Simulation and practical investigation of carbonic anhydrase stability in an industrial solvent system of methyl diethanolamine for carbon dioxide capture

References

• Almstedt, K., Lundqvist, M., Carlsson, J., Karlsson, M., Persson, B., Jonsson, B.-H., Carlsson, U., & Hammarström, P. (2004). Unfolding a folding disease: Folding, misfolding and aggregation of the marble brain syndrome-associated mutant H107Y of human carbonic anhydrase II. Journal of Molecular Biology, 342(2), 619–633. https://doi.org/10.1016/j.jmb.2004.07.024
   PubMed Web of Science ®Google Scholar
• Alterio, V., Di Fiore, A., D'Ambrosio, K., Supuran, C. T., & De Simone, G. (2012). Multiple binding modes of inhibitors to carbonic anhydrases: How to design specific drugs targeting 15 different isoforms? Chemical Reviews, 112(8), 4421–4468. https://doi.org/10.1021/cr200176r
   PubMed Web of Science ®Google Scholar
• Armstrong, J. M., Myers, D. V., Verpoorte, J. A., & Edsall, J. T. (1966). Purification and properties of human erythrocyte carbonic anhydrases. The Journal of Biological Chemistry, 241(21), 5137–5149.
   PubMed Web of Science ®Google Scholar
• Bharatiy, S. K., Hazra, M., Paul, M., Mohapatra, S., Samantaray, D., Dubey, R. C., Sanyal, S., Datta, S., & Hazra, S. (2016). In silico designing of an industrially sustainable carbonic anhydrase using molecular dynamics simulation. ACS Omega, 1(6), 1081–1103. https://doi.org/10.1021/acsomega.6b00041
   PubMed Web of Science ®Google Scholar
• Cabrita, L. D., Gilis, D., Robertson, A. L., Dehouck, Y., Rooman, M., & Bottomley, S. P. (2007). Enhancing the stability and solubility of TEV protease using in silico design. Protein Science: A Publication of the Protein Society, 16(11), 2360–2367. https://doi.org/10.1110/ps.072822507
   PubMed Web of Science ®Google Scholar
• Canchi, D. R., & García, A. E. (2013). Cosolvent effects on protein stability. Annual Review of Physical Chemistry, 64(1), 273–293. https://doi.org/10.1146/annurev-physchem-040412-110156
   PubMed Web of Science ®Google Scholar
• Cowan, D. (1997). Thermophilic proteins: Stability and function in aqueous and organic solvents. Comparative Biochemistry and Physiology. Part A, Physiology, 118(3), 429–438. https://doi.org/10.1016/s0300-9629(97)00004-2
   PubMed Web of Science ®Google Scholar
• Cuya, T., Gonçalves, A., da Silva, J. A. V., Ramalho, T. C., Kuca, K., & C.c. França, T. (2018). The role of the oximes HI-6 and HS-6 inside human acetylcholinesterase inhibited with nerve agents: A computational study. Journal of Biomolecular Structure & Dynamics, 36(13), 3444–3452. https://doi.org/10.1080/07391102.2017.1389307
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40, 82–92.
