Structural aspects of β-glucosidase of Myceliophthora thermophila (MtBgl3c) by homology modelling and molecular docking

References

• Acharya, S., & Chaudhary, A. (2012). Bioprospecting thermophiles for cellulase production: A review. Brazilian Journal of Microbiology : [Publication of the Brazilian Society for Microbiology], 43(3), 844–856. https://doi.org/https://doi.org/10.1590/S1517-83822012000300001
   PubMed Web of Science ®Google Scholar
• Agirre, J., Ariza, A., Offen, W. A., Turkenburg, J. P., Roberts, S. M., McNicholas, S., Harris, P. V., McBrayer, B., Dohnalek, J., Cowtan, K. D., Davies, G. J., & Wilson, K. S. (2016). Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. family GH3 β-D-glucosidases. Acta Crystallographica. Section D, Structural Biology, 72(Pt 2), 254–265. https://doi.org/https://doi.org/10.1107/S2059798315024237
   PubMedGoogle Scholar
• Bhat, M. K. (2000). Cellulases and related enzymes in biotechnology. Biotechnology Advances, 18(5), 355–383.
   PubMed Web of Science ®Google Scholar
• Bhatia, Y., Mishra, S., & Bisaria, V. S. (2002). Microbial beta-glucosidases: cloning, properties, and applications. Critical Reviews in Biotechnology, 22(4), 375–407. https://doi.org/https://doi.org/10.1080/07388550290789568
   PubMed Web of Science ®Google Scholar
• Bonfá, E. C., de Souza Moretti, M. M., Gomes, E., & Bonilla-Rodriguez, G. O. (2018). Biochemical characterization of an isolated 50 kDa beta-glucosidase from the thermophilic fungus Myceliophthora thermophila M.7. Biocatalysis and Agricultural Biotechnology, 13, 311–318. https://doi.org/https://doi.org/10.1016/j.bcab.2018.01.008
   Web of Science ®Google Scholar
• Bowers, K. J., Chow, D. E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the ACM/IEEE Conference on Supercomputing, 2006, pp. 43–-43.
   Google Scholar
• Chevenet, F., Brun, C., Bañuls, A.-L., Jacq, B., & Christen, R. (2006). TreeDyn: Towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics, 7(1), 439. https://doi.org/https://doi.org/10.1186/1471-2105-7-439
   PubMedGoogle Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science : a Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Dadheech, T., Shah, R., Pandit, R., Hinsu, A., Chauhan, P. S., Jakhesara, S., Kunjadiya, A., Rank, D., & Joshi, C. (2018). Cloning, molecular modeling and characterization of acidic cellulase from buffalo rumen and its applicability in saccharification of lignocellulosic biomass. International Journal of Biological Macromolecules, 113, 73–81. https://doi.org/https://doi.org/10.1016/j.ijbiomac.2018.02.100
   PubMed Web of Science ®Google Scholar
• Dadwal, A., Sharma, S., & Satyanarayana, T. (2019). Diversity in cellulose-degrading microbes and their cellulases: Role in ecosystem sustainability and potential applications. In Satyanarayana, T., Das, S. K., Johri, B. N. eds., Microbial diversity in ecosystem sustainability and biotechnological applications, vol. 2 (pp. 375–402) Springer.
   Google Scholar
• Dadwal, A., Sharma, S., & Satyanarayana, T. (2020). Progress in ameliorating beneficial characteristics of microbial cellulases by genetic engineering approaches for cellulose saccharification. Frontiers in Microbiology, 11, 1387 https://doi.org/https://doi.org/10.3389/fmicb.2020.01387
   PubMed Web of Science ®Google Scholar
• Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J. F., Guindon, S., Lefort, V., Lescot, M., Claverie, J. M., & Gascuel, O. (2008). Phylogeny.fr: Robust phylogenetic analysis for the non-specialist. Nucleic Acids Res, 36(Web Server issue), W465–469. https://doi.org/https://doi.org/10.1093/nar/gkn180
   PubMed Web of Science ®Google Scholar
• Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1179. https://doi.org/https://doi.org/10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Eswar, N., Marti-Renom, M. A., Webb, B., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Sali, A. (2006). Comparative protein structure modeling with modeller. Current protocols in bioinformatics, John Wiley & Sons Inc. 15, 5.6.1–5.6.30.
   Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In Walker, J. M. (Ed.) The proteomics protocols handbook (pp. 571–607). Humana Press.
