Capabilities of SEC-SAXS Method in Research of Polydisperse Systems: The Case of Apoferritin

Kovalchuk M.V., Blagov A. E., Dyakova Yu. A., Gruzinov A. Yu., Marchenkova M. A., Peters G. S., Pisarevsky Yu. V., Timofeev V. I., Volkov V. V. 2016. Investigation of the initial crystallization stage in lysozyme solutions by small-angle X-ray scattering. Cryst. Growth Des. 16 (4), 1792–1797. https://doi.org/10.1021/acs.cgd.5b01662

Article  CAS  Google Scholar 

Korasick D. A., Tanner J. J. 2018. Determination of protein oligomeric structure from small-angle X-ray scattering. Protein Sci. 27 (4), 814–824. https://doi.org/10.1002/pro.3376

Article  CAS  PubMed  PubMed Central  Google Scholar 

Korasick D. A., Singh H., Pemberton T. A., Luo M., Dhatwalia R., Tanner J. J. 2017. Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure, FEBS J. 284 (18), 3029–3049. https://doi.org/10.1111/febs.14165

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oda T., Aihara T., Wakabayashi K. 2016. Early nucleation events in the polymerization of actin, probed by time-resolved small-angle x-ray scattering. Sci. Rep. 6 (1), 34539. https://doi.org/10.1038/srep34539

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sudarev V.V., Dolotova S.M., Bukhalovich S.M., et al. 2023. Ferritin self-assembly, structure, function, and biotechnological applications. Int. J. Biol. Macromol. 224, 319–343. https://doi.org/10.1016/j.ijbiomac.2022.10.126

Article  CAS  PubMed  Google Scholar 

Richter G.W., Walker G.F. 1967. Reversible association of apoferritin molecules. Comparison of light-scattering and other data. Biochemistry. 6 (9), 2871–2881. https://doi.org/10.1021/bi00861a031

Article  CAS  PubMed  Google Scholar 

Williams M.A., Harrison P.M. 1968. Electron-microscopic and chemical studies of oligomers in horse ferritin. Biochem. J. 110 (2), 265–280. https://doi.org/10.1042/bj1100265

Article  CAS  PubMed  PubMed Central  Google Scholar 

BjÖRK I. 1973. Association-dissociation behaviour and hydrodynamic properties of apoferritin monomer and dimer. Eur. J. Biochem. 36 (1), 178–184. https://doi.org/10.1111/j.1432-1033.1973.tb02899.x

Article  PubMed  Google Scholar 

Niitsu Y., Listowsky I. 1973. Mechanisms for the formation of ferritin oligomers. Biochemistry. 12 (23), 4690–4695. https://doi.org/10.1021/bi00747a023

Article  CAS  PubMed  Google Scholar 

Lee S.S.C., Richter G.W. 1976. The monomers and oligomers of ferritin and apoferritin: Association and dissociation, Biochemistry. 15 (1), 65–70. https://doi.org/10.1021/bi00646a011

Article  CAS  PubMed  Google Scholar 

Singh B. P., Bohidar H. B., Chopra S. 1991. Heat aggregation studies of phycobilisomes, ferritin, insulin, and immunoglobulin by dynamic light scattering. Biopolymers. 31 (12), 1387–1396. https://doi.org/10.1002/bip.360311205

Article  CAS  PubMed  Google Scholar 

Yang D., Matsubara K., Yamaki M., Ebina S., Nagayama K. 1994. Heterogeneities in ferritin dimers as characterized by gel filtration, nuclear magnetic resonance, electrophoresis, transmission electron microscopy, and gene engineering techniques. Biochim. Biophys. Acta, Protein Struct. Mol. Enzymol. 1206 (2), 173–179. https://doi.org/10.1016/0167-4838(94)90205-4

Article  CAS  Google Scholar 

Petsev D.N., Thomas B.R., Yau S.-T., Vekilov P.G. 2000. Interactions and aggregation of apoferritin molecules in solution: Effects of added electrolytes, Biophys. J. 78 (4), 2060–2069. https://doi.org/10.1016/S0006-3495(00)76753-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zabelskii D. V., Vlasov A. V., Ryzhykau Y. L., Murugova T. N., et al. 2018. Ambiguities and completeness of SAS data analysis: investigations of apoferritin by SAXS/SANS EID and SEC-SAXS methods. J. Phys. Conf. Ser. 994 (1), 012017. https://doi.org/10.1088/1742-6596/994/1/012017

