Protein X-rays: Beating the law of averages

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  • Published: Feb 15, 2014
  • Author: David Bradley
  • Channels: X-ray Spectrometry
thumbnail image: Protein X-rays: Beating the law of averages

More dynamic

Computational biologists have demonstrated that taking an average X-ray snapshot of a crystallized protein masks much of the structural heterogeneity and the dynamics inherent in a protein. The work suggests that alternative approaches to averaging might be fruitful for extracting information about the form-derived function of many proteins.

Computational biologists have demonstrated that taking an average X-ray snapshot of a crystallized protein masks much of the structural heterogeneity and the dynamics inherent in a protein. The work suggests that alternative approaches might be needed to extract information about protein dynamics from X-ray data. Bojan Zagrovic and his team in the Max F. Perutz Laboratories at the University of Vienna and the Medical University of Vienna, Austria, describe details of their findings in the journal Nature Communications.

Usually, taking an average can simplify observations whether astronomical, economic or in X-ray crystallography. It provides a neat way to encapsulate data that would otherwise be overwhelming and perhaps unintelligible. "Moreover," Zagrovic told SpectroscopyNOW, "sometimes one simply cannot avoid averages: for example, in order to boost signal-to-noise ratio, structural biologists are often forced to study billions of copies of a single molecule at the same time and look at their average structure and dynamics. A protein crystal is one such example." However, as with taking an average on the bill when dining out with a group of friends it can hide all kinds of important details regarding the outliers who had more and those who had less than the "average". Similarly in science, averaging data from repeated experiments can hide the details and the dynamics of deviations from the norm, for instance.

Unfreezing proteins

When it comes to X-ray crystallography of proteins, the averaging is across billions of atoms within the crystal and masks much of the subtleties that are manifest in the protein in its native state rather than in the "frozen" crystalline form. "Take, for example, the average location of a goalie during a football match. Considering that the teams switch sides at halftime, it is roughly at the centre of the field, a clearly non-representative situation."

Graduate student Antonija Kuzmanic working with Zagrovic was hoping to improve the programs used in the analysis of X-ray crystallographic data to improve protein structure elucidation and simultaneously extract dynamic information. In work supported by a European Research Council (ERC) Starting Grant and in collaboration with Navraj Pannu of Leiden University, in The Netherlands, she simulated a protein crystal "in silico" and then analyzed it using conventional X-ray crystallography algorithms to extract the protein's structure. The team could then test how well the crystallography software currently "sees" what is really there in the simulated protein as a proxy for a real-life crystal analysis.

The wiggles

"We were really surprised to find that current software programs underestimates the level of dynamics - the atomic wiggle room - by up to six fold. This is a lot, it's as if we could suddenly turn our head 180 degrees rather than just to the left or right", Antonija Kuzmanic explains.

Structural biologist Garib Murshudov of the University of Cambridge, England, describes the work as "inspirational". He points out that the findings suggest that it is time to take another look at crystallography and what its working software can ascertain with regards to protein dynamics in crystals. More accurate ways to interpret X-ray crystallography data and determine the dynamics of proteins will improve the development of pharmaceuticals that are designed to target specific proteins. Approaches that go beyond the simple average representation of structures could provide a more realistic picture of what the protein looks like in nature and so help researchers develop medicines that can modify a protein's function more accurately and more potently.

"The next step is to try and figure out ways to more accurately capture protein dynamics from X-ray data," Zagrovic told us. "The main aim of our work is to understand how dynamic proteins really are on the microscopic level and how this relates to their function - our overarching hypothesis is that proteins, even well-structured ones, are significantly more dynamic than appreciated."

Related Links

Nature Commun, 2014, 5, 1-10: "X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals"

Article by David Bradley

The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.

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