Transmembrane Domains of Bitopic Proteins As a Key to Understand the Cellular Signaling

Мұқаба

Дәйексөз келтіру

Толық мәтін

Ашық рұқсат Ашық рұқсат
Рұқсат жабық Рұқсат берілді
Рұқсат жабық Рұқсат ақылы немесе тек жазылушылар үшін

Аннотация

This work presents in a systematic manner key modeling results corroborated by experimental biophysical data and obtained by the authors during long-term research on bitopic (single-pass) membrane proteins (BMP), which are the crucial elements of cell signaling. The manuscript does not claim to be a comprehensive review on the topic, whereby the authors did not aim to describe accurately the current state of the art, given the numerous reliable publications. Rather, it is an essay illustrating the authors’ understanding of the basic principles in organization of transmembrane protein domains (TMD) and their contribution to the cell functioning. Among the key topics highlighted in the present work are the fine-tuned processes of TMD oligomerization and direct contribution of the dynamic membrane environment to this process, the key role of TMD in the functioning of cell receptors and mutual relations between all components of protein-membrane complexes during the signal transduction in normal and pathological conditions.

Толық мәтін

Рұқсат жабық

Авторлар туралы

A. Polyansky

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Email: efremov@nmr.ru
Ресей, ul. Miklukho-Maklaya 16/10, Moscow, 117997

R. Efremov

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; National Research University Higher School of Economics; Moscow Institute of Physics and Technology (State University)

Хат алмасуға жауапты Автор.
Email: efremov@nmr.ru
Ресей, ul. Miklukho-Maklaya 16/10, Moscow, 117997; ul. Myasnitskaya 20, Moscow 101000; Institutsky per. 9/3, Dolgoprudny, 141701

