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Identification and characterization of a 2,2-dichloropropionic acid (2,2-DCP) degrading alkalotorelant bacterium strain BHS1 isolated from Blue Lake, Turkey Abdul Wahhab, Batool Hazim; Khairul Anuar, Nurul Fatin Syamimi; Abdul Wahab, Roswanira; Al Nimer, Marwan S.M.; Samsulrizal, Nurul HIdayah; Abdul Hamid, Azzmer Azzar; Edbeib, Mohamed Faraj; Kaya, Yilmaz; Huyop, Fahrul
Journal of Tropical Life Science Vol 10, No 3 (2020)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.10.03.08

An acid, 2,2-dichloropropionic acid (2,2-DCP) is an active ingredient in herbicide (DalaponÂ®). Using 2,2-DCP as a model substrate, an alkalotolerant bacterium was successfully isolated from the Blue Lake, Turkey. This bacterium is a potential bioremediation agent of recalcitrant xenobiotic halogenated compounds. This study aimed to prove the efficacy of the alkalotolerance Bacillus megaterium BHS1 in degrading 2,2-DCP as the sole source of carbon. Biolog GEN III system and 16S rRNA analysis were used for the identification of the bacterium. It was discovered that the strain BHS1 is Bacillus megaterium, and the bacterium that was observed to thrive in alkaline conditions (pH 7.0âˆ’14.0), supplemented with varying concentrations of 2,2-DCP (from 20 to 60 mM). Growth of strain BHS1 was exceptional in 40 mM of 2,2-DCP at pH 9, corresponding to a cell doubling time of 17.7 hour, whereas was fully inhibited at 50 mM 2,2-DCP. Since halogenated pollutants can make their way into highly alkaline environments, therefore, identifying threshold levels of strain BHS1 with respect to alkaline-tolerance and maximum level of 2,2-DCP may prove pertinent. This is to ensure that an optimal environment is created for the bacteria to degrade 2,2-DCP-contaminated water. In addition, this is the first study exploring a Bacillus species isolated from an alkaline environment adept in utilizing 2,2-DCP as a sole source of carbon. Hence, the ability of this strain to degrade other types of haloalkanoic acids constitutes a worthy future study.

Molecular Recognition of Polyaromatic Hydrocarbons (PAHs) by Naphthalene Dioxygenase through the Action of Rhamnolipid: PAHs Recognition by NDO with Rhamnolipid Azhary, Nabihah; Abdul Hamid, Azzmer Azzar; Mohd Ashaari, Mardiana
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.01

Rhamnolipids are a type of glycolipid biosurfactant that has garnered significant attention in various industries, including healthcare and petroleum. Their remarkable properties, such as highly biodegradable and good emulsification, have propelled extensive research on their potential role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). While numerous empirical studies have focused on PAH biodegradation, the molecular interactions between biosurfactants and PAHs remain elusive. This study aims to provide insights into the molecular recognition of PAHs by naphthalene dioxygenase (NDO) in the presence of rhamnolipid by molecular docking and molecular dynamics (MD) simulations. The results indicated that selected PAH compounds, phenanthrene (PHE), fluoranthene (FLU), and benzo[a]pyrene (BAP), interact with NDO’s active site mostly through hydrophobic interactions. The presence of rhamnolipid changes NDO’s structural conformation, which leads to a more stable binding between PAHs and NDO, as demonstrated during simulation runs. In addition, the MD simulation analysis by using root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent accessible surface area (SASA), and minimum distance parameters for the systems with rhamnolipid provided better results compared to the system without rhamnolipid, especially for NDO-BAP complex. Moreover, the number of consensuses interacting residues (Phe224, His195, Leu307) for the NDO-BAP complex with rhamnolipid presence was higher compared to without rhamnolipid (Val209, Leu253). Phe224 was identified as a consensus interacting residue for the NDO-BAP complex with rhamnolipid; assuming its important role for substrate binding when rhamnolipid is present. Hence, this study offers molecular insights into the role of biosurfactants during hydrocarbon degradation, especially for high molecular weight PAHs.

Three-Dimensional Structure of Human Epididymis Protein 4 (HE4): A Protein Modelling of an Ovarian Cancer Biomarker Through In Silico Approach: HE4 Protein Structure Modelling and Validation Abdul Rashid, Nur Nadiah; Mohd Nasir, Mohd Hamzah; Hamzah, Nurasyikin; Ismail, Che Muhammad Khairul Hisyam; Nor Hishamuddin, Siti Aishah Sufira; Mohamed Suffian, Izzat Fahimuddin; Abdul Hamid, Azzmer Azzar
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.13

