Objective Criteria for Estimation of Initial Parameters for the Modeling of Micelle and Liposome Structures from Small-Angle X-ray Scattering Data

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The structures of hydrophobic membrane proteins are studied using matrices, which serve as models of cell membranes and are formed by the appropriate amphiphilic molecules, e.g., by surfactant or lipid molecules. To study the structure of a protein incorporated into an artificial membrane, first of all it is necessary to determine the structure of the membrane. The ELLLIP and ELLMIC algorithms were previously developed to address this issue by small-angle X-ray scattering. These algorithms allow the construction of models of ellipsoidal vesicles based on the atomic structure of a lipid or surfactant monomer. However, the results of modeling depend, to a large extent, on the subjective assessment of the initial values of the structural parameters of the matrices and may be wrong due to the ambiguity in the solution of such problems. Here, we present an independent approach to the determination of the initial sizes of model membranes for their subsequent structural modeling, which is based on the analysis of the pair-distance distribution functions derived directly from the small-angle X-ray scattering curve.

作者简介

M. Petoukhov

Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia; Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071, Moscow, Russia

Email: pmxmvl@yandex.ru
Россия, Москва; Россия, Москва

E. Shtykova

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

编辑信件的主要联系方式.
Email: pmxmvl@yandex.ru
Россия, Москва

参考

  1. Jain P., Rauer S.B., Moller M. et al. // Biomacromolecules. 2022. V. 23. № 8. P. 3081. https://doi.org/10.1021/acs.biomac.2c00402
  2. Bayburt T.H., Sligar S.G. // FEBS Lett. 2010. V. 584. № 9. P. 1721. https://doi.org/10.1016/j.febslet.2009.10.024
  3. Knowles T.J., Finka R., Smith C. et al. // J. Am. Chem. Soc. 2009. V. 131. № 22. P. 7484. https://doi.org/10.1021/ja810046q
  4. Lee S.C., Knowles T.J., Postis V.L. et al. // Nat. Protoc. 2016. V. 11. № 7. P. 1149. https://doi.org/10.1038/nprot.2016.070
  5. Orwick M.C., Judge P.J., Procek J. et al. // Angew. Chem. Int. Ed. Engl. 2012. V. 51. № 19. P. 4653. https://doi.org/10.1002/anie.201201355
  6. Smirnova I.A., Sjostrand D., Li F. et al. // Biochim. Biophys. Acta. 2016. V. 1858. № 12. P. 2984. https://doi.org/10.1016/j.bbamem.2016.09.004
  7. Morrison K.A., Akram A., Mathews A. et al. // Biochem. J. 2016. V. 473. № 23. P. 4349. https://doi.org/10.1042/BCJ20160723
  8. Pautot S., Frisken B.J., Weitz D.A. // Proc. Natl. Acad. Sci. USA. 2003. V. 100. № 19. P. 10718. https://doi.org/10.1073/pnas.1931005100
  9. Hamada T., Miura Y., Komatsu Y. et al. // J. Phys. Chem. B. 2008. V. 112. № 47. P. 14678. https://doi.org/10.1021/jp807784j
  10. Cheng H.T., Megha, London E. // J. Biol. Chem. 2009. V. 284. № 10. P. 6079. https://doi.org/10.1074/jbc.M806077200
  11. Cheng H.T., London E. // Biophys. J. 2011. V. 100. № 11. P. 2671. https://doi.org/10.1016/j.bpj.2011.04.048
  12. Chiantia S., London E. // Biophys. J. 2012. V. 103. № 11. P. 2311. https://doi.org/10.1016/j.bpj.2012.10.033
  13. Elani Y., Purushothaman S., Booth P.J. et al. // Chem. Commun. (Camb.). 2015. V. 51. № 32. P. 6976. https://doi.org/10.1039/c5cc00712g
  14. Mineev K.S., Nadezhdin K.D. // Nanotechnol. Rev. 2017. V. 6. № 1. P. 15. https://doi.org/10.1515/ntrev-2016-0074
