New calculations solve an old problem with DNA

Dec. 21, 2012 — The normal DNA will switch to left-handed DNA when it is physically twisted, or when a lot of salt is added to the solution. Researchers at the University of Luxembourg were able to accurately calculate for the first time the amount of salt which is required to do this. Z-DNA in the cell leads to loss of function and cancer.

In a recent publication, researchers achieved new accuracy in the ability to measure energy differences between states of molecules, thus predicting which states will be observed.

It has been known since the seventies that excessive salt causes DNA to reverse its twist, from a right-handed spiral to a left-handed one. DNA in the Z form is treated by our natural repair enzymes as damaged, and is therefore usually deleted from the cell. Deletion of genetic material can lead to cancer or to other problems, so the B-Z transition is no mere curiosity. However such is the complexity of the DNA molecule that a theoretical explanation which correctly predicts the amount of salt to do this has never before been found.

Dr. Josh Berryman and Professor Tanja Schilling of the University of Luxembourg have now been able to find a method of calculation which predicts this transition with unprecedented accuracy. With this success in describing the most enigmatic of molecules, the team is optimistic that they will be able to perform similar mathematical analyses for a variety of other substances. "It will enable us to predict material properties such as melting temperatures or elasticity. And this will be done with high accuracy using our new technique. Hence, we can now design new materials and biomaterials on the computer more effectively than before," said Prof. Schilling.

Prof Schilling and Dr Berryman are physicists at the University's Physics and Material Sciences Research Unit, which comprises a team of 50 researchers.

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The above story is reprinted from materials provided by Université du Luxembourg, via AlphaGalileo.

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Joshua T. Berryman, Tanja Schilling. Free Energies by Thermodynamic Integration Relative to an Exact Solution, Used to Find the Handedness-Switching Salt Concentration for DNA. Journal of Chemical Theory and Computation, 2012; : 121130085236003 DOI: 10.1021/ct3005968

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Genetically enhanced biofuel crops? Plants engineered to have increased levels of beta-1,4-galactan may enhance biofuel production

Dec. 20, 2012 — Best known for its ability to transform simmering pots of sugared fruit into marmalades and jams, pectin is a major constituent of plant cell walls and the middle lamella, the sticky layer that glues neighboring plant cells together. Pectin imparts strength and elasticity to the plant and forms a protective barrier against the environment. Several different kinds of pectic compounds combine to form pectin. The relative proportion of each of these depends on the plant species, location within the plant, and environment. Pectic compounds decorated with ß-1,4-galactan (a chain of six-carbon sugars) are of considerable interest to the biofuels industry, because six-carbon sugars are readily converted into ethanol (biofuel) by fermenting microorganisms.

A new study published in The Plant Cell reveals a novel enzyme involved in the production of ß-1,4-galactans. This enzyme may be used to engineer plants with more desirable attributes for conversion to biofuel.

The major enzymes that catalyze pectin production are hard to pin down. Close to 70 enzymes are predicted to underlie pectin synthesis in plants; only about three of these have been identified definitively. Knowledge of these enzymes could be used to boost the production of pectins with desirable characteristics.

A team of researchers at the Joint BioEnergy Institute, University of California, Berkeley, and Technical University of Denmark set out to identify the enzymes that catalyze the production of ß-1,4-galactan. They screened a database of enzymes for galactosyltransferases, the enzymes that link six-carbon galactose sugars into a chain. They found a family of proteins, named GT92, that are present in some animals and all plants sequenced to date. The authors found that mutations in each of the three genes encoding the GT92 proteins in the model plant Arabidopsis led to a reduction in ß-1,4-galactan, whereas producing more of one of these proteins led to a 50% increase in ß-1,4-galactan levels. In many cases, modifying the composition of plant cell wall components leads to alterations in growth or stature. Strikingly, all of the plant lines overproducing this important six-carbon sugar appeared to be healthy. Biochemical tests of the enzymatic properties of purified Arabidopsis GT92 protein supported the hypothesis that GT92 proteins are important enzymes for ß-1,4-galactan synthesis in plants. This means that crops engineered to produce increased levels of GT92 proteins might contain more easily fermentable sugars, thereby potentially boosting the efficiency of biofuel production.

