Research on Protein Structure, 3rd of April 2003
-New purpose-built beam line-

We have already introduced the research on protein structure that uses the synchrotron radiation facility of KEK in various ways. As explained in our introduction to the Protein 3000 Project, a national project in Japan, the three-dimensional structure of protein can be identified mainly by using X-ray crystallography. X-ray synchrotron radiation that is strong and spatially focused has been used for over 20 years because it is optimal when illuminating a protein crystal for accurate measurement through the internal weak diffraction point (point of changing the direction of X-ray such as reflection). Life sciences, particularly those based on the 3-D structure of protein have recently been activated and promoted internationally on a large scale. In this situation, it has become difficult to carry out the rapid measurements of large-scale crystal or the measurement of micro crystal by use of beam line in conventional synchrotron radiation facilities.

Today, we introduce the NW12, the beam line for the structural biology research, created in the high-energy synchrotron radiation ring (PF-AR: Photon Factory Advanced Ring) of KEK synchrotron radiation facility in order to meet the expectations. The name, NW 12, reflects the fact that it makes use of the light source located at the 12th section on the northwest side of PF-AR. This beam line measures the diffraction data obtained from the exposure of X-ray synchrotron radiation to protein crystal. The calculation using computer of diffraction data obtained leads to the elucidation of protein structure. For rapid measurement, the beam line is equipped with special devices such as the inserting light source to eliminate light that is stronger than that of conventional synchrotron radiation and the CCD Detector to enable to read the diffraction data rapidly. For this, the exposure time and data recording time were shortened and the measurement time has been cut from over 3 hours at the time using the beam line in conventional PF to about 20 minutes.

There is only 2.2 micron or less of wobbling of the rotation axis of crystal in NW12. Because of its very high precision, measurement of microcrystal in even microns (a thousandth of 1 mm) is available. With the mirror that collimates X-ray synchrotron or the system to cool spectral structures by using liquid nitrogen (-196Ž), X-rays highly collimate, leading to the experiment using the multiwavelength anomalous dispersion (MAD) method with high precision. The MAD method is used to find clues to the structure through the use of the minute changes of signals that occur in the diffraction intensity when X-ray wavelength is changed, and is a potent structure determination method, which is difficult to carry out without synchrotron radiation, which its variable wavelength. Other state-of-the-art techniques, such as the X-ray shutter that can open and close for 10 millisecond or the spectrometer that has a variable wavelength without changing the outgoing site of the beam, have been incorporated into NW12.

In experimental study at the end of February, the structure of the protein called glycosyltransferases was clarified. It was possible to obtain the diffraction data at 2.0 angstrom resolution after measuring for only 20 minutes by using a crystal sized approximately 30 x 30 x 100 microns. Figure 3 shows the 3-dimentional structures obtained as a result of the structural analysis.

To carry out effectively the sequential measurement of large-scale crystals, the process of setting the crystal into the device should be accelerated. NW 12 is equipped with a control system that makes these process automated by introducing a robot. In the near future, through automating most of the process, the mechanism will be established to supply data immediately to researchers in structural biology.

Figure :
Picture of crystals of glycosyltransferases, which are approximately 30 x 30 x 100 microns

Figure 2
X-ray diffraction picture of glycosyltransferases
Each of the many spots of light, like a starry sky, has information about the location of each atom. The 3-dimentional structure of protein as shown in Figure 3 can be obtained using computer-assisted analysis.

Figure 3
The 3-dimentional structure of glycosyltransferases analyzed using NW12

Figure 4
Newly constructed NW 12 beam line for the structural biology research in PF-AR
Boxes called "hutches" that are seen at the front and the back of this picture hold the devices of the optical system and the measurement devices.

High magnification (60 KB)

Figure 5
High-speed CCD detector installed in the experimental hutch
Using this detector, the diffraction data as shown in Figure 2 can be obtained rapidly.

High magnification (41 KB)

1 micron = 0.001 millimeter
1 angstrom = 0.0000001 millimeter

For further inforvmation
Photon Factory (PF) Homepage

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Strategy of Natural Protein -Its 3-D structure-

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