H. Nakamura

M. Nakamura

R. Nishida

T. "Yasunaga

Y." Tamura

National Institute for Fusion Science (NIFS-Repository)

§ 33. A Visualization Tool of BiologicalMacromolecular Structures toward Insilica MicroscopyYasunaga, T., Nakamura, M., Nishida, R. (KyushuInst. of Tech.)Nakamura, H., Tamura, Y.Three-dimensional density maps of protein fromelectron cryo-micrographs are useful forelucidating the relationship between function andstructures, because the structures under thephysiological conditions can be observed usingelectron cryo-microscopy. The resolution of theirimages are, however, relatively worse (ananometer resolution in a typical case) than thatof X-ray crystallography, i.e., the atomic resolution.Thus, we consider that it is important forunderstanding proteins and their complexes tolink physiological, but not so high resolutional, 3Dimages from electron micrographs (EM) withatomic coordinates from X-ray crystallography, theother structural information and so on in anintegration and visualization tool. Databasesrelated to mutations of proteins should also beintegrated into the tool.Here we report that a new visualization tool ofproteins has been developed. Using the tool, wecan, stereoscopically, observe atomic coordinatesof proteins and the contour surface of 3D densitymaps from EM. Moreover, we can link the atomsof proteins with remote relational databases (suchas postgreSQI1) as shown in Fig. 1. When onesread some journal reports and are interested insome mutational information of an interestingprotein, they can note it into the database withpicking an atom of interest. Actually, we appliedthe tool to analyze the structure of actin-myosinrigor complexes for elucidating muscle contractionmechanism.354As the next generation of this application, weplan to improve the ability of visualization,especially, introduce virtual visualization usingstereo glasses such as CrystalEyes.XML-formatted databases will, also, be treated.Furthermore, 3D density maps from EM will notonly be visualized but also analyzed such asclassification, marking and so on.Pick--A: TYR: 188: CAPlease Write Your Memo! »>ActiveSite 0Fig. 1. The visualization tool developed here forvisualizing the atomic coordinates of proteins andlinking them with a remote relational database.Using the function shown here, some memos andnotes for the atom of interest can be stored intothe relational database. All tools have beendeveloped under Eos [1].[1] Yasunaga, T. and Wakabayashi T.: Extensibleand object-oriented system Eos supplies a newenvironment for image analysis of electronmicrographs of macromolecules., J 5truct Bi 01.116(1):155-60. (1996)

A Visualization Tool of Biological Macromolecular Structures toward in silico Microscopy

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