FEL’s light into life The value of IRIDE for life sciences

1. FEL’s light into life The value of IRIDE for life sciences Spokesperson Silvia Morante Physics Department University of Rome “Tor Vergata”

2. Things evolved • proposed IRIDE machine differs from SPARX •  some of the experiments are no more feasible • There are a number of FEL's already in operation in the world •  foreseen experiments successfully performed

3. WHERE in Europe

4. FLASH VUV/Xray FEL-DESY-Hamburg (2005) European X-FEL, DESY - Hamburg (2015) SwissFEL, Paul Scherrer Institute - Villigen FERMI FEL at Elettra, Trieste

5. FLASH: the world's first soft X-ray free-electron laser • wavelength range: (4.1 ÷ 45) nm • pulse duration: (50 ÷ 200) fs • available to the user community since 2005 • September 2010: laser light in the so-called water window (2.3 ÷ 4.4 nm) is generated • Opening the possibility of studying samples in solution

6. WHERELSE in the world

7. SLAC SSRL x-ray FEL - LCLS SACLA x-ray FEL - Riken

8. LCLS: Linac Coherent Light Source

10. 1. Redecke, Lars, et al. Science 339.6116 (2013): 227-230. 2. Barty, Anton, Jochen Küpper, and Henry N. Chapman. Annual review of physical chemistry 0 (2013). 3. Martin, A. V., et al. Optics Express 20.15 (2012): 16650-16661. 4. Martin, A. V., et al. Optics Express 20.12 (2012): 13501-13512. 5. Barty, Anton, et al. Nature Photonics 6.1 (2011): 35-40. 6. Johansson, Linda C., et al. Nature methods 9.3 (2012): 263-265. 7. Koopmann, Rudolf, et al. Nature methods 9.3 (2012): 259-262. 8. Aquila, Andrew, et al. Optics express 20.3 (2012): 2706-2716. 9. Boutet, Sébastien, et al.Science337.6092 (2012): 362-364. 10. Kassemeyer, Stephan, et al. Optics Express 20.4 (2012): 4149-4158. 11. Bajt, Saša, et al. JOSA A 29.3 (2012): 216-230. 12. Ziaja, B., et al. New Journal of Physics 14.11 (2012): 115015. 13. White, Thomas A., et al. Journal of Applied Crystallography 45.2 (2012): 335-341. 14. Andreasson, Jakob, et al. Physical Review E 83.1 (2011): 016403. 15. Ziaja, B., et al. Ultramicroscopy 111.7 (2011): 793-797. 16. Yoon, Chun Hong, et al. Optics Express 19.17 (2011): 16542-16549. 17. Filsinger, Frank, et al. Physical Chemistry Chemical Physics 13.6 (2011): 2076-2087. 18. Pedersoli, Emanuele, et al. Review of Scientific Instruments 82.4 (2011): 043711-043711. 19. Caleman, Carl, et al. Journal of Modern Optics 58.16 (2011): 1486-1497. 20. Seibert, M. Marvin, et al. Nature470.7332 (2011): 78-81. 21. Kirian, Richard A., et al. Acta Crystallographica Section A: Foundations of Crystallography 67.2 (2011): 131-140. 22. Son, Sang-Kil, Henry N. Chapman, and Robin Santra. Physical review letters 107.21 (2011): 218102. 23. Lomb, Lukas, et al. Physical Review B 84.21 (2011): 214111. 24. Chapman, Henry N., et al. Nature 470.7332 (2011): 73-77. 25. Kirian, Richard A., et al. Acta Crystallographica Section A: Foundations of Crystallography 67.2 (2011): 131-140. 26. Hau-Riege, Stefan P., et al Physical review letters 104.6 (2010): 064801. 27. Chapman, Henry N., and Keith A. Nugent. Nature photonics4.12 (2010): 833-839. 28. Saldin, D. K., et al. New Journal of Physics 12.3 (2010): 035014. 29. Chapman, Henry N.Nature 467.7314 (2010): 409-410. 30. Loh, N. D., et al. Physical review letters 104.22 (2010): 225501. 31. Saldin, D. K., et al. Phys. Rev. B 81 (2010): 174105. 32. Vinko, S. M., et al. Physical review letters 104.22 (2010): 225001. 33. Caleman, Carl, et al. ACS nano 5.1 (2010): 139-146. 34. Bogan, M. J., et al. Physical Review Special Topics-Accelerators and Beams 13.9 (2010): 094701. 35. Seibert, M. Marvin, et al. Journal of Physics B: Atomic, Molecular and Optical Physics 43.19 (2010): 194015.