According to lead scientist Henrik Scheller, "Bioenergy crops with high ß-1,4-galactan content would have significant advantages for the biofuels industry and we now have the knowledge to specifically increase ß-1,4-galactan content in the biomass of cell walls. This breakthrough was made possible by a collaboration involving members of the Feedstocks Division at JBEI and our collaborators in Denmark. We are very excited about this result and look forward to testing it in a bioenergy crop such as switchgrass or poplar trees."

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The above story is reprinted from materials provided by American Society of Plant Biologists.

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A. J. M. Liwanag, B. Ebert, Y. Verhertbruggen, E. A. Rennie, C. Rautengarten, A. Oikawa, M. C. F. Andersen, M. H. Clausen, H. V. Scheller. Pectin Biosynthesis: GALS1 in Arabidopsis thaliana Is a  -1,4-Galactan  -1,4-Galactosyltransferase. The Plant Cell, 2012; DOI: 10.1105/tpc.112.106625

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Unlocking new talents in nature: Protein engineers create new biocatalysts

Dec. 20, 2012 — Protein engineers at the California Institute of Technology (Caltech) have tapped into a hidden talent of one of nature's most versatile catalysts. The enzyme cytochrome P450 is nature's premier oxidation catalyst -- a protein that typically promotes reactions that add oxygen atoms to other chemicals. Now the Caltech researchers have engineered new versions of the enzyme, unlocking its ability to drive a completely different and synthetically useful reaction that does not take place in nature.

The new biocatalysts can be used to make natural products -- such as hormones, pheromones, and insecticides -- as well as pharmaceutical drugs, like antibiotics, in a "greener" way.

"Using the power of protein engineering and evolution, we can convince enzymes to take what they do poorly and do it really well," says Frances Arnold, the Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering and Biochemistry at Caltech and principal investigator on a paper about the enzymes that appears online in Science. "Here, we've asked a natural enzyme to catalyze a reaction that had been devised by chemists but that nature could never do."

Arnold's lab has been working for years with a bacterial cytochrome P450. In nature, enzymes in this family insert oxygen into a variety of molecules that contain either a carbon-carbon double bond or a carbon-hydrogen single bond. Most of these insertions require the formation of a highly reactive intermediate called an oxene.

Arnold and her colleagues Pedro Coelho and Eric Brustad noted that this reaction has a lot in common with another reaction that synthetic chemists came up with to create products that incorporate a cyclopropane -- a chemical group containing three carbon atoms arranged in a triangle. Cyclopropanes are a necessary part of many natural-product intermediates and pharmaceuticals, but nature forms them through a complicated series of steps that no chemist would want to replicate.

"Nature has a limited chemical repertoire," Brustad says. "But as chemists, we can create conditions and use reagents and substrates that are not available to the biological world."

The cyclopropanation reaction that the synthetic chemists came up with inserts carbon using intermediates called carbenes, which have an electronic structure similar to oxenes. This reaction provides a direct route to the formation of diverse cyclopropane-containing products that would not be accessible by natural pathways. However, even this reaction is not a perfect solution because some of the solvents needed to run the reaction are toxic, and it is typically driven by catalysts based on expensive transition metals, such as copper and rhodium. Furthermore, tweaking these catalysts to predictably make specific products remains a significant challenge -- one the researchers hoped nature could overcome with evolution's help.

Given the similarities between the two reaction systems -- cytochrome P450's natural oxidation reactions and the synthetic chemists' cyclopropanation reaction -- Arnold and her colleagues argued that it might be possible to convince the bacterial cytochrome P450 to create cyclopropane-bearing compounds through this more direct route. Their experiments showed that the natural enzyme (cytochrome P450) could in fact catalyze the reaction, but only very poorly; it generated a low yield of products, didn't make the specific mix of products desired, and catalyzed the reaction only a few times. In comparison, transition-metal catalysts can be used hundreds of times.

That's where protein engineering came in. Over the years, Arnold's lab has created thousands of cytochrome P450 variants by mutating the enzyme's natural sequence of amino acids, using a process called directed evolution. The researchers tested variants from their collections to see how well they catalyzed the cyclopropane-forming reaction. A handful ended up being hits, driving the reaction hundreds of times.

