Crystal structure analysis and molecular dynamics simulations of arginase from Thermus thermophilus

References

• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Ash, D. E. (2004). Structure and function of arginases. The Journal of Nutrition, 134(10 Suppl), 2760S–2767S. https://doi.org/10.1093/jn/134.10.2760S
   PubMed Web of Science ®Google Scholar
• Balamurugan, B., Roshan, M. N. A. M., Shaahul Hameed, B., Sumathi, K., Senthilkumar, R., Udayakumar, A., Venkatesh Babu, K. H., Kalaivani, M., Sowmiya, G., Sivasankari, P., Saravanan, S., Vasuki Ranjani, C., Gopalakrishnan, K., Selvakumar, K. N., Jaikumar, M., Brindha, T., Michael, D., & Sekar, K. (2007). PSAP: protein structure analysis package. Journal of Applied Crystallography, 40(4), 773–777. https://doi.org/10.1107/S0021889807021875
   Web of Science ®Google Scholar
• Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS A message passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• Bewley, M. C., & Flanagan, J. M. (2011). Arginase. Encyclopedia of Inorganic and Bioinorganic Chemistry. John Wiley and Sons, Inc.
   Google Scholar
• Bewley, M. C., Jeffrey, P. D., Patchett, M. L., Kanyo, Z. F., & Baker, E. N. (1999). Crystal structures of Bacillus caldovelox arginase in complex with substrate and inhibitors reveal new insights into activation, inhibition and catalysis in the arginase superfamily. Structure (London, England : 1993), 7(4), 435–448. https://doi.org/10.1016/S0969-2126(99)80056-2
   PubMed Web of Science ®Google Scholar
• Brunger, A. T. (2007). Version 1.2 of the Crystallography and NMR system. Nature Protocols, 2(11), 2728–2733. https://doi.org/10.1038/nprot.2007.406
   PubMed Web of Science ®Google Scholar
• Caldwell, R. W., Rodriguez, P. C., Toque, H. A., Narayanan, S. P., & Caldwell, R. B. (2018). Arginase: A multifaceted enzyme important in health and disease. Physiological Reviews, 98(2), 641–665.
   PubMed Web of Science ®Google Scholar
• Christianson, D. W. (2005). Arginase: Structure, mechanism, and physiological role in male and female sexual arousal. Accounts of Chemical Research, 38(3), 191–201. https://doi.org/10.1021/ar040183k
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (1998). The PyMOL molecular graphics system. http://www.pymol.org.
   Google Scholar
• Dowling, D. P., Di Costanzo, L., Gennadios, H. A., & Christianson, D. W. (2008). Evolution of the arginase fold and functional diversity. Cellular and Molecular Life Sciences : CMLS, 65(13), 2039–2055.
   PubMed Web of Science ®Google Scholar
• Dumorné, K., Córdova, D. C., Astorga-Eló, M., & Renganathan, P. (2017). Extremozymes: A potential source for industrial applications. Journal of Microbiology and Biotechnology, 27(4), 649–659.
   PubMed Web of Science ®Google Scholar
• Emsley, P., & Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 12 Pt 1), 2126–2132.
   PubMedGoogle Scholar
• Henne, A., Brüggemann, H., Raasch, C., Wiezer, A., Hartsch, T., Liesegang, H., Johann, A., Lienard, T., Gohl, O., Martinez-Arias, R., Jacobi, C., Starkuviene, V., Schlenczeck, S., Dencker, S., Huber, R., Klenk, H. P., Kramer, W., Merkl, R., Gottschalk, G., & Fritz, H. J. (2004). The genome sequence of the extreme thermophile Thermus thermophilus. Nature Biotechnology, 22(5), 547–553.
   PubMed Web of Science ®Google Scholar
• Holm, L., & Rosenström, P. (2010). Dali server: conservation mapping in 3D. Nucleic Acids Research, 38(Web Server issue), W545–549.
   PubMed Web of Science ®Google Scholar
• Huang, K., Zhang, S., Guan, X., Liu, J., Li, S., & Song, H. (2020). Thermostable arginase from Sulfobacillus acidophilus with neutral pH optimum applied for high-efficiency L-ornithine production. Applied Microbiology and Biotechnology, 104(15), 6635–6646.
