study aimed to use in silico site-directed mutagenesis to convert a carboxylesterase from Archaeoglobus fulgidus to BTA-hydrolase from Thermobifida fusca by replacing six amino acids in specific locations. This work was followed by molecular docking analysis with polyethylene terephthalate and polypropylene to compare their interactions. The best-docked enzyme-substrate complex was further subjected to molecular dynamics simulation to gauge the binding quality of the BTA-hydrolase, wild-type and mutant-carboxylesterase with only polyethylene terephthalate as a substrate. Results of molecular docking revealed lowest binding energy for the wild-type carboxylesterase-polypropylene complex (-7.5 kcal/mol). The root-mean-square deviation value was observed stable for BTA-hydrolase. Meanwhile, root-mean-square fluctuation was assessed with higher fluctuation for the mutated residue Lys178. Consequently, the Rg value for BTA-hydrolase-ligand complex (∼1.68 nm) was the lowest compared to the mutant and wild-type carboxylesterase. The collective data conveyed that mutations imparted a minimal change in the ability of the mutant carboxylesterase to bind to polyethylene terephthalate.
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Affiliation(s)
- Fatana Lameh
- Department of BotanyFaculty of BiologyKabul UniversityKabulAfghanistan
- Department of BiosciencesFaculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
| | - Abdul Qadeer Baseer
- Department of BiosciencesFaculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
- Department of BiologyFaculty of EducationKandahar UniversityKandaharAfghanistan
| | - Abubakar Garba Ashiru
- Department of ChemistryZamfara State College of EducationMaruNigeria
- Green Chemistry Research GroupDepartment of Chemistry, Faculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
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Romes NB, Abdul Wahab R, Abdul Hamid M, Oyewusi HA, Huda N, Kobun R. Thermodynamic stability, in-vitro permeability, and in-silico molecular modeling of the optimal Elaeis guineensis leaves extract water-in-oil nanoemulsion. Sci Rep 2021; 11:20851. [PMID: 34675286 PMCID: PMC8531315 DOI: 10.1038/s41598-021-00409-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/17/2021] [Indexed: 11/09/2022] Open
Abstract
Nanoemulsion is a delivery system used to enhance bioavailability of plant-based compounds across the stratum corneum. Elaeis guineensis leaves are rich source of polyphenolic antioxidants, viz. gallic acid and catechin. The optimal E. guineensis leaves extract water-in-oil nanoemulsion was stable against coalescence, but it was under significant influence of Ostwald ripening over 90 days at 25 °C. The in-vitro permeability revealed a controlled and sustained release of the total phenolic compounds (TPC) of EgLE with a cumulative amount of 1935.0 ± 45.7 µgcm-2 after 8 h. The steady-state flux and permeation coefficient values were 241.9 ± 5.7 µgcm-2 h-1 and 1.15 ± 0.03 cm.h-1, respectively. The kinetic release mechanism for TPC of EgLE was best described by the Korsmeyer-Peppas model due to the highest linearity of R2 = 0.9961, indicating super case II transport mechanism. The in-silico molecular modelling predicted that the aquaporin-3 protein in the stratum corneum bonded preferably to catechin over gallic acid through hydrogen bonds due to the lowest binding energies of - 57.514 kcal/mol and - 8.553 kcal/mol, respectively. Thus, the in-silico study further verified that catechin could improve skin hydration. Therefore, the optimal nanoemulsion could be used topically as moisturizer to enhance skin hydration based on the in-silico prediction.
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Affiliation(s)
- Nissha Bharrathi Romes
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia.
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia.
| | - Mariani Abdul Hamid
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
| | - Nurul Huda
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia.