   Google Scholar
• Geronimo, I., Ntarima, P., Piens, K., Gudmundsson, M., Hansson, H., Sandgren, M., & Payne, C. M. (2019). Kinetic and molecular dynamics study of inhibition and transglycosylation in Hypocrea jecorina family 3 β-glucosidases. The Journal of Biological Chemistry, 294(9), 3169–3180. https://doi.org/https://doi.org/10.1074/jbc.RA118.007027
   PubMed Web of Science ®Google Scholar
• Gill, S. C., & von Hippel, P. H. (1989). Calculation of protein extinction coefficients from amino acid sequence data. Analytical Biochemistry, 182(2), 319–326. https://doi.org/https://doi.org/10.1016/0003-2697(89)90602-7
   PubMed Web of Science ®Google Scholar
• Gomes, E., de Souza, A. R., Orjuela, G. L., Da Silva, R., de Oliveira, T. B., & Rodrigues, A. (2016). Applications and benefits of thermophilic microorganisms and their enzymes for industrial biotechnology, in Gene expression systems in fungi: Advancements and applications (Schmoll, M. and Dattenböck, C. Eds., pp. 459–492), Springer.
   Google Scholar
• Guindon, S., Lethiec, F., Duroux, P., & Gascuel, O. (2005). PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research, 33(Web Server issue), W557–W559. https://doi.org/https://doi.org/10.1093/nar/gki352
   PubMedGoogle Scholar
• Guruprasad, K., Reddy, B. V. B., & Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, 4(2), 155–161. https://doi.org/https://doi.org/10.1093/protein/4.2.155
   PubMedGoogle Scholar
• Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377–389. https://doi.org/https://doi.org/10.1021/ci800324m
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for Rapid, accurate docking and scoring. 2. enrichment factors in database Screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Hassan, N., Nguyen, T.-H., Intanon, M., Kori, L. D., Patel, B. K. C., Haltrich, D., Divne, C., & Tan, T. C. (2015). Biochemical and structural characterization of a thermostable β-glucosidase from Halothermothrix orenii for galacto-oligosaccharide synthesis. Applied Microbiology and Biotechnology, 99(4), 1731–1744. https://doi.org/https://doi.org/10.1007/s00253-014-6015-x
   PubMed Web of Science ®Google Scholar
• Henrissat, B., & Bairoch, A. (1993). New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochemical Journal, 293(3), 781–788. https://doi.org/https://doi.org/10.1042/bj2930781
   PubMed Web of Science ®Google Scholar
• Hu, X., Dong, Q., Yang, J., & Zhang, Y. (2016). Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. Bioinformatics (Oxford, England)), 32(21), 3260–3269. https://doi.org/https://doi.org/10.1093/bioinformatics/btw396
   PubMed Web of Science ®Google Scholar
• Huang, S. Y., & Zou, X. (2010). Advances and challenges in protein-ligand docking. International Journal of Molecular Sciences, 11(8), 3016–3034. https://doi.org/https://doi.org/10.3390/ijms11083016
   PubMed Web of Science ®Google Scholar
• Ikai, A. J. (1980). Thermostability and aliphatic index of globular proteins. Journal of Biochemistry, 88(6), 1895–1898.
   PubMed Web of Science ®Google Scholar
• Karnaouri, A., Topakas, E., Paschos, T., Taouki, I., & Christakopoulos, P. (2013). Cloning, expression and characterization of an ethanol tolerant GH3 β-glucosidase from Myceliophthora thermophila. PeerJ., 1, e46 https://doi.org/https://doi.org/10.7717/peerj.46
   PubMed Web of Science ®Google Scholar
• Karnaouri, A., Muraleedharan, M. N., Dimarogona, M., Topakas, E., Rova, U., Sandgren, M., & Christakopoulos, P. (2017). Recombinant expression of thermostable processive MtEG5 endoglucanase and its synergism with MtLPMO from Myceliophthora thermophila during the hydrolysis of lignocellulosic substrates. Biotechnology for Biofuels, 10, 126.https://doi.org/https://doi.org/10.1186/s13068-017-0813-1
   PubMed Web of Science ®Google Scholar
• Kaur, J., Chadha, B. S., Kumar, B. A., Kaur, G. S., & Saini, H. S. (2007). Purification and characterization of β-glucosidase from Melanocarpus sp. MTCC 3922. Electronic Journal of Biotechnology, 10(2), 0–270. https://doi.org/https://doi.org/10.2225/vol10-issue2-fulltext-4
   Web of Science ®Google Scholar
• Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157(1), 105–132. https://doi.org/https://doi.org/10.1016/0022-2836(82)90515-0
   PubMed Web of Science ®Google Scholar
