Thursday, January 5, 2012

MSU chemists become the first to solve an 84-year-old theory

Conservation of angular momentum is a of nature, one that astronomers use to detect the presence of satellites circling distant planets. In 1927, it was proposed that this principle should apply to , but a clear demonstration has never been achieved.

In the current issue of Science, MSU chemist Jim McCusker demonstrates for the first time the effect is real and also suggests how scientists could use it to control and predict chemical reaction pathways in general.

"The idea has floated around for decades and has been implicitly invoked in a variety of contexts, but no one had ever come up with a chemical system that could demonstrate whether or not the underlying concept was valid," McCusker said. "Our result not only validates the idea, but it really allows us to start thinking about chemical reactions from an entirely different perspective."

The experiment involved the preparation of two closely related that were specifically designed to undergo a chemical reaction known as , or FRET. Upon absorption of light, the system is predisposed to transfer that energy from one part of the molecule to another.

McCusker's team changed the identity of one of the atoms in the molecule from to cobalt. This altered the molecule's properties and shut down the reaction. The absence of any detectable energy transfer in the cobalt-containing compound confirmed the hypothesis.

"What we have successfully conducted is a proof-of-principle experiment," McCusker said. "One can easily imagine employing these ideas to other , and we're actually exploring some of these avenues in my group right now."

The researchers believe their results could impact a variety of fields including molecular electronics, biology and energy science through the development of new types of chemical reactions.

Provided by Michigan State University (news : web)

Biofuel research boosted by discovery of how cyanobacteria make energy

 A generally accepted, 44-year-old assumption about how certain kinds of bacteria make energy and synthesize cell materials has been shown to be incorrect by a team of scientists led by Donald Bryant, the Ernest C. Pollard Professor of Biotechnology at Penn State and a research professor in the Department of Chemistry and Biochemistry at Montana State University. The research, which will be published in the journal Science on Dec. 16, is expected to help scientists discover new ways of genetically engineering bacteria to manufacture biofuels -- energy-rich compounds derived from biological sources. Many textbooks, which cite the 44-year-old interpretation as fact, likely will be revised as a result of the new discovery.

Bryant explained that, in 1967, two groups of researchers concluded that an important energy-making cycle was incomplete in cyanobacteria -- photosynthetic bacteria formerly known as blue-green algae. This energy-producing cycle -- known as the tricarboxylic acid (TCA) cycle or the Krebs cycle -- includes a series of chemical reactions that are used for metabolism by most forms of life, including bacteria, molds, protozoa and animals. This series of chemical reactions eventually leads to the production of ATP -- molecules responsible for providing energy for cell metabolism.

"During studies 44 years ago, researchers concluded that cyanobacteria were missing an essential enzyme of the metabolic pathway that is found in most other life forms," Bryant explained. "They concluded that cyanobacteria lacked the ability to make one enzyme, called 2-oxoglutarate dehydrogenase, and that this missing enzyme rendered the bacteria unable to produce a compound -- called succinyl-coenzyme A -- for the next step in the TCA cycle. The absence of this reaction was assumed to render the organisms unable to oxidize metabolites for energy production, although they could still use the remaining TCA-cycle reactions to produce substrates for biosynthetic reactions. As it turns out, the researchers just weren't looking hard enough, so there was more work to be done."

Bryant suspected that the decades-old finding needed to be re-evaluated with a fresh set of eyes and new scientific tools. He explained that, after researchers in the 1960s concluded that cyanobacteria had an incomplete TCA cycle, that false assumption was compounded by later researchers who used modern genomics-research methods to confirm it.

"One idea we had was that the 1967 hypothesis never was corrected because modern genome-annotation methods were partly to blame," Bryant said. "Computer algorithms are used to search for strings of genetic code to identify genes. Sometimes important genes simply can be missed because of matching errors, which occur when very similar genes have very different functions. So if researchers don't use biochemical methods to validate computer-identified gene functions, they run the risk of making premature and often incorrect conclusions about what's there and what's not there."

To re-test the 1967 hypothesis, the team performed new biochemical and genetic analyses on a cyanobacterium called Synechococcus sp. PCC 7002, scouring its genome for genes that might be responsible for making alternative energy-cycle enzymes. The scientists discovered that Synechococcus indeed had genes that coded for one important alternative enzyme, succinic semialdehyde dehydrogenase, and that adjacent to the gene for this enzyme was a misidentified gene that subsequently was shown to encode a novel enzyme, 2-oxo-glutarate decarboxylase.

