Identification of key residues modulating the stereoselectivity of nitrile hydratase toward rac-mandelonitrile by semi-rational engineering

Biotechnology and Bioengineering
Zhongyi ChengZhemin Zhou

Abstract

Optically pure compounds are important in the synthesis of fine chemicals. Using directed evolution of enzymes to obtain biocatalysts that can selectively produce high-value chiral chemicals is often time-, money-, and resource-intensive; traditional semi-rational designs based on structural data and docking experiments are still limited due to the lack of accurate selection of hot-spot residues. In this study, through ligand-protein collision counts based on steered molecular dynamics simulation, we accurately identified four residues related to improving nitrile hydratase stereoselectivity toward rac-mandelonitrile (MAN). All the four selected residues had numerous collisions with rac-MAN. Five mutants significantly shifting stereoselectivity towards (S)-MAN were obtained from site-saturation mutagenesis, one of them, at position βPhe37, exhibiting efficient production of (S)-MAN with 96.8% eep , was isolated and further analyzed. The increased pulling force observed during SMD simulation was found to be in good coincidence with the formation of hydrogen bonds between (R)-MAN and residue βHis37. (R)-MAN had to break these barriers to enter the active site of nitrile hydratase and S selectivity was thus improved. The results i...Continue Reading

References

Mar 5, 1992·Nature·R LüthyD Eisenberg
Jan 1, 1994·Annual Review of Biophysics and Biomolecular Structure·K Svoboda, S M Block
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
May 20, 1998·Nature Structural Biology·S NagashimaI Endo
Apr 3, 2001·Current Opinion in Chemical Biology·A Archelas, R Furstoss
Apr 12, 2001·Current Opinion in Structural Biology·B IsralewitzK Schulten
Nov 9, 2001·Biochemical and Biophysical Research Communications·A MiyanagaT Wakagi
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Nov 23, 2005·Bioinformatics·Konstantin ArnoldTorsten Schwede
Mar 17, 2006·Biochemical and Biophysical Research Communications·A Ozlem Taştan Bishop, Trevor Sewell
Feb 1, 1958·Proceedings of the National Academy of Sciences of the United States of America·D E Koshland
Apr 26, 2006·Bioscience, Biotechnology, and Biochemistry·Hiromi TakaradaMasafumi Odaka
Nov 30, 2006·Chembiochem : a European Journal of Chemical Biology·Manfred T ReetzNikolaj Otte
Feb 1, 2008·Biophysical Journal·Karina Kubiak, Wieslaw Nowak
Sep 24, 2008·Proceedings of the National Academy of Sciences of the United States of America·Zhemin ZhouMichihiko Kobayashi
Oct 22, 2008·Nucleic Acids Research·Florian KieferTorsten Schwede
Mar 8, 2011·Organic & Biomolecular Chemistry·S van PeltR A Sheldon
May 2, 2014·Nucleic Acids Research·Marco BiasiniTorsten Schwede
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Jun 20, 2014·Biochemical and Biophysical Research Communications·Youtian CuiZhemin Zhou
Jun 28, 2016·Journal of Molecular Modeling·Tin Trung NguyenMai Suan Li
Jul 22, 2016·Chembiochem : a European Journal of Chemical Biology·Jan-Ytzen van der MeerGerrit J Poelarends
Aug 9, 2016·Methods in Enzymology·C L RamírezA E Roitberg
Dec 15, 2016·Journal of Chemical Information and Modeling·Jakub Jakowiecki, Slawomir Filipek

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Citations

May 12, 2020·Frontiers in Bioengineering and Biotechnology·Zhongyi ChengZhemin Zhou
Dec 14, 2019·Scientific Reports·Karolina Mikulska-RuminskaWieslaw Nowak
Oct 23, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Zhongyi ChengLukasz Peplowski
Jul 5, 2021·Biotechnology Advances·Lunjie WuYi-Lei Zhao

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