[1] D.M. Larsen, C. Nyffenegger, M.M. Swiniarska, A. Thygesen, M.L. Strube, A.S. Meyer, J.D. Mikkelsen, Thermostability enhancement of an endo-1, 4-β-galactanase from Talaromyces stipitatus by site-directed mutagenesis, Appl. Microbiol. Biotechnol. 99(10)(2015)4245-4253. [2] S. Jemli, D. Ayadi-Zouari, H. Ben Hlima, S. Bejar, Biocatalysts:Application and engineering for industrial purposes, Crit. Rev. Biotechnol. 36(2)(2016)246-258. [3] S. Boutet, L. Lomb, G.J. Williams, T.R.M. Barends, A. Aquila, R.B. Doak, U. Weierstall, D.P. DePonte, J. Steinbrener, R.L. Shoeman, M. Messerschmidt, A. Barty, T.A. White, S. Kassemeyer, R.A. Kirian, M.M. Seibert, P.A. Montanez, C. Kenney, R. Herbst, P. Hart, J. Pines, G. Haller, S.M. Gruner, H.T. Philipp, M.W. Tate, M. Hromalik, L.J. Koerner, N. van Bakel, J. Morse, W. Ghonsalves, D. Arnlund, M.J. Bogan, C. Caleman, R. Fromme, C.Y. Hampton, M.S. Hunter, L.C. Johansson, G. Katona, C. Kupitz, M.N. Liang, A.V. Martin, K. Nass, L. Redecke, F. Stellato, N. Timneanu, D.J. Wang, N.A. Zatsepin, D. Schafer, J. Defever, R. Neutze, P. Fromme, J.C.H. Spence, H.N. Chapman, I. Schlichting, High-resolution protein structure determination by serial femtosecond crystallography, Science 337(6092)(2012)362-364. [4] N.J. Greenfield, Using circular dichroism spectra to estimate protein secondary structure, Nat. Protoc. 1(6)(2006)2876-2890. [5] E.M. Nordwald, G.S. Armstrong, J.L. Kaar, NMR-guided rational engineering of an ionic-liquid-tolerant lipase, ACS Catal. 4(11)(2014)4057-4064. [6] L.Y. Zhang, L.J. Wang, Y.T. Kao, W.H. Qiu, Y. Yang, O. Okobiah, D.P. Zhong, Mapping hydration dynamics around a protein surface, Proc. Natl. Acad. Sci. U. S. A. 104(47)(2007)18461-18466. [7] M. Fioroni, M.D. Diaz, K. Burger, S. Berger, Solvation phenomena of a tetrapeptide in water/trifluoroethanol and water/ethanol mixtures:A diffusion NMR, intermolecular NOE, and molecular dynamics study, J. Am. Chem. Soc. 124(26)(2002)7737-7744. [8] Y. Maeda, IR spectroscopic study on the hydration and the phase transition of poly (vinyl methyl ether) in water, Langmuir 17(5)(2001)1737-1742. [9] J.T. King, K.J. Kubarych, Site-specific coupling of hydration water and protein flexibility studied in solution with ultrafast 2D-IR spectroscopy, J. Am. Chem. Soc. 134(45)(2012)18705-18712. [10] S. Dutta Banik, M. Nordblad, J.M. Woodley, G.H. Peters, A correlation between the activity of Candida antarctica lipase B and differences in binding free energies of organic solvent and substrate, ACS Catal. 6(10)(2016)6350-6361. [11] P.P. Wangikar, P.C. Michels, D.S. Clark, J.S. Dordick, Structure and function of subtilisin BPN'solubilized in organic solvents, J. Am. Chem. Soc. 119(1)(1997)70-76. [12] M.L. Foresti, M. Galle, M.L. Ferreira, L.E. Briand, Enantioselective esterification of ibuprofen with ethanol as reactant and solvent catalyzed by immobilized lipase:experimental and molecular modeling aspects, J. Chem. Technol. Biotechnol. 