Observation of a single protein by ultrafast X-ray diffraction

Tomas Ekeberg; Dameli Assalauova; Johan Bielecki; Rebecca Boll; Benedikt J. Daurer; Lutz A. Eichacker; Linda E. Franken; Davide E. Galli; Luca Gelisio; Lars Gumprecht; Laura H. Gunn; Janos Hajdu; Robert Hartmann; Dirk Hasse; Alexandr Ignatenko; Jayanath Koliyadu; Olena Kulyk; Ruslan Kurta; Markus Kuster; Wolfgang Lugmayr; Jannik Lübke; Adrian P. Mancuso; Tommaso Mazza; Carl Nettelblad; Yevheniy Ovcharenko; Daniel E. Rivas; Max Rose; Amit K. Samanta; Philipp Schmidt; Egor Sobolev; Nicusor Timneanu; Sergey Usenko; Daniel Westphal; Tamme Wollweber; Lena Worbs; Paul Lourdu Xavier; Hazem Yousef; Kartik Ayyer; Henry N. Chapman; Jonas A. Sellberg; Carolin Seuring; Ivan A. Vartanyants; Jochen Küpper; Michael Meyer; Filipe R. N. C. Maia

doi:10.1038/s41377-023-01352-7

Your Location：

Home >

Browse articles >

Observation of a single protein by ultrafast X-ray diffraction

Article

- Observation of a single protein by ultrafast X-ray diffraction
- Observation of a single protein by ultrafast X-ray diffraction
- LSA 2024年13卷第1期页码：80-90
- Affiliations：
- Author bio：
  
  ayfilipe.maia@icm.uu.se
- Funds：
  
  Vetenskapsrådet (Swedish Research Council);Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation);Deutsche Forschungsgemeinschaft (German Research Foundation);Human Frontiers Science Program (RGP0010/2017)
- DOI：10.1038/s41377-023-01352-7
  中图分类号：
- 收稿日期：2023-11-03，
  
  修回日期：2023-12-05，
  
  录用日期：2023-12-06，
  
  网络出版日期：2024-01-12，
  
  纸质出版日期：2024-12
- Accepted：
Scan QR Code
Observation of a single protein by ultrafast X-ray diffraction[J]. LSA, 2024,13(1):80-90.

Tomas Ekeberg, Dameli Assalauova, Johan Bielecki, et al. Observation of a single protein by ultrafast X-ray diffraction[J]. Light: science & applications, 2024, 13(1): 80-90.
Observation of a single protein by ultrafast X-ray diffraction[J]. LSA, 2024,13(1):80-90. DOI： 10.1038/s41377-023-01352-7.

Tomas Ekeberg, Dameli Assalauova, Johan Bielecki, et al. Observation of a single protein by ultrafast X-ray diffraction[J]. Light: science & applications, 2024, 13(1): 80-90. DOI： 10.1038/s41377-023-01352-7.

摘要

Abstract

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory

the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier

and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then

a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations

while keeping the sample at room temperature

may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein

that of

Escherichia coli

GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays

and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern

it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins

opening the way to single-molecule time-resolved studies on the femtosecond timescale.

关键词

Keywords

references

R. Mankowsky et al. , Nonlinear lattice dynamics as a basis for enhanced superconductivity in YBa2Cu3O6.5 . Nature 516 , 71 - 73 ( 2014 ). http://doi.org/10.1038/nature13875 http://doi.org/10.1038/nature13875

Z.H. Loh et al. , Observation of the fastest chemical processes in the radiolysis of water . Science 367 , 179 - 182 ( 2020 ). http://doi.org/10.1126/science.aaz4740 http://doi.org/10.1126/science.aaz4740

H.N. Chapman et al. , Femtosecond X-ray protein nanocrystallography . Nature 470 , 73 - 77 ( 2011 ). http://doi.org/10.1038/nature09750 http://doi.org/10.1038/nature09750

J. Tenboer et al. , Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein . Science 346 , 1242 - 1246 ( 2014 ). http://doi.org/10.1126/science.1259357 http://doi.org/10.1126/science.1259357

E. Nogales , The development of cryo-EM into a mainstream structural biology technique . Nat. Methods 13 , 24 - 27 ( 2016 ). http://doi.org/10.1038/nmeth.3694 http://doi.org/10.1038/nmeth.3694

