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Research Articles

A molecular dynamics study of Beta-Glucosidase B upon small substrate binding

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Pages 1486-1494 | Received 21 Apr 2015, Accepted 05 Aug 2015, Published online: 15 Sep 2015

References

  • Andrew, J. A., Jie, C., Shina, C. L. K., & Arieh, W. (2011). Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proceedings of the National Academy of Sciences, 108, 14115–14120. doi:10.1073/pnas.1111252108
  • Arieh, W. (1981). Calculations of enzymic reactions: Calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry, 20, 3167–3177. doi:10.1021/bi00514a028
  • Chuenchor, W., Pengthaisong, S., Robinson, R. C., Yuvaniyama, J., Svasti, J., & Cairns, J. R. (2011). The structural basis of oligosaccharide binding by rice BGlu1 beta-glucosidase. Journal of Structural Biology, 173, 169–179.10.1016/j.jsb.2010.09.021
  • Esen, A., & Blanchard, D. J. (2000). A specific beta-glucosidase-aggregating factor is responsible for the beta-glucosidase null phenotype in maize. Plant Physiology, 122, 563–572.10.1104/pp.122.2.563
  • Gallivan, J. P., & Dougherty, D. A. (1999). Cation-pi interactions in structural biology. Proceedings of the National Academy of Sciences, 96, 9459–9464.10.1073/pnas.96.17.9459
  • Isorna, P., Polaina, J., Latorre-García, L., Cañada, F. J., González, B., & Sanz-Aparicio, J. (2007). Crystal structures of Paenibacillus polymyxa β-glucosidase B complexes reveal the molecular basis of substrate specificity and give new insights into the catalytic machinery of family I glycosidases. Journal of Molecular Biology, 371, 1204–1218.10.1016/j.jmb.2007.05.082
  • Ketudat Cairns, J. R., & Esen, A. (2010). β-Glucosidases. Cellular and Molecular Life Sciences, 67, 3389–3405.10.1007/s00018-010-0399-2
  • Lins, R. D., & Hunenberger, P. H. (2005). A new GROMOS force field for hexopyranose-based carbohydrates. Journal of Computational Chemistry, 26, 1400–1412. doi:10.1002/jcc.20275
  • Maria, P. F., Jie, C., & Arieh, W. (2011). Challenges and advances in validating enzyme design proposals: The case of kemp eliminase catalysis. Biochemistry, 50, 3849–3858. doi:10.1021/bi200063a
  • Matej, R., Miha, P., Robert, V., & Janez, M. (2014). Examining electrostatic preorganization in monoamine oxidases A and B by structural comparison and pKa calculations. Journal of Physical Chemistry B, 118, 4326–4332. doi:10.1021/jp500795p
  • Mazlan, N. S. F., & Ahmad Khairudin, N. B. (2014). Docking study of β-glucosidase B (BglB) from P. polymyxca with cellobiose and cellotetrose. Journal of Medical Bioengineering, 3, 78–83.
  • Nutt, Anu. (2006). Hydrolytic and oxidative mechanisms involved in cellulose degradation (PhD Thesis). Sweden: Uppsala Universitet. Retrieved from http://www.diva-portal.org/smash/get/diva2:168387/FULLTEXT01.pdf
  • Opassiri, R., Pomthong, B., Onkoksoong, T., Akiyama, T., Esen, A., & Ketudat Cairns, J. R. (2006). Analysis of rice glycosyl hydrolase family 1 and expression of Os4bglu12 beta-glucosidase. BMC Plant Biology, 6, 33.10.1186/1471-2229-6-33
  • 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, 1605–1612.10.1002/(ISSN)1096-987X
  • Schrondinger, L. (2010). The PyMOL molecular graphics system (Version 1.7.4) [Computer software]. Retrieved from https://www.pymol.org
  • Schüttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60, 1355–1363.10.1107/S0907444904011679
  • Tiwari, M., Lee, K.-M., Kalyani, D., Singh, R. K., Kim, H., Lee, J.-K., & Ramachandran, P. (2012). Role of Glu445 in the substrate binding of β-glucosidase. Process Biochemistry, 47, 2365–2372. doi:10.1016/j.procbio.2012.09.015
  • Withers, S. (2001). Mechanisms of glycosyl transferases and hydrolases. Carbohydrate Polymers, 44, 325–337.10.1016/S0144-8617(00)00249-6
  • Zhao, G., Dong, X.-Y., & Sun, Y. (2009). Ligands for mixed-mode protein chromatography: Principles characteristics and design. Journal of Biotechnology, 144, 3–11.10.1016/j.jbiotec.2009.04.009

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