リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation

Okuda, Aya Shimizu, Masahiro Morishima, Ken Inoue, Rintaro Sato, Nobuhiro Urade, Reiko Sugiyama, Masaaki 京都大学 DOI:10.1038/s41598-021-85219-0

2021.03.11

概要

Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other.

この論文で使われている画像

参考文献

1. Apic, G., Gough, J. & Teichmann, S. A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310,

311–325 (2001).

2. Orengo, C. A. & Thornton, J. M. Protein families and their evolution—A structural perspective. Annu. Rev. Biochem. 74, 867–900

(2005).

3. Mann, M. & Jensen, O. N. Proteomic analysis of post-translational modifications. Nat. Biotechnol. 21, 255–261 (2003).

4. Melero, J. A. & Smith, A. E. Possible transcriptional control of three polypeptides which accumulate in a temperature-sensitive

mammalian cell line. Nature 272, 725–727 (1978).

5. Lee, A. S. The accumulation of three specific proteins related to glucose-regulated proteins in a temperature-sensitive hamster

mutant cell line K12. J. Cell Physiol. 106, 119–125 (1981).

6. Bennett, C. F., Balcarek, J. M., Varrichio, A. & Crooke, S. T. Molecular cloning and complete amino-acid sequence of form-I

phosphoinositide-specific phospholipase C. Nature 334, 268–270 (1988).

7. Martin, J. L. et al. A metabolite of halothane covalently binds to an endoplasmic reticulum protein that is highly homologous to

phosphatidylinositol-specific phospholipase C-α but has no activity. Biochem. Biophys. Res Commun. 178, 679–685 (1991).

8. Srivastava, S. P., Chen, N., Liu, Y. & Holtzman, J. L. Purification and characterization of a new isozyme of thiol:protein-disulfide

oxidoreductase from rat hepatic microsomes. J. Biol. Chem. 266, 20337–20344 (1991).

9. Urade, R. et al. Protein degradation by the phosphoiiiositide-specific phospholipase C-α family from rat liver endoplasmic reticulum. J. Biol. Chem. 267, 15152–15159 (1992).

10. Srivastava, S. P., Fuchs, J. A. & Holtzman, J. L. The reported cDNA sequence for phospholipase C α encodes protein disulfide

isomerase, isozyme Q-2 and not phospholipase-C. Biochem. Biophys. Res Commun. 193, 971–978 (1993).

11. Mazzarella, R. A. et al. Erp61 is GRP58, a stress-inducible luminal endoplasmic reticulum protein, but is devoid of phosphatidylinositide-specific phospholipase C activity. Arch. Biochem. Biophys. 308, 454–460 (1994).

12. Hirano, N. et al. Molecular cloning and characterization of a cDNA for bovine phospholipase C-α: proposal of redesignation of

phospholipase C-α. Biochem Biophys. Res. Commun. 204, 375–382 (1994).

13. Hirano, N. et al. Molecular cloning of the human glucose-regulated protein ERp57/GRP58, a thiol-dependent reductase. Identification of its secretory form and inducible expression by the oncogenic transformation. Eur. J. Biochem. 234, 336–342 (1995).

14. Kozlov, G., Määttänen, P., Thomas, D. Y. & Gehring, K. A structural overview of the PDI family of proteins. FEBS J. 277, 3924–3936

(2010).

15. Ellgaard, L. & Ruddock, L. W. The human protein disulphide isomerase family: Substrate interactions and functional properties.

EMBO Rep. 6, 28–32 (2005).

16. Lu, J. & Holmgred, A. The thioredoxin superfamily in oxidative protein folding. Antioxid. Redox Signal. 21, 457–470 (2014).

17. Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. The Phyre2 web portal for protein modeling, prediction and

analysis. Nat. Protoc. 10, 845–858 (2015).

18. Dong, G. et al. Insights into MHC class I peptide loading from the structure of the tapasin-ERp57 thiol oxidoreductase heterodimer.

Immunity 30, 21–32 (2009).

19. Jeffries, C. M. et al. Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron

scattering experiments. Nat. Protoc. 11, 2122–2153 (2016).

20. David, G. & Pérez, J. Combined sampler robot and high-performance liquid chromatography: A fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline. J. Appl. Ctyst. 42, 892–900 (2009).

21. Morishima, K. et al. Integral approach to biomacromolecular structure by analytical-ultracentrifugation and small-angle scattering.

Commun. Biol. 3, 294 (2020).

22. Inoue, R. et al. Newly developed Laboratory-based Size exclusion chromatography Small-angle X-ray scattering System (La-SSS).

Sci. Rep. 9, 12610 (2019).

