Three-Dimensional Structure of the Orange-Red Fluorescent Biomarker DiB3-F53L
- Autores: Rossohin A.V1,2, Artemiev I.V1, Arhipova S.F1, Pletnev V.Z1, Pletneva N.V1
-
Afiliações:
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
- Research Center of Neurology, Institute of Brain
- Edição: Volume 51, Nº 6 (2025)
- Páginas: 1088-1092
- Seção: ЭКСПЕРИМЕНТАЛЬНЫЕ СТАТЬИ
- URL: https://ogarev-online.ru/0132-3423/article/view/356316
- DOI: https://doi.org/10.7868/S1998286025060071
- ID: 356316
Citar
Acesso aberto
Acesso está concedido
Somente assinantes
Resumo
The 3D structure of the fluorescent protein DiB3-F53L, an orange-red fluorescent non-covalent complex of a genetically engineered variant of the bacterial protein lipocalin Blc with a synthetic GFP-like chromophore M739, was studied by the molecular dynamics (MD) computational method. The chromophore was shown to interact more strongly with the mutated DiB3-F53L protein than with the native DiB3 protein. Calculations revealed the amino acids surrounding the chromophore at the binding site that contribute most strongly to the chromophore-protein interaction energy. The DiB3-F53L protein complex with the M739 chromophore exhibits increased fluorescence brightness compared to the known parent biomarker DiB3, making it a promising marker for labeling biological objects in cell biology, as well as a starting point for the subsequent design of new, brighter biological markers.
Palavras-chave
Sobre autores
A. Rossohin
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; Research Center of Neurology, Institute of Brain
Email: altrossokhin@yandex.ru
Moscow, Russia; Moscow, Russia
I. Artemiev
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
S. Arhipova
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
V. Pletnev
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
Email: vzpletnev@gmail.com
Moscow, Russia
N. Pletneva
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
Bibliografia
- Rothe C., Skerra A. // BioDrugs. 2018. V. 32. P. 233–243. https://doi.org/10.1007/s40259-018-0278-1
- 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
- Muslinkina L., Gavrikov A.S., Bozhanova N.G., Mishin A.S., Baranov M.S., Meiler J., Pletneva N.V., Pletnev VZ., Pletnev S. // ACS Chem. Biol. 2020. V. 15. P. 2456–2465. https://doi.org/10.1021/acschenbio.0c00440
- Bozhanova N.G., Baranov M.S., Klementieva N.V., Sarkisyan K.S., Gavrikov A.S., Yampolsky I.V., Zagaynova E.V., Lukyanov S.A., Lukyanov K.A., Mishin A.S. // Chem. Sci. 2017. V. 8. P. 7138–7142. https://doi.org/10.1039/C7SC016281
- Emsley P., Lohkamp B., Scott W.G., Cowtan K. // Acta Crystal. Section D. Biol. Crystal. 2010. V. 66. P. 486–501. https://doi.org/10.1107/S0907444910007493
- Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., Schulten K. // J. Computat. Chem. 2005. V. 26. P. 1781–1802.
- Humphrey W., Dalke A., Schulten K. // J. Mol. Graph. 1996. V. 14. P. 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
- Lee J., Cheng X., Swails J.M., Yeom M.S., Eastman P.K., Lemkal J.A., Wei S., Buckner J., Jeong J.C., Qi Y., Jo S., Pande Y.S., Cass D.A., Brooks C.L., 3rd, MacKerell A.D., Jr., Klauda J.B., Im W. // J. Chem. Theory Computat. 2016. V. 12. P. 405–413. https://doi.org/10.1021/acs.jctc.5b00935
- Darden T., York D., Pedersen L. // J. Chem. Phys. 1993. V. 103. P. 8577–8593. https://doi.org/10.1063/1.464397
- Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. // J. Chem. Phys. 1995. V. 98. P. 10089–10092. https://doi.org/10.1063/1.470117
- Karplus M., Petsko G.A. // Mol. Dynam. Simulat. Biol. Nat. 1990. V. 347. P. 631–639. https://doi.org/10.1038/347631a0
- Isralewitz B., Baudry J., Gullingsrud J., Kosztin D., Schulten K. // J. Mol. Graph. Model. 2001. V. 19. P. 13–25. https://doi.org/10.1016/s1093-3263(00)00133-9
Arquivos suplementares
