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 「Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach」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

Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach

Yunoki, Yasuhiro Matsumoto, Atsushi Morishima, Ken Martel, Anne Porcar, Lionel Sato, Nobuhiro Yogo, Rina Tominaga, Taiki Inoue, Rintaro Yagi-Utsumi, Maho Okuda, Aya Shimizu, Masahiro Urade, Reiko Terauchi, Kazuki Kono, Hidetoshi Yagi, Hirokazu Kato, Koichi Sugiyama, Masaaki 京都大学 DOI:10.1038/s42003-022-03143-z

2022

概要

In the cyanobacterial circadian clock system, KaiA, KaiB and KaiC periodically assemble into a large complex. Here we determined the overall structure of their fully assembled complex by integrating experimental and computational approaches. Small-angle X-ray and inverse contrast matching small-angle neutron scatterings coupled with size-exclusion chromatography provided constraints to highlight the spatial arrangements of the N-terminal domains of KaiA, which were not resolved in the previous structural analyses. Computationally built 20 million structural models of the complex were screened out utilizing the constrains and then subjected to molecular dynamics simulations to examine their stabilities. The final model suggests that, despite large fluctuation of the KaiA N-terminal domains, their preferential positionings mask the hydrophobic surface of the KaiA C-terminal domains, hindering additional KaiA-KaiC interactions. Thus, our integrative approach provides a useful tool to resolve large complex structures harboring dynamically fluctuating domains.

この論文で使われている画像

参考文献

1.

2.

3.

4.

5.

6.

7.

8.

9.

10.

11.

12.

13.

14.

15.

16.

17.

18.

19.

Bonomi, M. & Vendruscolo, M. Determination of protein structural

ensembles using cryo-electron microscopy. Curr. Opin. Struct. Biol. 56, 37–45

(2019).

Patil, N. K., Bohannon, J. K., Hernandez, A., Patil, T. K. & Sherwood, E. R.

Regulation of leukocyte function by citric acid cycle intermediates. J. Leukoc.

Biol. 106, 105–117 (2019).

Sora, V. et al. Structure and dynamics in the ATG8 family from experimental

to computational techniques. Front. Cell Dev. Biol. 8, 420 (2020).

Ziegler, S. J., Mallinson, S. J., John, P. C. S. & Bomble, Y. J. Advances in

integrative structural biology: Towards understanding protein complexes in

their cellular context. Comput. Struct. Biotechnol. J. 19, 214–225 (2020).

Yamaguchi, H. Q., Ode, K. L. & Ueda, H. R. A design principle for

posttranslational chaotic oscillators. iScience 24, 101946 (2021).

Ishiura, M. et al. Expression of a gene cluster kaiABC as a circadian feedback

process in cyanobacteria. Science 281, 1519–1523 (1998).

Nakajima, M. et al. Reconstitution of circadian oscillation of cyanobacterial

KaiC phosphorylation in vitro. Science 308, 414–415 (2005).

Chang, Y. G. et al. Circadian rhythms. A protein fold switch joins the

circadian oscillator to clock output in cyanobacteria. Science 349, 324–328

(2015).

Oyama, K., Azai, C., Nakamura, K., Tanaka, S. & Terauchi, K. Conversion

between two conformational states of KaiC is induced by ATP hydrolysis as a

trigger for cyanobacterial circadian oscillation. Sci. Rep. 6, 32443 (2016).

Vakonakis, I. et al. NMR structure of the KaiC-interacting C-terminal domain

of KaiA, a circadian clock protein: implications for KaiA-KaiC interaction.

Proc. Natl Acad. Sci. USA 101, 1479–1484 (2004).

Ye, S., Vakonakis, I., Ioerger, T. R., LiWang, A. C. & Sacchettini, J. C. Crystal

structure of circadian clock protein KaiA from Synechococcus elongatus. J.

Biol. Chem. 279, 20511–20518 (2004).

Hitomi, K., Oyama, T., Han, S., Arvai, A. S. & Getzoff, E. D. Tetrameric

architecture of the circadian clock protein KaiB. A novel interface for

intermolecular interactions and its impact on the circadian rhythm. J. Biol.

Chem. 280, 19127–19135 (2005).