| | - Rovina Kobun
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia
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Oyewusi HA, Huyop F, Wahab RA, Hamid AAA. In silico assessment of dehalogenase from Bacillus thuringiensis H2 in relation to its salinity-stability and pollutants degradation. J Biomol Struct Dyn 2021; 40:9332-9346. [PMID: 34014147 DOI: 10.1080/07391102.2021.1927846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Increased scientific interest has led to the rise in biotechnological uses of halophilic and halotolerant microbes for hypersaline wastewater bioremediation. Hence, this study performed molecular docking, molecular dynamic (MD) simulations, and validation by Molecular Mechanic Poisson-Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis H2. We aimed to identify the interactions of DehH2 with substrates haloacids, haloacetates, and chlorpyrifos under extreme salinity (35% NaCl). MD simulations revealed that DehH2 preferentially degraded haloacids and haloacetates (-6.3 to -4.7 kcal/mol) by forming three or four hydrogen bonds to the catalytic triad, Asp125, Arg201, and Lys202. Conversely, chlorpyrifos was the least preferred substrate in both MD simulations and MM-PBSA calculations. MD simulation results ranked the DehH2-L-2CP complex (RMSD □0.125-0.23 nm) as the most stable while the least was the DehH2-chlorpyrifos complex (RMSD 0.32 nm; RMSF 0.0 - 0.29). The order of stability was as follows: DehH2-L-2CP > DehH2-MCA > DehH2-D-2CP > DehH2-3CP > DehH2-2,2-DCP > DehH2-2,3-DCP > DehH2-TCA > DehH2-chlorpyrifos. The MM-PBSA calculations further affirmed the DehH2-L-2CP complex's highest stability with the lowest binding energy of -45.14 kcal/mol, followed closely by DehH2-MCA (-41.21 kcal/mol), DehH2-D-2CP (-31.59 kcal/mol), DehH2-3CP (-30.75 kcal/mol), DehH2-2,2- DCP (-29.72 kcal/mol), DehH2-2,3-DCP (-22.20 kcal/mol) and DehH2-TCA (-18.46 kcal/mol). The positive binding energy of the DehH2-chlorpyrifos complex (+180.57 kcal/mol) proved the enzyme's non-preference for the substrate. The results ultimately illustrated the unique specificity of the DehH2 to degrade the above-said pollutants under a hypersaline condition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan Pahang, Malaysia
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Wahhab BHA, Samsulrizal NH, Edbeib MF, Wahab RA, Al-Nimer MSM, Hamid AAA, Oyewusi HA, Kaya Y, Notarte KIR, Shariff AHM, Huyop F. Genomic analysis of a functional haloacid-degrading gene of Bacillus megaterium strain BHS1 isolated from Blue Lake (Mavi Gölü, Turkey). ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01625-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Bacillus megaterium strain BHS1, isolated from an alkaline water sample taken from Mavi Gölü (Blue Lake, Turkey), can grow on minimal medium containing 2,2-dichloropropionic acid. We characterized this bacterium at the genomic level.
Methods
The HiSeq platform was used to carry out genome sequencing, de novo assembly, and scaffolding with strain BHS1. Next, genome data were analyzed to demarcate DNA regions containing protein-coding genes and determine the function of certain BHS1 genes. Finally, results from a colorimetric chloride ion–release assay demonstrated that strain BHS1 produces dehalogenase.
Results
De novo assembly of the BHS1 genomic sequence revealed a genome size of ~ 5.37 Mb with an average G+C content of 38%. The predicted nuclear genome harbors 5509 protein-coding genes, 1353 tRNA genes, 67 rRNA genes, and 6 non-coding (mRNA) genes. Genomic mapping of strain BHS1 revealed its amenability to synthesize two families of dehalogenases (Cof-type haloacid dehalogenase IIB family hydrolase and haloacid dehalogenase type II), suggesting that these enzymes can participate in the catabolism of halogenated organic acids. The mapping identified seven Na+/H+ antiporter subunits that are vital for adaptation of the bacterium to an alkaline environment. Apart from a pairwise analysis to the well-established L-2-haloacid dehalogenases, whole-cell analysis strongly suggested that the haloacid dehalogenase type II might act stereospecifically on L-2-chloropropionic acid, D,L-2-chloropropionic acid, and 2,2-dichloropropionic acid. Whole-cell studies confirmed the utilization of these three substrates and the gene’s role in dehalogenation.
Conclusions
To our knowledge, this is the first report of the full genome sequence for strain BHS1, which enabled the characterization of selected genes having specific metabolic activities and their roles in the biodegradation of halogenated compounds.
