Molecular Dynamics Study of Thymidine Phosphorylase from E. coli in the Apo Form and in Complexes with Substrates

Crystallography Reports volume 64, pages98–104(2019)Cite this article

Abstract

Models of E. coli thymidine phosphorylase in complexes with the substrates — the complex with phosphate and the complex with phosphate and thymidine — were obtained by molecular docking calculations. The influence of the substrates on domain movements in the dimeric thymidine phosphorylase molecule was probed by molecular dynamics simulations. The two subunits were shown to function asynchronously. In the thymidine phosphorylase/phosphate and thymidine phosphorylase/phosphate/thymidine complexes, phosphate is more weakly bound in the active site and moves away from the phosphate-binding site during the 60-ns trajectory, whereas thymidine remains in the active site but undergoes conformational changes.

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ACKNOWLEDGMENTS

This work was supported by the Ministry of Science and Higher Education within the State assignment FSRC “Crystallography and Photonics” RAS.

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Affiliations

  1. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 119333, Moscow, Russia

    D. D. Sidorov-Biryukov, D. D. Podshivalov, V. I. Timofeev, N. E. Zhukhlistova & I. P. Kuranova

  2. National Research Centre “Kurchatov Institute”, 123098, Moscow, Russia

    D. D. Podshivalov, V. I. Timofeev & I. P. Kuranova

  3. M. V. Lomonosov Moscow State University, 119991, Moscow, Russia

    D. D. Podshivalov

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  1. D. D. Sidorov-Biryukov
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  2. D. D. Podshivalov
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  3. V. I. Timofeev
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  4. N. E. Zhukhlistova
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  5. I. P. Kuranova
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Correspondence to I. P. Kuranova.

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Translated by T. Safonova

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Sidorov-Biryukov, D.D., Podshivalov, D.D., Timofeev, V.I. et al. Molecular Dynamics Study of Thymidine Phosphorylase from E. coli in the Apo Form and in Complexes with Substrates. Crystallogr. Rep. 64, 98–104 (2019). https://doi.org/10.1134/S1063774518060287

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