J. Frank , Time-resolved cryo-electron microscopy: recent progress . J. Struct. Biol. 200 , 303 - 306 ( 2017 ). http://doi.org/10.1016/j.jsb.2017.06.005 http://doi.org/10.1016/j.jsb.2017.06.005

R. Neutze et al. , Potential for biomolecular imaging with femtosecond X-ray pulses . Nature 406 , 752 - 757 ( 2000 ). http://doi.org/10.1038/35021099 http://doi.org/10.1038/35021099

M. Hayer-Hartl , A. Bracher , F.U. Hartl , The GroEL-GroES chaperonin machine: a nano-cage for protein folding . Trends Biochem. Sci. 41 , 62 - 76 ( 2016 ). http://doi.org/10.1016/j.tibs.2015.07.009 http://doi.org/10.1016/j.tibs.2015.07.009

K. Braig et al. , The crystal structure of the bacterial chaperonin GroEL at 2.8 Å . Nature 371 , 578 - 586 ( 1994 ). http://doi.org/10.1038/371578a0 http://doi.org/10.1038/371578a0

A.A. Rostom , C.V. Robinson , Detection of the intact groel chaperonin assembly by mass spectrometry . J. Am. Chem. Soc. 121 , 4718 - 4719 ( 1999 ). http://doi.org/10.1021/ja990238r http://doi.org/10.1021/ja990238r

R.J. Rose et al. , High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies . Nat. Methods 9 , 1084 - 1086 ( 2012 ). http://doi.org/10.1038/nmeth.2208 http://doi.org/10.1038/nmeth.2208

R.H.H. van den Heuvel et al. , Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry . Anal. Chem. 78 , 7473 - 7483 ( 2006 ). http://doi.org/10.1021/ac061039a http://doi.org/10.1021/ac061039a

F. Sobott , C.V. Robinson , Characterising electrosprayed biomolecules using tandem-MS—the noncovalent GroEL chaperonin assembly . Int. J. Mass Spectrom. 236 , 25 - 32 ( 2004 ). http://doi.org/10.1016/j.ijms.2004.05.010 http://doi.org/10.1016/j.ijms.2004.05.010

A.M. Roseman et al. , The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL . Cell 87 , 241 - 251 ( 1996 ). http://doi.org/10.1016/S0092-8674(00)81342-2 http://doi.org/10.1016/S0092-8674(00)81342-2

S.J. Ludtke et al. , Seeing GroEL at 6 Å resolution by single particle electron cryomicroscopy . Structure 12 , 1129 - 1136 ( 2004 ). http://doi.org/10.1016/j.str.2004.05.006 http://doi.org/10.1016/j.str.2004.05.006

M.M. Seibert et al. , Single mimivirus particles intercepted and imaged with an X-ray laser . Nature 470 , 78 - 81 ( 2011 ). http://doi.org/10.1038/nature09748 http://doi.org/10.1038/nature09748

A. Aquila et al. , The linac coherent light source single particle imaging road map . Struct. Dyn. 2 , 041701 ( 2015 ). http://doi.org/10.1063/1.4918726 http://doi.org/10.1063/1.4918726

B.J. Daurer et al. , Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses . IUCrJ 4 , 251 - 262 ( 2017 ). http://doi.org/10.1107/S2052252517003591 http://doi.org/10.1107/S2052252517003591

K. Ayyer et al. , Low-signal limit of X-ray single particle diffractive imaging . Opt. Express 27 , 37816 - 37833 ( 2019 ). http://doi.org/10.1364/OE.27.037816 http://doi.org/10.1364/OE.27.037816

T. Ekeberg et al. , Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser . Phys. Rev. Lett. 114 , 098102 ( 2015 ). http://doi.org/10.1103/PhysRevLett.114.098102 http://doi.org/10.1103/PhysRevLett.114.098102

G. van der Schot et al. , Imaging single cells in a beam of live cyanobacteria with an X-ray laser . Nat. Commun. 6 ,( 2015 ). http://doi.org/10.1038/ncomms6704 http://doi.org/10.1038/ncomms6704

J. Bielecki et al. , Electrospray sample injection for single-particle imaging with x-ray lasers . Sci. Adv. 5 , eaav8801 ( 2019 ). http://doi.org/10.1126/sciadv.aav8801 http://doi.org/10.1126/sciadv.aav8801

