Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase

Current Research in Structural Biology - Tập 4 - Trang 256-270 - 2022
Jennifer C. Van Wyk1,2,3, B. Trevor Sewell4,5, Michael J. Danson6, Tsepo L. Tsekoa1,2,7, Muhammed F. Sayed1,2, Don A. Cowan1,2,8
1Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, South Africa
2Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
3Keratech LLC, Hair and Skin Research Lab, Pittsburgh, PA 15219, USA
4Electron Microscopy Unit, University of Cape Town, Cape Town, 7700, South Africa
5Department of Integrative Biomedical Sciences, University of Cape Town, Observatory 7925 South Africa
6Department of Biology and Biochemistry, University of Bath
7Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria 0001 Gauteng, South Africa
8Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa

Tài liệu tham khảo

Anderson, 1993, Hydrophobic core repacking and aromatic–aromatic interaction in the thermostable mutant of T4 lysozyme Ser 117→ Phe, Protein Sci., 2, 1285, 10.1002/pro.5560020811 Arnott, 2000, Thermostability and thermoactivity of citrate synthases from the thermophilic and hyperthermophilic archaea, Thermoplasma acidophilum and Pyrococcus furiosus, J. Mol. Biol., 304, 657, 10.1006/jmbi.2000.4240 Bloom, 2005, Evolving strategies for enzyme engineering, Curr. Opin. Struct. Biol., 15, 447, 10.1016/j.sbi.2005.06.004 Bogin, 1998, Enhanced thermal stability of Clostridium beijerinckii alcohol dehydrogenase after strategic substitution of amino acid residues with prolines from the homologous thermophilic Thermoanaerobacter brockii alcohol dehydrogenase, Protein Sci., 7, 1156, 10.1002/pro.5560070509 Cameron, 2003 Cameron, 2005, Molecular analysis of the nitrile catabolism operon of the thermophile Bacillus pallidus RAPc8, Biochim. Biophys. Acta, 1725, 35, 10.1016/j.bbagen.2005.03.019 Chen, 2013, Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions, J. Biotechnol., 164, 354, 10.1016/j.jbiotec.2013.01.021 Cowan, 2003, Comparative biology of mesophilic and thermophilic nitrile hydratases, Adv. Appl. Microbiol., 52, 123, 10.1016/S0065-2164(03)01005-0 Cramp, 1999, Molecular characterisation of a novel thermophilic nitrile hydratase, Biochim. Biophys. Acta, 1431, 249, 10.1016/S0167-4838(99)00010-2 Cui, 2014, Improvement of stability of nitrile hydratase via protein fragment swapping, Biochem. Biophys. Res. Commun., 450, 401, 10.1016/j.bbrc.2014.05.127 Daniel, 2008, 1 Daugherty, 2000, Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies, Proc. Natl. Acad. Sci. USA, 97, 2029, 10.1073/pnas.030527597 Drummond, 2005, Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins, J. Mol. Biol., 350, 806, 10.1016/j.jmb.2005.05.023 Elcock, 1998, The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins, J. Mol. Biol., 284, 489, 10.1006/jmbi.1998.2159 Eyring, 1935, The activated complex in chemical reactions, J. Chem. Phys., 3, 107, 10.1063/1.1749604 Forood, 1993, Stabilization of alpha-helical structures in short peptides via end capping, Proc. Natl. Acad. Sci. USA, 90, 838, 10.1073/pnas.90.3.838 García, 2002, α-Helical stabilization by side chain shielding of backbone hydrogen bonds, Proc. Natl. Acad. Sci. USA, 99, 2782, 10.1073/pnas.042496899 Georgiou, 2001, Analysis of large libraries of protein mutants using flow cytometry, Adv. Protein Chem., 55, 293, 10.1016/S0065-3233(01)55007-X Ghosh, 2003, Role of backbone hydration and salt-bridge formation in stability of α-helix in solution, Biophys. J., 85, 3187, 10.1016/S0006-3495(03)74736-5 Gong, 2017, Nitrile-converting enzymes as a tool to improve biocatalysis in organic synthesis: recent insights and promises, Crit. Rev. Biotechnol., 37, 69, 10.3109/07388551.2015.1120704 Haney, 1997, Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus, Proteins Struct. Funct. Genet., 28, 117, 10.1002/(SICI)1097-0134(199705)28:1<117::AID-PROT12>3.0.CO;2-M Hendsch, 1994, Do salt bridges stabilize proteins? A continuum electrostatic analysis, Protein Sci.: Pub. Protein. Soc., 3, 211, 10.1002/pro.5560030206 Hendsch, 1996, Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests, Biochemistry, 35, 7621, 10.1021/bi9605191 Hiraga, 1997, Roles of hydrogen bonding residues in the interaction between the α and β subunits in the tryptophan synthase complex: