A new approach for solving protein structures

Sep 06, 2012 by Laura Mgrdichian
A new approach for solving protein structures
A native protein structure as determined using the multiple-crystal SAD method. The complex of four protein chains is shown as a ribbon diagram and is colored violet. The anomalously scattering substructure, containing 28 sulfur atoms and three sulfate ions, is represented as spheres (yellow for sulfur, yellow/red for sulfate).

(Phys.org)—Using synchrotron x-ray beams to solve the molecular structures of proteins and other large biological molecules has yielded many advances in medicine, such as drug therapies for cancer. Improvements in the techniques available to scientists could lead to even more exciting advances. Recently, scientists from NSLS, the New York Structural Biology Center and Columbia University discovered a new method to determine molecular structures that would have been difficult or impossible to solve otherwise. Their work is reported in the May 25 online edition of Science.

The process of using to determine protein structures, known as macromolecular crystallography, begins by growing pure crystals of the molecule. Crystals, being regular arrays of these molecules, generate diffraction patterns when exposed to x-rays, and these diffraction data can be measured accurately and used to extract structural information – a very complex task.

When a has similar structure relatives, the process is easier. But when it does not, scientists face the "phase problem," the loss of critical information describing the "phase" of the incident x-rays waves – that is, the waves' positions relative to each other. When a detector records the , it can measure intensity, but not phase, and without phases the structure cannot be completely solved.

When no related structure exists, there are other ways to evaluate the phases. Two of these methods are x-ray crystallographic techniques: multiwavelength anomalous diffraction (MAD), in which x-rays of more than one wavelength are used; and single-wavelength anomalous diffraction (SAD), which uses x-rays of just one wavelength. (MAD and SAD were developed by this study's corresponding author, Columbia biophysicist Wayne Hendrickson.)

Both techniques typically involve adding selenium into the (via the amino acid derivative selenomethionine, which incorporates easily into proteins) and scanning the x-ray beam across the atom's edge. Selenium is a heavier atom than those usually found in proteins – carbon, nitrogen, and oxygen, for example – and it absorbs and re-emits x-rays with element-specific resonance. From the resonant , scientists can determine the phase. (The selenomethionine substitution method for MAD phasing was also developed by Hendrickson.)

Here, working at NSLS beamline X4A, the group developed a way to solve the phase problem without adding a heavy element to the crystal, and instead were able to use proteins in their native state. They used off-resonance scattering from the proteins' own sulfur atoms, which is much feebler than that from selenium, but yet strong enough to be workable. They applied SAD to several crystals (between five and 13 for each protein studied) using lower-than-usual x-ray energies and then combined the relatively weak diffraction signals.

The four proteins they solved varied in size and contained different amounts of sulfur (between three and 28 sulfur sites on each molecule). The group's success with each one suggests that their work has opened a doorway for a potentially vast new landscape of discoveries in macromolecular crystallography.

"The idea of using sulfur SAD phasing is an old one, but its impact has been limited until now," said Hendrickson. "We are excited by the dramatic improvements in signal-to-noise and phasing efficacy that derive from multi-crystal averaging."

At the future NSLS successor, NSLS-II, which will offer an extremely bright x-ray beam and the most advanced synchrotron tools, Hendrickson and his group expect to make further progress with this technique. NSLS-II's x-ray beam will be much smaller and more intense, allowing scientists to use smaller crystals. At the same time, the beam is also more likely to damage a single protein crystal before all the data has been collected. Therefore, a technique that uses multiple crystals could work exceptionally well.

Explore further: X-rays probe LHC for cause of short circuit

add to favorites email to friend print save as pdf

Related Stories

Fastest X-ray images of tiny biological crystals

Jan 05, 2012

(PhysOrg.com) -- An international research team headed by DESY scientists from the Center for Free-Electron Laser Science (CFEL) in Hamburg, Germany, has recorded the shortest X-ray exposure of a protein crystal ...

New strategy could lead to dose reduction in X-ray imaging

Nov 22, 2011

For more than a century, the use of X-rays has been a prime diagnostic tool when it comes to human health. As it turns out, X-rays also are a crucial component for studying and understanding molecules, and a new approach ...

Powders show their strength

Oct 09, 2007

[PIC=:left]Growing a single crystal of a protein can be very difficult. Thanks to recent developments, a powder sample may be enough to solve a structure.

Unveiling the structure of microcrystals

Oct 04, 2007

Microcrystals take the form of tiny grains resembling powder, which is extremely difficult to study. For the first time, researchers from the European Synchrotron Radiation Facility (ESRF) and the Centre National ...

New technique to see crystals like never before

Nov 30, 2011

An international team of scientists led by the Fresnel Institute and the ESRF (European Synchrotron Radiation Facility) in Grenoble has developed a new technique allowing to observe the nanometer-sized structure ...

Recommended for you

X-rays probe LHC for cause of short circuit

Mar 27, 2015

The LHC has now transitioned from powering tests to the machine checkout phase. This phase involves the full-scale tests of all systems in preparation for beam. Early last Saturday morning, during the ramp-down, ...

New insights found in black hole collisions

Mar 27, 2015

New research provides revelations about the most energetic event in the universe—the merging of two spinning, orbiting black holes into a much larger black hole.

Swimming algae offer insights into living fluid dynamics

Mar 27, 2015

None of us would be alive if sperm cells didn't know how to swim, or if the cilia in our lungs couldn't prevent fluid buildup. But we know very little about the dynamics of so-called "living fluids," those ...

Fluctuation X-ray scattering

Mar 26, 2015

In biology, materials science and the energy sciences, structural information provides important insights into the understanding of matter. The link between a structure and its properties can suggest new ...

Hydrodynamics approaches to granular matter

Mar 26, 2015

Sand, rocks, grains, salt or sugar are what physicists call granular media. A better understanding of granular media is important - particularly when mixed with water and air, as it forms the foundations of houses and off-shore ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.