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Integrated Computational Studies on Mutational Effects of a Nylon-Degrading Enzyme

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Quantum Systems in Physics, Chemistry, and Biology

Part of the book series: Progress in Theoretical Chemistry and Physics ((PTCP,volume 30))

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Abstract

We investigate the mutational effects on a particular mutant of the nylon oligomer hydrolase (NylB), Y170F, whose enzymatic activity is about 1/80 times smaller than that of the wild type (WT). To this aim, we have investigated them by several computational schemes and analyzed obtained data to reveal mutational effects due to Y170F. First, classical molecular dynamics (MD) simulations were performed to measure the stability of substrate-enzyme complexes. Owing to a replacement of Tyr170 by Phe170, it is found that water molecules flow to an active site, which might avoid the substrate degradation. Next, by using QM/MM Car-Parrinello molecular dynamics (QM/MM CPMD) complemented with meta-dynamics (Meta-D), we provide a detailed insight into the underlying acylation mechanism. Our results show that while in the WT the Tyr170 residue points the NH group towards the proton-acceptor site of an artificial amide bond, hence ready to react, in the Y170F this does not occur. The reason is ascribed to the absence of Tyr170 in the mutant, replaced by phenylalanine, unable to form H-bonds with the amide bond, thus resulting in an increase of the activation barrier by 11 kcal/mol. Nonetheless, despite the lack of H-bond between the Y170F and the mutant, also in this case the highest free energy barrier for the induced-fit is similar to that of WT revealed by Parallel Cascade MD (PaCS-MD) with free energy analyses. This seems to suggest that, in the induced-fit process, kinetics is little affected by the mutation. We also evaluated interaction energy between the substrate and amino acid residues in NylB and its changes upon the induced-fit processes by using fragment molecular orbital (FMO) method.

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Acknowledgements

We would like to express acknowledgement to Profs. S. Negoro, Y. Higuchi, and H. Shibata for their valuable suggestions from the experimental side and Profs. Y. Mochizuki, T. Matsui, M. Boero, M. Nakano, and Mr H. Ando for their tight collaboration for the integrated theoretical analyses. These works were supported from the Japan Society for the Promotion of Science (JSPS) Research Fellowship for Young Scientists, Grant-in-Aid for Scientific Research (Nos. 26102525, 26107004, and 22360350). Computer resources were provided from Research Center for Computational Science, Okazaki, Japan and Center of Computational Materials Science, Institute for Solid State Physics, The University of Tokyo, Japan.

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Authors and Affiliations

  1. Department of Materials Engineering Sciences, Graduate School of Sciences, Osaka University, Osaka, Japan

    Takeshi Baba & Yasuteru Shigeta

  2. Center for Basic Education and Integrated Learning, Kanagawa Institute of Technology, Atsugi, Japan

    Katsumasa Kamiya

  3. Department of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan

    Yasuteru Shigeta

Authors
  1. Takeshi Baba
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  2. Katsumasa Kamiya
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  3. Yasuteru Shigeta
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Corresponding author

Correspondence to Yasuteru Shigeta .

Editor information

Editors and Affiliations

  1. Chemistry and Pharmacy, University of Sofia, Sofia, Bulgaria

    Alia Tadjer

  2. Inst for Nuclear Res & Nuclear Ener, Sofia, Bulgaria

    Rossen Pavlov

  3. Laboratoire de Chimie Physique, CNRS & UPMC Laboratoire de Chimie Physique, Paris, France

    Jean Maruani

  4. Department of Quantum Chemistry, Uppsala University, Uppsala, Sweden

    Erkki J. Brändas

  5. CSIC, Madrid, Spain

    Gerardo Delgado-Barrio

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Baba, T., Kamiya, K., Shigeta, Y. (2017). Integrated Computational Studies on Mutational Effects of a Nylon-Degrading Enzyme. In: Tadjer, A., Pavlov, R., Maruani, J., Brändas, E., Delgado-Barrio, G. (eds) Quantum Systems in Physics, Chemistry, and Biology. Progress in Theoretical Chemistry and Physics, vol 30. Springer, Cham. https://doi.org/10.1007/978-3-319-50255-7_19

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