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EPSP synthase flexibility is determinant to its function: computational molecular dynamics and metadynamics studies

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Abstract

Flexibility is involved in a wide range of biological processes, such as protein assembly and binding recognition. EPSP synthase is an enzyme that must undergo a large conformational change to accommodate its ligands into its binding cavity. However, although the structure of EPSP synthase has been determined, its plasticity has not been explored in depth. Therefore, in this work, we extensively examined the influence of the flexibility of Mycobacterium tuberculosis EPSP (MtEPSP) synthase on the function of this protein using classical and replica-exchange metadynamics simulations. We were able to identify five well-populated conformational clusters for MtEPSP synthase: two corresponding to open, one to ajar, and two to closed conformations. We also pinpointed three hydrophobic regions that are responsible for guiding transitions among these states. Taken together, the new findings presented here indicate how the hydrophobic regions modulate the flexibility of MtEPSP synthase, and they highlight the importance of considering these dynamic features in drug design projects employing this enzyme as a target.

The flexibility of EPSP synthase as a function of the pincer angles

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Acknowledgments

We would like to thank Predrag Kukic for helpful discussion about the manuscript, and Ivani Pauli, Rafael A. Caceres, and José Fernando R. Bachega for their valuable suggestions.

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Authors and Affiliations

  1. Laboratory for Bioinformatics, Modelling and Simulation of Biosystems (LABIO), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681 – LABIO, Prédio 32, Sala 602, Partenon, Porto Alegre, RS, CEP: 90619-900, Brazil

    Luís Fernando Saraiva Macedo Timmers & Osmar Norberto de Souza

  2. Laboratory of PharmInformatics, PUCRS, Porto Alegre, RS, Brazil

    Luís Fernando Saraiva Macedo Timmers & Osmar Norberto de Souza

  3. Graduate Program in Cellular and Molecular Biology (PPGBCM), PUCRS, Porto Alegre, RS, Brazil

    Luís Fernando Saraiva Macedo Timmers, Luiz A. Basso, Diógenes S. Santos & Osmar Norberto de Souza

  4. São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil

    Antônio M. S. Neto & Rinaldo W. Montalvão

  5. Research Centre of Molecular and Functional Biology (CPBMF), PUCRS, Porto Alegre, RS, Brazil

    Luís Fernando Saraiva Macedo Timmers, Luiz A. Basso, Diógenes S. Santos & Osmar Norberto de Souza

  6. Graduate Program in Medicine and Health Sciences (PPGMCS), PUCRS, Porto Alegre, RS, Brazil

    Luís Fernando Saraiva Macedo Timmers & Luiz A. Basso

Authors
  1. Luís Fernando Saraiva Macedo Timmers
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  2. Antônio M. S. Neto
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  3. Rinaldo W. Montalvão
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The manuscript was written through the contributions of all the authors. All authors gave their approval to the final version of the manuscript.

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Correspondence to Osmar Norberto de Souza.

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Funding sources

This project was supported fully or in part by grants from the National Research Council of Brazil (CNPq) to O.N.S. (308,124/2015–4) and to D.S.S and L.A.B. via The National Institute of Science and Technology in Tuberculosis (DECIT/SCTIE/MS - MCT - CNPq - FNDCT - CAPES), and from FAPERGS to O.N.S. (TO2054–2551/13–0). D.S.S., L.A.B., and O.N.S. are Research Career Awardees of the CNPq. L.F.S.M.T. acknowledges Ph.D. scholarships awarded by CAPES. L.F.S.M.T. also thanks CNPq for a split Ph.D. fellowship (229,676/2013–8). R.W.M. acknowledges the São Paulo Research Foundation (FAPESP, grant #2011/11343–0). A.M.S.N. acknowledges Ph.D. scholarships awarded by FAPESP (grant #2013/18398–0).

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PA1 distribution from classical MD simulations (50 ns and 300 ns) and metadynamics simulation (PDF file).

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Timmers, L.F.S.M., Neto, A.M.S., Montalvão, R.W. et al. EPSP synthase flexibility is determinant to its function: computational molecular dynamics and metadynamics studies. J Mol Model 23, 197 (2017). https://doi.org/10.1007/s00894-017-3372-2

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  • DOI: https://doi.org/10.1007/s00894-017-3372-2

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