The Human Epididymis Protein 4 (HE4) biomarker has been extensively investigated for its potential in diagnosing ovarian cancer (OC). For the application of diagnostic techniques and drug delivery, it is crucial to understand the protein tertiary structure. However, the Protein Data Bank (PDB) does not currently contain the three-dimensional (3D) structure of HE4. Therefore, an in silico analysis was conducted to model the HE4 protein using AlphaFold, I-TASSER, and Robetta servers, with the sequence retrieved from UniProt (ID: Q14508). These three servers employed deep learning algorithms, threading templates, and de novo methods, respectively. Subsequently, Molecular Dynamics (MD) simulation using the GROMACS software package improved each 3D structure model, resulting in optimised and refined structures: RF1, RF2, and RF3. PROCHECK and ERRAT programmes were employed to assess the structure quality. The Ramachandran plots from PROCHECK indicated that 100% of residues were within the allowed regions for all servers except for I-TASSER. For the refined structures, RF1 and RF3, all residues were concentrated within the allowed regions. According to the ERRAT programme, the RF1 model exhibited the highest overall quality factor of 97.701, followed by RF3 and AlphaFold models with scores of 94.643 and 93.750, respectively. After these validations, RF1 emerged as the most accurately predicted 3D structure of HE4 and has one tunnel identified by CAVER 3.0 tool that facilitates the transportation of small particles to the active site, supported by FTsite and PrankWeb binding site predictions. This model holds potential for various computational studies, including the development of OC diagnostic kits. It will enhance our comprehension of the interactions between the protein and other biomolecules.

Molecular Recognition of Polyaromatic Hydrocarbons (PAHs) by Naphthalene Dioxygenase through the Action of Rhamnolipid: PAHs Recognition by NDO with Rhamnolipid Azhary, Nabihah; Abdul Hamid, Azzmer Azzar; Mohd Ashaari, Mardiana
Journal of Tropical Life Science Vol. 14 No. 3 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.01

Rhamnolipids are a type of glycolipid biosurfactant that has garnered significant attention in various industries, including healthcare and petroleum. Their remarkable properties, such as highly biodegradable and good emulsification, have propelled extensive research on their potential role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). While numerous empirical studies have focused on PAH biodegradation, the molecular interactions between biosurfactants and PAHs remain elusive. This study aims to provide insights into the molecular recognition of PAHs by naphthalene dioxygenase (NDO) in the presence of rhamnolipid by molecular docking and molecular dynamics (MD) simulations. The results indicated that selected PAH compounds, phenanthrene (PHE), fluoranthene (FLU), and benzo[a]pyrene (BAP), interact with NDO’s active site mostly through hydrophobic interactions. The presence of rhamnolipid changes NDO’s structural conformation, which leads to a more stable binding between PAHs and NDO, as demonstrated during simulation runs. In addition, the MD simulation analysis by using root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent accessible surface area (SASA), and minimum distance parameters for the systems with rhamnolipid provided better results compared to the system without rhamnolipid, especially for NDO-BAP complex. Moreover, the number of consensuses interacting residues (Phe224, His195, Leu307) for the NDO-BAP complex with rhamnolipid presence was higher compared to without rhamnolipid (Val209, Leu253). Phe224 was identified as a consensus interacting residue for the NDO-BAP complex with rhamnolipid; assuming its important role for substrate binding when rhamnolipid is present. Hence, this study offers molecular insights into the role of biosurfactants during hydrocarbon degradation, especially for high molecular weight PAHs.

Three-Dimensional Structure of Human Epididymis Protein 4 (HE4): A Protein Modelling of an Ovarian Cancer Biomarker Through In Silico Approach: HE4 Protein Structure Modelling and Validation Abdul Rashid, Nur Nadiah; Mohd Nasir, Mohd Hamzah; Hamzah, Nurasyikin; Ismail, Che Muhammad Khairul Hisyam; Nor Hishamuddin, Siti Aishah Sufira; Mohamed Suffian, Izzat Fahimuddin; Abdul Hamid, Azzmer Azzar
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.13

The Human Epididymis Protein 4 (HE4) biomarker has been extensively investigated for its potential in diagnosing ovarian cancer (OC). For the application of diagnostic techniques and drug delivery, it is crucial to understand the protein tertiary structure. However, the Protein Data Bank (PDB) does not currently contain the three-dimensional (3D) structure of HE4. Therefore, an in silico analysis was conducted to model the HE4 protein using AlphaFold, I-TASSER, and Robetta servers, with the sequence retrieved from UniProt (ID: Q14508). These three servers employed deep learning algorithms, threading templates, and de novo methods, respectively. Subsequently, Molecular Dynamics (MD) simulation using the GROMACS software package improved each 3D structure model, resulting in optimised and refined structures: RF1, RF2, and RF3. PROCHECK and ERRAT programmes were employed to assess the structure quality. The Ramachandran plots from PROCHECK indicated that 100% of residues were within the allowed regions for all servers except for I-TASSER. For the refined structures, RF1 and RF3, all residues were concentrated within the allowed regions. According to the ERRAT programme, the RF1 model exhibited the highest overall quality factor of 97.701, followed by RF3 and AlphaFold models with scores of 94.643 and 93.750, respectively. After these validations, RF1 emerged as the most accurately predicted 3D structure of HE4 and has one tunnel identified by CAVER 3.0 tool that facilitates the transportation of small particles to the active site, supported by FTsite and PrankWeb binding site predictions. This model holds potential for various computational studies, including the development of OC diagnostic kits. It will enhance our comprehension of the interactions between the protein and other biomolecules.

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