Investigating the detailed structure of large biomolecules with a non-damaging X-ray technique

Jul 18, 2014
Figure 1: Using ultrashort x-ray pulses generated by the x-ray free electron laser (XFEL) at the SPring-8 synchrotron facility allows the structure of complex biomolecules to be investigated without radiation damage. Credit: k4d/iStock/Thinkstock

Biological molecules such as proteins can contain hundreds of thousands of atoms, which makes it very difficult to understand their function in detail. Identifying the exact atomic structure of these complex molecules is essential for biological studies and drug discovery, but the high-intensity x-ray beams needed to study them inevitably cause significant radiation damage to the molecules being investigated.

Hideo Ago and colleagues from the RIKEN SPring-8 Center, along with researchers from other institutions in Japan, have now developed an technique that allows one of the most powerful modern x-ray machines, the x-ray free electron laser (XFEL) at the SPring-8 synchrotron facility, to be used to study large, without radiation damage.

X-ray diffraction experiments involve measuring the scatter of x-rays from in a crystal. Since the atoms in a crystal are ordered in periodically repeating arrangements, the reflected x-rays form regular patterns that can be traced back to the arrangement of the atoms in the crystal, allowing the molecular structure to be determined.

"The dilemma of conventional x-ray protein crystallography, however, is that the x-ray intensities required for a precise structure determination also cause severe radiation damage to the protein molecules," explains Ago.

The XFEL at the SPring-8 facility offers a solution. The ultra-intense, femtosecond x-ray pulses generated by the XFEL are so short that they do not interact with proteins long enough to cause structural changes. Although the individual interactions are weak, if the crystals are thick enough, the pulses have sufficient cumulative interaction to give clear x-ray diffraction patterns and resolve the details of even highly complex molecules.

To avoid damage from successive pulses hitting the same spot in the crystal, the x-ray spot size is made very small and successive measurements are taken at different locations in the crystal. Averaging the x-ray patterns obtained from various locations then allows the optimized crystal structure to be determined.

As an example, the researchers successfully studied the oxygen reaction center in the bovine enzyme cytochrome c oxidase, which is particularly susceptible to and had therefore defied previous attempts at precise structural characterization.

In future, this method could be employed for the study of a number of important , particularly in biology, says Ago. "Our system is very useful for studying the catalytic function of enzymes and proteins. Famous examples include the proteins involved in photosynthesis, and we would like to study the exact mechanism behind their amazingly efficient light-harvesting ability."

Explore further: X-ray imaging reveals a complex core

More information: Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E. et al. "Determination of damage-free crystal structure of an X-ray–sensitive protein using an XFEL." Nature Methods 11, 734–736 (2014). DOI: 10.1038/nmeth.2962

add to favorites email to friend print save as pdf

Related Stories

X-ray imaging reveals a complex core

Jul 04, 2014

Macromolecular complexes composed of self-assembling proteins and nucleic acids hold promise for a wide range of applications, including drug delivery, sensing and molecular electronics. Scientists have developed ...

First X-ray lasing of SACLA

Jun 17, 2011

RIKEN and the Japan Synchrotron Radiation Research Institute (JASRI) have successfully produced a first beam of X-ray laser light with a wavelength of 1.2 Angstroms. This light was created using SACLA, a cutting-edge X-ray ...

Recommended for you

And so they beat on, flagella against the cantilever

Sep 16, 2014

A team of researchers at Boston University and Stanford University School of Medicine has developed a new model to study the motion patterns of bacteria in real time and to determine how these motions relate ...

Tandem microwave destroys hazmat, disinfects

Sep 16, 2014

Dangerous materials can be destroyed, bacteria spores can be disinfected, and information can be collected that reveals the country of origin of radiological isotopes - all of this due to a commercial microwave ...

Cornell theorists continue the search for supersymmetry

Sep 16, 2014

(Phys.org) —It was a breakthrough with profound implications for the world as we know it: the Higgs boson, the elementary particle that gives all other particles their mass, discovered at the Large Hadron ...

How did evolution optimize circadian clocks?

Sep 12, 2014

(Phys.org) —From cyanobacteria to humans, many terrestrial species have acquired circadian rhythms that adapt to sunlight in order to increase survival rates. Studies have shown that the circadian clocks ...

User comments : 0