References
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
- Adamcsek, B., Palla, G., Farkas, I. J., Derényi, I., & Vicsek, T. (2006). CFinder: Locating cliques and overlapping modules in biological networks. Bioinformatics (Oxford, England), 22(8), 1021–1023. https://doi.org/10.1093/bioinformatics/btl039
- Alponti, J. S., Fonseca Maldonado, R., & Ward, R. J. (2016). Thermostabilization of Bacillus subtilis GH11 xylanase by surface charge engineering. International Journal of Biological Macromolecules, 87, 522–528. https://doi.org/10.1016/j.ijbiomac.2016.03.003
- Bateman, A. (2019). UniProt: A worldwide hub of protein knowledge. Nucleic Acids Research, 47(D1), D506–D515. https://doi.org/10.1093/nar/gky1049
- Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D., & Zardecki, C. (2002). The protein data bank. Acta Crystallographica. Section D, Biological Crystallography, 58(Pt 6 No 1), 899–907. https://doi.org/10.1107/s0907444902003451
- Bhat, S. K., Purushothaman, K., Kini, K. R., & Gopala Rao Appu Rao, A. R. (2021). Design of mutants of GH11 xylanase from Bacillus pumilus for enhanced stability by amino acid substitutions in the N-terminal region: An in silico analysis. Journal of Biomolecular Structure and Dynamics, Mar 22:1–14. https://doi.org/10.1080/07391102.2021.1899988
- Bjellqvist, B., Basse, B., Olsen, E., & Celis, J. E. (1994). Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis, 15(3–4), 529–539. https://doi.org/10.1002/elps.1150150171
- Collins, T., Gerday, C., & Feller, G. (2005). Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiology Reviews, 29(1), 3–23. https://doi.org/10.1016/j.femsre.2004.06.005
- Cui, H., Eltoukhy, L., Zhang, L., Markel, U., Jaeger, K. E., Davari, M. D., & Schwaneberg, U. (2021). Less unfavorable salt bridges on the enzyme surface result in more organic cosolvent resistance. Angewandte Chemie (International ed. in English), 60(20), 11448–11456. https://doi.org/10.1002/anie.202101642
- Dumon, C., Varvak, A., Wall, M. A., Flint, J. E., Lewis, R. J., Lakey, J. H., Morland, C., Luginbühl, P., Healey, S., Todaro, T., DeSantis, G., Sun, M., Parra-Gessert, L., Tan, X., Weiner, D. P., & Gilbert, H. J. (2008). Engineering hyperthermostability into a GH11 xylanase is mediated by subtle changes to protein structure. The Journal of Biological Chemistry, 283(33), 22557–22564. https://doi.org/10.1074/jbc.M800936200
- Garcia-Campayo, V., Mccrae, S., Zhang, J., Flint, H. J., & Wood, T. M. (1993). Mode of action, kinetic properties and physicochemical characterization of two different domains of a bifunctional (1--> 4)-beta-D-xylanase from Ruminococcus flavefaciens expressed separately in Escherichia coli. 296(Pt 1), 235–243.
