Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey

References

• Adamu, A., Shamsir, M. S., Wahab, R. A., Parvizpour, S., & Huyop, F. (2017). Multi-template homology-based structural model of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1. Journal of Biomolecular Structure & Dynamics, 35(15), 3285–3296. https://doi.org/10.1080/07391102.2016.1254115
   PubMed Web of Science ®Google Scholar
• Adamu, A., Wahab, R. A., & Huyop, F. (2016). l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1. Springer Plus, 5(1), 695. https://doi.org/10.1186/s40064-016-2328-9
   PubMedGoogle Scholar
• Ang, T. F., Maiangwa, J., Salleh, A. B., Normi, Y. M., & Leow, T. C. (2018). Dehalogenases: From improved performance to potential microbial dehalogenation applications. Molecules, 23(5), 1100. https://doi.org/10.3390/molecules23051100
   PubMed Web of Science ®Google Scholar
• Anuar, N. F. S. K., Wahab, R. A., Huyop, F., Halim, K. B. A., & Hamid, A. A. A. (2020). In silico mutation on a mutant lipase from Acinetobacter haemolyticus towards enhancing alkaline stability. Journal of Biomolecular Structure & Dynamics, 38(15), 4493–4507. https://doi.org/10.1080/07391102.2019.1683074
   PubMed Web of Science ®Google Scholar
• Bahaman, A. H., Wahab, R. A., Abdul Hamid, A. A., Abd Halim, K. B., & Kaya, Y. (2021). 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. Journal of Biomolecular Structure & Dynamics, 39(7), 2628–2641. https://doi.org/10.1080/07391102.2020.1751713
   PubMed Web of Science ®Google Scholar
• Baig, M. H., Sudhakar, D. R., Kalaiarasan, P., Subbarao, N., Wadhawa, G., Lohani, M., Khan, M. K. A., & Khan, A. U. (2014). Insight into the effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase: A molecular dynamics study. PloS One, 9(12), e112456. https://doi.org/10.1371/journal.pone.0112456
   PubMed Web of Science ®Google Scholar
• Basri, D. F., Shabry, A. S. M., & Meng, C. K. (2015). Leaves extract from Canarium odontophyllum Miq.(dabai) exhibits cytotoxic activity against human colorectal cancer cell HCT 116. Natural Products Chemistry and Research, 3(2), 1–4.
   Google Scholar
• Batumalaie, K., Edbeib, M. F., Mahat, N. A., Huyop, F., & Wahab, R. A. (2018). In silico and empirical approaches toward understanding the structural adaptation of the alkaline-stable lipase KV1 from Acinetobacter haemolyticus. Journal of Biomolecular Structure & Dynamics, 36(12), 3077–3093. https://doi.org/10.1080/07391102.2017.1377635
   PubMed Web of Science ®Google Scholar
• Cairns, S. S., Cornish, A., & Cooper, R. A. (1996). Cloning, Sequencing and expression in Escherichia coli of two Rhizobium sp. genes encoding haloalkanoate dehalogenases of opposite stereospecificity. European Journal of Biochemistry, 235(3), 744–749. https://doi.org/10.1111/j.1432-1033.1996.t01-1-00744.x
   PubMedGoogle Scholar
• Edbeib, M. F., Aksoy, H. M., Kaya, Y., Wahab, R. A., & Huyop, F. (2020a). Haloadaptation: Insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases. Journal of Biomolecular Structure & Dynamics, 38(12), 3452–3461. https://doi.org/10.1080/07391102.2019.1657498
   PubMed Web of Science ®Google Scholar
• Edbeib, M. F., Wahab, R. A., Huyop, F. Z., Aksoy, H. M., & Kaya, Y. (2020b). Further analysis of Burkholderia pseudomallei MF2 and identification of putative dehalogenase gene by PCR. Indonesian Journal of Chemistry, 20(2), 386–394. https://doi.org/10.22146/ijc.43262
   Web of Science ®Google Scholar
• Fan, H., & Mark, A. E. (2004). Refinement of homology‐based protein structures by molecular dynamics simulation techniques. Protein Science: A Publication of the Protein Society, 13(1), 211–220. https://doi.org/10.1110/ps.03381404
   PubMed Web of Science ®Google Scholar
• Feig, M. (2017). Computational protein structure refinement: Almost there, yet still so far to go. Wiley Interdisciplinary Reviews: Computational Molecular Science, 7(3), e1307. https://doi.org/10.1002/wcms.1307
   PubMed Web of Science ®Google Scholar
• Flannelly, D. F., Aoki, T. G., & Aristilde, L. (2015). Short-time dynamics of pH-dependent conformation and substrate binding in the active site of beta-glucosidases: A computational study. Journal of Structural Biology, 191(3), 352–364. https://doi.org/10.1016/j.jsb.2015.07.002