84(10)(2009)1461-1473. [13] N. Doukyu, H. Ogino, Organic solvent-tolerant enzymes, Biochem. Eng. J. 48(3)(2010)270-282. [14] A.S. Kim, L.T. Kakalis, N. Abdul-Manan, G.A. Liu, M.K. Rosen, Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein, Nature 404(6774)(2000)151-158. [15] X.Y. Chen, B. He, M. Feng, D.W. Zhao, J. Sun, Immobilized laccase on magnetic nanoparticles for enhanced lignin model compounds degradation, Chin. J. Chem. Eng. 28(8)(2020)2152-2159. [16] C.Y. Zhang, Y. Sun, X.Y. Dong, Conjugation of a zwitterionic polymer with dimethyl chains to lipase significantly increases the enzyme activity and stability, Chin. J. Chem. Eng. 47(2022)48-53. [17] F. Kartal, M.H.A. Janssen, F. Hollmann, R.A. Sheldon, A. Kılınc, Improved esterification activity of Candida rugosa lipase in organic solvent by immobilization as Cross-linked enzyme aggregates (CLEAs), J. Mol. Catal. B 71(3-4)(2011)85-89. [18] V. Stepankova, S. Bidmanova, T. Koudelakova, Z. Prokop, R. Chaloupkova, J. Damborsky, Strategies for stabilization of enzymes in organic solvents, ACS Catal. 3(12)(2013)2823-2836. [19] C. Zheng, Z.J. Li, H.F. Yang, T.Y. Zhang, H.Q. Niu, D. Liu, J.Z. Wang, H.J. Ying, Computation-aided rational design of a halophilic choline kinase for cytidine diphosphate choline production in high-salt condition, J. Biotechnol. 290(2019)59-66. [20] X.L. Wang, J.H. Du, B.C. Zhao, H.Y. Wang, S.Q. Rao, G.C. Du, J.W. Zhou, J. Chen, S. Liu, Significantly improving the thermostability and catalytic efficiency of Streptomyces mobaraenesis transglutaminase through combined rational design, J. Agric. Food Chem. 69(50)(2021)15268-15278. [21] H.Y. Cui, L.L. Zhang, L. Eltoukhy, Q.J. Jiang, S.K. Korkunç, K.E. Jaeger, U. Schwaneberg, M.D. Davari, Enzyme hydration determines resistance in organic cosolvents, ACS Catal. 10(24)(2020)14847-14856. [22] T. Koudelakova, S. Bidmanova, P. Dvorak, A. Pavelka, R. Chaloupkova, Z. Prokop, J. Damborsky, Haloalkane dehalogenases:Biotechnological applications, Biotechnol. J. 8(1)(2013)32-45. [23] S. Murshid, G.P. Dhakshinamoorthy, Application of an immobilized microbial consortium for the treatment of pharmaceutical wastewater:Batch-wise and continuous studies, Chin. J. Chem. Eng. 29(2021)391-400. [24] F. Xue, C.F. Li, Q. Xu, Biocatalytic approaches for the synthesis of optically pure vic-halohydrins, Appl. Microbiol. Biotechnol. 105(9)(2021)3411-3421. [25] I. Gul, W. Le, Z. Jie, R.Q. Fang, M. Bilal, L.X. Tang, Recent advances on engineered enzyme-conjugated biosensing modalities and devices for halogenated compounds, Trac. Trends Anal. Chem. 134(2021)116145. [26] S. Mazzucchelli, M. Colombo, P. Verderio, E. Rozek, F. Andreata, E. Galbiati, P. Tortora, F. Corsi, D. Prosperi, Orientation-controlled conjugation of haloalkane dehalogenase fused homing peptides to multifunctional nanoparticles for the specific recognition of cancer cells, Angew. Chem. Int. Ed. 52(11)(2013)3121-3125. [27] V. Stepankova, J. Damborsky, R. Chaloupkova, Organic co-solvents affect activity, stability and enantioselectivity of haloalkane dehalogenases, Biotechnol. J. 8(6)(2013)719-729. [28] Y.Z. Zhao, W.L. Yu, H. Zheng, X. Guo, N. Guo, T. Hu, J.Y. Zhong, PEGylation with the thiosuccinimido butylamine linker significantly increases the stability of haloalkane dehalogenase DhaA, J. Biotechnol. 254(2017)25-33. [29] T. Koudelakova, R. Chaloupkova, J. Brezovsky, Z. Prokop, E. Sebestova, M. Hesseler, M. Khabiri, M. Plevaka, D. Kulik, I. Kuta Smatanova, P. Rezacova, R. Ettrich, U.T. Bornscheuer, J. Damborsky, Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel, Angew. Chem. Int. Ed. 52(7)(2013)1959-1963. [30] M. Lahoda, J.R. Mesters, A. Stsiapanava, R. Chaloupkova, M. Kuty, J. Damborsky, I. Kuta Smatanova, Crystallographic analysis of 1, 2, 3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31, Acta Crystallogr. Sect. D Biol. Crystallogr. 