Әдебиет тізімі

  1. Engel A., Gaub H.E. // Ann. Rev. Biochem. 2008. V. 77. P. 127–148. https://doi.org/10.1146/annurev.biochem.77.062706. 154450
  2. Deisenhofer J., Epp O., Miki K., Huber R., Michel H. // Nature. 1985. V. 318. P. 618–624. https://doi.org/10.1038/318618a0
  3. Ernst O.P., Lodowski D.T., Elstner M., Hegemann P., Brown L.S., Kandori H. // Chem. Rev. 2014. V. 114. P. 126–163. https://doi.org/10.1021/cr4003769
  4. Kandori H. // Biophys. Rev. 2020. V. 12. P. 355–361. https://doi.org/10.1007/s12551-020-00645-0
  5. Nadezhdin K.D., Neuberger A., Trofimov Y.A., Krylov N.A., Sinica V., Kupko N., Vlachova V., Zakharian E., Efremov R.G., Sobolevsky A.I. // Nat. Struct. Mol. Biol. 2021. V. 28. P. 564–572. https://doi.org/10.1038/s41594-021-00615-4
  6. Cymer F., Schneider D. // Cell Adh. Migr. 2010. V. 4. P. 299–312. https://doi.org/10.4161/cam.4.2.11191
  7. Bugge K., Lindorff-Larsen K., Kragelund B.B. // FEBS J. 2016. V. 283. P. 4424–4451. https://doi.org/10.1111/febs.13793
  8. MacKenzie K.R., Prestegard J.H., Engelman D.M. // Science. 1997. V. 276. P. 131–133. https://doi.org/10.1126/science.276.5309.131
  9. Henderson R., Unwin P.N.T. // Nature. 1975. V. 257. P. 28–32. https://doi.org/10.1038/257028a0
  10. Consortium T.U. // Nucleic Acids Res. 2022. V. 51. P. D523–D531. https://doi.org/10.1093/nar/gkac1052
  11. Kahn T.W., Engelman D.M. // Biochemistry. 1992. V. 31. P. 6144–6151. https://doi.org/10.1021/bi00141a027
  12. White S.H., von Heijne G. // Annu. Rev. Biophys. 2008. V. 37. P. 23–42. https://doi.org/10.1146/annurev.biophys.37.032807. 125904
  13. Polyansky A.A., Chugunov A.O., Volynsky P.E., Krylov N.A., Nolde D.E., Efremov R.G. // Bioinformatics. 2013. V. 30. P. 889–890. https://doi.org/10.1093/bioinformatics/btt645
  14. Russ W.P., Engelman D.M. // J. Mol. Biol. 2000. V. 296. P. 911–919. https://doi.org/10.1006/jmbi.1999.3489
  15. Kordyukova L.V., Serebryakova M.V., Polyansky A.A., Kropotkina E.A., Alexeevski A.V., Veit M., Efremov R.G., Filippova I.Y., Baratova L.A. // Biochim. Biophys. Acta. 2011. V. 1808. P. 1843–1854. https://doi.org/10.1016/j.bbamem.2011.03.005
  16. Zhang L., Polyansky A., Buck M. // PLoS One. 2015. V. 10. P. e0121513. https://doi.org/10.1371/journal.pone.0121513
  17. Aliper E.T., Krylov N.A., Nolde D.E., Polyansky A.A., Efremov R.G. // Int. J. Mol. Sci. 2022. V. 23. P. 9221. https://doi.org/10.3390/ijms23169221
  18. Polyansky A.A., Efremov R.G. // Comput. Struct. Biotechnol. J. 2023. V. 21. P. 2837–2844. https://doi.org/10.1016/j.csbj.2023.04.021
  19. Polyansky A.A., Bocharov E.V., Velghe A.I., Kuznetsov A.S., Bocharova O.V., Urban A.S., Arseniev A.S., Zagrovic B., Demoulin J.B., Efremov R.G. // Biochim. Biophys. Acta Gen. Subj. 2019. V. 1863. P. 82–95. https://doi.org/10.1016/j.bbagen.2018.09.011
  20. Albrecht C., Kuznetsov A.S., Appert-Collin A., Dhaideh Z., Callewaert M., Bershatsky Y.V., Urban A.S., Bocharov E.V., Bagnard D., Baud S., Blaise S., RomierCrouzet B., Efremov R.G., Dauchez M., Duca L., Gueroult M., Maurice P., Bennasroune A. // Front. Cell Dev. Biol. 2020. V. 8. https://doi.org/10.3389/fcell.2020.611121
  21. Jumper J., Evans R., Pritzel A., Green T., Figurnov M., Ronneberger O., Tunyasuvunakool K., Bates R., Žídek A., Potapenko A., Bridgland A., Meyer C., Kohl S.A.A., Ballard A.J., Cowie A., Romera-Paredes B., Nikolov S., Jain R., Adler J., Back T., Petersen S., Reiman D., Clancy E., Zielinski M., Steinegger M., Pacholska M., Berghammer T., Bodenstein S., Silver D., Vinyals O., Senior A.W., Kavukcuoglu K., Kohli P., Hassabis D. // Nature. 2021. V. 596. P. 583–589. https://doi.org/10.1038/s41586-021-03819-2