H.N. Chapman et al. , Femtosecond diffractive imaging with a soft-X-ray free-electron laser . Nat. Phys. 2 , 839 - 843 ( 2006 ). http://doi.org/10.1038/nphys461 http://doi.org/10.1038/nphys461

T. Tschentscher et al. , Photon beam transport and scientific instruments at the european XFEL . Appl. Sci. 7 , 592 ( 2017 ). http://doi.org/10.3390/app7060592 http://doi.org/10.3390/app7060592

M.F. Hantke et al. , Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams . IUCrJ 5 , 673 - 680 ( 2018 ). http://doi.org/10.1107/S2052252518010837 http://doi.org/10.1107/S2052252518010837

M. Kuster et al. , The 1-Megapixel pnCCD detector for the Small Quantum Systems Instrument at the European XFEL: system and operation aspects . J. Synchrotron Radiat. 28 , 576 - 587 ( 2021 ). http://doi.org/10.1107/S1600577520015659 http://doi.org/10.1107/S1600577520015659

L. Strüder et al. , Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources . Nucl. Instrum. Methods Phys. Res. Sect. A: Accel. Spectrom. Detect. Assoc. Equip. 614 , 483 - 496 ( 2010 ). http://doi.org/10.1016/j.nima.2009.12.053 http://doi.org/10.1016/j.nima.2009.12.053

W. Decking et al. , A MHz-repetition-rate hard X-ray free-electron laser driven by a superconducting linear accelerator . Nat. Photonics 14 , 391 - 397 ( 2020 ). http://doi.org/10.1038/s41566-020-0607-z http://doi.org/10.1038/s41566-020-0607-z

C. Chaudhry , A.L. Horwich , A.T. Brunger , P.D. Adams , Exploring the structural dynamics of the E. coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states . J. Mol. Biol. 342 , 229 - 245 ( 2004 ). http://doi.org/10.1016/j.jmb.2004.07.015 http://doi.org/10.1016/j.jmb.2004.07.015

C.J. Hogan et al. , Tandem differential mobility analysis-mass spectrometry reveals partial gas-phase collapse of the GroEL complex . J. Phys. Chem. B 115 , 3614 - 3621 ( 2011 ). http://doi.org/10.1021/jp109172k http://doi.org/10.1021/jp109172k

E.G. Marklund , D.S.D. Larsson , D. van der Spoel , A. Patriksson , C. Caleman , Structural stability of electrosprayed proteins: temperature and hydration effects . Phys. Chem. Chem. Phys. 11 , 8069 - 8078 ( 2009 ). http://doi.org/10.1039/b903846a http://doi.org/10.1039/b903846a

Esser, T. K. et al. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. Preprint at BioRxiv https://doi.org/10.1101/2023.08.17.553673 10.1101/2023.08.17.553673 (2023).

S.P. Hau-Riege et al. , Sacrificial tamper slows down sample explosion in FLASH diffraction experiments . Phys. Rev. Lett. 104 , 064801 ( 2010 ). http://doi.org/10.1103/PhysRevLett.104.064801 http://doi.org/10.1103/PhysRevLett.104.064801

F.R.N.C. Maia , T. Ekeberg , N. Tîmneanu , D. van der Spoel , J. Hajdu , Structural variability and the incoherent addition of scattered intensities in single-particle diffraction . Phys. Rev. E 80 , 031905 ( 2009 ). http://doi.org/10.1103/PhysRevE.80.031905 http://doi.org/10.1103/PhysRevE.80.031905

M. Porro et al. , The MiniSDD-based 1-Megapixel Camera of the DSSC Project for the European XFEL . IEEE Trans. Nucl. Sci. 68 , 1334 - 1350 ( 2021 ). http://doi.org/10.1109/TNS.2021.3076602 http://doi.org/10.1109/TNS.2021.3076602

Gessler, P. et al. Overview of acquisition and control electronics and concepts for experiments and beam transport at the European XFEL. In Proceedings of the 17th Biennial International Conference on Accelerator and Large Experimental Physics Control Systems . New York, https://doi.org/10.18429/jacow-icalepcs2019-thapp05 10.18429/jacow-icalepcs2019-thapp05 (2020).