   PubMed Web of Science ®Google Scholar
• Fortin, N., Fulthorpe, R. R., Allen, D. G., & Greer, C. W. (1998). Molecular analysis of bacterial isolates and total community DNA from kraft pulp mill effluent treatment systems. Canadian Journal of Microbiology, 44(6), 537–546. https://doi.org/10.1139/w98-036
   PubMed Web of Science ®Google Scholar
• Fu, Y., Zhao, J., & Chen, Z. (2018). Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: A case of oligopeptide binding protein. Computational and Mathematical Methods in Medicine, 2018, 1–12. https://doi.org/10.1155/2018/3502514
   Web of Science ®Google Scholar
• Fuentes, D., Muñoz, N. M., Guo, C., Polak, U., Minhaj, A. A., Allen, W. J., Gustin, M. C., & Cressman, E. N. (2018). A molecular dynamics approach towards evaluating osmotic and thermal stress in the extracellular environment. International Journal of Hyperthermia: The Official Journal of European Society for Hyperthermic Oncology, North American Hyperthermia Group, 35(1), 559–567. https://doi.org/10.1080/02656736.2018.1512161
   PubMed Web of Science ®Google Scholar
• Hamid, A., Wong, E. L., Joyce-Tan, K. H., Shamsir, M. S., Haziyamin, T., Hamid, T. A., & Huyop, F. (2013). Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-CP. Biotechnology & Biotechnological Equipment, 27(2), 3725–3736. https://doi.org/10.5504/BBEQ.2012.0142
   Web of Science ®Google Scholar
• Harisna, A. H., Edbeib, M. F., Adamu, A., Hamid, A. A. A., Wahab, R. A. B., & Huyop, F. (2017). In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1. Malaysian Journal of Microbiology, 13(1), 50–60., https://doi.org/10.21161/mjm.90116
   Google Scholar
• Hisano, T., Hata, Y., Fujii, T., Liu, J.-Q., Kurihara, T., Esaki, N., & Soda, K. (1996). Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL AN α/β hydrolase structure that is different from the α/β hydrolase fold. The Journal of Biological Chemistry, 271(34), 20322–20330. https://doi.org/10.1074/jbc.271.34.20322
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Huyop, F., Jing, N. H., & Cooper, R. A. (2008). Overexpression, purification and analysis of dehalogenase D of Rhizobium sp. Canadian Journal of Pure and Applied Sciences, 2(2), 389–392.
   Google Scholar
• Huyop, F. Z., Tan, Y. Y., & Ismail, M. (2004). Overexpression and characterisation of non-stereospecific haloacid Dehalogenase E (DehE) of Rhizobium sp. Asia Pacific Journal of Molecular Biology and Biotechnology, 12(1 & 2), 15–20.
   Google Scholar
• Isa, M. A., Mustapha, A., Qazi, S., Raza, K., Allamin, I. A., Ibrahim, M. M., & Mohammed, M. M. (2022). In silico molecular docking and molecular dynamic simulation of potential inhibitors of 3C-like main proteinase (3CLpro) from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) using selected African medicinal plants. Advances in Traditional Medicine, 22(1), 107–123. https://doi.org/10.1007/s13596-020-00523-w
   Google Scholar
• Ismail, S. N. F., Edbeib, M. F., Wahab, R. A., & Huyop, F. (2018). Purification and characterization of dehalogenase from Bacillus cereus SN1 isolated from cow dung. Malaysian Journal of Microbioliogy, 14(3), 244–253.
   Google Scholar
• Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583–589. https://doi.org/10.1038/s41586-021-03819-2
   PubMed Web of Science ®Google Scholar
• Khersonsky, O., Lipsh, R., Avizemer, Z., Ashani, Y., Goldsmith, M., Leader, H., Dym, O., Rogotner, S., Trudeau, D. L., Prilusky, J., Amengual-Rigo, P., Guallar, V., Tawfik, D. S., & Fleishman, S. J. (2018). Automated design of efficient and functionally diverse enzyme repertoires. Molecular Cell, 72(1), 178–186.e5. e175. https://doi.org/10.1016/j.molcel.2018.08.033
   PubMed Web of Science ®Google Scholar
• Kumar, C. V., Swetha, R. G., Anbarasu, A., & Ramaiah, S. (2014). Computational analysis reveals the association of threonine 118 methionine mutation in PMP22 resulting in CMT-1A. Advances in Bioinformatics, 2014, 1–10. https://doi.org/10.1155/2014/502618
   Google Scholar
• Landa-Acuña, D., Acosta, R. A. S., Hualpa Cutipa, E., Vargas de la Cruz, C., & Luis Alaya, B. (2020). Bioremediation: A low-cost and clean-green technology for environmental management. Microbial bioremediation and biodegradation (pp. 153–171). Springer.