Article  CAS  Google Scholar 

Graewert M.A., Da Vela S., Gräwert T.W., Molodenskiy D.S., Blanchet C.E., Svergun D.I., Jeffries C.M. 2020. Adding size exclusion chromatography (SEC) and light scattering (LS) devices to obtain high-quality small angle X-ray scattering (SAXS) data. Crystals. 10 (11), 975. https://doi.org/10.3390/cryst10110975

Article  CAS  Google Scholar 

Bucciarelli S., Midtgaard S.R., Nors Pedersen M., Skou S., Arleth L., Vestergaard B. 2018. Size-exclusion chromatography small-angle X-ray scattering of water-soluble proteins on a laboratory instrument. J. Appl. Crystallogr. 51 (6), 1623–1632. https://doi.org/10.1107/S1600576718014462

Article  CAS  PubMed  PubMed Central  Google Scholar 

Blanchet C.E., Round A., Mertens H.D.T., Ayyer K., et al. 2023. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS). Commun. Biol. 6 (1), 1057. https://doi.org/10.1038/s42003-023-05416-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brennich M. E., Kieffer J., Bonamis G., De Maria Antolinos A., Hutin S., Pernot P., Round A. 2016. Online data analysis at the ESRF bioSAXS beamline, BM29. J. Appl. Crystallogr. 49 (1), 203–212. https://doi.org/10.1107/S1600576715024462

Article  CAS  Google Scholar 

Hopkins J. B., Gillilan R. E., Skou S. 2017. BioXTAS RAW: Improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis, J. Appl. Crystallogr. 50 (5), 1545–1553. https://doi.org/10.1107/S1600576717011438

Article  CAS  PubMed  PubMed Central  Google Scholar 

Svergun D.I. 1992. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25 (4), 495–503. https://doi.org/10.1107/S0021889892001663

Article  CAS  Google Scholar 

Hajizadeh N.R., Franke D., Jeffries C.M., Svergun D.I. 2018. Consensus Bayesian assessment of protein molecular mass from solution X-ray scattering data. Sci. Rep. 8, 7204. https://doi.org/10.1038/s41598-018-25355-2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Harris C.R., Millman K.J., van der Walt S.J., Gommers R., et al. 2020. Array programming with NumPy. Nature. 585 (7825), 357–362. https://doi.org/10.1038/s41586-020-2649-2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Virtanen P., Gommers R., Oliphant T.E., Haberland M., et al. 2020. SciPy 1.0: Fundamental algorithms for scientific computing in Python. Nat. Methods. 17 (3), 261–272. https://doi.org/10.1038/s41592-019-0686-2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hunter J.D. 2007. Matplotlib: A 2D graphics environment. Comput. Sci. Eng. 9 (3), 90–95. https://doi.org/10.1109/MCSE.2007.55

Article  Google Scholar 

McKinney W. 2010. Data structures for statistical computing in python. Proceedings of the 9th Python in Science Conference, p. 56–61. https://doi.org/10.25080/Majora-92bf1922-00a

The pandas development team. 2020. pandas-dev/pandas: Pandas (v1.5.3) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.7549438

Buitinck L., Louppe G., Blondel M., Pedregosa F., et al. 2013. API design for machine learning software: Experiences from the scikit-learn project. arXiv preprint arXiv:1309.0238. https://doi.org/10.48550/arXiv.1309.0238

Svergun D.I., Feigin L.A. 1986. Rentgenovskoe i neitronnoe malouglovoe rasseyanie (Small angle X-ray and neutron scattering. Moscow: Nauka) [Translated into English (Structure analysis by small-angle X-ray and neutron scattering. New York: Plenum Press, 1987)].

Yau S.T., Vekilov P.G. 2000. Quasi-planar nucleus structure in apoferritin crystallization. Nature. 406 (6795), 494–497. https://doi.org/10.1038/35020035

Article  CAS  PubMed  Google Scholar 

Comments (0)

No login
gif