   Google Scholar
• Deutsch, H. F. (1987). Carbonic anhydrases. The International Journal of Biochemistry, 19(2), 101–113. https://doi.org/10.1016/0020-711x(87)90320-x
   PubMedGoogle Scholar
• Di Fiore, A., Alterio, V., Monti, S. M., De Simone, G., & D'Ambrosio, K. (2015). Thermostable carbonic anhydrases in biotechnological applications. International Journal of Molecular Sciences, 16(7), 15456–15480. https://doi.org/10.3390/ijms160715456
   PubMed Web of Science ®Google Scholar
• Dierckx, S., & Huyghebaert, A. (2002). Effects of sucrose and sorbitol on the gel formation of a whey protein isolate. Food Hydrocolloids, 16(5), 489–497. https://doi.org/10.1016/S0268-005X(01)00129-1
   Web of Science ®Google Scholar
• Du, X., Sang, P., Xia, Y.-L., Li, Y., Liang, J., Ai, S.-M., Ji, X.-L., Fu, Y.-X., & Liu, S.-Q. (2017). Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 35(7), 1500–1517. https://doi.org/10.1080/07391102.2016.1188155
   PubMed Web of Science ®Google Scholar
• Fernández, P. A., Roleda, M. Y., Rautenberger, R., & Hurd, C. L. (2018). Carbonic anhydrase activity in seaweeds: Overview and recommendations for measuring activity with an electrometric method, using Macrocystis pyrifera as a model species. Marine Biology, 165(5), 1–12. https://doi.org/10.1007/s00227-018-3348-5
   Web of Science ®Google Scholar
• Fisher, Z., Boone, C. D., Biswas, S. M., Venkatakrishnan, B., Aggarwal, M., Tu, C., Agbandje-McKenna, M., Silverman, D., & McKenna, R. (2012). Kinetic and structural characterization of thermostabilized mutants of human carbonic anhydrase II. Protein Engineering, Design & Selection: PEDS, 25(7), 347–355. https://doi.org/10.1093/protein/gzs027
   PubMed Web of Science ®Google Scholar
• Fraczkiewicz, R., & Braun, W. (1998). Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. Journal of Computational Chemistry, 19(3), 319–333. https://doi.org/10.1002/(SICI)1096-987X(199802)19:3<319::AID-JCC6>3.3.CO;2-3
   Web of Science ®Google Scholar
• Gekko, K., & Timasheff, S. N. (1981). Mechanism of protein stabilization by glycerol: Preferential hydration in glycerol-water mixtures. Biochemistry, 20(16), 4667–4676. https://doi.org/10.1021/bi00519a023
   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
• Illanes, A. (2008). Enzyme Biocatalysis: Principles and Applications. Springer Science & Business Media.
   Google Scholar
• Kim, H. S., Le, Q. A. T., & Kim, Y. H. (2010a). Development of thermostable lipase B from Candida antarctica (CalB) through in silico design employing B-factor and RosettaDesign. Enzyme and Microbial Technology, 47(1–2), 1–5. https://doi.org/10.1016/j.enzmictec.2010.04.003
   Web of Science ®Google Scholar
• Kim, S., Sung, J., Yeon, J., Choi, S. H., & Jin, M. S. (2019). Crystal structure of a highly thermostable alpha-carbonic anhydrase from persephonella marina EX-H1. Molecules and Cells, 42(6), 460–469. https://doi.org/10.14348/molcells.2019.0029
   PubMed Web of Science ®Google Scholar
• Kim, S. J., Lee, J. A., Joo, J. C., Yoo, Y. J., Kim, Y. H., & Song, B. K. (2010b). The development of a thermostable CiP (Coprinus cinereus peroxidase) through in silico design. Biotechnology Progress, 26(4), 1038–1046. https://doi.org/10.1002/btpr.408
   PubMed Web of Science ®Google Scholar
• Knolls, D., & Hermans, J. (1983). Polymer–protein interactions.
   Google Scholar
• Krishnamurthy, V. M., Kaufman, G. K., Urbach, A. R., Gitlin, I., Gudiksen, K. L., Weibel, D. B., & Whitesides, G. M. (2008). Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chemical Reviews, 108(3), 946–1051. https://doi.org/10.1021/cr050262p
   PubMed Web of Science ®Google Scholar
• Lawal, O., Bello, A., & Idem, R. (2005). The role of methyl diethanolamine (MDEA) in preventing the oxidative degradation of CO2 loaded and concentrated aqueous monoethanolamine (MEA)− MDEA blends during CO2 absorption from flue gases. Industrial & Engineering Chemistry Research, 44(6), 1874–1896. https://doi.org/10.1021/ie049261y
   Web of Science ®Google Scholar
• Le, Q. A. T., Joo, J. C., Yoo, Y. J., & Kim, Y. H. (2012). Development of thermostable Candida antarctica lipase B through novel in silico design of disulfide bridge. Biotechnology and Bioengineering, 109(4), 867–876. https://doi.org/10.1002/bit.24371
   PubMed Web of Science ®Google Scholar
• Lee, L. L., & Lee, J. C. (1987). Thermal stability of proteins in the presence of poly (ethylene glycols). Biochemistry, 26(24), 7813–7819. https://doi.org/10.1021/bi00398a042
   PubMed Web of Science ®Google Scholar
• Liu, Y., & Bolen, D. (1995). The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes. Biochemistry, 34(39), 12884–12891. https://doi.org/10.1021/bi00039a051
   PubMed Web of Science ®Google Scholar
• Mirjafari, P., Asghari, K., & Mahinpey, N. (2007). Investigating the application of enzyme carbonic anhydrase for CO2 sequestration purposes. Industrial & Engineering Chemistry Research, 46(3), 921–926. https://doi.org/10.1021/ie060287u
   Web of Science ®Google Scholar
• Nikbakht, M. R., Ashrafi-Kooshk, M. R., Jaafari, M., Ghasemi, M., & Khodarahmi, R. (2014). Does long-term administration of a beta-blocker (timolol) induce fibril-based cataract formation in-vivo? Iranian Journal of Pharmaceutical Research: IJPR, 13(2), 599–612.