   Google Scholar
• Larsson, P., Wallner, B., Lindahl, E., & Elofsson, A. (2008). Using multiple templates to improve quality of homology models in automated homology modeling. Protein Science: A Publication of the Protein Society, 17(6), 990–1002. https://doi.org/10.1110/ps.073344908
   PubMed Web of Science ®Google Scholar
• Lee, H. S., Qi, Y., & Im, W. (2015). Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study. Scientific Reports, 5(1), 1–7. https://doi.org/10.1038/srep08926
   Google Scholar
• Lemmon, G., & Meiler, J. (2013). Towards ligand docking including explicit interface water molecules. PLoS One, 8(6), e67536. https://doi.org/10.1371/journal.pone.0067536
   PubMed Web of Science ®Google Scholar
• Liao, K. H., Chen, K.-B., Lee, W.-Y., Sun, M.-F., Lee, C.-C., & Chen, C. Y.-C. (2014). Ligand-based and structure-based investigation for Alzheimer’s disease from traditional Chinese medicine. Evidence-Based Complementary and Alternative Medicine: eCAM, 2014, 364819. https://doi.org/10.1155/2014/364819
   PubMed Web of Science ®Google Scholar
• Lobanov, M. Y., Bogatyreva, N., & Galzitskaya, O. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., Oostenbrink, C., & Mark, A. E. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037. https://doi.org/10.1021/ct200196m
   PubMed Web of Science ®Google Scholar
• Marianayagam, N. J., Sunde, M., & Matthews, J. M. (2004). The power of two: Protein dimerization in biology. Trends in Biochemical Sciences, 29(11), 618–625. https://doi.org/10.1016/j.tibs.2004.09.006
   PubMed Web of Science ®Google Scholar
• Mishra, R., Mazumder, A., Mazumder, R., Mishra, P. S., & Chaudhary, P. (2019). Docking study and result conclusion of heterocyclic derivatives having urea and acyl moiety. Asian Journal of Biomedical and Pharmaceutical Sciences, 9(67), 13. https://doi.org/10.35841/2249-622X.67.19-082
   Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Muslem, W. H., Edbeib, M. F., Wahab, R. A., Khalili, E., Zakaria, I. I., & Huyop, F. (2017). The potential of a novel β-specific dehalogenase from Bacillus cereus WH2 as a bioremediation agent for the removal of β-haloalkanoic acids. Malaysian Journal of Microbiology, 13(4), 298–307. https://doi.org/10.21161/mjm.98816
   Web of Science ®Google Scholar
• Nakamura, T., Yamaguchi, A., Kondo, H., Watanabe, H., Kurihara, T., Esaki, N., Hirono, S., & Tanaka, S. (2009). Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and AB initio fragment molecular orbital calculations. Journal of Computational Chemistry, 30(16), 2625–2634. https://doi.org/10.1002/jcc.21273
   PubMed Web of Science ®Google Scholar
• Nardi-Dei, V., Kurihara, T., Park, C., Esaki, N., & Soda, K. (1997). Bacterial DL-2-haloacid dehalogenase from Pseudomonas sp. strain 113: Gene cloning and structural comparison with D-and L-2-haloacid dehalogenases. Journal of Bacteriology, 179(13), 4232–4238. https://doi.org/10.1128/jb.179.13.4232-4238.1997
   PubMed Web of Science ®Google Scholar
• Nemati, M., Abdulghader, M. F., Gicana, R. G., Lamis, R. J. S., Ibrahim, N., & Hamid, A. A. A., Huyop, F. (2013). Identification of putative Cof-like hydrolase associated with dehalogenase in Enterobacter cloacae MN1 isolated from the contaminated sea-side area of the Philippines. Malaysian Journal of Microbiology, 9(3), 253–259., https://doi.org/10.21161/mjm.51113
   Google Scholar
• Oyewusi, H. A., Akinyede, K. A., Wahab, R. A., & Huyop, F. (2021b). In silico analysis of predicted dehalogenase from the marine Halomonas smyrnensis AAD6T genome in relation to its bioremediation potential. Journal of Biomolecular Structure and Dynamics, 1–17.
