Email this article Decomposition of Small-Angle Scattering Profiles from Two Conformational States of 3-Isopropylmalate Dehydrogenase Using Evolving Factor Analysis
- Authors: Konarev P.V.1,2, Volkov V.V.1,3
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Affiliations:
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia
- National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia
- National Research Centre “Kurchatov Institute,”, 123182, Moscow, Russia
- Issue: Vol 68, No 6 (2023)
- Pages: 946-950
- Section: ДИФРАКЦИЯ И РАССЕЯНИЕ ИОНИЗИРУЮЩИХ ИЗЛУЧЕНИЙ
- URL: https://journals.rcsi.science/0023-4761/article/view/231843
- DOI: https://doi.org/10.31857/S0023476123600155
- EDN: https://elibrary.ru/XRTPYF
- ID: 231843
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Abstract
The separation of two conformational states of 3-isopropylmalate dehydrogenase molecules from Thermus thermophilus in solution on a gel chromatographic column, attached to a sample cell of a small-angle X-ray scattering synchrotron beamline, has been simulated. The scattering intensity profiles from the open and closed forms of the enzyme molecules were restored by evolving factor analysis (EFA) using the synthetic data set with added Poisson noise at the relative level of 3–5%. Thus, the efficiency of the EFA algorithm is confirmed in the case of two-component mixtures consisting of particles with the same molecular masses.
About the authors
P. V. Konarev
Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia; National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia
Email: peter_konarev@mail.ru
Россия, Москва; Россия, Москва
V. V. Volkov
Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia; National Research Centre “Kurchatov Institute,”, 123182, Moscow, Russia
Author for correspondence.
Email: vvo@crys.ras.ru
Россия, Москва; Россия, Москва
References
- Svergun D.I., Koch M.H.J., Timmins P.A., May R.P. Small angle X-ray and neutron scattering from solutions of biological macromolecules. Oxford University Press, 2013. 358 p.
- Herranz-Trillo F., Groenning M., van Maarschalkerweerd A. et al. // Structure. 2017. V. 25. P. 5. https://doi.org/10.1016/j.str.2016.10.013
- Keller H.R., Massart D.L. // Chemom. Intell. Lab. Syst. 1992. V. 12. P. 209. https://doi.org/10.1016/0169-7439(92)80002-L
- Hopkins J.B., Gillilan R.E., Skou S.J. // J. Appl. Cryst. 2017. V. 50. P. 1545. https://doi.org/10.1107/S1600576717011438
- Konarev P.V., Graewert M.A., Jeffries C.Y. et al. // Protein Sci. 2022. V. 31. P. 269. https://doi.org/10.1002/pro.4237
- Panjkovich A., Svergun D.I. // Bioinformatics. 2018. V. 34. P. 1944. https://doi.org/10.1093/bioinformatics/btx846
- Konarev P.V., Volkov V.V. // Physics of Atomic Nuclei. 2022. V. 85. P. 2127. https://doi.org/10.1134/S1063778822090198
- Hayashi-Iwasaki Y., Oshima T. // Methods Enzymol. 2000. V. 324. P. 301. https://doi.org/10.1016/s0076-6879(00)24240-7
- Graczer E., Merlin A., Singh R.K. et al. // Mol. Biosyst. 2011. V. 7. P. 1646. https://doi.org/10.1039/C0MB00346H
- Pallo A., Olah J., Graczer E. et al. // FEBS J. 2014. V. 281. P. 5063. https://doi.org/10.1111/febs.13044
- Svergun D.I., Barberato C., Koch M.H.J. // J. Appl. Cryst. 1995. V. 28. P. 768. https://doi.org/10.1107/S0021889895007047
- Graczer E., Konarev P.V., Szimler. T. et al. // FEBS Lett. 2011. V. 585. P. 3297. https://doi.org/10.1016/j.febslet.2011.09.013
- Golub G.H., Reinsch C. // Numer. Math. 1970. V. 14. P. 403. https://doi.org/10.1007/bf02163027
- Ahrens J.H., Dieter U. // ACM Trans Math Software. 1982. V. 8. P. 163. https://doi.org/10.1145/355993.355997
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