Infrared spectroscopy allows scientists to analyze protein structure on ultrafast timescale

Now, MIT researchers have developed a way to analyze proteins that doesn’t require any pre-treatment. The technique is also extremely fast, allowing scientists to see, for the first time, how a protein changes its shape over picoseconds, or trillionths of a second.

The researchers, led by chemistry professor Andrei Tokmakoff and postdoc Carlos Baiz, describe their new technique this month in the journal Analyst. Their approach builds on a technology known as two-dimensional infrared spectroscopy, which works by shining pulses of infrared light on a molecule and measuring the resulting molecular vibrations. In the new paper, the researchers came up with a way to analyze that data and correlate it with common structural elements found in proteins.

Once assembled, proteins tend to fold into one of two secondary structures, known as alpha helices and beta pleated sheets. In this study, the researchers distinguished between those two structures by examining how bonds between carbon and oxygen — found in each of the amino acids that make up proteins — vibrate when exposed to infrared light. 

In an alpha helix, the carbon-oxygen bonds run parallel to the protein’s backbone; in a beta sheet, those bonds are perpendicular to the sheet. Because of that difference, the bonds vibrate at different frequencies when struck with infrared light. This allows the researchers to calculate the percentage of the amino acids that belong to a helical structure and the percentage that form a beta sheet.

The researchers confirmed the accuracy of their calculations by analyzing a set of proteins whose structures are already known. Their method does not currently reveal the exact structure of a protein, but the researchers are working on ways to determine the arrangements of the sheets and helices from the spectroscopic data.

“In principle, the full structure of the protein is represented in the spectrum. The trick is how to get out the information,” says Baiz, lead author of the paper.

One way to do that is to analyze data from a broader range of infrared wavelengths. The researchers are also developing methods to get information about other bonds within the amino acids.

Because the new method can be performed over millionths of a second, it can be used to study how proteins fold and unfold when denatured by heat. After hitting a protein with a laser blast to heat it up, the researchers can capture a series of snapshots of how the protein unfolds over this very short time period.

“This is the first method that will allow us to take snapshots of the structure of the protein as it’s denatured,” Baiz says. “Usually the way people look at proteins is they start with the unfolded state and they end up with the folded state, so you have two static structures. What we can do now is look at all the structures along the pathway.”

Munira Khalil, an assistant professor of chemistry at the University of Washington, says the ability to track structural changes over time is the technique’s biggest strength. “One big question is how do proteins fold — at what point does it go from a completely disordered structure to an ordered structure?” says Khalil, who was not involved in this research.

This would be particularly useful for studying proteins that cause disease when misfolded, such as the tau protein found in patients with Alzheimer’s disease and the prion that causes Creutzfeldt-Jakob disease.

The method can also measure the structural changes that occur as proteins bind to each other. “If the protein is like a rock, and doesn’t change, then it’s never really going to bind its target or do anything. Those are the types of processes we can look at — the conformational changes that drive biological function,” Baiz says.

Provided by Massachusetts Institute of Technology (news : web)

This story is republished courtesy of MIT News (http://web.mit.edu/newsoffice/), a popular site that covers news about MIT research, innovation and teaching.

Materials Inspired by Mother Nature: One-Pound Boat That Could Float 1,000 Pounds

 Combining the secrets that enable water striders to walk on water and give wood its lightness and great strength has yielded an amazing new material so buoyant that, in everyday terms, a boat made from 1 pound of the substance could carry five kitchen refrigerators, about 1,000 pounds.

One of the lightest solid substances in the world, which is also sustainable, it was among the topics of a symposium in San Diego March 25 at the 243rd National Meeting & Exposition of the American Chemical Society, the world's largest scientific society. The symposium focused on an emerging field called biomimetics, in which scientists literally take inspiration from Mother Nature, probing and adapting biological systems in plants and animals for use in medicine, industry and other fields.

Olli Ikkala, Ph.D., described the new buoyant material, engineered to mimic the water strider's long, thin feet and made from an "aerogel" composed of the tiny nano-fibrils from the cellulose in plants. Aerogels are so light that some of them are denoted as "solid smoke." The nanocellulose aerogels also have remarkable mechanical properties and are flexible.