   Web of Science ®Google Scholar
• Oyewusi, H. A., Huyop, F., & Wahab, R. A. (2020c). Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. Journal of Biomolecular Structure and Dynamics, 40(5), 1979–1994. https://doi.org/10.1080/07391102.2020.1835727
   PubMed Web of Science ®Google Scholar
• Oyewusi, H. A., Huyop, F., Wahab, R. A., & Hamid, A. A. A. (2021c). In silico assessment of dehalogenase from Bacillus thuringiensis H2 in relation to its salinity-stability and pollutants degradation. Journal of Biomolecular Structure and Dynamics, 40(19), 9332–9346. https://doi.org/10.1080/07391102.2021.1927846
   PubMed Web of Science ®Google Scholar
• Oyewusi, H. A., Wahab, R. A., & Huyop, F. (2020b). Dehalogenase-producing halophiles and their potential role in bioremediation. Marine Pollution Bulletin, 160, 111603. https://doi.org/10.1016/j.marpolbul.2020.111603
   PubMed Web of Science ®Google Scholar
• Oyewusi, H. A., Wahab, R. A., & Huyop, F. (2021a). Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria. Molecular Biology Reports, 48(3), 2687–2701. https://doi.org/10.1007/s11033-021-06239-7
   PubMed Web of Science ®Google Scholar
• Oyewusi, H. A., Wahab, R. A., Kaya, Y., Edbeib, M. F., & Huyop, F. (2020a). Alternative bioremediation agents against haloacids, haloacetates and chlorpyrifos using novel halogen-degrading bacterial isolates from the hypersaline lake Tuz. Catalysts, 10(6), 651. https://doi.org/10.3390/catal10060651
   Web of Science ®Google Scholar
• Park, H., Ovchinnikov, S., Kim, D. E., DiMaio, F., & Baker, D. (2018). Protein homology model refinement by large-scale energy optimization. Proceedings of the National Academy of Sciences of the United States of America, 115(12), 3054–3059. https://doi.org/10.1073/pnas.1719115115
   PubMed Web of Science ®Google Scholar
• Pontius, J., Richelle, J., & Wodak, S. J. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology, 264(1), 121–136. https://doi.org/10.1006/jmbi.1996.0628
   PubMed Web of Science ®Google Scholar
• Ridder, I. S., Rozeboom, H. J., Kingma, J., Janssen, D. B., & Dijkstra, B. W. (1995). Crystallization and preliminary X-ray analysis of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10. Protein Science, 4(12), 2619–2620. https://doi.org/10.1002/pro.5560041220
   PubMed Web of Science ®Google Scholar
• Rosdi, M. N. M., Arif, S. M., Bakar, M. H. A., Razali, S. A., Zulkifli, R. M., & Ya’akob, H. (2018). Molecular docking studies of bioactive compounds from Annona muricata Linn as potential inhibitors for Bcl-2, Bcl-w and Mcl-1 antiapoptotic proteins. Apoptosis: An International Journal on Programmed Cell Death, 23(1), 27–40. https://doi.org/10.1007/s10495-017-1434-7
   PubMed Web of Science ®Google Scholar
• Ruvinsky, A. M., Kirys, T., Tuzikov, A. V., & Vakser, I. A. (2012). Structure fluctuations and conformational changes in protein binding. Journal of Bioinformatics and Computational Biology, 10(2), 1241002. https://doi.org/10.1142/S0219720012410028
   PubMed Web of Science ®Google Scholar
• Rye, C. A., Isupov, M. N., Lebedev, A. A., & Littlechild, J. A. (2009). Biochemical and structural studies of a L-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii. Extremophiles: Life under Extreme Conditions, 13(1), 179–190. https://doi.org/10.1007/s00792-008-0208-0
   PubMed Web of Science ®Google Scholar
• Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein–ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/10.1093/nar/gkv315
   PubMed Web of Science ®Google Scholar
• Schmidberger, J. W., Oakley, A. J., Tsang, J. S., & Wilce, M. C. (2005). Purification, crystallization and preliminary crystallographic analysis of DehIVa, a dehalogenase from Burkholderia cepacia MBA4. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications, 61(Pt 3), 271–273. https://doi.org/10.1107/S1744309105002472
   PubMedGoogle Scholar