E. Motuk et al. , Design and development of electronics for the EuXFEL clock and control system . J. Instrum. 7 , C01062 ( 2012 ). http://doi.org/10.1088/1748-0221/7/01/C01062 http://doi.org/10.1088/1748-0221/7/01/C01062

T. Maltezopoulos et al. , Operation of X-ray gas monitors at the European XFEL . J. Synchrotron Radiat. 26 , 1045 - 1051 ( 2019 ). http://doi.org/10.1107/S1600577519003795 http://doi.org/10.1107/S1600577519003795

B.J. Daurer , M.F. Hantke , C. Nettelblad , F.R.N.C. Maia , Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time . J. Appl. Crystallogr. 49 , 1042 - 1047 ( 2016 ). http://doi.org/10.1107/S1600576716005926 http://doi.org/10.1107/S1600576716005926

M.J. Abraham et al. , GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers . SoftwareX 1–2 , 19 - 25 ( 2015 ). http://doi.org/10.1016/j.softx.2015.06.001 http://doi.org/10.1016/j.softx.2015.06.001

M.F. Hantke , T. Ekeberg , F.R.N.C. Maia , Condor: a simulation tool for flash X-ray imaging . J. Appl. Crystallogr. 49 , 1356 - 1362 ( 2016 ). http://doi.org/10.1107/S1600576716009213 http://doi.org/10.1107/S1600576716009213

N.-T.D. Loh , V. Elser , Reconstruction algorithm for single-particle diffraction imaging experiments . Phys. Rev. E 80 , 026705 ( 2009 ). http://doi.org/10.1103/PhysRevE.80.026705 http://doi.org/10.1103/PhysRevE.80.026705

P. Virtanen et al. , SciPy 1.0: fundamental algorithms for scientific computing in Python . Nat. Methods 17 , 261 - 272 ( 2020 ). http://doi.org/10.1038/s41592-019-0686-2 http://doi.org/10.1038/s41592-019-0686-2

J. Freeke , C.V. Robinson , B.T. Ruotolo , Residual counter ions can stabilise a large protein complex in the gas phase . Int. J. Mass Spectrom. 298 , 91 - 98 ( 2010 ). http://doi.org/10.1016/j.ijms.2009.08.001 http://doi.org/10.1016/j.ijms.2009.08.001

J. Zivanov et al. , New tools for automated high-resolution cryo-EM structure determination in RELION-3 . eLife 7 , e42166 ( 2018 ). http://doi.org/10.7554/eLife.42166 http://doi.org/10.7554/eLife.42166

A. Punjani et al. , cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination . Nat. Methods 14 , 290 - 296 ( 2017 ). http://doi.org/10.1038/nmeth.4169 http://doi.org/10.1038/nmeth.4169

S.Q. Zheng et al. , MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy . Nat. Methods 14 , 331 - 332 ( 2017 ). http://doi.org/10.1038/nmeth.4193 http://doi.org/10.1038/nmeth.4193

K. Zhang , Gctf: real-time CTF determination and correction . J. Struct. Biol. 193 , 1 - 12 ( 2016 ). http://doi.org/10.1016/j.jsb.2015.11.003 http://doi.org/10.1016/j.jsb.2015.11.003

S.-H. Roh et al. , Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM . Proc. Natl Acad. Sci. USA 114 , 8259 - 8264 ( 2017 ). http://doi.org/10.1073/pnas.1704725114 http://doi.org/10.1073/pnas.1704725114

E.F. Pettersen et al. , UCSF Chimera—a visualization system for exploratory research and analysis . J. Comput. Chem. 25 , 1605 - 1612 ( 2004 ). http://doi.org/10.1002/jcc.20084 http://doi.org/10.1002/jcc.20084

T. Wagner et al. , SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM . Commun. Biol. 2 , 218 ( 2019 ). http://doi.org/10.1038/s42003-019-0437-z http://doi.org/10.1038/s42003-019-0437-z

F.R.N.C. Maia , The Coherent X-ray Imaging Data Bank . Nat. Methods 9 , 854 - 855 ( 2012 ). http://doi.org/10.1038/nmeth.2110 http://doi.org/10.1038/nmeth.2110

M.O. Wiedorn et al. , Post-sample aperture for low background diffraction experiments at X-ray free-electron lasers . J. Synchrotron Radiat. 24 , 1296 - 1298 ( 2017 ). http://doi.org/10.1107/S1600577517011961 http://doi.org/10.1107/S1600577517011961

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

暂无数据