70(2)(2014)209-217. [31] R. Guerois, J.E. Nielsen, L. Serrano, Predicting changes in the stability of proteins and protein complexes:A study of more than 1000 mutations, J. Mol. Biol. 320(2)(2002)369-387. [32] C. Kutzner, S. Pall, M. Fechner, A. Esztermann, B.L. de Groot, H. Grubmüller, More Bang for your buck:Improved use of GPU nodes for GROMACS 2018, J. Comput. Chem. 40(27)(2019)2418-2431. [33] K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J.L. Klepeis, R.O. Dror, D.E. Shaw, Improved side-chain torsion potentials for the Amber ff99SB protein force field, Proteins 78(8)(2010)1950-1958. [34] T.A. Lu, F.W. Chen, Multiwfn:A multifunctional wavefunction analyzer, J. Comput. Chem. 33(5)(2012)580-592. [35] W. Humphrey, A. Dalke, K. Schulten, VMD:Visual molecular dynamics, J. Mol. Graph. 14(1)(1996)33-38. [36] I. Massova, P.A. Kollman, Computational alanine scanning to probe proteineprotein interactions:A novel approach to evaluate binding free energies, J. Am. Chem. Soc. 121(36)(1999)8133-8143. [37] A. Ben Chorin, G. Masrati, A. Kessel, A. Narunsky, J. Sprinzak, S. Lahav, H. Ashkenazy, N. Ben-Tal, ConSurf-DB:An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins, Protein Sci. 29(1)(2020)258-267. [38] D.E.V. Pires, D.B. Ascher, T.L. Blundell, mCSM:Predicting the effects of mutations in proteins using graph-based signatures, Bioinformatics 30(3)(2014)335-342. [39] E. Capriotti, P. Fariselli, R. Casadio, I-Mutant2.0:Predicting stability changes upon mutation from the protein sequence or structure, Nucleic Acids Res. 33(Web Server issue)(2005) W306-W310. [40] V. Dockalova, E.M. Sanchez-Carnerero, Z. Dunajova, E. Palao, M. Slanska, T. Buryska, J. Damborsky, P. Klan, Z. Prokop, Fluorescent substrates for hal-oalkane dehalogenases:Novel probes for mechanistic studies and protein labeling, Comput. Struct. Biotechnol. J. 18(2020)922-932. [41] H.Y. Cui, T.H.J. Stadtmüller, Q.J. Jiang, K.E. Jaeger, U. Schwaneberg, M.D. Davari, How to engineer organic solvent resistant enzymes:Insights from combined molecular dynamics and directed evolution study, ChemCatChem 12(16)(2020)4073-4083. [42] A.R.S. Prasad, R.F. Luduena, P.M. Horowitz, Detection of energy transfer between tryptophan residues in the tubulin molecule and bound bis (8-anilinonaphthalene-1-sulfonate), an inhibitor of microtubule assembly, that binds to a flexible region on tubulin, Biochemistry 25(12)(1986)3536-3540. [43] C. Duy, J. Fitter, How aggregation and conformational scrambling of unfolded states govern fluorescence emission spectra, Biophys. J. 90(10)(2006)3704-3711. [44] T. Magsumov, A. Fatkhutdinova, T. Mukhametzyanov, I. Sedov, The effect of dimethyl sulfoxide on the lysozyme unfolding kinetics, thermodynamics, and mechanism, Biomolecules 9(10)(2019)547. [45] F. Salehi, R. Emamzadeh, M. Nazari, S.M.M. Rasa, Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site, Int. J. Biol. Macromol. 93(2016)1253-1260. [46] F. Secundo, S. Fial a, M.W. Fraaije, G. de Gonzalo, M. Meli, F. Zambianchi, G. Ottolina, Effects of water miscible organic solvents on the activity and conformation of the baeyer-villiger monooxygenases from Thermobifida fusca and Acinetobacter calcoaceticus:A comparative study, Biotechnol. Bioeng. 108(3)(2011)491-499. [47] M.Wilding,N.Hong,M.Spence,A.M.Buckle,C.J.Jackson,Proteinengineering:The potential of remote mutations, Biochem. Soc. Trans. 47(2)(2019)701-711. |