• Laughrey, Z. R., Kiehna, S. E., Riemen, A. J., & Waters, M. L. (2008). Carbohydrate-pi interactions: what are they worth? Journal of the American Chemical Society, 130(44), 14625–14633. https://doi.org/https://doi.org/10.1021/ja803960x
   PubMed Web of Science ®Google Scholar
• Li, Y., Liu, N., Yang, H., Zhao, F., Yu, Y., Tian, Y., & Lu, X. (2014). Cloning and characterization of a new β-glucosidase from a metagenomic library of Rumen of cattle feeding with Miscanthus sinensis. BMC Biotechnology, 14, 85 https://doi.org/https://doi.org/10.1186/1472-6750-14-85
   PubMed Web of Science ®Google Scholar
• Liu, D., Zhang, R., Yang, X., Zhang, Z., Song, S., Miao, Y., & Shen, Q. (2012). Characterization of a thermostable β-glucosidase from Aspergillus fumigatus Z5, and its functional expression in Pichia pastoris X33. Microb Cell Fact, 11, 25 https://doi.org/https://doi.org/10.1186/1475-2859-11-25
   PubMed Web of Science ®Google Scholar
• Lovell, S. C., Davis, I. W., Arendall, I. I. I., W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S., & Richardson, D. C. (2003). Structure validation by C-alpha geometry: Phi,psi and C-beta deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437–450. https://doi.org/https://doi.org/10.1002/prot.10286
   PubMed Web of Science ®Google Scholar
• Lüthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356(6364), 83–85. https://doi.org/https://doi.org/10.1038/356083a0
   PubMed Web of Science ®Google Scholar
• Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808. https://doi.org/https://doi.org/10.1021/jm060522a
   PubMed Web of Science ®Google Scholar
• Mohsin, I., Poudel, N., Li, D.-C., & Papageorgiou, A. C. (2019). Crystal structure of a GH3 β-glucosidase from the thermophilic fungus Chaetomium thermophilum. International Journal of Molecular Sciences, 20(23), 5962. https://doi.org/https://doi.org/10.3390/ijms20235962
   Web of Science ®Google Scholar
• Morgenstern, I., Powlowski, J., Ishmael, N., Darmond, C., Marqueteau, S., Moisan, M. C., Quenneville, G., & Tsang, A. (2012). A molecular phylogeny of thermophilic fungi. Fungal Biology, 116(4), 489–502. https://doi.org/https://doi.org/10.1016/j.funbio.2012.01.010
   PubMed Web of Science ®Google Scholar
• Olajuyigbe, F. M., Nlekerem, C. M., & Ogunyewo, O. A. (2016). Production and characterization of highly thermostable β-glucosidase during the biodegradation of methyl cellulose by Fusarium oxysporum. Biochemistry Research International., 2016, 1–8. https://doi.org/https://doi.org/10.1155/2016/3978124
   Web of Science ®Google Scholar
• Patel, A. K., Singhania, R. R., Sim, S. J., & Pandey, A. (2019). Thermostable cellulases: Current status and perspectives. Bioresource Technology, 279, 385–392. https://doi.org/https://doi.org/10.1016/j.biortech.2019.01.049
   PubMed Web of Science ®Google Scholar
• Payne, C. M., Resch, M. G., Chen, L., Crowley, M. F., Himmel, M. E., Taylor, L. E., Sandgren, M., Ståhlberg, J., Stals, I., Tan, Z., & Beckham, G. T. (2013). Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose. Proceedings of the National Academy of Sciences of the United States of America, 110(36), 14646–14651. https://doi.org/https://doi.org/10.1073/pnas.1309106110
   PubMed Web of Science ®Google Scholar
• 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 analyses. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Phadtare, P., Joshi, S., & Satyanarayana, T. (2017). Recombinant thermo-alkali-stable endoglucanase of Myceliopthora thermophila BJA (rMt-egl): biochemical characteristics and applicability in enzymatic saccharification of agro-residues. International Journal of Biological Macromolecules, 104(Pt A), 107–116. https://doi.org/https://doi.org/10.1016/j.ijbiomac.2017.05.167
   PubMedGoogle Scholar
• Ramanathan, K., Verma, K., Gupta, N., & Shanthi, V. (2018). Discovery of therapeutic lead molecule against β-tubulin using computational approach. Interdisciplinary Sciences, Computational Life Sciences, 10(4), 734–747. https://doi.org/https://doi.org/10.1007/s12539-017-0233-8
   PubMed Web of Science ®Google Scholar
• Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42(Web Server issue), W320–W324. https://doi.org/https://doi.org/10.1093/nar/gku316
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Schwede, T. (2013). Homology modeling of protein structures. In Roberts, G.C.K. ed., Encyclopedia of biophysics (pp. 992–998). Springer.
