2017 Fiscal Year Research-status Report
Database of Molecular Shapes and Diffraction Patterns for X-ray Free Electron Laser Data Analysis
| Project/Area Number |
17K07305
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| Research Institution | Nagoya University |
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Principal Investigator |
TAMA FLORENCE 名古屋大学, 理学研究科, 教授 (20648191)
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| Project Period (FY) |
2017-04-01 – 2020-03-31
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| Keywords | single molecules / 2D images / 3D structure |
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| Outline of Annual Research Achievements |
Advancements in biophysical experimental techniques have pushed the limits in terms of the types of phenomena that can be characterized, the amount of data that can be produced and the resolution at which we can visualize them. Single particle techniques such as Electron Microscopy (EM) and X-ray free electron laser (XFEL) scattering require a large number of 2D images collected to resolve three-dimensional (3D) structures. In this study, we propose a quick strategy to retrieve potential 3D shapes, as low-resolution models, from a few 2D experimental images by searching a library of 2D projection images generated from existing 3D structures.
We developed the protocol to assemble a non-redundant set of 3D shapes for generating the 2D image library, and to retrieve potential match 3D shapes for query images, using EM data as a test. In our strategy, we disregard differences in volume size, giving previously unknown structures and conformations a greater number of 3D biological shapes as possible matches. We tested the strategy using images from three EM models as query images for searches against a library of 22750 2D projection images generated from 250 random EM models. We found that our ability to identify 3D shapes that match the query images depends on how complex the outline of the 2D shapes are and whether they are represented in the search image library.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
We have demonstrated that a few 2D EM images could be used to retrieve a 3D shape. The computational approach has been submitted and is currently under revision.
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| Strategy for Future Research Activity |
Through our computational method, we are able to quickly retrieve a 3D shape from a few 2D projection images. Our approach has the potential for exploring other types of 2D single particle structural data such as from XFEL scattering experiments, for providing a tool to interpret low-resolution data that may be insufficient for 3D reconstruction, and for estimating the mixing of states or conformations that could exists in such experimental data. We are currently working toward achieving those aims and more specifically finding the appropriate measures that could be used to derive 3D shape from a few XFEL patterns. In addition, we plan to make the database available to the public.
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| Causes of Carryover |
Did not purchase server as the database wasn't fully completed and I prefer to wait to get the latest computer as it might be more powerful.
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