Iwase, R. et al. Functionally important substructures of circadian clock protein

KaiB in a unique tetramer complex. J. Biol. Chem. 280, 43141–43149 (2005).

Mori, T. et al. Circadian clock protein KaiC forms ATP-dependent hexameric

rings and binds DNA. Proc. Natl Acad. Sci. USA 99, 17203–17208 (2002).

Hayashi, F. et al. ATP-induced hexameric ring structure of the cyanobacterial

circadian clock protein KaiC. Genes Cells 8, 287–296 (2003).

Pattanayek, R. et al. Visualizing a circadian clock protein: crystal structure of

KaiC and functional insights. Mol. Cell 15, 375–388 (2004).

Yunoki, Y. et al. ATP hydrolysis by KaiC promotes its KaiA binding in the

cyanobacterial circadian clock system. Life Sci. Alliance https://doi.org/

10.26508/lsa.201900368 (2019).

Pattanayek, R. et al. Analysis of KaiA-KaiC protein interactions in the cyanobacterial circadian clock using hybrid structural methods. EMBO J. 25,

2017–2028 (2006).

Pattanayek, R. et al. Combined SAXS/EM based models of the S. elongatus

post-translational circadian oscillator and its interactions with the output Hiskinase SasA. PLoS ONE 6, e23697 (2011).

ARTICLE

20. Phong, C., Markson, J. S., Wilhoite, C. M. & Rust, M. J. Robust and tunable

circadian rhythms from differentially sensitive catalytic domains. Proc. Natl

Acad. Sci. USA 110, 1124–1129 (2013).

21. Sugiyama, M. et al. Structural characterization of the circadian clock protein

complex composed of KaiB and KaiC by inverse contrast-matching smallangle neutron scattering. Sci. Rep. 6, 35567 (2016).

22. Kageyama, H. et al. Cyanobacterial circadian pacemaker: Kai protein complex

dynamics in the KaiC phosphorylation cycle in vitro. Mol. Cell 23, 161–171

(2006).

23. Mori, T. et al. Elucidating the ticking of an in vitro circadian clockwork. PLoS

Biol. 5, e93 (2007).

24. Akiyama, S., Nohara, A., Ito, K. & Maeda, Y. Assembly and disassembly

dynamics of the cyanobacterial periodosome. Mol. Cell 29, 703–716 (2008).

25. Snijder, J. et al. Structures of the cyanobacterial circadian oscillator frozen in a

fully assembled state. Science 355, 1181–1184 (2017).

26. Tseng, R. et al. Structural basis of the day-night transition in a bacterial

circadian clock. Science 355, 1174–1180 (2017).

27. Brettschneider, C. et al. A sequestration feedback determines dynamics and

temperature entrainment of the KaiABC circadian clock. Mol. Syst. Biol. 6, 389

(2010).

28. Mori, T. et al. Revealing circadian mechanisms of integration and resilience by

visualizing clock proteins working in real time. Nat. Commun. 9, 3245 (2018).

29. Nishimura, H. et al. Mutations in KaiA, a clock protein, extend the period of

circadian rhythm in the cyanobacterium Synechococcus elongatus PCC 7942.

Microbiology (Reading) 148, 2903–2909 (2002).

30. Chen, Q., Liu, S., Yang, L., Zhang, L. & Li, J. The reversible function switching

of the circadian clock protein KaiA is encoded in its structure. Biochim.

Biophys. Acta 1861, 2535–2542, (2017).

31. Fejgin, L. A. & Svergun, D. I. Structure Analysis by Small-angle X-ray and

Neutron Scattering. (Plenum Press, 1987).

32. Svergun, D. I. Restoring low resolution structure of biological macromolecules from

solution scattering using simulated annealing. Biophys. J. 76, 2879–2886 (1999).

33. Bernadó, P., Shimizu, N., Zaccai, G., Kamikubo, H. & Sugiyama, M. Solution

scattering approaches to dynamical ordering in biomolecular systems.

Biochim. Biophys. Acta 1862, 253–274 (2018).

34. Bonomi, M., Heller, G. T., Camilloni, C. & Vendruscolo, M. Principles of

protein structural ensemble determination. Curr. Opin. Struct. Biol. 42,

106–116 (2017).

