Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software

Scientific Reports

Volumn 5, Issue , 2015, Pages 8193-

  Nakano, Shogo ^a,b   Asano, Yasuhisa ^a,b  

^a TOYAMA PREFECTURAL UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

LYASE; MANDELONITRILE LYASE;

ALGORITHM; CHEMISTRY; CIRCULAR DICHROISM; COMPUTER PROGRAM; GENETICS; KINETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR EVOLUTION; PROTEIN FOLDING; PROTEIN STABILITY; TEMPERATURE;

ALDEHYDE-LYASES; ALGORITHMS; CIRCULAR DICHROISM; CLONING, MOLECULAR; EVOLUTION, MOLECULAR; KINETICS; PROTEIN FOLDING; PROTEIN STABILITY; SOFTWARE; TEMPERATURE;

EID: 84923107265     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep08193     Document Type: Article

References (45)

1. Akanuma, S. et al. Experimental evidence for the thermophilicity of ancestral life. Proc. Natl. Acad. Sci. U S A 110, 11067-11072, doi:10.1073/pnas.1308215110 (2013).
2. Rothlisberger, D. et al. Kemp elimination catalysts by computational enzyme design. Nature 453, 190-195, doi:10.1038/nature06879 (2008).
3. Blaber, M. & Lee, J. Designing proteins from simple motifs: opportunities in Top-Down Symmetric Deconstruction. Curr. Opin. Struct. Biol. 22, 442-450, doi:10.1016/j.sbi.2012.05.008 (2012).
4. Lin, Y. W. et al. Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin. Proc. Natl. Acad. Sci. U S A 107, 8581-8586, doi:DOI 10.1073/pnas.1000526107 (2010).
5. Yeung, N. et al. Rational design of a structural and functional nitric oxide reductase. Nature 462, 1079-1082, doi:10.1038/nature08620 (2009).
6. Privett, H. K. et al. Iterative approach to computational enzyme design. Proc. Natl. Acad. Sci. U S A 109, 3790-3795, doi:10.1073/pnas.1118082108 (2012).
7. Broom,A. et al.Modular evolution and the origins of symmetry: reconstruction of a three-fold symmetric globular protein. Structure 20, 161-171, doi:10.1016/j.str.2011.10.021 (2012).
8. Sullivan, B. J. et al. Stabilizing proteins from sequence statistics: the interplay of conservation and correlation in triosephosphate isomerase stability. J. Mol. Biol. 420, 384-399, doi:10.1016/j.jmb.2012.04.025 (2012).
9. Jackel, C., Bloom, J. D., Kast, P., Arnold, F. H. & Hilvert, D. Consensus protein design without phylogenetic bias. J. Mol. Biol. 399, 541-546, doi:10.1016/j.jmb.2010.04.039 (2010).
10. Rath, A. & Davidson, A. R. The design of a hyperstable mutant of the Abp1p SH3 domain by sequence alignment analysis. Protein Sci. 9, 2457-2469, doi:10.1110/ps.9.12.2457 (2000).
11. Merz, T. et al. Stabilizing ionic interactions in a full-consensus ankyrin repeat protein. J. Mol. Biol. 376, 232-240, doi:10.1016/j.jmb.2007.11.047 (2008).
12. Sullivan, B. J., Durani, V. & Magliery, T. J. Triosephosphate isomerase by consensus design: dramatic differences in physical properties and activity of related variants. J. Mol. Biol. 413, 195-208, doi:10.1016/j.jmb.2011.08.001 (2011).
13. Magliery, T. J. & Regan, L. Beyond consensus: statistical free energies reveal hidden interactions in the design of a TPR motif. J. Mol. Biol. 343, 731-745, doi:10.1016/j.jmb.2004.08.026 (2004).
14. Socolich, M. et al. Evolutionary information for specifying a protein fold. Nature 437, 512-518, doi:Doi 10.1038/Nature03991 (2005).
15. Russ, W. P., Lowery, D. M., Mishra, P., Yaffe, M. B. & Ranganathan, R. Natural-like function in artificial WW domains. Nature 437, 579-583, doi:10.1038/nature03990 (2005).
16. Magliery, T. J., Lavinder, J. J. & Sullivan, B. J. Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems. Curr. Opin. Chem. Biol. 15, 443-451, doi:10.1016/j.cbpa.2011.03.015 (2011).
17. Dadashipour, M. & Asano, Y. Hydroxynitrile Lyases: Insights into Biochemistry, Discovery, and Engineering. ACS Catalysis 1, 1121-1149, doi:Doi 10.1021/Cs200325q (2011).
18. Gruber, K., Gartler, G., Krammer, B., Schwab, H. & Kratky, C. Reaction mechanism of hydroxynitrile lyases of the alpha/beta-hydrolase superfamily - The three-dimensional structure of the transient enzyme-substrate complex certifies the crucial role of LYS236. J. Biol. Chem. 279, 20501-20510, doi:DOI 10.1074/jbc.M401575200 (2004).
19. Buhler, H.,Miehlich, B. & Effenberger, F. Inversion of stereoselectivity by applying mutants of the hydroxynitrile lyase from Manihot esculenta. Chembiochem 6, 711-717, doi:10.1002/cbic.200400302 (2005).
20. Asano, Y., Dadashipour, M., Yamazaki, M., Doi, N. & Komeda, H. Functional expression of a plant hydroxynitrile lyase in Escherichia coli by directed evolution: creation and characterization of highly in vivo soluble mutants. Protein Engineering Design & Selection 24, 607-616, doi:DOI 10.1093/protein/gzr030 (2011).
