Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron...
-
Upload
debra-harriet-farmer -
Category
Documents
-
view
229 -
download
0
Transcript of Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron...
![Page 1: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/1.jpg)
Single Particle X-ray Diffraction- the Present and the Future
John MiaoStanford Synchrotron Radiation Laboratory
Stanford Linear Accelerator Center
![Page 2: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/2.jpg)
![Page 3: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/3.jpg)
Nobel Prizes awarded to research related to the phase problem
F. Zernike (Physics in 1953), “for his invention of phase contrast method”.
M. F. Perutz & J. C. Kendrew (Chemistry in 1962), “for their studies of the structures of globular proteins”.
D. Gabor (Physics in 1971), “for his invention and development of the holographic method”.
J. Karle & H. Hauptman (Chemistry in 1985) “for their contributions to the Direct Methods”.
![Page 4: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/4.jpg)
A 200 m crystal (a = 50 Å, 4 104 unit cells)
| ℱ
|
Real Reciprocal
![Page 5: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/5.jpg)
A 0.1 m crystal (a = 50 Å, 20 unit cells)
| ℱ
|
Real Reciprocal
![Page 6: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/6.jpg)
The Essence of the Oversampling Phasing Method
Real Space ℱ Reciprocal Space
Bragg-peak sampling
Oversampling
J. Miao, D. Sayre & H. N. Chapman, J. Opt. Soc. Am. A 15, 1662 (1998).
![Page 7: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/7.jpg)
The Oversampling Phasing Method
![Page 8: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/8.jpg)
An Iterative Algorithm
JJ. Fienup, Appl. Opt. 21, 2758 (1982). JJ. Miao, J. Kirz & D. Sayre, Acta Cryst. D 56, 1312 (2000).
![Page 9: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/9.jpg)
(a) A SEM image of a double-layered sample made of Ni (~2.7 x 2.5 x 1 m3)
(b) A coherent diffraction pattern from (a) (the resolution at the edge is 8 nm)
(c) An image reconstructed from (b)
J. Miao et al., Phys. Rev. Lett. 89, 088303 (2002).
![Page 10: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/10.jpg)
The Reconstructed 3D structure
The reconstructed top pattern The reconstructed bottom pattern
An iso-surface rendering of the reconstructed 3D structure
![Page 11: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/11.jpg)
Direct determination of the absolute electron
density of nanostructured materials
2
2
20 )()( kFr
rPIkI e
I0: Measured by an X-ray photodiode
I( ): Measured by a direct-illumination CCDk
![Page 12: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/12.jpg)
(a) Coherent diffraction pattern from a porous silica particle
(b) The reconstructed absolute electron density
(c) The absolute electron density distribution
within a 100 x 100 nm2 area
![Page 13: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/13.jpg)
Imaging Whole E. Coli Bacteria
(b) A Coherent X-ray diffraction pattern
from E. Coli
(c) An image reconstructed from (b).
(a) Light and fluorescence microscopy images
of E. Coli labeled with YFP and manganese oxide
![Page 14: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/14.jpg)
Radiation damage
SSolemn & Baldwin, Science 218, 229-235 (1982). With picosecond pulse duration X-rays, biological specimens
remain morphological unchanged to an accuracy of a few nm. NNeutze, Wouts, Spoel, Weckert & Hajdu, Nature 400, 752-757 (2000).
With an X-FEL of pulse leng. < 50 fs and 3 x 1012 photons focused down to a spot of ~ 0.1 m, a 2D diffraction pattern could be recorded from a biomolecule before the radiation damage manifests itself.
![Page 15: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/15.jpg)
Orientation determination Use the methods developed in cryo-EM to determine the
molecular orientation based on many 2D diffraction patterns.
Crowther, Phil. Trans. Roy. Soc. Lond. B. 261, 221 (1971).
J. Frank, in Three-Dimensional Electron Microscopy of Macromolecular Assemblies, Academic Press (1996).
Use laser fields to physically align each molecule.
J. J. Larsen, K. N. Hald, Bjerre, H. Stapelfeldt & T. Seideman, Phys. Rev. Lett. 85, 2470-2473 (2000).
![Page 16: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/16.jpg)
![Page 17: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/17.jpg)
The 3D electron density map of a rubisco molecule
The active site of the molecule
![Page 18: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/18.jpg)
Procedures to Obtain Oversampled 3D Diffraction Patterns
(i) Calculated oversampled 2D diffraction patterns from
106 identical molecules.
(ii) Assumed that the orientation of each 2D diffraction pattern is known.
(ii) Assembled an oversampled 3D diffraction pattern from these
oversampled 2D diffraction patterns.
(iv) Added Poisson noise to the 3D diffraction pattern.
zyx
zyx
kkkzyxcalculated
kkkzyxnoisyzyxcalculated
IkkkI
kkkIkkkI
R
,,
,,
),,(
),,(),,(
![Page 19: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/19.jpg)
(a) One section of the oversampled 3D diffraction Pattern with RI = 9.8% and 3x3x3 central pixels removed
(b) Top view of (a)
![Page 20: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/20.jpg)
The reconstructed 3D electron density map The reconstructed active site
J. Miao, K. O. Hodgson & D. Sayre, Proc. Natl. Acad. Sci. USA 98, 6641 (2001).
![Page 21: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/21.jpg)
Reconstruction of the 3D diffraction pattern obtained from 3 x 105 identical molecules with RI = 16.6% and 3 x 3 x 3 central pixels removed.
![Page 22: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/22.jpg)
(a) The active site of the
molecule from PDB
(b) The reconstruction
with RI = 9.8%
(c) The reconstruction
with RI = 16.6%
![Page 23: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/23.jpg)
SSummary
• A new imaging methodology (i.e. single particle diffraction) has been developed by combining coherent X-rays with the
oversampling method.
• The 2D and 3D imaging resolution of 8 nm and 50 nm has been achieved.
• These results will pave a way for the development of atomic resolution 3D X-ray diffraction microscopy.
• In combination with the X-ray free electron lasers, single particle diffraction could be used to determine the 3D structure of single biomolcules at near atomic resolution.
![Page 24: Single Particle X-ray Diffraction - the Present and the Future John Miao Stanford Synchrotron Radiation Laboratory Stanford Linear Accelerator Center.](https://reader035.fdocuments.net/reader035/viewer/2022062423/5697bf731a28abf838c7ed0d/html5/thumbnails/24.jpg)
Acknowledgements
• B. Johnson & K. Hodgson, Stanford Synchrotron Radiation Lab., Stanford University
• J. Kirz & D. Sayre, SUNY at Stony Brook• C. Larabell, UC San Francisco & Lawrence Berkeley
National Lab.• M. LeGros, E. Anderson, Lawrence Berkeley National
Lab.• B. Lai, Advanced Photon Source, Argonne National Lab.• T. Ishikawa, Y. Nishino, RIKEN/SPring-8, Japan • J. Amonette, Pacific Northwest National Lab.