2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching.
In this study, we develop an approach termed "2D hybrid analysis" for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.
Molecular Simulation and Modeling Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan. matsumoto.atsushi@qst.go.jp.
Atsushi
A
Matsumoto
Institute for Protein Research, Laboratory of Protein Synthesis and Expression, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Naoyuki
N
Miyazaki
Institute for Protein Research, Laboratory of Protein Synthesis and Expression, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Junichi
J
Takagi
Institute for Protein Research, Laboratory of Protein Synthesis and Expression, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Kenji
K
Iwasaki
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D021621:Imaging, Three-Dimensional / Q000379:methods*; D016023:Integrins / Q000737:chemistry; D008854:Microscopy, Electron; D008956:Models, Chemical; D008958:Models, Molecular
D016023:Integrins