Protein pulling -- Learning how proteins fold by pulling them apart

Rice University physicists have unveiled an innovative way of finding out how proteins get their shape based on how they unfold when pulled apart. The experimental method could be of widespread use in the field of protein folding science, which has grown dramatically in the past decade, due in part to the discovery that misfolded proteins play a key role in diseases like Alzheimer's and Parkinson's.

Rice's new findings, which were three years in the making, are available online and slated to appear in an upcoming issue of Physical Review Letters. The article describes a new method scientists can use to map out exactly how much free energy is required throughout the folding process.

"We believe the method can be applied to any protein," said lead author Ching-Hwa Kiang, assistant professor of physics and astronomy. "Many people are working on this problem, and when we present our work at scientific conferences it often creates a good deal of excitement."

If DNA is the blueprint for life, then proteins are the machines built from those blueprints. All living cells produce proteins by stringing together strands of amino acids based on the sequences of their DNA. Proteins are created in linear chains, like strands of pearls, with each amino acid representing a bead on the strand. However, knowing the order of the amino acids in the strand gives no clue about how a protein functions. That's because every protein folds into a three-dimensional shape within about one second of being made, and it is this shape that dictates the protein's function.

By studying how much free energy it takes for a protein to fold into its final shape, scientists hope to learn more about how amino acid sequences affect protein function and how folding goes awry, as with some diseases.

At the halfway point between it's folded and unfolded state, a protein is like a rollercoaster balanced at the crest of the highest hill on the track. Like the rollercoaster, the protein requires a certain amount of energy to make it over the hill and wind its course to a final resting place -- its folded state. If it lacks the energy to clear the hill, it will slide back into a partially folded or misfolded state.

Kiang and graduate student Nolan Harris's new approach to probing these energy states yields something akin to a map of the rollercoaster's path. For example, theirs is the only experimental method that can reveal the slope and height of the energy barrier that the protein must overcome.

"Other experimental methods give researchers a pretty clear picture of the energy states at the beginning and the end -- the two equilibrium states," Kiang said. "Our approach helps fill in what happens in between, when the system is between folded and unfolded."

Kiang and Harris's experiments were conducted on one piece of a protein named Titin. The Titin piece, dubbed I27, contains 89 amino acids. Harris suspended thousands of intact, folded I27s in a dilute saline solution and let the solution sit long enough for the proteins to become stuck to the bottom of the sample dish. The needle from an atomic force microscope (AFM) was repeatedly dipped into the solution. The tip of the AFM operates much like a phonograph needle. The AFM needle is on the end of a cantilever arm that bobs up and down over the sample. The tip of the AFM needle is just a few atoms wide. Bobbing down, it randomly grabbed I27s that were pulled into their string-like, unfolded shape as the needle rose.

Harris measured the force exerted on the cantilever arm each time an I27 was unfolded. To get the energy maps, he wrote software incorporating a statistical mechanics equation called the "Jarzynski equality." The equation related the non-equilibrium energy from the unfolding events to the equilibrium profiles along the trajectory from the folded to the unfolded state. Kiang said the software, and the use of the Jarzynski equality, makes the new method unique and useful.

"Christopher Jarzynski only discovered this relationship 10 years ago," Kiang said. "It's a very powerful technique."

Source: Rice University

Related stories:

Landmark discovery of 'engine' that drives cell movement
This research by Thomas Leung, Ph.D., and his team in the GSK-IMCB Group at the Institute of Molecular and Cell Biology (IMCB), under Singapore's Agency for Science, Technology and Research, is fundamental to the understanding of how assembles its internal machinery required for cell movement.
Food for thought -- regulating energy supply to the brain during fasting
If the current financial climate has taught us anything, it's that a system where over-borrowing goes unchecked eventually ends in disaster. It turns out this rule applies as much to our bodies as it does to economics. Instead of cash, our body deals in energy borrowed from muscle and given to the brain.
When a light goes on during thought processes
(PhysOrg.com) -- Thought processes made visible: An international team of scientists headed by Mazahir Hasan of the Max Planck Institute for Medical Research in Heidelberg has succeeded in optically detecting individual action potentials in the brains of living animals. The scientists introduced fluorescent indicator proteins into the brain cells of mice via viral gene vectors: the illumination of the fluorescent proteins indicates both when and which neurons are communicating with each other.
New technology paves the way for the future of identifying proteins inside cells
A new technology which enables scientists to identify proteins by making a map of the energy flow inside the protein is revealed today in Proceedings of the National Academy of Sciences (PNAS) journal.
Photosynthesizing bacteria with a day-night cycle contain rare chromosome
Researchers sequencing the DNA of blue-green algae found a linear chromosome harboring genes important for producing biofuels. Simultaneously analyzing the complement of proteins revealed more genes on the linear and the typical circular chromosomes then they'd have found with DNA sequencing alone.
Giant grass offers clues to growing corn in cooler climes, researchers report
A giant perennial grass used as a biofuels source has a much longer growing season than corn, and researchers think they've found the secret of its success. Their findings offer a promising avenue for developing cold-tolerant corn, an advance that would significantly boost per-acre yields. The new study, from researchers at University of Illinois, appears this month in Plant Physiology Preview.
Thumbs up -- a tiny ancestral remnant lends developmental edge to humans
Subtle genetic changes that confer an evolutionary advantage upon a species, such as the dexterity characteristic of the human hand, while difficult to detect and even harder to reproduce in a model system, have nevertheless generated keen interest amongst evolutionary biologists. In findings published online in the September 5 edition of the journal Science, researchers from the U.S. Department of Energy's Lawrence Berkeley National Laboratory and their collaborators, have uncovered a specifically human 13-nucelotide change concealed in the vast three-billion-letter landscape of the human genome.
Energy-saving bacteria resist antibiotics
Bacteria save energy by producing proteins that moonlight, having different roles at different times, which may also protect the microbes from being killed. The moonlighting activity of one enzyme from the tuberculosis bacterium makes it partially resistant to a family of broad-spectrum antibiotics, according to a paper published in the September issue of the journal Microbiology.

News discussion:

Physics news