Transmission Electron Microscopy 3D Construction by IPET Method TCBG GPU Workshop
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1 Transmission Electron Microscopy 3D Construction by IPET Method TCBG GPU Workshop Xing Zhang 8/4/2013 Molecular Foundry Lawrence Berkeley National Laboratory Department of Applied Physics Xi an Jiaotong University
2 Out line
3 Protein Dynamics The dynamic nature and structural heterogeneity of proteins is essential for their functions. Dynamic proteins, like antibody, have a big conformation space. Fab Fab Fc
4 SCIENTIFIC REPORTS 3 : 1089 DOI: /srep01089
5 However, conventional structural determination technologies, such as X-ray, NMR and singleparticle electron cryo-microscopy (cryo-em) are limited by structural heterogeneity because they all involved in averaging process of hundreds to thousands of different particles.
6 Electron Microscopy Cryo- Tomography (ET)
7 Negative stain and Cryo-EM View unaltered macromolecular assemblies by freezing them Sample is studied at cryogenic temperatures Show biological specimen in their native environment Improving steadily since vitreous ice can be produced
8 Tomography 3D Reconstruction
9 3D reconstruction is a challenge with Cryo-TEM data for small protein Low dose, low contrast High noise ratio 0.05 Distortion in large area How to make good alignment and reduce noise lever?
10 Individual-particle Electron Tomography (IPET) Lei Zhang, Gang Ren PLoS ONE January 2012 Volume 7 Issue 1 e30249
11 The Core Algorithm of the Local Refinement Program Original tilt series Translated tilt series 3D reconstruction FSC Dynamic Gaussian low-pass filter Dynamic 3D & 2D masks Filtered and masked Tilt series Filtered and masked projections as references Translation parameters
12 The Flow Diagram of Our Local Refinement Program Align the ET micrographs Correct the CTF Project the 3D 3D particleshape mask Back-project to 3D Window the target particle 2D crosscorrelation Project the 3D Generate initial 3D Interpolation Round three Interpolation Refine the trans. param. of tilt series 2D circle mask Low-pass filter & 2D Corr. 2D particleshape mask Refine the center of tilt-series Round one Round two Final 3D Back-project to 3D Project the 3D 3D particleshape mask Back-project to 3D
13 Creating a Series of Simulating Cryo-ET Tilt Images of One Individual Particle - A 100kDa Transporter Projections of the Model CTF effects Translation Errors Add Noise S:N=1:5
14 The 3D reconstruction by IPET method A B C D Initial Iteration 1 Iteration 2 E F G H Round 1 Round 2 Round 3 Round 3 Fitting Object I J
15 Antibody 3D reconstruction
16 Antibody Dynamic
17 GPU implementation?
18 The 3D reconstruction is very time consuming To finish one 3D construction by IPET method need hundreds of iterations which means more than 5 hours, just for 120 tilted images (400*400 pixel) Key algorithm(s) involved in traditional CPU approach Pixel by pixel matrix operations, Fourier transform, Cross-Correlation calculation, interpolation and function fitting calculation GPU acceleration Imaging processing is very suit for GPU implementation, because their internal parallel property
19 Goals Increase calculation speed by verify SPIDER code and apply GPU accelerate The speed limiting steps: 3D volume rotation, FFT, Cross- Correlation calculation, Fourier space interpolation
20 Our Group member: Gang (Gary) Ren, Ph.D. Staff Scientist, Molecular Foundry Principal Investigator Dr. Lei Zhang Dr. Bo Peng Dr. Huimin Tong Mr. Xing Zhang (ME) Mr. Zhuoyang Lu Mr. Meng Zhang Mr. Dongsheng Lei Mr. Matthew J. Rames Group home page:
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