  22. Sahoo A.R., Souza P.C.T., Meng Z., Buck M. // Structure. 2023. V. 31. P. 735–745.e2. https://doi.org/10.1016/j.str.2023.03.014
  23. Muhle-Goll C., Hoffmann S., Afonin S., Grage S.L., Polyansky A.A., Windisch D., Zeitler M., Bürck J., Ulrich A.S. // J. Biol. Chem. 2012. V. 287. P. 26178– 26186. https://doi.org/10.1074/jbc.M111.325555
  24. Polyansky A.A., Volynsky P.E., Efremov R.G. // J. Am. Chem. Soc. 2012. V. 134. P. 14390–14400. https://doi.org/10.1021/ja303483k
  25. Bocharov E.V., Bragin P.E., Pavlov K.V., Bocharova O.V., Mineev K.S., Polyansky A.A., Volynsky P.E., Efremov R.G., Arseniev A.S. // Biochemistry. 2017. V. 56. P. 1697–1705. https://doi.org/10.1021/acs.biochem.6b01085
  26. Roepstorff K., Thomsen P., Sandvig K., van Deurs B. // J. Biol. Chem. 2002. V. 277. P. 18954–18960. https://doi.org/10.1074/jbc.M201422200
  27. Sottocornola E., Misasi R., Mattei V., Ciarlo L., Gradini R., Garofalo T., Berra B., Colombo I., Sorice M. // FEBS J. 2006. V. 273. P. 1821–1830. https://doi.org/10.1111/j.1742-4658.2006.05203.x
  28. Rohwedder A., Knipp S., Roberts L.D., Ladbury J.E. // Sci. Rep. 2021. V. 11. P. 6160. https://doi.org/10.1038/s41598-021-85578-8
  29. Roy A., Patra S.K. // Stem Cell Rev. Rep. 2022. V. 19. P. 2–25. https://doi.org/10.1007/s12015-022-10448-3
  30. Volynsky P.E., Polyansky A.A., Fakhrutdinova G.N., Bocharov E.V., Efremov R.G. // J. Am. Chem. Soc. 2013. V. 135. P. 8105–8108. https://doi.org/10.1021/ja4011942
  31. Kuznetsov A.S., Polyansky A.A., Fleck M., Volynsky P.E., Efremov R.G. // J. Chem. Theory Comput. 2015. V. 11. P. 4415–4426. https://doi.org/10.1021/acs.jctc.5b00206
  32. Velghe A.I., Van Cauwenberghe S., Polyansky A.A., Chand D., Montano-Almendras C.P., Charni S., Hallberg B., Essaghir A., Demoulin J.B. // Oncogene. 2014. V. 33. P. 2568–2576. https://doi.org/10.1038/onc.2013.218
  33. Russ W.P., Engelman D.M. // Proc. Natl. Acad. Sci. USA. 1999. V. 96. P. 863–868. https://doi.org/10.1073/pnas.96.3.863
  34. De Baets G., Van Doorn L., Rousseau F., Schymkowitz J. // PLoS Comput. Biol. 2015. V. 11. P. e1004374. https://doi.org/10.1371/journal.pcbi.1004374
  35. Suomivuori C.-M., Latorraca N.R., Wingler L.M., Eismann S., King M.C., Kleinhenz A.L.W., Skiba M.A., Staus D.P., Kruse A.C., Lefkowitz R.J., Dror R.O. // Science. 2020. V. 367. P. 881–887. https://doi.org/10.1126/science.aaz0326
  36. Chen P.H., Unger V., He X. // J. Mol. Biol. 2015. V. 427. P. 3921–3934. https://doi.org/10.1016/j.jmb.2015.10.003
  37. Arkhipov A., Shan Y., Das R., Endres N.F., Eastwood M.P., Wemmer D.E., Kuriyan J., Shaw D.E. // Cell. 2013. V. 152. P. 557–569. https://doi.org/10.1016/j.cell.2012.12.030
  38. Fleck M., Polyansky A.A., Zagrovic B. // J. Chem. Theory Comput. 2016. V. 12. P. 2055–2065. https://doi.org/10.1021/acs.jctc.5b01217
  39. Westerfield J.M., Barrera F.N. // J. Biol. Chem. 2020. V. 295. P. 1792–1814. https://doi.org/10.1074/jbc.REV119.009457
  40. Mitchell C.J., Johnson T.S., Deber C.M. // Biophys. J. 2022. V. 121. P. 3253–3262. https://doi.org/10.1016/j.bpj.2022.07.026
  41. Love J., Mancia F., Shapiro L., Punta M., Rost B., Girvin M., Wang D.-N., Zhou M., Hunt J.F., Szyperski T., Gouaux E., MacKinnon R., McDermott A., Honig B., Inouye M., Montelione G., Hendrickson W.A. // J. Struct. Funct. Genomics. 2010. V. 11. P. 191–199. https://doi.org/10.1007/s10969-010-9094-7

Қосымша файлдар

Қосымша файлдар
Әрекет
1. JATS XML
Жүктеу
2. Fig. 1. Structural, dynamic and functional aspects of the study of TM domains of BMB using molecular biophysical modeling methods. TMD and the full-length PDGFRA receptor are used for illustration.

Жүктеу (606KB)
Метадеректер

© Russian Academy of Sciences, 2024