11. A NATION WIDE COLLABORATION

12. BioFel Collaboration Fifteen laboratories Eight towns

13. Milano BioFel Collaboration Roma Teramo L’Aquila Ancona Bari Padova Firenze

14. ManyDepartments and Laboratories are involved • Physics • Chemistry • Biochemistry • MolecularBiology • Biotechnology • Pharmacology • Crystallography • Nanoscience • Nanotechnology • ClinicalBiochemistry • Biomedical Science • Experimental Medicine Multi-disciplinarity is the key-word

15. The IRIDE bio-scientific case 1) Serial crystallography on nanocrystals. 2) X-ray Absorption (and/or Emission) Spectroscopy 3) Sub-picosecond pumps&probe structural and spectrometric investigations 4) Wide and Small angle X-ray scattering of biological molecules 5) Low density atomic and molecular processes with two photon spectroscopy 6) X-ray microscopy with nanometer resolution 7) Femtosecond Raman scectroscopy 8) Single molecule imaging with soft and hard X-rays 9) ...

16. Outline • General motivation •  biological complexity • Some open questions in biology • membrane proteins and aggregates • intrinsically unfolded proteins • … • The bio-FEL case • a couple of examples • Conclusions…?

17. Citric acid cycle or Krebs cycle Mitochondria + O2 COOH | C=O | CH2 | COOH CO2 CO2

18. malate Citrate synthase Aconitase a-ketoglutarate Isocitrate fumarase succinate succinyl-CoA synthetase Step1: Citrate synthase Step2: Aconitase Step8: malate dehydrogenase Step3: isocitrate dehydrogenase Step7: fumarase Step4: a-ketoglutarate dehydrogenase complex Step6: succinate dehydrogenase Step5: succinyl-CoA synthetase

19. Play in Concerto most biological processes require interactions among several actors interactions may require and/or promote the actors to modify their own structure

20. Many biologically relevant target complexes are difficult or impossible to crystalize • Two large classes of proteins: • membrane proteins • intrinsically unfolded proteins

21. 25% of human genes encode for membrane proteins Human genome: 25% 75% 67% of known drug targets are membrane proteins 67% 33% Known drug targets: membrane proteins soluble proteins Membrane proteins as drug targets ~ 2% of XRD proteinstructures are of membrane proteins A large blank area in structural biology that has to be filled!

22. Intrinsically unfolded proteins They challenged the protein structure paradigm: Stable structure  correct functioning Disordered proteins fulfill well defined tasks • adopting and stabilizing their three dimensional structure after binding to other macromolecules • maintaining flexible regions connecting two transmembrane domains • functioning as "molecular switches" in regulating certain biological function • … • Sometimes they go astray undergoing an aggregation process  pathological state (amyloidosis). The bottleneck is always to grow (sufficiently large) crystals

23. Serial Crystallography @ IRIDE • XRD: the most used technique to solve 3D structures of proteins

25. Serial Crystallography @ IRIDE • XRD: the most used technique to solve 3D structures of proteins • Sufficiently large crystals are difficult to obtain • In principle, one has only to wait for a sufficiently long time Small (sub-micron sized) crystals damaged before giving valuable diffraction Short pulses: diffraction-before-desctruction High resolution: diffraction better than 2Å! Small objects: down to <300 nm protein crystals

26. Nanocrystallography Precipitates obtained during the crystallization trials are full of crystals of extremely small size. Photosystem I 3th generation Synchrotron radiation facilities  sufficiently big crystal  13 years nanocrystals  few weeks

27. “Femtosecond X-ray protein nano-crystallography.” (2011) Nature 470: 73-77. More than 100,000,000 diffraction patterns collected nanocrystals ∼200 nm to 2 μm. By using pulses briefer than the timescale of most damage processes

28. briefer than the timescale needed for the pain signal to reach the brain!!

29. Time evolution of T4 lysozyme explosion FWHMX-ray pulse = 2 fs Integrated X-ray intensity = 3.8 x 106 photons per Å2. First two structures (before and after the pulse) are practically identical. Neutze et al., Nature, 406 (2000) Very short pulse to overcomeradiationdamage Very high intensity to overcomecrystallizationproblem  Towards single moleculeexperiments

30. Time resolved Serial Crystallography The ultra-short FEL pulse are naturally suited for time-resolved measurements

31. Francesco Stellato

32. X-ray Absorption (and/or Emission) Spectroscopy

33. SASE FEL photon energy varies shot-to-shot. A 1% variation would be enough to collect XANES spectra exploiting this natural jitter of the radiation. The design IRIDE parameters will allow to study many L-edges and also K-edges up to Zn using the 5th harmonic A single pulse spectrometer is required to measure wavelength and intensity of each pulse. Protein Solution Stream Pump pulse A serial crystallography-like setup, with a liquid jet delivering particles or molecules under the beam, can be easily adapted and will naturally allow pump-probe measurements. FEL beam Fluorescence photons

34. X-ray spectroscopy can be coupled with serial crystallography experiments X-ray emission spectroscopy measurements have already been carried out at the LCLS on photosystem II crystals Kern J. et al. "Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature." Science (2013).

35. Conclusions…?

36. Thank you for your attention