Stanford collaboration creates new X-ray 'molecular observatory'

By Brad Plummer

Just as astronomers use specialized observatories to study distant galaxies, chemists and molecular biologists need advanced tools for studying nanoscale structures that are in some ways as inaccessible as the far reaches of the cosmos. Now, thanks to a collaboration among Stanford University, the California Institute of Technology (Caltech) and the Gordon and Betty Moore Foundation, researchers have a new tool for studying in great detail the molecules that make up living systems. The new Molecular Observatory for Structural Molecular Biology, at the Department of Energy's Stanford Synchrotron Radiation Laboratory (SSRL), will help unlock the secrets of organic molecules on the atomic level with an unprecedented degree of precision.

On March 23, collaboration leaders gathered at SSRL before a crowd of a hundred staff members for an official dedication of the new $12.5 million molecular observatory. Attendees included Stanford President John Hennessy, Caltech President Jean-Lou Chameau and Intel co-founder and philanthropist Gordon Moore.

"Instrumentation seems to be the place where we can make the biggest impact, where new capabilities make possible great leaps forward," said Moore, addressing the crowd. "It enables scientists to do things otherwise unavailable to them."

The observatory capitalizes on a device called an undulator to create powerful beams of X-rays. Typically, undulators contain alternating rows of strong magnets that clamp around the outside of the accelerator's pipe, through which electrons flow. The magnets force the beam of electrons inside the pipe to slalom back and forth and emit intense X-rays. According to physicists at SSRL, the new undulator differs from others in use at the lab because the rows of magnets are placed inside the accelerator pipe, under vacuum, allowing them to squeeze closer together around the beam and exert a stronger field on the electrons. The result is an ultra-bright beam of X-rays that can be focused into a tiny spot and trained onto biologic samples, revealing their details with tremendous resolution.

The science of protein crystallographya widely used method for creating images of organic moleculesrelies on tightly controlled, highly focused X-ray beams to probe the structure of materials. The process involves crystallizing a sample of molecules, blasting it with X-rays and analyzing the diffraction pattern captured by a detector. Protein crystallography studies often require scanning hundreds of samples to map out the properties of one complex molecule. With the new observatory, the intense brightness of the X-rays means samples will need shorter exposure times. Subsequently, more samples can be processed quickly.

The new observatory also boasts an automated sample-handling system that can be controlled remotely, allowing researchers from around the world to conduct research without having to travel to the Stanford Linear Accelerator Center (SLAC) in Menlo Park, Calif., which houses SSRL. With this system, a robotic arm removes a sample stored in liquid nitrogen and places it in front of the X-ray beam, obviating the need for researchers to enter the experimental station to place samples manually. The software developed to operate the system remotely, called Blu-Ice, was developed by the crystallography group at SSRL and is the first system of its kind. Once a batch of samples has arrived at the lab, scientists working remotely have full control of over how the samples are scanned. Presently, seven remote-access systems are in use at beamlines around SSRL.

The molecular observatory promises to push the boundaries of atomic- and molecular-scale imaging. By working out the blueprint of macromolecules such as proteins, DNA and RNA, scientists can better address fundamental questions, such as how the chemistry of life is achieved and regulated within cells.

"The new beam line will enable Caltech scientists and SSRL's users to address problems at the cutting edge of structural biology research," said Keith Hodgson, photon science director at SLAC. "We are very grateful to the Gordon and Betty Moore Foundation for their visionary investment."

SSRL and Caltech will share research time on the new observatory. SLAC is operated by Stanford and is funded in part by the Department of Energy's Office of Science.

Brad Plummer is a science writer at SLAC.