Coherent Diffraction Imaging of Biological Materials

Transcription

1 Coherent Diffraction Imaging of Biological Materials Jianwei Miao Dept. of Physics and Astronomy & California NanoSystems Institute UCLA Workshop on Science with Free Electron Lasers SINAP, Shanghai, Aug , 2011

2 Coherent Diffraction Imaging of a Single Virus at 22 nm Resolution Performed on BL29XUL at SPring-8 (E = 5 kev) Song, Jiang, Mancuso, Amirbekian, Peng, Sun, Shah, Zhou, Ishikawa & Miao, PRL 101, (2008).

3 Consistency of the Independent Reconstructions Missing data confined within the centro-speckle Miao, Nishino, Kohmura, Johnson, Song, Risbud, Ishikawa, PRL 95, (2005). Xu, Salha, Jiang, Song, Ishikawa, Miao et al., J. Synch. Rad. 18, 293 (2011).

4 Identifying the Viral Capsid Inside the Herpesvirus Virion Quantitative X-ray diffraction imaging of a single herpesvirus AFM image of a herpesvirus prepared at the same conditions

5 What Cryo-EM Can Do Nowadays? Zhang et al., 3.3 Å cryo-em structure of a nonenveloped virus reveals a priming mechanism for cell entry. Cell 141, 472 (2010). Liu et al., Atomic structure of human adenovirus by cryoem reveals networks of protein interactions. Science 329, 1038 (2010). Medalia et al., Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography, Science 298, 1209 (2002). Cryo-EM: Resolution at 2 5 nm Sample thinner than 0.5 µm

6 Coherent X-ray Diffraction Imaging of Whole Cells Phase Retrieval EST EST: Equally-Sloped Tomography Miao, Förster, Levi, Phys. Rev. B. 72, (2005). Lee et al., J. Struct. Biol. 164, 221 (2008). Fahimian, Mao, Cloetens, Miao, Phys. Med. Bio. 55, 5383 (2010).

7 3D Visualization of the Internal Structure of the Yeast Spore Jiang, Song, Chen, Xu, Raines, Fahimian, Lu, Lee, Nakashima, Urano, Ishikawa, Tamanoi, Miao., PNAS 107, (2010).

8 Iso-Surface Renderings of a Fission Yeast Spore

9 Detailed 3D View of Some Cellular Organelles

10 Cryo-CDI Instrument at SPring-8 Nakasako, Yamamoto, Ishikawa et al.

11 Cryo-Sample Holder

12 Light Microscope Images of Human B Cells (Lymphocytes) Before Plunge Freezing

13 Coherent X-ray Diffraction Patterns and a Reconstruction of a Frozen-Hydrated Human B Cell Reconstruction of 0 pattern

14 Ankylography: 3D Structure Determination from a Single View Ankylography: Derived from Greek words ankylos - curved and graphein - writing. Raines, Salha, Sandberg, Jiang, Rodríguez, Bahamian, Kapteyn, Du, Miao, Nature 463, (2010). (Source Codes: Super-resolution crystallography: Schroder, Levitt, Brunger, Nature 464, (2010). Discrete tomography: Van Aert et al., Nature 470, (2011). Real Space Reciprocal Space The way of our thinking should not be confined by the Fourier transform.

15 Geometrical Difference between the grid points within a spherical shell of 1 voxel thick (black dots) and those on an infinitesimally thin shell (red dots) Oversampling deg. (O d ): Ratio of the black dots to the number of voxels sampling an object.

16 Constraints Used in the Ankylographic Reconstruction Algorithm (i) Optimization of the random initial phase set. Start with a large number of independent initial random phase sets and select the best one with the smallest R-factor. (ii) Uniformity outside the support. By incorporating this constraint, we reduce the density oscillation inside the support and improve the quality of the reconstructions. (iii) Continuity inside the support. The reconstructed images should be continuous and there exist no sharp points or edges in the reconstructions. (iv) Amplitude extension. First compute a reconstruction from the lower-resolution diffraction pattern, and then compute a higher resolution reconstruction using the lower-resolution reconstruction information. Repeat this procedure until a full reconstruction is reached.

17 3D Spatial Resolution in Ankylography d d x z = = d y = λ 2 2sin θ λ sin(2θ max max )

18 Numerical Simulations on Ankylographic Reconstruction of a Sodium Silicate Glass Nanoparticle Red, purple and yellow: O, Na and Si atoms Particle Size: Å 3 λ = 2 Å Incident flux = photons 2θ max = 90 d x = d y = d z = 2 Å Poisson noise added Sample array: 14 3 voxels Reciprocal-space array: 64 3 voxels 204 atoms

19 Two Perpendicular Slices of the Reconstructed Sodium Silicate Glass Particle

20 3D Structure of a Poliovirus Displayed at 2 3 nm Resolution

21 Simulated 2D Spherical Diff. Pattern of an Individual Poliovirus from a Single X-FEL Pulse λ = 1.77 nm Flux = photons/pulse Focal spot: 100 nm Poisson noise added 2θ max = 62.7 d x = d y = 2 nm and d z = 3.3 nm Sample array: voxels Reciprocal-space array: voxels

22 Numerical Simulation on 3D Structure of the Poliovirus from a Single X-ray Pulse

23 Soft X-ray Laser Used for Experimental Demonstration of Ankylography λ = 46.9nm λ / λ = 4 10 Andor CCD detector ( pixels, 13.5 µm 13.5 µm pixel size).

24 Projection of the Oversampled Diffraction Pattern from a Planar Detector onto the Spherical Shell

25 Experimental Diffraction Pattern on a Spherical Shell voxels Diffraction angle at the corner: 48.3 Diffraction angle at the edge: 35.9 Reconstruction error R-factor (Intensities within the spherical shell): 8%

26 Demonstration of Ankylography Using Experimental Data Obtained with a Soft X-ray Laser Raines, Salha, Sandberg, Jiang, Rodríguez, Fahimian, Kapteyn, Du & Miao, Nature 463, 214 (2010).

27 Summary CDI has been applied to imaging a single herpesvirus at a resolution of 22 nm at SPring-8. The independent reconstructions are very consistent. With X-FELs, significant higher resolution should be achievable. Over the past decade, a reliable experimental method has been established at SPring-8 to measure high-quality coherent X-ray diffraction patterns with small missing centers, allowing consistent phase retrieval. Performed quantitative 3D imaging of a whole, unstained yeast spore cell at a resolution of nm and identified the 3D morphology and structure of cellular organelles. With X-FELs (larger coherence length and high coherent flux), it is possible to obtain the 3D structure of whole frozen-hydrated mammalian and human cells whole at sub-10 nm resolution, potentially allowing to identify large protein complexes. Ankylography: 3D structural determination of small objects without the requirement of identical copies. For larger objects, further theoretical, experimental and algorithm developments are needed.

28 Acknowledgements RIKEN/SPring-8 T. Ishikawa, C. Song, Y. Kumara, M. Yamamoto, K. Yonekura Univ. of Colorado, Boulder M. M. Murnane, H. C. Kapteyn Shandong Univ. H. Jiang SINAP, CAS T. Earnest IHEP, CAS Yuhui Dong UCLA Microbiology, Immunology, and Molecular Genetics F. Tamanoi, Z. H. Zhou UCLA, Molecular and Medical Pharmacology R. Sun Keio University M. Nakasako UCLA, Dept. of Mathematics S. Osher Academia Sinica, Taiwan T. K. Lee Univ. of North Texas J. Du Coherent Imaging Group at UCLA