  15. Garavito R.M., Ferguson-Miller S. // J. Biol. Chem. 2001. V. 276. № 35. P. 32403. https://doi.org/10.1074/jbc.R100031200
  16. Seddon A.M., Curnow P., Booth P.J. // Biochim. Biophys. Acta. 2004. V. 1666. № 1–2. P. 105. https://doi.org/10.1016/j.bbamem.2004.04.011
  17. Tanford C., Reynolds J.A. // Biochim. Biophys. Acta. 1976. V. 457. № 2. P. 133. https://doi.org/10.1016/0304-4157(76)90009-5
  18. MacKenzie K.R., Prestegard J.H., Engelman D.M. // Science. 1997. V. 276. № 5309. P. 131. https://doi.org/10.1126/science.276.5309.131
  19. Pages G., Torres A.M., Ju P. et al. // Eur. Biophys. J. 2009. V. 39. № 1. P. 111. https://doi.org/10.1007/s00249-009-0433-1
  20. Strandberg E., Ozdirekcan S., Rijkers D.T. et al. // Biophys. J. 2004. V. 86. № 6. P. 3709. https://doi.org/10.1529/biophysj.103.035402
  21. Feigin L.A., Svergun D.I. Structure analysis by small-angle x-ray and neutron scattering. New York: Plenum Press, 1987. 335 p.
  22. Shtykova E.V., Volkov V.V., Wang H.J. et al. // Langmuir. 2006. V. 22. № 19. P. 7994. https://doi.org/10.1021/la060879h
  23. Jensen G.V., Lund R., Gummel J. et al. // J. Am. Chem. Soc. 2013. V. 135. № 19. P. 7214. https://doi.org/10.1021/ja312469n
  24. Dwivedi D., Lepkova K. SAXS and SANS Techniques for Surfactant Characterization: Application in Corrosion Science. Application and Characterization of Surfactants. University of Tabriz: IntechOpen, 2017. 316 p.
  25. Us’yarov O.G. // Colloid. J. 2016. V. 78. P. 698. https://doi.org/10.1134/S1061933X16050227
  26. Razuvaeva E.V., Kulebyakina A.I., Streltsov D.R. et al. // Langmuir. 2018. V. 34. № 50. P. 15470. https://doi.org/10.1021/acs.langmuir.8b03379
  27. Сыбачин А.В., Локова А.Ю., Спиридонов В.В. et al. // Высокомолекулярные соединения. Серия А. 2019. V. 61. № 3. P. 244. https://doi.org/10.1134/S2308112019030179
  28. Zalygin A., Solovyeva D., Vaskan I. et al. // ChemistryOpen. 2020. V. 9. № 6. P. 641. https://doi.org/10.1002/open.201900276
  29. Konarev P.V., Petoukhov M.V., Dadinova L.A. et al. // J. Appl. Cryst. 2020. V. 53. P. 236. https://doi.org/10.1107/S1600576719015656
  30. Петухов М.В., Конарев П.В., Дадинова Л.А. et al. // Кристаллография. 2020. V. 65. № 2. P. 260. https://doi.org/10.31857/S0023476120020198
  31. Kordyukova L.V., Konarev P.V., Fedorova N.V. et al. // Membranes (Basel). 2021. V. 11. № 10. P. 772. https://doi.org/10.3390/membranes11100772
  32. Manalastas-Cantos K., Konarev P.V., Hajizadeh N.R. et al. // J. Appl. Cryst. 2021. V. 54. P. 343. https://doi.org/10.1107/S1600576720013412
  33. Shilova L.A., Knyazev D.G., Fedorova N.V. et al. // Biochemistry (Moscow). Suppl. Ser. A. Membr. Cell Biol. 2017. V. 11. № 3. P. 225. https://doi.org/10.1134/S1990747817030072
  34. Blanchet C.E., Spilotros A., Schwemmer F. et al. // J. Appl. Cryst. 2015. V. 48. № 2. P. 431. https://doi.org/10.1107/S160057671500254X
  35. Konarev P.V., Volkov V.V., Sokolova A.V. et al. // J. Appl. Cryst. 2003. V. 36. P. 1277. https://doi.org/10.1107/S0021889803012779
  36. Svergun D.I. // J. Appl. Cryst. 1992. V. 25. P. 495. https://doi.org/10.1107/S0021889892001663
  37. Svergun D.I., Semenyuk A.V., Feigin L.A. // Acta Cryst. A. 1988. V. 44. P. 244. https://doi.org/10.1107/S0108767387011255
  38. Svergun D.I., Barberato C., Koch M.H.J. // J. Appl. Cryst. 1995. V. 28. P. 768. https://doi.org/10.1107/S0021889895007047
  39. Svergun D.I. // Biophys. J. 1999. V. 76. № 6. P. 2879. https://doi.org/10.1016/S0006-3495(99)77443-6

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