35. Rout, M. P. & Sali, A. Principles for integrative structural biology studies. Cell

177, 1384–1403 (2019).

36. Lattman, E. E., Grant, T. D. & Snell, E. H. in Biological Small Angle Scattering:

Theory and Practice. Vol. 29 (Oxford University Press, 2018).

37. 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.

Crystallogr. 42, 892–900 (2009).

38. Ryan, T. M. et al. An optimized SEC-SAXS system enabling high X-ray dose

for rapid SAXS assessment with correlated UV measurements for

biomolecular structure analysis. J. Appl. Crystallogr. 51, 97–111 (2018).

39. Inoue, R. et al. Newly developed laboratory-based size exclusion chromatography

small-angle x-ray scattering system (La-SSS). Sci. Rep. 9, 1–12 (2019).

40. Paissoni, C., Jussupow, A. & Camilloni, C. Martini bead form factors for

nucleic acids and their application in the refinement of protein–nucleic acid

complexes against SAXS data. J. Appl. Crystallogr. 52, 394–402 (2019).

41. Jussupow, A. et al. The dynamics of linear polyubiquitin. Sci. Adv. 6, eabc3786

(2020).

42. Okuda, A. et al. Solution structure of multi-domain protein ER-60 studied by

aggregation-free SAXS and coarse-grained-MD simulation. Sci. Rep. 11, 1–13

(2021).

43. Sugiyama, M. et al. Conformational characterization of a protein complex

involving intrinsically disordered protein by small-angle neutron scattering

using the inverse contrast matching method: a case study of interaction

between α-synuclein and PbaB tetramer as a model chaperone. J. Appl.

Crystallogr. 47, 430–435 (2014).

44. Yogo, R. et al. Characterization of conformational deformation-coupled

interaction between immunoglobulin G1 Fc glycoprotein and a low-affinity

Fcγ receptor by deuteration-assisted small-angle neutron scattering. Biochem.

Biophys. Rep. 12, 1–4 (2017).

45. Sekiguchi, T. et al. Mutational and combinatorial control of self-assembling

and disassembling of human proteasome α subunits. Int. J. Mol. Sci. 20, 2308

(2019).

46. Inoue, R. et al. Elucidation of the mechanism of subunit exchange in αB

crystallin oligomers. Sci. Rep. 11, 1–9 (2021).

47. Shimizu, N. et al. in AIP Conference Proceedings. 050017 (AIP Publishing LLC,

2016).

48. Johansen, N. T., Pedersen, M. C., Porcar, L., Martel, A. & Arleth, L.

Introducing SEC–SANS for studies of complex self-organized biological

systems. Acta Crystallogr. Sect. D Struct. Biol. 74, 1178–1191 (2018).

COMMUNICATIONS BIOLOGY | (2022)5:184 | https://doi.org/10.1038/s42003-022-03143-z | www.nature.com/commsbio

11

ARTICLE

A Self-archived copy in

Kyoto University Research Information Repository

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

COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-022-03143-z

49. Sato, N. et al. A feasibility study of inverse contrast-matching small-angle neutron

scattering method combined with size exclusion chromatography using antibody

interactions as model systems. J. Biochem. 169, 701–708 (2021).

50. Morishima, K. et al. Integral approach to biomacromolecular structure by

analytical-ultracentrifugation and small-angle scattering. Commun. Biol. 3,

1–7 (2020).

51. Mandell, D. J., Coutsias, E. A. & Kortemme, T. Sub-angstrom accuracy in

protein loop reconstruction by robotics-inspired conformational sampling.

Nat. Methods 6, 551–552 (2009).

52. Huang, P.-S. et al. RosettaRemodel: a generalized framework for flexible

backbone protein design. PLoS ONE 6, e24109 (2011).

53. Hünenberger, P. H., Mark, A. E. & van Gunsteren, W. F. Fluctuation and

cross-correlation analysis of protein motions observed in nanosecond

molecular dynamics simulations. J. Mol. Biol. 252, 492–503 (1995).

54. Iwasaki, H., Nishiwaki, T., Kitayama, Y., Nakajima, M. & Kondo, T. KaiAstimulated KaiC phosphorylation in circadian timing loops in cyanobacteria.