asn-104 of the α subunit IS especially important, J. Biol. Chem., 272, 4935, 10.1074/jbc.272.8.4935 Hooft, 1996, Errors in protein structures, Nature, 381, 272, 10.1038/381272a0 Hourai, 2003, Crystal structure of nitrile hydratase from a thermophilic Bacillus smithii, Biochem. Biophys. Res. Commun., 312, 340, 10.1016/j.bbrc.2003.10.124 Jones, 1991, Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr. A, 47, 110, 10.1107/S0108767390010224 Jones, 2000, Protein domain interfaces: characterization and comparison with oligomeric protein interfaces, Protein Eng., 13, 77, 10.1093/protein/13.2.77 Karshikoff, 2001, Ion pairs and the thermotolerance of proteins from hyperthermophiles: a ‘traffic rule’for hot roads, Trends Biochem. Sci., 26, 550, 10.1016/S0968-0004(01)01918-1 Kataeva, 2003, Calcium and domain interactions contribute to the thermostability of domains of the multimodular cellobiohydrolase, CbhA, a subunit of the Clostridium thermocellum cellulosome, Biochem. J., 372, 151, 10.1042/bj20021621 Khaustova, 2010, Noninvasive biochemical monitoring of physiological stress by Fourier transform infrared saliva spectroscopy, Analyst, 135, 3183, 10.1039/c0an00529k Langhorst, 2000, Analysis of a water mediated protein-protein interactions within RNase T1, Biochemistry, 39, 6586, 10.1021/bi992131m Levy, 2006, Water mediation in protein folding and molecular recognition, Annu. Rev. Biophys. Biomol. Struct., 35, 389, 10.1146/annurev.biophys.35.040405.102134 Liu, 2008, Insights into thermal stability of thermophilic nitrile hydratases by molecular dynamics simulation, J. Mol. Graph. Model., 27, 529, 10.1016/j.jmgm.2008.09.004 Luo, 1997, Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water, Biochemistry, 36, 8413, 10.1021/bi9707133 Marqusee, 1994, Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in lambda repressor, Protein Sci.: Pub. Protein. Soc., 3, 2217, 10.1002/pro.5560031207 Mattos, 2002, Protein–water interactions in a dynamic world, Trends Biochem. Sci., 27, 203, 10.1016/S0968-0004(02)02067-4 McCoy, 2007, Phaser crystallographic software, J. Appl. Crystallogr., 40, 658, 10.1107/S0021889807021206 Miyanaga, 2001, Crystal structure of cobalt-containing nitrile hydratase, Biochem. Biophys. Res. Commun., 288, 1169, 10.1006/bbrc.2001.5897 Mizuguchi, 1998, JOY: protein sequence-structure representation and analysis, Bioinformatics, 14, 617, 10.1093/bioinformatics/14.7.617 Murshudov, 1997, Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr. Sect. D Biol. Crystallogr., 53, 240, 10.1107/S0907444996012255 Myers, 1996, Hydrogen bonding stabilizes globular proteins, Biophys. J., 71, 2033, 10.1016/S0006-3495(96)79401-8 Nagasawa, 1990, Application of nitrile converting enzymes for the production of useful compounds, Pure Appl. Chem., 62, 1441, 10.1351/pac199062071441 Nakasako, 1999, Tertiary and quaternary structures of photoreactive Fe-type nitrile hydratase from Rhodococcus sp. N-771: roles of hydration water molecules in stabilizing the structures and the structural origin of the substrate specificity of the enzyme, Biochemistry, 38, 9887, 10.1021/bi982753s Padmakumar, 1999, Bioconversion of acrylonitrile to acrylamide using a thermostable nitrile hydratase, Appl. Biochem. Biotechnol., 77–79, 671, 10.1385/ABAB:79:1-3:671 Pappenberger, 1997, Disruption of an ionic network leads to accelerated thermal denaturation of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima, J. Mol. Biol., 274, 676, 10.1006/jmbi.1997.1421 Pawar, 2014, PVA/chitosan–glutaraldehyde cross-linked nitrile hydratase as reusable biocatalyst for conversion of nitriles to amides, J. Mol. Catal. B Enzym., 101, 115, 10.1016/j.molcatb.2014.01.005 Payne, 1997, A stereoselective cobalt-containing nitrile hydratase, Biochemistry, 36, 5447, 10.1021/bi962794t Pei, 2018, Evidence for the participation of an extra α-helix at β-subunit surface in the thermal stability of Co-type nitrile hydratase, Appl. Microbiol. Biotechnol., 102, 7891, 10.1007/s00253-018-9191-2 Pereira, 1998, A novel thermostable nitrile hydratase, Extremophiles, 2, 347, 10.1007/s007920050078 Pflugrath, 1999, The finer things in X-ray diffraction data collection, Acta. Crystallogr. D Biol. Crystallogr., 55, 1718, 10.1107/S090744499900935X Puchkaev, 2003, Aromatic stacking as a