   PubMedGoogle Scholar
• Huang, K., Zhang, T., Jiang, B., Mu, W., & Miao, M. (2016). Characterization of a thermostable arginase from Rummeliibacillus pycnus SK31.001. Journal of Molecular Catalysis B: Enzymatic, 133, S68–S75. https://doi.org/10.1016/j.molcatb.2016.11.020
   Google Scholar
• Hünenberger, P. H. (2005). Thermostat algorithms for molecular dynamics simulations. In C. Holm, K. Kremer (Eds.), Advanced computer simulation. Advances in polymer science. Vol. 173. Springer.
   Google Scholar
• Ivanenkov, Y. A., & Chufarova, N. V. (2014). Small-molecule arginase inhibitors. Pharmaceutical Patent Analyst, 3(1), 65–85.
   PubMedGoogle Scholar
• Kleiger, G., & Eisenberg, D. (2002). GXXXG and GXXXA motifs stabilize FAD and NAD(P)-binding Rossmann folds through C(alpha)-H… O hydrogen bonds and Van der Waals interactions. Journal of Molecular Biology, 323(1), 69–76. https://doi.org/10.1016/S0022-2836(02)00885-9
   PubMed Web of Science ®Google Scholar
• Li, M., Qin, J., Xiong, K., Jiang, B., & Zhang, T. (2022). Review of arginase as a promising biocatalyst: characteristics, preparation, applications and future challenges. Critical reviews in biotechnology, 42(5), 651–667. https://doi.org/10.1080/07388551.2021.1947962
   Google Scholar
• López-López, O., Cerdán, M.-E., & González-Siso, M.-I. (2015). Thermus thermophilus as a Source of Thermostable Lipolytic Enzymes. Microorganisms, 3(4), 792–808.
   PubMedGoogle Scholar
• Mahmoudi, M., Arab, A. A., Zahiri, J., & Parandian, Y. (2016). An overview of the protein thermostability prediction: Databases and tools. Journal of Nanomedicine Research, 3(6), 00072.
   Google Scholar
• Nose, S., & Klein, M. L. (1983). Constant pressure molecular-dynamics for molecular-systems. Molecular Physics, 50(5), 1055–1076. https://doi.org/10.1080/00268978300102851
   Web of Science ®Google Scholar
• Otwinowski, Z., & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods in Enzymology, 276, 307–326. [Database] https://doi.org/10.1016/S0076-6879(97)76066-X
   PubMed Web of Science ®Google Scholar
• Pucci, F., Kwasigroch, J. M., & Rooman, M. (2017). SCooP: an accurate and fast predictor of protein stability curves as a function of temperature. Bioinformatics (Oxford, England), 33(21), 3415–3422. https://doi.org/10.1093/bioinformatics/btx417
   PubMed Web of Science ®Google Scholar
• Sabnis, R. W. (2020). Novel arginase inhibitors for treating cancer and respiratory inflammatory diseases. ACS Medicinal Chemistry Letters, 11(12), 2370–2371. https://doi.org/10.1021/acsmedchemlett.0c00593
   PubMedGoogle Scholar
• Sin, Y. Y., Baron, G., Schulze, A., & Funk, C. D. (2015). Arginase-1 deficiency. Journal of Molecular Medicine (Berlin, Germany), 93(12), 1287–1296.
   PubMed Web of Science ®Google Scholar
• Song, W., Niu, P., Chen, X., & Liu, L. (2014). Enzymatic production of L-ornithine from L-arginine with recombinant thermophilic arginase. Journal of Molecular Catalysis B: Enzymatic, 110, 1–7. https://doi.org/10.1016/j.molcatb.2014.09.005
   Google Scholar
• Vagin, A., & Teplyakov, A. (1997). MOLREP: An automated program for molecular replacement. Journal of Applied Crystallography, 30(6), 1022–1025. https://doi.org/10.1107/S0021889897006766
   Google Scholar
• Zhang, X., Liu, J., Yu, X., Wang, F., Yi, L., Li, Z., Liu, Y., & Ma, L. (2015). High-level expression of human arginase I in Pichia pastoris and its immobilization on chitosan to produce L-ornithine. BMC Biotechnology, 15, 66.
   PubMed Web of Science ®Google Scholar