- Ge, M., Xia, X., & Pan, X. (2008). Salt bridges in the hyperthermophilic protein Ssh10b are resilient to temperature increases. The Journal of Biological Chemistry, 283(46), 31690–31696. https://doi.org/10.1074/jbc.M805750200
- Gouet, P., Robert, X., & Courcelle, E. (2003). ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Research, 31(13), 3320–3323. https://doi.org/10.1093/nar/gkg556
- Hakulinen, N., Turunen, O., Jänis, J., Leisola, M., & Rouvinen, J. (2003). Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability. European Journal of Biochemistry, 270(7), 1399–1412. https://doi.org/10.1046/j.1432-1033.2003.03496.x
- Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). Trabajo práctico No 13. Varianzas en función de variable independiente categórica. Nature Protocols, 10(6), 845–858. https://doi.org/10.1038/nprot.2015-053
- Kim, T., Chan, J., & Je, Y. (2012). Hydrophobic interaction network analysis for thermostabilization of a mesophilic xylanase. Journal of Biotechnology, 161(1), 49–59. https://doi.org/10.1016/j.jbiotec.2012.04.015
- Krska, D., & Larsbrink, J. (2020). Investigation of a thermostable multi-domain xylanase-glucuronoyl esterase enzyme from Caldicellulosiruptor kristjanssonii incorporating multiple carbohydrate-binding modules. Biotechnology for Biofuels, 13(1), 68–13. https://doi.org/10.1186/s13068-020-01709-9
- Lee, C., Wang, H., Hwang, J., & Tseng, C. (2014). Protein thermal stability enhancement by designing salt bridges: A combined computational and experimental study. 9(11), e11275. https://doi.org/10.1371/journal.pone.0112751
- Li, H., Kankaanpää, A., Xiong, H., Hummel, M., Sixta, H., Ojamo, H., & Turunen, O. (2013). Thermostabilization of extremophilic Dictyoglomus thermophilum GH11 xylanase by an N-terminal disulfide bridge and the effect of ionic liquid [emim]OAc on the enzymatic performance. Enzyme and Microbial Technology, 53(6–7), 414–419. https://doi.org/10.1016/j.enzmictec.2013.09.004
- Notredame, C., Higgins, D. G., & Heringa, J. (2000). T-coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1), 205–217. https://doi.org/10.1006/jmbi.2000.4042
- Paës, G., Berrin, J.-G., & Beaugrand, J. (2012). GH11 xylanases: Structure/function/properties relationships and applications. Biotechnology Advances, 30(3), 564–592. https://doi.org/10.1016/j.biotechadv.2011.10.003
- Paës, G., Cortés, J., Siméon, T., Donohue, M. J. O., & Tran, V. (2012). Thumb-loops up for catalysis: A structure/function investigation of a functional loop movement in a GH11 xylanase. Computational and Structural Biotechnology, 1(2), 1–10. https://doi.org/10.5936/csbj.201207001
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera: A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
- Purmonen, M., Valjakka, J., Takkinen, K., Laitinen, T., & Rouvinen, J. (2007). Molecular dynamics studies on the thermostability of family 11 xylanases. Protein Engineering, Design & Selection: PEDS, 20(11), 551–559. https://doi.org/10.1093/protein/gzm056
- Tina, K. G., Bhadra, R., & Srinivasan, N. (2007). PIC : Protein interactions calculator. Nucleic Acids Research, 35, 473–476. https://doi.org/10.1093/nar/gkm423
- Turunen, O., Etuaho, K., Fenel, F., Vehmaanperä, J., Wu, X., Rouvinen, J., & Leisola, M. (2001). A combination of weakly stabilizing mutations with a disulfide bridge in the α-helix region of Trichoderma reesei endo-1,4-β-xylanase II increases the thermal stability through synergism. Journal of Biotechnology, 88(1), 37–46. 10.1016/S0168-1656(01)00253-X
- Umemoto, H., Ihsanawati, Inami, M., Yatsunami, R., Fukui, T., Kumasaka, T., & Nakamura, S. (2007). Contribution of salt bridges to alkaliphily of Bacillus alkaline xylanase. Nucleic Acids Symposium Series, 51(1), 461–462. https://doi.org/10.1093/nass/nrm231
- Umemoto, H., Inami, M., Yatsunami, R., Kumasaka, T., Tanaka, N., & Nakamura, S. (2014). Improvement of alkaliphily of Bacillus alkaline xylanase by introducing amino acid substitutions both on catalytic cleft and protein surface. Bioscience, Biotechnology, and Biotechnology, 74(4), 965–967. https://doi.org/10.1271/bbb.80869
- Vogt, G., Woell, S., & Argos, P. (1997). Protein thermal stability, hydrogen bonds, and ion pairs. Journal of Molecular Biology, 269(4), 631–643. https://doi.org/10.1006/jmbi.1997.1042
- Wu, X., Zhang, Q., Zhang, L., Liu, S., Chen, G., Zhang, H., & Wang, L. (2020). Insights into the role of exposed surface charged residues in the alkali-tolerance of GH11 xylanase. Frontiers in Microbiology, 11, 872. https://doi.org/10.3389/fmicb.2020.00872
- Zhang, F., Chen, J.-J., Ren, W.-Z., Lin, L.-B., Zhou, Y., Zhi, X.-Y., Tang, S.-K., & Li, W.-J. (2012). Cloning, expression, and characterization of an alkaline thermostable GH11 xylanase from Thermobifida halotolerans YIM 90462T. Journal of Industrial Microbiology & Biotechnology, 39(8), 1109–1116. https://doi.org/10.1007/s10295-012-1119-8