"These materials have really spectacular properties that could be used in practical ways," said Ikkala. He is with Helsinki University of Technology in Espoo, Finland. Potential applications range from cleaning up oil spills to helping create such products as sensors for detecting environmental pollution, miniaturized military robots, and even children's toys and super-buoyant beach floats.

Ikkala's presentation was among almost two dozen reports in the symposium titled, "Cellulose-Based Biomimetic and Biomedical Materials," that focused on the use of specially processed cellulose in the design and engineering of materials modeled after biological systems. Cellulose consists of long chains of the sugar glucose linked together into a polymer, a natural plastic-like material. Cellulose gives wood its remarkable strength and is the main component of plant stems, leaves and roots. Traditionally, cellulose's main commercial uses have been in producing paper and textiles -- cotton being a pure form of cellulose. But development of a highly processed form of cellulose, termed nanocellulose, has expanded those applications and sparked intense scientific research. Nanocellulose consists of the fibrils of nanoscale diameters so small that 50,000 would fit across the width of the period at the end of this sentence.

"We are in the middle of a Golden Age, in which a clearer understanding of the forms and functions of cellulose architectures in biological systems is promoting the evolution of advanced materials," said Harry Brumer, Ph.D., of Michael Smith Laboratories, University of British Columbia, Vancouver. He was a co-organizer of the symposium with J. Vincent Edwards, Ph.D., a research chemist with the Agricultural Research Service, U.S. Department of Agriculture in New Orleans, Louisiana. "This session on cellulose-based biomimetic and biomedical materials is really very timely due to the sustained and growing interest in the use of cellulose, particularly nanoscale cellulose, in biomaterials."

Ikkala pointed out that cellulose is the most abundant polymer on Earth, a renewable and sustainable raw material that could be used in many new ways. In addition, nanocellulose promises advanced structural materials similar to metals, such as high-tech spun fibers and films.

"It can be of great potential value in helping the world shift to materials that do not require petroleum for manufacture," Ikkala explained. "The use of wood-based cellulose does not influence the food supply or prices, like corn or other crops. We are really delighted to see how cellulose is moving beyond traditional applications, such as paper and textiles, and finding new high-tech applications."

One application was in Ikkala's so-called "nanocellulose carriers" that have such great buoyance. In developing the new material, Ikkala's team turned nanocellulose into an aerogel. Aerogels can be made from a variety of materials, even the silica in beach sand, and some are only a few times denser than air itself. By one estimate, if Michelangelo's famous statue David were made out of an aerogel rather than marble, it would be less than 5 pounds.

The team incorporated into the nanocellulose aerogel features that enable the water strider to walk on water. The material is not only highly buoyant, but is capable of absorbing huge amounts of oil, opening the way for potential use in cleaning up oil spills. The material would float on the surface, absorbing the oil without sinking. Clean-up workers, then, could retrieve it and recover the oil.

The American Chemical Society is a non-profit organization chartered by the U.S. Congress. With more than 164,000 members, ACS is the world's largest scientific society and a global leader in providing access to chemistry-related research through its multiple databases, peer-reviewed journals and scientific conferences. Its main offices are in Washington, D.C., and Columbus, Ohio.

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The above story is reprinted from materials provided by American Chemical Society (ACS), via Newswise.

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Double chemical action yields double success

Halogen elements such as chlorine or bromine can boost the synthetic capabilities of many molecules once attached to their frameworks. Techniques known as substitution reactions can then switch the halogens for other groups, such as aromatic species. However, chemists have scarcely studied halogenated disilenes because theoretical calculations indicate that they are inherently volatile. 

Recently however, Tamao and colleagues developed compounds that are extraordinarily adept at stabilizing disilenes. Known as ‘Rind’ ligands, these molecules have a unique fused-ring structure that locks silicon double bonds into place. They also have chemically tunable side chains that optimize compatibility with a variety of substrates and solvents. Based on these capabilities, Tamao and team postulated that their technique could capture the halogenated targets.

Experiments proved that their instincts were correct: combining a Rind-protected bromine–silicon precursor with a reducing agent successfully produced the sought-after dibromo-disilene crystals. But closer examination of the new product’s reactivity revealed a surprise. Simply mixing it with an acetylene derivative caused the disilene to cleave in half and join to both sides of the carbon triple bond, producing a triangle-shaped unsaturated ring.