Proc. Natl Acad. Sci. USA 99, 15788–15793 (2002).

55. Kim, Y. I., Dong, G., Carruthers, C. W. Jr., Golden, S. S. & LiWang, A. The

day/night switch in KaiC, a central oscillator component of the circadian clock

of cyanobacteria. Proc. Natl Acad. Sci. USA 105, 12825–12830 (2008).

56. Kitayama, Y., Iwasaki, H., Nishiwaki, T. & Kondo, T. KaiB functions as an

attenuator of KaiC phosphorylation in the cyanobacterial circadian clock

system. EMBO J. 22, 2127–2134 (2003).

57. Nishiwaki, T. et al. A sequential program of dual phosphorylation of KaiC as a

basis for circadian rhythm in cyanobacteria. EMBO J. 26, 4029–4037 (2007).

58. Valentini, E., Kikhney, A. G., Previtali, G., Jeffries, C. M. & Svergun, D. I.

SASBDB, a repository for biological small-angle scattering data. Nucleic Acids

Res. 43, D357–D363 (2015).

59. Bekker, G.-J., Kawabata, T. & Kurisu, G. The Biological Structure Model

Archive (BSM-Arc): an archive for in silico models and simulations. Biophys.

Rev. 12, 371–375 (2020).

60. Chang, Y. G., Kuo, N. W., Tseng, R. & LiWang, A. Flexibility of the Cterminal, or CII, ring of KaiC governs the rhythm of the circadian clock of

cyanobacteria. Proc. Natl Acad. Sci. USA 108, 14431–14436 (2011).

61. Murakami, R. et al. Cooperative binding of KaiB to the KaiC hexamer ensures

accurate circadian clock oscillation in cyanobacteria. Int. J. Mol. Sci. https://

doi.org/10.3390/ijms20184550 (2019).

62. Okuda, A. et al. Deuteration aiming for neutron scattering. Biophys.

Physicobiol., 18, 16–27 (2021).

63. Schuck, P. Size-distribution analysis of macromolecules by sedimentation

velocity ultracentrifugation and lamm equation modeling. Biophys. J. 78,

1606–1619 (2000).

64. Orthaber, D., Bergmann, A. & Glatter, O. SAXS experiments on absolute scale

with Kratky systems using water as a secondary standard. J. Appl. Crystallogr.

33, 218–225 (2000).

65. Dewhurst, C. GRASP. https://www.ill.eu/users/support-labs-infrastructure/

software-scientific-tools/grasp. (Institut Laue-Langevin, 2020).

66. Berendsen, H. J., van der Spoel, D. & van Drunen, R. GROMACS: a messagepassing parallel molecular dynamics implementation. Computer Phys.

Commun. 91, 43–56 (1995).

67. Lindahl, E., Hess, B. & Van Der Spoel, D. GROMACS 3.0: a package for molecular

simulation and trajectory analysis. Mol. Model. Annu. 7, 306–317 (2001).

68. Van Der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem.

26, 1701–1718 (2005).

69. Hess, B., Kutzner, C., Van Der Spoel, D. & Lindahl, E. GROMACS 4:

algorithms for highly efficient, load-balanced, and scalable molecular

simulation. J. Chem. Theory Comput. 4, 435–447 (2008).

70. Pronk, S. et al. GROMACS 4.5: a high-throughput and highly parallel open

source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013).

71. Páll, S., Abraham, M. J., Kutzner, C., Hess, B. & Lindahl, E. Tackling exascale

software challenges in molecular dynamics simulations with GROMACS. In

Solving software challenges for exascale, (eds Markidis, S. & Laure, E.), 3–27,

(Springer, 2015).

72. Abraham, M. J. et al. GROMACS: High performance molecular simulations

through multi-level parallelism from laptops to supercomputers. SoftwareX 1,

19–25 (2015).

73. Maier, J. A. et al. ff14SB: improving the accuracy of protein side chain and

backbone parameters from ff99SB. J. Chem. Theory Comput. 11, 3696–3713 (2015).

74. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M.

L. Comparison of simple potential functions for simulating liquid water. J.

Chem. Phys. 79, 926–935 (1983).

75. Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity

rescaling. J. Chem. Phys. 126, 014101 (2007).