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Dutta B, Deska J, Bandopadhyay R, Shamekh S. In silico characterization of bacterial chitinase: illuminating its relationship with archaeal and eukaryotic cousins. J Genet Eng Biotechnol 2021; 19:19. [PMID: 33495874 PMCID: PMC7835276 DOI: 10.1186/s43141-021-00121-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/14/2021] [Indexed: 11/23/2022]
Abstract
Background Chitin is one of the most abundant biopolymers on Earth, only trailing second after cellulose. The enzyme chitinase is responsible for the degradation of chitin. Chitinases are found to be produced by wide range of organisms ranging from archaea to higher plants. Though chitin is a major component of fungal cell walls and invertebrate exoskeletons, bacterial chitinase can be industrially generated at low cost, in facile downstream processes at high production rate. Microbial chitinases are more stable, active, and economically practicable compared to the plant- and animal-derived enzymes. Results In the present study, computationally obtained results showed functional characteristics of chitinase with particular emphasis on bacterial chitinase which is fulfilling all the required qualities needed for commercial production. Sixty-two chitinase sequences from four different groups of organisms were collected from the RCSB Protein Data Bank. Considering one suitable exemplary sequence from each group is being compared with others. Primary, secondary, and tertiary structures are determined by in silico models. Different physical parameters, viz., pI, molecular weight, instability index, aliphatic index, GRAVY, and presence of functional motifs, are determined, and a phylogenetic tree has been constructed to elucidate relationships with other groups of organisms. Conclusions This study provides novel insights into distribution of chitinase among four groups and their characterization. The results represent valuable information toward bacterial chitinase in terms of the catalytic properties and structural features, can be exploited to produce a range of chitin-derived products. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00121-6.
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Affiliation(s)
- Bhramar Dutta
- Juva Truffle Center, Huttulantie 1C, Juva, Finland.,Department of Botany, The University of Burdwan, Golapbag, Purba Bardhaman, West Bengal 713104, India
| | - Jan Deska
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 11000 (Otakaari 1B), FI 00076, Aalto, Finland
| | - Rajib Bandopadhyay
- Department of Botany, The University of Burdwan, Golapbag, Purba Bardhaman, West Bengal 713104, India.
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11
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Oyewusi HA, Huyop F, Wahab RA. Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. J Biomol Struct Dyn 2020; 40:1979-1994. [PMID: 33094694 DOI: 10.1080/07391102.2020.1835727] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The high dependency and surplus use of agrochemical products have liberated enormous quantities of toxic halogenated pollutants into the environment and threaten the well-being of humankind. Herein, this study performed molecular docking, molecular dynamic (MD) simulations, molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis, to identify the order of which the enzyme degrades different substrates, haloacids, haloacetate and chlorpyrifos. The study discovered that the DehH2 favored the degradation of haloacids and haloacetates (-3.3 - 4.6 kcal/mol) and formed three hydrogen bonds with Asp125, Arg201 and Lys202. Despite the inconclusive molecular docking result, chlorpyrifos was consistently shown to be the least favored substrate of the DehH2 in MD simulations and MM-PBSA calculations. Results of MD simulations revealed the DehH2-haloacid- (RMSD 0.15 - 0.25 nm) and DehH2-haloacetates (RMSF 0.05 - 0.25 nm) were more stable, with the DehH2-L-2CP complex being the most stable while the least was the DehH2-chlorpyrifos (RMSD 0.295 nm; RMSF 0.05 - 0.59 nm). The Molecular Mechanics Poisson-Boltzmann Surface Area calculations showed the DehH2-L-2CP complex (-24.27 kcal/mol) having the lowest binding energy followed by DehH2-MCA (-22.78 kcal/mol), DehH2-D-2CP (-21.82 kcal/mol), DehH2-3CP (-21.11 kcal/mol), DehH2-2,2-DCP (-18.34 kcal/mol), DehH2-2,3-DCP (-8.34 kcal/mol), DehH2-TCA (-7.62 kcal/mol), while chlorpyrifos was unable to spontaneously bind to DehH2 (+127.16 kcal/mol). In a nutshell, the findings of this study offer valuable insights into the rational tailoring of the DehH2 for expanding its substrate specificity and catalytic activity in the near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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12
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Bahaman AH, Wahab RA, Abdul Hamid AA, Abd Halim KB, Kaya Y. Molecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation. J Biomol Struct Dyn 2020; 39:2628-2641. [DOI: 10.1080/07391102.2020.1751713] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Aina Hazimah Bahaman