"As it turns out, these two enzymes work together to complete the TCA cycle in a slightly different way," Bryant said. "That is, rather than making 2-oxoglutarate dehydrogenase, these bacteria produce both 2-oxoglutarate decarboxylase and succinic semialdehyde dehydrogenase. That combination of enzymes allows these organisms to move to the next intermediate -- succinate -- and to complete the TCA cycle." Bryant also said that his team found that the genes coding for the two enzymes are present in all cyanobacterial genomes except those of a few marine species. Bryant's co-author on the Science paper is Shuyi Zhang, a graduate student in the Department of Biochemistry and Molecular Biology at Penn State.

Bryant hopes to use the findings of his research to investigate new ways of producing biofuels. "Now that we understand better how cyanobacteria make energy, it might be possible to genetically engineer a cyanobacterial strain to synthesize 1,3-butanediol -- an organic compound that is the precursor for making not just biofuels but also plastics," Bryant said.

Bryant also said that his team's discoveries about cyanobacteria show how science is an ever-evolving process, and that firm conclusions never should be drawn from studies with negative results.

"Sadly, the conclusion that cyanobacteria have an incomplete TCA cycle is written into many textbooks as fact, simply because the research teams in 1967 misinterpreted their failure to find a particular enzyme," Bryant said. "But in science there is never really an end. There always is something new to discover."

The research was supported by the Air Force Office of Scientific Research and the Genomic Science Program of the U.S. Department of Energy.

Story Source:

The above story is reprinted from materials provided by Penn State.

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

Journal Reference:

S. Zhang, D. A. Bryant. The Tricarboxylic Acid Cycle in Cyanobacteria. Science, 2011; 334 (6062): 1551 DOI: 10.1126/science.1210858

Badwater Basin: Death Valley microbe may spark novel biotech and nanotech uses

 Nevada, the "Silver State," is well-known for mining precious metals. But scientists Dennis Bazylinski and colleagues at the University of Nevada Las Vegas (UNLV) do a different type of mining.

They sluice through every water body they can find, looking for new forms of microbial magnetism.

In a basin named Badwater on the edge of Death Valley National Park, Bazylinski and researcher Christopher Lefevre hit pay dirt.

Lefevre is with the French National Center of Scientific Research and University of Aix-Marseille II.

In a recent issue of the journal Science, Bazylinski, Lefevre and others report that they identified, isolated and grew a new type of magnetic bacteria that could lead to novel biotech and nanotech uses.

Magnetotactic bacteria are simple, single-celled organisms that are found in almost all bodies of water.

As their name suggests, they orient and navigate along magnetic fields like miniature swimming compass needles.

This is due to the nano-sized crystals of the minerals magnetite or greigite they produce.

The presence of these magnetic crystals makes the bacteria and their internal crystals--called magnetosomes--useful in drug delivery and medical imaging.

The research was funded by the U.S. National Science Foundation (NSF), the U.S. Department of Energy and the French Foundation for Medical Research.

"The finding is significant in showing that this bacterium has specific genes to synthesize magnetite and greigite, and that the proportion of these magnetosomes varies with the chemistry of the environment," said Enriqueta Barrera, program director in NSF's Division of Earth Sciences.

While many magnetite-producing bacteria can be grown and easily studied, Bazylinski and his team were the first to cultivate a greigite-producing species. Greigite is an iron sulfide mineral, the equivalent of the iron oxide magnetite.

"Because greigite-producing bacteria have never been isolated, the crystals haven't been tested for the types of biomedical and other applications that currently use magnetite," said Bazylinski.

"Greigite is an iron sulfide that may be superior to magnetite in some applications due to its slightly different physical and magnetic properties. Now we have the opportunity to find out."

Researchers found the greigite-producing bacterium, called BW-1, in water samples collected more than 280 feet below sea level in Badwater Basin. Lefevre and Bazylinski later isolated and grew it leading to the discovery that BW-1 produces both greigite and magnetite.

A detailed look at its DNA revealed that BW-1 has two sets of magnetosome genes, unlike other such bacteria, which produce only one mineral and have only one set of magnetosome genes.

This suggests that the production of magnetite and greigite in BW-1 is likely controlled by separate sets of genes. That could be important in the mass production of either mineral for specific applications.