• Schmidberger, J. W., Wilce, J. A., Tsang, J. S., & Wilce, M. C. (2007). Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4. Journal of Molecular Biology, 368(3), 706–717. https://doi.org/10.1016/j.jmb.2007.02.015
   PubMed Web of Science ®Google Scholar
• Senior, A. W., Evans, R., Jumper, J., Kirkpatrick, J., Sifre, L., Green, T., Qin, C., Žídek, A., Nelson, A. W. R., Bridgland, A., Penedones, H., Petersen, S., Simonyan, K., Crossan, S., Kohli, P., Jones, D. T., Silver, D., Kavukcuoglu, K., & Hassabis, D. (2020). Improved protein structure prediction using potentials from deep learning. Nature, 577(7792), 706–710. https://doi.org/10.1038/s41586-019-1923-7
   PubMed Web of Science ®Google Scholar
• Shen, J., Zhang, W., Fang, H., Perkins, R., Tong, W., & Hong, H. (2013). Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes [Paper presentation].Paper Presented at the BMC Bioinformatics,. https://doi.org/10.1186/1471-2105-14-S14-S6
   Google Scholar
• Slater, J. H., Bull, A. T., & Hardman, D. J. (1995). Microbial dehalogenation. Biodegradation, 6(3), 181–189. https://doi.org/10.1007/BF00700456
   Web of Science ®Google Scholar
• Śledź, P., & Caflisch, A. (2018). Protein structure-based drug design: From docking to molecular dynamics. Current Opinion in Structural Biology, 48, 93–102. https://doi.org/10.1016/j.sbi.2017.10.010
   PubMed Web of Science ®Google Scholar
• Stringfellow, J. M., Cairns, S. S., Cornish, A., & Cooper, R. A. (1997). Haloalkanoate dehalogenase II (DehE) of a Rhizobium sp.-molecular analysis of the gene and formation of carbon monoxide from trihaloacetate by the enzyme. European Journal of Biochemistry, 250(3), 789–793. https://doi.org/10.1111/j.1432-1033.1997.00789.x
   PubMedGoogle Scholar
• Sudi, I. Y., Hamid, A. A. A., Shamsir, M. S., Jamaluddin, H., Wahab, R. A., & Huyop, F. (2014). Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D- and L-2-chloropropionate. Biotechnology, Biotechnological Equipment, 28(4), 608–615. https://doi.org/10.1080/13102818.2014.937907
   PubMed Web of Science ®Google Scholar
• Thasif, S., Hamdan, S., & Huyop, F. (2009). Degradation of D, L-2-chloropropionic acid by bacterial dehalogenases that shows stereospecificity and its partial enzymatic characteristics. Biotechnology 8(2), 264–269. https://doi.org/10.3923/biotech.2009.264.269
   Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Wahhab, B. H. A., Anuar, N. F. S. K., Wahab, R. A., A., Nimer, M. S., Samsulrizal, Nh, Hamid, A. A. A., Edbeib, M. F., Kaya, Y., & Huyop, F. (2020). Identification and characterization of a 2, 2-dichloropropionic acid (2, 2-DCP) degrading alkalotorelant bacterium strain BHS1 isolated from Blue Lake Turkey. Journal of Tropical Life Science, 10(3), 245–252.
   Google Scholar
• Wang, Y., Feng, Y., Cao, X., Liu, Y., & Xue, S. (2018). Insights into the molecular mechanism of dehalogenation catalyzed by D-2-haloacid dehalogenase from crystal structures. Scientific Reports, 8(1), 1454. https://doi.org/10.1038/s41598-017-19050-x
   PubMed Web of Science ®Google Scholar
• Xu, Z., Yang, Y., & Huang, B. (2017). A teaching approach from the exhaustive search method to the Needleman–Wunsch algorithm. Biochemistry and Molecular Biology Education: A Bimonthly Publication of the International Union of Biochemistry and Molecular Biology, 45(3), 194–204. https://doi.org/10.1002/bmb.21027
   PubMed Web of Science ®Google Scholar
• Yang, J., & Zhang, Y. (2015). I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Research, 43(W1), W174–W181. https://doi.org/10.1093/nar/gkv342
   PubMed Web of Science ®Google Scholar
• Zakary, S., Mashal, H., Osmani, A. R., Oyewusi, H. A., Huyop, F., & Nasim, M. M, (2022). In silico molecular characterization of a putative haloacid dehalogenase Type II from genomic of Mesorhizobium loti strain TONO: In silico molecular characterization of a putative haloacid dehalogenase Type II. Journal of Tropical Life Science, 12(2), 241–252. https://doi.org/10.11594/jtls.12.02.10
   Google Scholar