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
- Enzyme Technology and Green Synthesis Group, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
- Enzyme Technology and Green Synthesis Group, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Kuantan, Malaysia
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Pahang, Malaysia
| | - Khairul Bariyyah Abd Halim
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Kuantan, Malaysia
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Pahang, Malaysia
| | - Yilmaz Kaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
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13
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Anuar NFSK, Wahab RA, Huyop F, Amran SI, Hamid AAA, Halim KBA, Hood MHM. Molecular docking and molecular dynamics simulations of a mutant Acinetobacter haemolyticus alkaline-stable lipase against tributyrin. J Biomol Struct Dyn 2020; 39:2079-2091. [DOI: 10.1080/07391102.2020.1743364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nurul Fatin Syamimi Khairul Anuar
- Faculty of Science, Department of Bioscience, Universiti Teknologi Malaysia, Johor, Malaysia
- Faculty of Science, Department of Chemistry, Enzyme Technology and Green Synthesis Research Group, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, Johor, Malaysia
- Faculty of Science, Department of Chemistry, Enzyme Technology and Green Synthesis Research Group, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Huyop
- Faculty of Science, Department of Bioscience, Universiti Teknologi Malaysia, Johor, Malaysia
- Faculty of Science, Department of Chemistry, Enzyme Technology and Green Synthesis Research Group, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Syazwani Itri Amran
- Faculty of Science, Department of Bioscience, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Kuantan, Malaysia
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Malaysia
| | - Khairul Bariyyah Abd Halim
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Kuantan, Malaysia
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Malaysia
| | - Mohammad Hakim Mohammad Hood
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Kuantan, Malaysia
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Malaysia
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14
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Anuar NFSK, Wahab RA, Huyop F, Halim KBA, Hamid AAA. In silico mutation on a mutant lipase from Acinetobacter haemolyticus towards enhancing alkaline stability. J Biomol Struct Dyn 2019; 38:4493-4507. [DOI: 10.1080/07391102.2019.1683074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Nurul Fatin Syamimi Khairul Anuar
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor, Bahru, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Bahru, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Bahru, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Fahrul Huyop
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor, Bahru, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Khairul Bariyyah Abd Halim
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota Kuantan, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kuliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota Kuantan, Malaysia
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15
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Bahaman AH, Abdul Wahab R, Hamid AAA, Halim KBA, Kaya Y, Edbeib MF. Substrate docking and molecular dynamic simulation for prediction of fungal enzymes from Trichoderma species-assisted extraction of nanocellulose from oil palm leaves. J Biomol Struct Dyn 2019; 38:4246-4258. [DOI: 10.1080/07391102.2019.1679667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Aina Hazimah Bahaman
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Enzyme Technology and Green Synthesis Group, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Enzyme Technology and Green Synthesis Group, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Pahang, Malaysia
| | - Khairul Bariyyah Abd Halim
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Pahang, Malaysia
| | - Yilmaz Kaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Kyrgyzstan
| | - Mohamed Faraj Edbeib
- Department of Animal Production, Faculty of Agriculture, Baniwalid University, Baniwalid, Libya
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16