According to co-author Tsukasa Matsuo, this reaction provided strong evidence that the halogenated disilene could easily dissociate. To confirm this behavior, Katsunori Suzuki, another co-author, dissolved two dibromo-disilenes, each protected by a different Rind ligand, into solution. After one day at room temperature, the researchers observed an extraordinary event: the spontaneously cleaved fragments, known as bromo-silylenes, had reconnected into new disilenes containing both Rind ligands (Fig. 1). This type of ‘cross-over’ reaction, also known as olefin metathesis, is extremely useful to chemists and normally requires expensive metal catalysts to proceed.

The researchers exploited the synthetic potential of the dynamic dibromo-disilenes by capturing the reactive silylene fragment with a base, and then used this complex to construct aromatic-substituted conjugated silicon molecules inaccessible through other techniques. “These results open a new platform for development of functional disilene materials and devices,” says Matsuo.

More information: Suzuki, K., Matsuo, T., Hashizume, D. & Tamao, K. Room-temperature dissociation of 1,2-dibromodisilenes to bromosilylenes. Journal of the American Chemical Society 133, 19710–19713 (2011).

Matsuo, T., et al. Synthesis and structures of a series of bulky “Rind-Br” based on a rigid fused-ring s-hydrindacene skeleton. Bulletin of the Chemical Society of Japan 84, 1178–1191 (2011).

Provided by RIKEN (news : web)

A basic -- and slightly acidic -- solution for hydrogen storage

 Sometimes, solutions for hard problems can turn out to be pretty basic. That's especially true for a team of researchers at the Office of Science's Brookhaven National Laboratory (Brookhaven Lab), where the solution for a hard problem they were working on turned out to be pretty basic…and also a bit acidic.

The hard problem they were working on was how to store hydrogen fuel. Hydrogen gas (H2) is a clean and powerful fuel, but it's also extremely light, which makes it difficult and costly to store. It's typically held in high pressure tanks, although researchers at another Office of Science lab recently found a possible way to keep it in naturally-formed frozen cages.

In a paper published March 18th in Nature Chemistry, researchers at Brookhaven Lab led by chemist Etsuko Fujita announced that they had found a safe and reversible way to store hydrogen under mild (and therefore hopefully much more economical) conditions, using a newly developed catalyst.

Their work began by seeing acids and bases in an unconventional way -- as potential carriers of hydrogen fuel. Students often learn about acids and bases as part of their science fair projects. The 'volcanic' reaction of vinegar (a mild acid) and baking soda (a mild base) has given many students an early interest in the sciences. That was true for Jonathan Hull, a lead researcher on the paper, who was intrigued by seeing a similar reaction blow the corks off wine bottles.

However, many acids and bases are actually watery solutions filled with hydrogen. In an acidic solution, the hydrogen atoms wander free. They're usually missing their electron too, which gives them a positive charge (atoms and molecules with either a positive or a negative charge are called ions). In a basic solution, the hydrogen atoms are usually connected with something else, a negative ion of some sort. And yes, when an acid and a base react with each other, they typically create something neutral, like water.

The catalyst created by researchers at Brookhaven Lab connects hydrogen gas and carbon dioxide, "storing" the hydrogen linked to (adduct to) carbon dioxide in a mildly basic solution. The reaction can be reversed -- and the hydrogen fuel released -- by adding a bit of acid. The entire process can be run, and easily reversed, in a watery solution under mild temperatures and pressures with no toxic byproducts, and at a faster rate than any previous catalyst.

As a consequence, Brookhaven Lab's new catalyst might be used in future hydrogen fuel vehicles, though additional testing will be needed to see if it can be economically scaled up to industrial production. It may show up in other high powered systems too -- time and technology will tell.

This new catalyst shows the best of the Office of Science and its labs at work: Researchers taking on truly challenging problems, and finding basic (and sometimes slightly acidic) solutions.

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The above story is reprinted from materials provided by DOE/US Department of Energy. The original article was written by Charles Rousseaux.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Jonathan F. Hull, Yuichiro Himeda, Wan-Hui Wang, Brian Hashiguchi, Roy Periana, David J. Szalda, James T. Muckerman, Etsuko Fujita. Reversible hydrogen storage using CO2 and a proton-switchable iridium catalyst in aqueous media under mild temperatures and pressures. Nature Chemistry, 2012; DOI: 10.1038/nchem.1295