Alternative Chromophore Binding Sites in Non-Covalent Fluorescent Complexes of Bacterial Lipocalin

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

The three-dimensional structure of DiB3, a fluorescent non-covalent complex of a genetically engineered variant of the bacterial protein lipocalin Blc with a synthetic GFP-like chromophore M739, was determined by the calculation method of molecular mechanics. Compared to the crystal structure of the related DiB1 complex, an alternative binding site for the M739 chromophore was found in the structure of the DiB3 complex.

About the authors

E. A. Goryacheva

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

Author for correspondence.
Email: goryacheva@ibch.ru
Russia, 117997, Moscow, ul. Miklukho-Maklaya 16/10

I. V. Artemyev

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

Email: goryacheva@ibch.ru
Russia, 117997, Moscow, ul. Miklukho-Maklaya 16/10

S. F. Arhipova

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

Email: goryacheva@ibch.ru
Russia, 117997, Moscow, ul. Miklukho-Maklaya 16/10

A. V. Rossohin

Research Center of Neurology

Email: goryacheva@ibch.ru
Russia, 105064, Moscow, per. Obuha 5

A. R. Gilvanov

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

Email: goryacheva@ibch.ru
Russia, 117997, Moscow, ul. Miklukho-Maklaya 16/10

V. Z. Pletnev

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

Email: goryacheva@ibch.ru
Russia, 117997, Moscow, ul. Miklukho-Maklaya 16/10

N. V. Pletnevа

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences

Email: goryacheva@ibch.ru
Russia, 117997, Moscow, ul. Miklukho-Maklaya 16/10

References

  1. Rothe C., Skerra A. // BioDrugs. 2018. V. 32. P. 233–243. https://doi.org/10.1007/s40259-018-0278-1
  2. Campanacci V., Bishop R.E., Blangy S., Tegoni M., Cambillau C. // FEBS Lett. 2006. V. 580. P. 877−883. https://doi.org/10.1016/j.febslet.2006.07.086
  3. Muslinkina L., Gavrikov A.S., Bozhanova N.G., Mishin A.S., Baranov M.S., Meiler J., Pletneva N.V., Pletnev V.Z., Pletnev S. // ACS Chem. Biol. 2020. V. 15. P. 2456−2465. https://doi.org/10.1021/acschembio.0c00440
  4. Bozhanova N.G., Mikhail S., Baranov M.S., Klementieva N.V., Gavrikov A.S., Sarkisyan K.S., Yampolsky I.V., Zagaynova E.V., Lukyanov S.A., Konstantin A., Lukyanov K.A., Mishin A.S. // Chem. Sci. 2017. V. 8. P. 7138–7142. https://doi.org/10.1039/C7SC01628J
  5. Ghosh S., Yu C.L., Ferraro D.J., Sudha S., Pal S.K., Schaefer W.F., Gibson D.T., Ramaswamy S. // Proc. Natl. Acad. Sci. USA. 2016. V. 13. P. 11513–11518. https://doi.org/10.1073/pnas.1525622113
  6. Garden D.P., Zhorov B.S. // J. Comput. Aided Mol. Des. 2010. V. 24. P. 91–105. https://doi.org/10.1007/s10822-009-9317-9
  7. Emsley P., Lohkamp B., Scott W.G., Cowtan K. // Acta Crystallogr. D Biol. Crystallogr. 2010. V. 66. P. 486–501. https://doi.org/10.1107/s0907444910007493
  8. Schiefner A., Chatwell L., Breustedt D.A., Skerra A. // Acta Crystallogr. D Biol. Crystallogr. 2010. V. 66. P. 1308–1315. https://doi.org/10.1107/s0907444910039375
  9. Bozhanova N.G., Calcutt M.W., Beavers W.N., Brown B.P., Skaar E.P., Meiler J. // FEBS Lett. 2021. V. 595. P. 206–219. https://doi.org/10.1002/1873-3468.14001
  10. Li Z., Scheraga H.A. // Proc. Natl. Acad. Sci. USA. 1987. V. 84. P. 6611–6615. https://doi.org/10.1073/pnas.84.19.6611
  11. Weiner J., Kollman P.A., Case D.A., Singh U.C., Chio C., Alagona G., Profeta S., Weiner P.K. // J. Am. Chem. Soc. 1984. V. 106. P. 765–784. https://doi.org/10.1021/ja00315a051
  12. Dewar M.J.S., Zoebisch E.G., Healy E.F., Stewart J.J.P. // J. Am. Chem. Soc. 1985. V. 107. P. 3902–3909. https://doi.org/10.1021/ja00299a024
  13. Stewart J.J.P. // Chem. Prog. Exch. 1990. V. 10. P. 86.

Supplementary files

Supplementary Files
Action
1. JATS XML
Download
2.

Download (168KB)
Indexing metadata
3.

Download (10KB)
Indexing metadata
4.

Download (347KB)
Indexing metadata
5.

Download (722KB)
Indexing metadata

Copyright (c) 2023 Е.А. Горячева, И.В. Артемьев, С.Ф. Архипова, А.В. Россохин, А. Р. Гильванов, В.З. Плетнев, Н.В. Плетнева