determinant of the thermal stability of CYP119 from Sulfolobus solfataricus, Arch. Biochem. Biophys., 409, 52, 10.1016/S0003-9861(02)00402-2 Rodier, 2005, Hydration of protein–protein interfaces, Proteins: Struct., Funct., Bioinf., 60, 36, 10.1002/prot.20478 Russell, 1997, The crystal structure of citrate synthase from the hyperthermophilic archaeon Pyrococcus furiosus at 1.9 Å resolution, Biochemistry, 36, 9983, 10.1021/bi9705321 Salminen, 1996, An unusual route to thermostability disclosed by the comparison of Thermus thermophilus and Escherichia coli inorganic pyrophosphatases, Protein Sci., 5, 1014, 10.1002/pro.5560050604 Sambrook, 2001, Molecular cloning: a laboratory manual, vols. 1–3 Shan, 1996, The energetics of hydrogen bonds in model systems: implications for enzymatic catalysis, Science, 272, 97, 10.1126/science.272.5258.97 Sterner, 2001, Thermophilic adaptation of proteins, Crit. Rev. Biochem. Mol. Biol., 36, 39, 10.1080/20014091074174 Takano, 1999, Contribution of intra-and intermolecular hydrogen bonds to the conformational stability of human lysozyme, Biochemistry, 38, 12698, 10.1021/bi9910169 Takashima, 1998, Nitrile hydratase from a thermophilic Bacillus smithii, J. Ind. Microbiol. Biotechnol., 20, 220, 10.1038/sj.jim.2900514 Taştan Bishop, 2006, A new approach to possible substrate binding mechanisms for nitrile hydratase, Biochem. Biophys. Res. Commun., 343, 319, 10.1016/j.bbrc.2006.02.150 Thomas, 2002, Biocatalysis: applications and potentials for the chemical industry, Trends Biotechnol., 20, 238, 10.1016/S0167-7799(02)01935-2 Tigerström, 2004, Effects of a novel disulfide bond and engineered electrostatic interactions on the thermostability of azurin, Biochemistry, 43, 12563, 10.1021/bi048926x Tsekoa, L. 2005. Structure, Enzymology and Genetic Engineering of Bacillus Sp. Nitrile Hydratase, University of the Western Cape. Tsekoa, 2004, Purification, crystallization and preliminary X-ray diffraction analysis of thermostable nitrile hydratase: research letter, South Afr. J. Sci., 100, 488 Van Den Burg, 2003, Extremophiles as a source for novel enzymes, Curr. Opin. Microbiol., 6, 213, 10.1016/S1369-5274(03)00060-2 Vetriani, 1998, Protein thermostability above 100 C: a key role for ionic interactions, Proc. Natl. Acad. Sci. USA, 95, 12300, 10.1073/pnas.95.21.12300 Vieille, 2001, Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability, Microbiol. Mol. Biol. Rev., 65, 1, 10.1128/MMBR.65.1.1-43.2001 Vihinen, 1987, Relationship of protein flexibility to thermostability, Protein Eng., 1, 477, 10.1093/protein/1.6.477 Vogt, 1997, Protein thermal stability, hydrogen bonds, and ion pairs, J. Mol. Biol., 269, 631, 10.1006/jmbi.1997.1042 Waldburger, 1995, Are buried salt bridges important for protein stability and conformational specificity?, Nat. Struct. Mol. Biol., 2, 122, 10.1038/nsb0295-122 Wilding, 2015, An investigation of nitrile transforming enzymes in the chemo-enzymatic synthesis of the taxol sidechain, Org. Biomol. Chem., 13, 7803, 10.1039/C5OB01191D Wintrode, 2001, Patterns of adaptation in a laboratory evolved thermophilic enzyme, Biochim. Biophys. Acta, 1549, 1, 10.1016/S0167-4838(01)00226-6 Xiao, 1999, Electrostatic contributions to the stability of hyperthermophilic proteins, J. Mol. Biol., 289, 1435, 10.1006/jmbi.1999.2810 Xudong, 2009, Deactivation kinetics of nitrile hydratase in free resting cells, Chin. J. Chem. Eng., 17, 822, 10.1016/S1004-9541(08)60282-7 Yamaki, 1997, Cloning and sequencing of a nitrile hydratase gene from Pseudonocardia thermophila JCM3095, J. Ferment. Bioeng., 83, 474, 10.1016/S0922-338X(97)83004-8 Yano, 2003, Preliminary characterization and crystal structure of a thermostable cytochrome P450 from Thermus thermophilus, J. Biol. Chem., 278, 608, 10.1074/jbc.M206568200 Zaccolo, 1999, The effect of high-frequency random mutagenesis on in vitro protein evolution: a study on TEM-1 β-lactamase, J. Mol. Biol., 285, 775, 10.1006/jmbi.1998.2262 ZAvodszky, 1998, Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins, Proc. Natl. Acad. Sci. USA, 95, 7406, 10.1073/pnas.95.13.7406 Zhou, 2002, Toward the physical basis of thermophilic proteins: linking of enriched polar interactions and reduced heat capacity of unfolding, Biophys. J., 83, 3126, 10.1016/S0006-3495(02)75316-2