According to Bazylinski, the greigite-producing bacteria represent a new, previously unrecognized group of sulfate-reducing bacteria that "breathe" the compound sulfate rather than oxygen as most living organisms do.

"With how much is known about sulfate-reducing bacteria, it's surprising that no one has described this group," he said.

Working with Bazylinski and Lefevre on the project are David Pignol of the French National Center of Scientific Research and University of Aix-Marseille II; Nicolas Menguy of Pierre and Marie Curie University, France; Fernanda Abreu and Ulysses Lins of the Federal University of Rio de Janeiro, Brazil; Mihaly PĆ³sfai of the University of Pannonia, Hungary; Tanya Prozorov of Ames Laboratory, Iowa; and Richard Frankel of California Polytechnic State University, San Luis Obispo.

Story Source:

The above story is reprinted from materials provided by National Science Foundation.

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

Journal Reference:

C. T. Lefevre, N. Menguy, F. Abreu, U. Lins, M. Posfai, T. Prozorov, D. Pignol, R. B. Frankel, D. A. Bazylinski. A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria. Science, 2011; 334 (6063): 1720 DOI: 10.1126/science.1212596

New method for watching proteins fold

 A protein's function depends on both the chains of molecules it is made of and the way those chains are folded. And while figuring out the former is relatively easy, the latter represents a huge challenge with serious implications because many diseases are the result of misfolded proteins. Now, a team of chemists at the University of Pennsylvania has devised a way to watch proteins fold in "real-time," which could lead to a better understanding of protein folding and misfolding in general.

The research was conducted by Feng Gai, professor in the Department of Chemistry in the School of Arts and Sciences, along with graduate students Arnaldo Serrano, also of Chemistry, and Robert Culik of the Department of Biochemistry and Molecular Biophysics at Penn's Perelman School of Medicine. They collaborated with Michelle R. Bunagan of the College of New Jersey's Department of Chemistry.

Their research was published in the international edition of the journal Angewandte Chemie, where it was featured on the cover and bestowed VIP (very important paper) status.

"One of the reasons that figuring out what happens when proteins fold is difficult is that we don't have the equivalent of a high-speed camera that can capture the process, " Gai said. "If the process were slow, we could take multiple 'pictures' over time and see the mechanism at work. Unfortunately, no one has this capability; the folding occurs faster than the blink of an eye."

Gai's team uses infrared spectroscopy -- a technique that measures how much light different parts of a molecule absorbs -- to analyze proteins' structure and how this changes. In this case, the researchers looked at a model protein known as Trp-cage with an infrared laser setup.

In this experiment, Gai's team used two lasers to study structural changes as a function of time. The first laser acts as the starting gun; by heating the molecule, it causes its structure to change. The second laser acts as the camera, following the motions of the protein's constituent amino acids.

"The protein is made of different groups of atoms, and the different groups can be thought of as springs," Gai said. "Each spring has a different frequency with which it moves back and forth, which is based on the mass of the atom on either end. If the mass is bigger, the spring oscillates slower. Our 'camera' can detect the speed of that motion and we can relate it to the atoms it is made of and how that segment of the protein chain moves."

Even in a simple protein like Trp-cage, however, there are many identical bonds, and the researchers need to be able to distinguish one from another in order to see which of them are moving while the protein folds. One strategy they used to get around this problem was to employ the molecular equivalent of a tracking device.

"We use an amino acid with a carbon isotope marker," Culik said. "If it's incorporated into the protein correctly, we'll know where it is."

With a single carbon atom of the Trp-cage slightly heavier than the others, the research team can use its signature to infer the position of the other atoms as they fold. The researchers could then "tune" the frequency of their laser to match different parts of the protein, allowing them to isolate them in their analyses.

Similar isotopes could be inserted in more complicated molecules, allowing their folds to also be viewed with infrared spectroscopy.

"This technique enhances our structural resolution. It allows us to see which part is moving," Gai said. "That would allow us to see exactly how a protein is misfolding in a disease, for example."

The research was supported by the National Institutes of Health.

Story Source:

The above story is reprinted from materials provided by University of Pennsylvania.

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

Journal Reference:

Robert M. Culik, Arnaldo L. Serrano, Michelle R. Bunagan, Feng Gai. Achieving Secondary Structural Resolution in Kinetic Measurements of Protein Folding: A Case Study of the Folding Mechanism of Trp-cage. Angewandte Chemie, 2011; 123 (46): 11076 DOI: 10.1002/ange.201104085