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Edbeib MF, Aksoy HM, Kaya Y, Wahab RA, Huyop F. Haloadaptation: insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases. J Biomol Struct Dyn 2019; 38:3452-3461. [PMID: 31422756 DOI: 10.1080/07391102.2019.1657498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Halophiles are extremophilic microorganisms that grow optimally at high salt concentrations by producing a myriad of equally halotolerant enzymes. Structural haloadaptation of these enzymes adept to thriving under high-salt environments, though are not fully understood. Herein, the study attempts an in silico investigation to identify and comprehend the evolutionary structural adaptation of a halotolerant dehalogenase, DehHX (GenBank accession number: KR297065) of the halotolerant Pseudomonas halophila, over its non-halotolerant counterpart, DehMX1 (GenBank accession number KY129692) produced by Pseudomonas aeruginosa. GC content of the halotolerant DehHX DNA sequence was distinctively higher (58.9%) than the non-halotolerant dehalogenases (55% average GC). Its acidic residues, Asp and Glu were 8.27% and 12.06%, respectively, compared to an average 5.5% Asp and 7% Glu, in the latter; but lower contents of basic and hydrophobic residues in the DehHX. The secondary structure of DehHX interestingly revealed a lower incidence of α-helix forming regions (29%) and a higher percentage of coils (57%), compared to 49% and 29% in the non-halotolerant homologues, respectively. Simulation models showed the DehHX is stable under a highly saline environment (25% w/v) by adopting a highly negative-charged surface with a concomitant weakly interacting hydrophobic core. The study thus, established that a halotolerant dehalogenase undergoes notable evolutionary structural changes related to GC content over its non-halotolerant counterpart, in order to adapt and thrive under highly saline environments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed Faraj Edbeib
- Department of Animal Production, Faculty of Agriculture, Baniwalid University, Baniwalid, Libya.,Department of Plant Protection, Agricultural Faculty, Ondokuz Mayis University, Samsun, Turkey
| | - Hasan Murat Aksoy
- Department of Plant Protection, Agricultural Faculty, Ondokuz Mayis University, Samsun, Turkey
| | - Yilmaz Kaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey.,Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Fahrul Huyop
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey.,Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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17
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Muslem WH, Edbeib MF, Aksoy HM, Kaya Y, Hamid AAA, Hood MHM, Wahab RA, Huyop F. Biodegradation of 3-chloropropionic acid (3-CP) by Bacillus cereus WH2 and its in silico enzyme-substrate docking analysis. J Biomol Struct Dyn 2019; 38:3432-3441. [DOI: 10.1080/07391102.2019.1655482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Wafaa Hassan Muslem
- Department of Biology, College of Science, Al-Mustansiriyah University, Baghdad, Iraq
| | - Mohamed Faraj Edbeib
- Faculty of Agriculture, Department of Animal Production, Baniwalid University, Bani Walid, Libya
- Agricultural Faculty, Department of Plant Protection, Ondokuz Mayis University, Samsun, Turkey
| | - Hasan Murat Aksoy
- Agricultural Faculty, Department of Plant Protection, Ondokuz Mayis University, Samsun, Turkey
| | - Yilmaz Kaya
- Agricultural Faculty, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
- Faculty of Science, Department of Biology, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | | | | | - Roswanira Abdul Wahab
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Fahrul Huyop
- Agricultural Faculty, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
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18
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Biophysical characterization of a recombinant lipase KV1 from Acinetobacter haemolyticus in relation to pH and temperature. Biochimie 2018; 152:198-210. [PMID: 30036604 DOI: 10.1016/j.biochi.2018.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/18/2018] [Indexed: 01/05/2023]
Abstract
Spectroscopic and calorimetric methods were employed to assess the stability and the folding aspect of a novel recombinant alkaline-stable lipase KV1 from Acinetobacter haemolyticus under varying pH and temperature. Data on far ultraviolet-circular dichroism of recombinant lipase KV1 under two alkaline conditions (pH 8.0 and 12.0) at 40 °C reveal strong negative ellipticities at 208, 217, 222 nm, implying its secondary structure belonging to a α + β class with 47.3 and 39.0% ellipticity, respectively. Results demonstrate that lipase KV1 adopts its most stable conformation at pH 8.0 and 40 °C. Conversely, the protein assumes a random coil structure at pH 4.0 and 80 °C, evident from a strong negative peak at ∼ 200 nm. This blue shift suggests a general decline in enzyme activity in conjunction with the partially or fully unfolded state that invariably exposed more hydrophobic surfaces of the lipase protein. The maximum emission at ∼335 nm for pH 8.0 and 40 °C indicates the adoption of a favorable protein conformation with a high number of buried tryptophan residues, reducing solvent exposure. Appearance of an intense Amide I absorption band at pH 8.0 corroborates an intact secondary structure. A lower enthalpy value for pH 4.0 over pH 8.0 and 12.0 in the differential scanning calorimetric data corroborates the stability of the lipase at alkaline conditions, while a low Km (0.68 ± 0.03 mM) for tributyrin verifies the high affinity of lipase KV1 for the substrate. The data, herein offer useful insights into future structure-based tunable catalytic activity of lipase KV1.
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