   Google Scholar
• Shan, Y., Klepeis, J. L., Eastwood, M. P., Dror, R. O., & Shaw, D. E. (2005). Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. The Journal of Chemical Physics, 122(5), 54101.https://doi.org/https://doi.org/10.1063/1.1839571
   PubMed Web of Science ®Google Scholar
• Shen, M., & Sali, A. (2006). Statistical potential for assessment and prediction of protein structures. Protein Sci, 15(11), 2507–2524. https://doi.org/https://doi.org/10.1110/ps.062416606
   PubMed Web of Science ®Google Scholar
• Srivastava, N., Srivastava, M., Mishra, P. K., Gupta, V. K., Molina, G., Rodriguez-Couto, S., Manikanta, A., & RaMteke, P. W. (2018). Applications of fungal cellulases in biofuel production: Advances and limitations. Renewable and Sustainable Energy Reviews, 82, 2379–2386. https://doi.org/https://doi.org/10.1016/j.rser.2017.08.074
   Web of Science ®Google Scholar
• Suzuki, K., Sumitani, J.-I., Nam, Y.-W., Nishimaki, T., Tani, S., Wakagi, T., Kawaguchi, T., & Fushinobu, S. (2013). Crystal structures of glycoside hydrolase family 3 β-glucosidase 1 from Aspergillus aculeatus. The Biochemical Journal, 452(2), 211–221. https://doi.org/https://doi.org/10.1042/BJ20130054
   PubMedGoogle Scholar
• Talavera, G., & Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56(4), 564–577. https://doi.org/https://doi.org/10.1080/10635150701472164
   PubMed Web of Science ®Google Scholar
• Teugjas, H., & Väljamäe, P. (2013). Selecting β-glucosidases to support cellulases in cellulose saccharification. Biotechnology for Biofuels, 6, 1–13.
   PubMed Web of Science ®Google Scholar
• Tian, L., Liu, S., Wang, S., & Wang, L. (2016). Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. Scientific Reports, 6(1)
   Google Scholar
• Verma, K., & Ramanathan, K. (2015a). Exploring the impact of F270V mutation in the β-tubulin (Bos Taurus) structure and its function: A computational perspective. Biotechnology Letters, 37(5), 1003–1011. https://doi.org/https://doi.org/10.1007/s10529-015-1765-9
   PubMed Web of Science ®Google Scholar
• Verma, K., & Ramanathan, K. (2015b). Investigation of paclitaxel resistant R306C mutation in β-Tubulin—A Computational Approach . Journal of Cellular Biochemistry, 116(7), 1318–1324. https://doi.org/https://doi.org/10.1002/jcb.25087
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Wilson, D. B. (2009). Cellulases and biofuels. Current Opinion in Biotechnology, 20(3), 295–299. [Database] https://doi.org/https://doi.org/10.1016/j.copbio.2009.05.007
   PubMed Web of Science ®Google Scholar
• Xiang, Z. (2006). Advances in homology protein structure modeling. Current Protein & Peptide Science, 7(3), 217–227. https://doi.org/https://doi.org/10.2174/138920306777452312
   PubMed Web of Science ®Google Scholar
• Xiao, Z., Zhang, X., Gregg, D. J., & Saddler, J. N. (2004). Effects of sugar inhibition on cellulases and β-glucosidase during enzymatic hydrolysis of softwood substrates. Applied Biochemistry and Biotechnology, 115(1-3), 1115–1126. https://doi.org/https://doi.org/10.1385/ABAB:115:1-3:1115
   Google Scholar
• Yang, X., Ma, R., Shi, P., Huang, H., Bai, Y., Wang, Y., Yang, P., Fan, Y., & Yao, B. (2014). Molecular characterization of a highly-active thermophilic β-glucosidase from Neosartorya fischeri P1 and Its application in the hydrolysis of soybean isoflavone glycosides. PLoS One, 9(9), e106785.https://doi.org/https://doi.org/10.1371/journal.pone.0106785
   PubMed Web of Science ®Google Scholar
• Zhang, L., Fu, Q., Li, W., Wang, B., Yin, X., Liu, S., Xu, Z., & Niu, Q. (2017). Identification and characterization of a novel β-glucosidase via metagenomic analysis of Bursaphelenchus xylophilus and its microbial flora. Scientific Reports, 7(1), 14850.https://doi.org/https://doi.org/10.1038/s41598-017-14073-w
   PubMed Web of Science ®Google Scholar
• Zhao, J., Guo, C., Tian, C., & Ma, Y. (2015). Heterologous expression and characterization of a GH3 β-glucosidase from thermophilic fungi Myceliophthora thermophila in Pichia pastoris. Appl Biochem Biotechnol, 177(2), 511–527. https://doi.org/https://doi.org/10.1007/s12010-015-1759-z
   PubMed Web of Science ®Google Scholar