21. Nakano, S., Dadashipour, M. & Asano, Y. Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics. Biochim. Biophys. Acta 1844, 2059-2067, doi:10.1016/j.bbapap.2014.09.004 (2014).
22. Schmidt, A., Gruber, K., Kratky, C. & Lamzin, V. S. Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis. J. Biol. Chem. 283, 21827-21836, doi:10.1074/jbc.M801056200 (2008).
23. Holt, J. & Hanefeld, U. Enantioselective Enzyme-Catalysed Synthesis of Cyanohydrins. Current Organic Synthesis 6, 15-37, doi:10.2174/157017909787314858 (2009).
24. Purkarthofer, T., Skranc, W., Schuster, C. & Griengl, H. Potential and capabilities of hydroxynitrile lyases as biocatalysts in the chemical industry. Appl. Microbiol. Biotechnol. 76, 309-320, doi:10.1007/s00253-007-1025-6 (2007).
25. Nedrud, D. M. et al. Uncovering divergent evolution of alpha/beta-hydrolases: a surprising residue substitution needed to convert hydroxynitrile lyase into an esterase. Chem. Sci. 5, 4265-4277, doi:10.1039/c4sc01544d (2014).
26. Padhi, S. K. et al. Switching from an esterase to a hydroxynitrile lyase mechanism requires only two amino acid substitutions. Chem. Biol. 17, 863-871, doi:10.1016/j.chembiol.2010.06.013 (2010).
27. Edgar, R. C. & Batzoglou, S. Multiple sequence alignment. Curr. Opin. Struct. Biol. 16, 368-373, doi:DOI 10.1016/j.sbi.2006.04.004 (2006).
28. Hughes, J., Carvalho, F. J. & Hughes, M. A. Purification, characterization, and cloning of alpha-hydroxynitrile lyase from cassava (Manihot esculenta Crantz). Arch. Biochem. Biophys. 311, 496-502 (1994).
29. Hasslacher, M. et al. Molecular cloning of the full-length cDNA of (S)-hydroxynitrile lyase from Hevea brasiliensis. Functional expression in Escherichia coli and Saccharomyces cerevisiae and identification of an active site residue. J. Biol. Chem. 271, 5884-5891 (1996).
30. Forouhar, F. et al. Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity. Proc. Natl. Acad. Sci. U S A 102, 1773-1778, doi:10.1073/pnas.0409227102 (2005).
31. Cui, F. C., Pan, X. L. & Liu, J. Y. Catalytic mechanism of hydroxynitrile lyase from Hevea brasiliensis: a theoretical investigation. J. Phys. Chem. B 114, 9622-9628, doi:10.1021/jp100373e (2010).
32. Magliery, T. J. & Regan, L. Combinatorial approaches to protein stability and structure. Eur. J. Biochem. 271, 1595-1608, doi:10.1111/j.1432-1033.2004.04075.x (2004).
33. Jimenez-Oses, G. et al. The role of distant mutations and allosteric regulation on LovD active site dynamics. Nat. Chem. Biol. 10, 431-436, doi:10.1038/nchembio.1503 (2014).
34. Bhabha, G. et al. A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332, 234-238, doi:10.1126/science.1198542 (2011).
35. Cheeseman, J. D., Tocilj, A., Park, S., Schrag, J. D. & Kazlauskas, R. J. Structure of an aryl esterase from Pseudomonas fluorescens. Acta Crystallogr. D Biol. Crystallogr. 60, 1237-1243, doi:10.1107/S0907444904010522 (2004).
36. Toth-Petroczy, A. & Tawfik, D. S. Slow protein evolutionary rates are dictated by surface-core association. Proc. Natl. Acad. Sci. U S A 108, 11151-11156, doi:10.1073/pnas.1015994108 (2011).
37. Bershtein, S., Goldin, K. & Tawfik, D. S. Intense neutral drifts yield robust and evolvable consensus proteins. J. Mol. Biol. 379, 1029-1044, doi:10.1016/j.jmb.2008.04.024 (2008).
38. Amitai, G., Gupta, R. D. & Tawfik, D. S. Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J. 1, 67-78, doi:10.2976/1.2739115/10.2976/1 (2007).
39. Harms, M. J. & Thornton, J. W. Analyzing protein structure and function using ancestral gene reconstruction. Curr. Opin. Struct. Biol. 20, 360-366, doi:10.1016/j.sbi.2010.03.005 (2010).
40. Dean, A. M. & Thornton, J. W. Mechanistic approaches to the study of evolution: the functional synthesis. Nat. Rev. Genet. 8, 675-688, doi:10.1038/nrg2160 (2007).
41. Crameri, A., Raillard, S. A., Bermudez, E. & Stemmer, W. P. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288-291, doi:10.1038/34663 (1998).
42. Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic. Acids Res. 22, 4673-4680 (1994).
43. Dadashipour, M. et al. S-selective hydroxynitrile lyase from a plant Baliospermum montanum: molecular characterization of recombinant enzyme. J. Biotechnol. 153, 100-110, doi:10.1016/j.jbiotec.2011.02.004 (2011).
44. Greenfield, N. J. Analysis of the kinetics of folding of proteins and peptides using circular dichroism. Nat. Protoc. 1, 2891-2899, doi:10.1038/nprot.2006.244 (2006).
45. Rink, R. et al. Mutation of Tyrosine Residues Involved in the Alkylation Half Reaction of Epoxide Hydrolase from Agrobacterium radiobacter AD1 Results in Improved Enantioselectivity. J. Am. Chem. Soc. 121, 7417-7418, doi:10.1021/ja990501o (1999).