New crystallization method to ease study of protein structures

March 10, 2008
New crystallization method to ease study of protein structures
Ribbon representation of NE2398, a protein from the Nitrosomonas europaea bacterium. Dotted lines represent the parts of the protein digested with protease. Blue molecules represent other molecules in the crystal lattice.

Researchers at the Midwest Center for Structural Genomics (MCSG), the Structural Genomics Consortium (SGC) and the Structural Biology Center (SBC) at the U.S. Department of Energy's Argonne National Laboratory have developed a new technique for crystallizing proteins that will ease experimentation into protein structures.

In order to study protein structures, biologists must turn what is essentially a soup of purified protein into crystals that have a consistent and ordered structure. Each protein consists of a chain of amino acid subunits that twists into helices, ribbons and loops. Some proteins have less tidy molecular structures than others; in these, disordered amino acid chains dangle off the protein like split ends.

Crystallizing proteins that contain many of these flexible regions takes much more work and patience than working with more organized ones, said Argonne senior biologist Andrzej Joachimiak, who led the Argonne research effort. "We've tried to find a way to remove the disordered parts using computer modeling, but that's been a challenging process," he said. "This new experimental method is fast, inexpensive and can be applied to many different targets, from bacterial pathogens to human proteins."

In order to try to boost the efficiency of the crystallization process, Joachimiak and his colleagues at the MCSG and SGC inserted a protease—a certain type of enzyme that breaks down the bonds that connect a protein's amino acids.

Once added, the protease preferentially bound to the proteins at the disordered regions, snipping off the loose ends like a molecular barber. The researchers successfully crystallized and examined nine of these newly shorn proteins that previously had resisted attempts to study them using X-ray crystallography.

"This simple technique offers an opportunity to uncover and characterize the structures of dozens of proteins that up until now we had to study using much more laborious and expensive approaches," Joachimiak said.

This process, known as "limited in situ proteolysis," represents one of several potential "salvage pathways" that biophysicists could use to create more usable protein crystals and reduce waste, Joachimiak said. Currently, scientists' efforts to manufacture and then study a workable crystal on Argonne's Advanced Photon Source yield structural data only about 15 percent of the time. By using proteases to digest part of the protein sample, the Argonne scientists achieved a six percent boost in efficiency.

Joachimiak cautioned that scientists do not have a way to successfully crystallize every protein, even with the use of proteolysis. "There will still be some that are resistant," he admitted, "but we are making enormous strides in our understanding of how exactly these essential substances work."

A research paper, "In situ proteolysis for protein crystallization and structure determination," that detailed the study appeared in the December 4 issue of Nature Methods. The study's X-ray data were collected at the SBC beamlines at the Advanced Photon Source. The MCSG and SGC represent a collaboration of Argonne scientists as well as scientists from Canada and Europe.

Source: Argonne National Laboratory

Explore further: Hacking the bacterial social network

Related Stories

Hacking the bacterial social network

October 25, 2017

Whenever we use our smartphones to check social media, we face loads of bacteria on the devices—even more than on toilet seats, according to a University of Arizona study. Those bacteria may have their own form of social ...

Crystals in a pink X-ray beam

November 3, 2017

A newly developed experimental set-up allows the X-ray structure determination of biomolecules such as proteins with far smaller samples and shorter exposure times than before. At so-called synchrotron sources, protein crystal ...

Researchers devise a new way of producing hydrogen fuel

September 4, 2017

A U.S.-based team of researchers including MIPT scientists has assembled a nanoscale biological structure capable of producing hydrogen from water using light. They inserted a photosensitive protein into nanodiscs—circular ...

New Argonne study may shed light on protein-drug interactions

January 15, 2008

Proteins, the biological molecules involved in virtually every action of every organism, may themselves move in surprising ways, according to a recent study from the U.S. Department of Energy’s Argonne National Laboratory ...

Inside a high-stakes experiment in protein crystallization

April 14, 2015

On April 18, 2014, former astronaut and UAB Professor Lawrence DeLucas, O.D., Ph.D., stood at Cape Canaveral and watched several hundred crystallization experiments blast into orbit aboard the SpaceX Falcon 9 rocket. Then ...

Recommended for you

How to cut your lawn for grasshoppers

November 22, 2017

Picture a grasshopper landing randomly on a lawn of fixed area. If it then jumps a certain distance in a random direction, what shape should the lawn be to maximise the chance that the grasshopper stays on the lawn after ...

Plague likely a Stone Age arrival to central Europe

November 22, 2017

A team of researchers led by scientists at the Max Planck Institute for the Science of Human History has sequenced the first six European genomes of the plague-causing bacterium Yersinia pestis dating from the Late Neolithic ...

Ancient barley took high road to China

November 21, 2017

First domesticated 10,000 years ago in the Fertile Crescent of the Middle East, wheat and barley took vastly different routes to China, with barley switching from a winter to both a winter and summer crop during a thousand-year ...


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.