76. Franke, D. et al. ATSAS 2.8: a comprehensive data analysis suite for smallangle scattering from macromolecular solutions. J. Appl. Crystallogr. 50,

1212–1225 (2017).

12

77. Svergun, D. et al. Protein hydration in solution: experimental observation by

x-ray and neutron scattering. Proc. Natl Acad. Sci. USA 95, 2267–2272 (1998).

Acknowledgements

SEC-SAXS experiments at Photon Factory were performed under Proposal No. 2017G100

and 2018G680. SEC-iCM-SANS, and iCM-SANS at Institut Laue Langevin were performed

under Proposals No. 8-03-854, 8-03-884, 8-03-924, and 8-03-938. Analytical ultracentrifuge

and SAXS experiment at Institute for Integrated Radiation and Nuclear Science, Kyoto

University (KURNS) were performed under Proposal Numbers, 31006, R2024, and R3063 to

H.Y. and R3003 to M.Y.-U. This work was supported by the JSPS Research Fellowship for

Young Scientists (to Y.Y. and R.Y.) and the Grants-in-Aid for Scientific Research (Grant

Numbers, JP18J21063 to Y.Y., JP18K06101 to A.Mat., JP19K16088 and JP21K15051 to K.M.,

JP17K07816 to N.S., JP20K06579 and JP19KK0071 to R.I., JP20K22629 to M.Sh.,

JP18H05229 and JP18H03681 to M.Su., and JP18H05534 to M.Su. and H.K.) from the

Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. The study

was partially supported by the Platform Project for Supporting Drug Discovery and Life

Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research

(BINDS)) from AMED (JP21am0101106, support number 2121) to A.Mat. and H.K. This

study was also supported by Joint Research of the Exploratory Research Center on Life and

Living Systems (ExCELLS) (ExCELLS program No. 21-408 to K.M., No. 20-326 and 21-315

to M.Su., and No. 20-308 and 21-308 to H.Y.), by Joint Research by Institute for Molecular

Science (IMS program No. 19-205, 20-207 and 21-217 to M.Su.), by Research Fund for

Young Scientists in Kyoto University (to K.M.) and by Fund for Project Research in KURNS

(to Y.Y., K.M., M.Sh., and A.O.). This work was also partially supported by the project for

Construction of the basis for the advanced materials science and analytical study by the

innovative use of quantum beam and nuclear sciences in KURNS. Computations were

carried out at National Institutes for Quantum Science and Technology, at Japan Atomic

Energy Agency, and at Tokyo Institute of Technology Global Scientific Information and

Computing Center.

Author contributions

This research was designed by H.K., H.Y., K.K., and M.Su. Sample preparation was

performed by Y.Y., A.O., R.U., K.T., and H.Y. SEC-SAXS experiment was performed by

R.I., M.Y.-U., M.Sh., and M.Su. SEC-iCM-SANS experiments were performed by A.Mar.,

L.P., N.S., R.Y., T.T., and M.Su. AUC experiment was performed by Y.Y. and K.M.

Computational modeling and molecular dynamics simulation were performed by A.Mat.

and H.K. Integrative analysis was performed by Y.Y., A.Mat., H.K., H.Y., K.K., and M.Su.

All the 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/s42003-022-03143-z.

Correspondence and requests for materials should be addressed to Hidetoshi Kono,

Hirokazu Yagi, Koichi Kato or Masaaki Sugiyama.

Peer review information Communications Biology thanks Carlo Camilloni and Ralf

Biehl for their contribution to the peer review of this work. Primary Handling Editor:

Gene Chong. Peer reviewer reports are available.

Reprints and permission information is available at http://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 license, and indicate if changes were made. The images or other third party

material in this article are included in the article’s Creative Commons license, unless

indicated otherwise in a credit line to the material. If material is not included in the

article’s Creative Commons license 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 license, visit http://creativecommons.org/

licenses/by/4.0/.

© The Author(s) 2022

COMMUNICATIONS BIOLOGY | (2022)5:184 | https://doi.org/10.1038/s42003-022-03143-z | www.nature.com/commsbio

...

参考文献をもっと見る

全国の大学の
卒論・修論・学位論文

一発検索!

この論文の関連論文を見る