   PubMed Web of Science ®Google Scholar
• Noel, M., & Combes, D. (2003). Rhizomucor miehei lipase: Differential scanning calorimetry and pressure/temperature stability studies in presence of soluble additives. Enzyme and Microbial Technology, 33(2–3), 299–308. https://doi.org/10.1016/S0141-0229(03)00123-6
   Web of Science ®Google Scholar
• Paul, M., Hazra, M., Barman, A., & Hazra, S. (2014). Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein “CheY”. Journal of Biomolecular Structure & Dynamics, 32(6), 928–949. https://doi.org/10.1080/07391102.2013.799438
   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 analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Prasad, R., & Zhou, H.-X. (2020). Membrane association and functional mechanism of synaptotagmin-1 in triggering vesicle fusion. Biophysical Journal, 119(6), 1255–1265. https://doi.org/10.1016/j.bpj.2020.08.008
   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/10.1093/nar/gku316
   PubMed Web of Science ®Google Scholar
• Schiffer, C. A., & Dötsch, V. (1996). The role of protein-solvent interactions in protein unfolding. Current Opinion in Biotechnology, 7(4), 428–432. https://doi.org/10.1016/s0958-1669(96)80119-4
   PubMed Web of Science ®Google Scholar
• 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(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Shapovalov, M. S., & Dunbrack, R. L. J. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure (London, England: 1993), 19(6), 844–858. https://doi.org/10.1016/j.str.2011.03.019
   PubMed Web of Science ®Google Scholar
• Shiraki, K., Tomita, S., & Inoue, N. (2015). Small amine molecules: Solvent design toward facile improvement of protein stability against aggregation and inactivation. Current Pharmaceutical Biotechnology, 17(2), 116–125. https://doi.org/10.2174/1389201017666151029110229
   PubMed Web of Science ®Google Scholar
• Sterpone, F., & Melchionna, S. (2012). Thermophilic proteins: Insight and perspective from in silico experiments. Chemical Society Reviews, 41(5), 1665–1676. https://doi.org/10.1039/c1cs15199a
   PubMed Web of Science ®Google Scholar
• Supuran, C. T., Casini, A., & Scozzafava, A. (2003). Protease inhibitors of the sulfonamide type: Anticancer, antiinflammatory, and antiviral agents. Medicinal Research Reviews, 23(5), 535–558. https://doi.org/10.1002/med.10047
   PubMed Web of Science ®Google Scholar
• Tanford, C. (1969). Extension of the theory of linked functions to incorporate the effects of protein hydration. Journal of Molecular Biology, 39(3), 539–544. https://doi.org/10.1016/0022-2836(69)90143-0
   PubMed Web of Science ®Google Scholar
• Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363–W367. https://doi.org/10.1093/nar/gky473
   PubMed Web of Science ®Google Scholar
• Tomita, S., & Shiraki, K. (2011). Why do solution additives suppress the heat‐induced inactivation of proteins? Inhibition of chemical modifications. Biotechnology Progress, 27(3), 855–862. https://doi.org/10.1002/btpr.597
   PubMed Web of Science ®Google Scholar
• Tu, C., Silverman, D. N., Forsman, C., Jonsson, B. H., & Lindskog, S. (1989). Role of histidine 64 in the catalytic mechanism of human carbonic anhydrase II studied with a site-specific mutant. Biochemistry, 28(19), 7913–7918. https://doi.org/10.1021/bi00445a054
   PubMed Web of Science ®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
• Yao, Y., Liu, J., Zheng, F., & Zhan, C.-G. (2015). Reaction pathway for cocaine hydrolase-catalyzed hydrolysis of (+)-cocaine. Theoretical Chemistry Accounts, 135(1), 15. https://doi.org/10.1007/s00214-015-1788-2
   PubMed Web of Science ®Google Scholar