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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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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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Oyewusi HA, Akinyede KA, Abdul Wahab R, Huyop F. In silico analysis of a putative dehalogenase from the genome of halophilic bacterium Halomonas smyrnensis AAD6T. J Biomol Struct Dyn 2023; 41:319-335. [PMID: 34854349 DOI: 10.1080/07391102.2021.2006085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Microbial-assisted removal of natural or synthetic pollutants is the prevailing green, low-cost technology to treat polluted environments. However, the challenge with enzyme-assisted bioremediation is the laborious nature of dehalogenase-producing microorganisms' bioprospecting. This bottleneck could be circumvented by in-silico analysis of certain microorganisms' whole-genome sequences to predict their protein functions and enzyme versatility for improved biotechnological applications. Herein, this study performed structural analysis on a dehalogenase (DehHsAAD6) from the genome of Halomonas smyrnensis AAD6 by molecular docking and molecular dynamic (MD) simulations. Other bioinformatics tools were also employed to identify substrate preference (haloacids and haloacetates) of the DehHsAAD6. The DehHsAAD6 preferentially degraded haloacids and haloacetates (-3.2-4.8 kcal/mol) and which formed three hydrogen bonds with Tyr12, Lys46, and Asp182. MD simulations data revealed the higher stability of DehHsAAD6-haloacid- (RMSD 0.22-0.3 nm) and DehHsAAD6-haloacetates (RMSF 0.05-0.14 nm) complexes, with the DehHsAAD6-L-2CP complex being the most stable. The detail of molecular docking calculations ranked complexes with the lowest binding free energies as: DehHsAAD6-L-2CP complex (-4.8 kcal/mol) = DehHsAAD6-MCA (-4.8 kcal/mol) < DehHsAAD6-TCA (-4.5 kcal/mol) < DehHsAAD6-2,3-DCP (-4.1 kcal/mol) < DehHsAAD6-D-2CP (-3.9 kcal/mol) < DehHsAAD6-2,2-DCP (-3.5 kcal/mol) < DehHsAAD6-3CP (-3.2 kcal/mol). In a nutshell, the study findings offer valuable perceptions into the elucidation of possible reaction mechanisms of dehalogenases for extended substrate specificity and higher catalytic activity.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 P.M.B, Ado Ekiti, Ekiti State, Nigeria
| | - Kolajo Adedamola Akinyede
- Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria.,Department of Medical Bioscience, University of the Western Cape, Bellville, Cape Town, 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
| | - 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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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: 11] [Impact Index Per Article: 2.8] [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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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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Fuentes D, Fahrenholtz SJ, Guo C, MacLellan CJ, Layman RR, Rivière B, Stafford RJ, Cressman E. Mathematical modeling of mass and energy transport for thermoembolization. Int J Hyperthermia 2020; 37:356-365. [PMID: 32308071 PMCID: PMC10558277 DOI: 10.1080/02656736.2020.1749317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 12/27/2022] Open
Abstract
Background: Thermoembolization presents a unique treatment alternative for patients diagnosed with hepatocellular carcinoma. The approach delivers a reagent that undergoes an exothermic chemical reaction and combines the benefits of embolic as well as thermal- and chemical-ablative therapy modalities. The target tissue and vascular bed are subjected to simultaneous hyperthermia, ischemia, and chemical denaturation in a single procedure. To guide optimal delivery, we developed a mathematical model for understanding the competing diffusive and convective effects observed in thermoembolization delivery protocols.Methods: A mixture theory formulation was used to mathematically model thermoembolization as chemically reacting transport of an electrophile, dichloroacetyl chloride (DCACl), within porous living tissue. Mass and energy transport of each relevant constituent are considered. Specifically, DCACl is injected into the vessels and exothermically reacts with water in the blood or tissue to form dichloroacetic acid and hydrochloric acid. Neutralization reactions are assumed instantaneous in this approach. We validated the mathematical model predictions of temperature using MR thermometry of the thermoembolization procedure performed in ex vivo kidney.Results: Mathematical modeling predictions of tissue death were highly dependent on the vascular geometry, injection pressure, and intrinsic amount of exothermic energy released from the chemical species, and were able to recapitulate the temperature distributions observed in MR thermometry.Conclusion: These efforts present a first step toward formalizing a mathematical model for thermoembolization and are promising for providing insight for delivery protocol optimization. While our approach captured the observed experimental temperature measurements, larger-scale experimental validation is needed to prioritize additional model complexity and fidelity.
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Affiliation(s)
- David Fuentes
- Department of Imaging Physics, Anderson Cancer Center, The University of Texas MD, Houston, TX, USA
- Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Samuel J. Fahrenholtz
- Department of Imaging Physics, Anderson Cancer Center, The University of Texas MD, Houston, TX, USA
| | - Chunxiao Guo
- Department of Interventional Radiology, Anderson Cancer Center, The University of Texas MD, Houston, TX, USA
| | - Christopher J. MacLellan
- Department of Imaging Physics, Anderson Cancer Center, The University of Texas MD, Houston, TX, USA
| | - Rick R. Layman
- Department of Imaging Physics, Anderson Cancer Center, The University of Texas MD, Houston, TX, USA
| | - Beatrice Rivière
- Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - R. Jason Stafford
- Department of Imaging Physics, Anderson Cancer Center, The University of Texas MD, Houston, TX, USA
| | - Erik Cressman
- Department of Interventional Radiology, Anderson Cancer Center, The University of Texas MD, Houston, TX, USA
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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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