23. Kozlov, G. et al. Crystal structure of the bb’ domains of the protein disulfide isomerase ERp57. Structure. 14, 1331–1339 (2006).

24. Takada, S. et al. Modeling structural dynamics of biomolecular complexes by coarse-grained molecular simulations. Acc. Chem.

Res. 48, 3026–3035 (2015).

25. Shimizu, M. et al. Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights. Proc.

Natl. Acad. Sci. USA 113, E8021–E8030 (2016).

26. Urade, R. et al. ER-60 domains responsible for interaction with calnexin and calreticulin. Biochemistry 43, 8858–8868 (2004).

27. Laemmli, U. Cleavage of structural proteins during assembly of head of bacteriophage-T4. Nature 227, 680–685 (1970).

28. Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling.

Biophys. J. 78, 1606–1619 (2000).

29. Sawicki, M. SEDfit: Software for spectral energy distribution fitting of photometric data. Publ. Astron. Soc. Pac. 124, 1208–1218

(2012).

30. Shimizu, N. et al. Software development for analysis of small-angle X-ray scattering data. AIP Conf. Proc. 1741, 50017 (2016).

31. Li, W., Wang, W. & Takada, S. Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains.

Proc. Natl. Acad. Sci. USA 111, 10550–10555 (2014).

32. The PyMOL Molecular Graphics System, Version 1.8, Schrödinger, LLC.

33. Tanaka, T., Hori, N. & Takada, S. How co-translational folding of multi-domain protein is affected by elongation schedule: Molecular simulations. PLoS. Comput. Biol. 11, e1004356 (2015).

34. Terakawa, T. & Takada, S. RESPAC: Method to determine partial charges in coarse-grained protein model and its application to

DNA-binding proteins. J. Chem. Theory. Comput. 10, 711–721 (2014).

35. Kenzaki, H. et al. Cafemol: A coarse-grained biomolecular simulator for simulating proteins at work. J. Chem. Theory. Comput. 7,

1979–1989 (2011).

36. Semenyuk, A. V. & Svergun, D. I. GNOM – a program package for small-angle scattering data processing. J. Appl. Ctyst. 24, 537–540

(1991).

Acknowledgements

This study was supported by MEXT/JSPS KAKENHI Grants (JP20K22629 to M. Shimizu; JP19K16088 to K.

M.; JP17K07361, JP19KK0071, and JP20K06579 to R. I.; JP17K07816 to N. S.; JP18H05229, JP18H05534, and

JP18H03681 to M. Sugiyama). and the Sasakawa Scientific Research Grant from The Japan Science Society

assigned to A. O. The study was also partially supported by a project for the construction of the basis for advanced

materials science and analytical study by the innovative use of quantum beams and nuclear sciences at the

Institute for Integrated Radiation and Nuclear Science, Kyoto University (KURNS) and a Grant for research

promotion in KURNS to A. O., M. Shimizu, and K. M. SAXS measurements using the SAXS at KURNS were

Scientific Reports |

Vol:.(1234567890)

(2021) 11:5655 |

https://doi.org/10.1038/s41598-021-85219-0

12

www.nature.com/scientificreports/

A Self-archived copy in

Kyoto University Research Information Repository

https://repository.kulib.kyoto-u.ac.jp

performed under proposal No. R2121 to N. S. We thank Prof. Shoji Takada at Kyoto University for providing

the computational resources.

Author contributions

A.O. and R.U. assembled and performed the sample preparation. A.O., K.M., R.I., and N.S. performed SAXS

measurements and analysed the SAXS profiles. A.O. and K.M. performed the AUC measurements and analysed the profiles. A.O. performed MALDI-TOF MS and LC-ESI-TOF MS and analysed the data. M. Shimizu

performed CG-MD simulations and analysed the simulation data. R.U. and M.S. designed the research, and all

authors wrote the paper.

Competing interests The authors declare no competing interests.

Additional information

Supplementary Information The online version contains supplementary material available at https​://doi.

org/10.1038/s4159​8-021-85219​-0.

Correspondence and requests for materials should be addressed to R.U. or M.S.

Reprints and permissions information is available at www.nature.com/reprints.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and

institutional affiliations.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International

License, which permits use, sharing, adaptation, distribution and reproduction in any medium or

format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the

Creative Commons licence, and indicate if changes were made. The images or other third party material in this

article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the

material. If material is not included in the article’s Creative Commons licence and your intended use is not

permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from

the copyright holder. To view a copy of this licence, visit http://creat​iveco​mmons​.org/licen​ses/by/4.0/.

© The Author(s) 2021

Scientific Reports |

(2021) 11:5655 |

https://doi.org/10.1038/s41598-021-85219-0

13

Vol.:(0123456789)

...

参考文献をもっと見る