Being able to catalyze a reaction is a crucial first step, but for a chemical process to be truly useful it has to generate high yields of specific products. Many chemical compounds exist in more than one form, so although the chemical formulas of various products may be identical, they might, for example, be mirror images of each other or have slightly different bonding structures, leading to dissimilar behavior. Therefore, being able to control what forms are produced and in what ratio -- a quality called selectivity -- is especially important.

Controlling selectivity is difficult. It is something that chemists struggle to do, while nature excels at it. That was another reason Arnold and her team wanted to investigate cytochrome P450's ability to catalyze the reaction.

"We should be able to marry the impressive repertoire of catalysts that chemists have invented with the power of nature to do highly selective chemistry under green conditions," Arnold says.

So the researchers further "evolved" enzyme variants that had worked well in the cyclopropanation reaction, to come up with a spectrum of new enzymes. And those enzymes worked -- they were able to drive the reaction many times and produced many of the selectivities a chemist could desire for various substrates.

Coelho says this work highlights the utility of synthetic chemistry in expanding nature's catalytic potential. "This field is still in its infancy," he says. "There are many more reactions out there waiting to be installed in the biological world."

The paper, "Olefin cyclopropanation via carbene insertion catalyzed by engineered cytochrome P450 enzymes," was also coauthored by Arvind Kannan, now a Churchill Scholar at Cambridge University; Brustad is now an assistant professor at the University of North Carolina at Chapel Hill. The work was supported by a grant from the U.S. Department of Energy and startup funds from UNC Chapel Hill.

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The above story is reprinted from materials provided by California Institute of Technology. The original article was written by Kimm Fesenmaier.

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Journal Reference:

P. S. Coelho, E. M. Brustad, A. Kannan, F. H. Arnold. Olefin Cyclopropanation via Carbene Transfer Catalyzed by Engineered Cytochrome P450 Enzymes. Science, 2012; DOI: 10.1126/science.1231434

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Engineers seek ways to convert methane into useful chemicals

Dec. 20, 2012 — Little more than a decade ago, the United States imported much of its natural gas. Today, the nation is tapping into its own natural gas reserves and producing enough to support most of its current needs for heating and power generation, and is beginning to export natural gas to other countries.

The trend is expected to continue, as new methods are developed to extract natural gas from vast unrecovered reserves embedded in shale. Natural gas can be used to generate electricity, and it burns cleaner than coal.

"With petroleum reserves in decline, natural gas production is destined to increase to help meet worldwide energy demands," said Matthew Neurock, a chemical engineering professor in the University of Virginia's School of Engineering and Applied Science. "But petroleum -- in addition to being used to make fuels -- is also used to make ethylene, propylene and other building blocks used in the production of a wide range of other chemicals. We need to develop innovative processes that can readily make these chemical intermediates from natural gas." The problem is, there currently are no cost-effective ways to do this. Methane, the principal component of natural gas, is rather inert and requires high temperatures to activate its strong chemical bonds; therefore the practical and successful conversion of methane to useful chemical intermediates has thus far eluded chemists and engineers.

Neurock is working with colleagues at Northwestern University to invent novel ways and catalytic materials to activate methane to produce ethylene. This week the collaborators published a paper in the online edition of the journal Nature Chemistry detailing the use of sulfur as a possible "soft" oxidant for catalytically converting methane into ethylene, a key "intermediate" for making chemicals, polymers, fuels and, ultimately, products such as films, surfactants, detergents, antifreeze, textiles and others.

"We show, through both theory -- using quantum mechanical calculations -- and laboratory experiments, that sulfur can be used together with novel sulfide catalysts to convert methane to ethylene, an important intermediate in the production of a wide range of materials," Neurock said.

Chemists and engineers have attempted to develop catalysts and catalytic processes that use oxygen to make ethylene, methanol and other intermediates, but have had little success as oxygen is too reactive and tends to over-oxidize methane to common carbon dioxide.

Neurock said that sulfur or other "softer" oxidants that have weaker affinities for hydrogen may be the answer, in that they can help to limit the over-reaction of methane to carbon disulfide. In the team's process, methane is reacted with sulfur over sulfide catalysts used in petroleum processes. Sulfur is used to remove hydrogen from the methane to form hydrocarbon fragments, which subsequently react together on the catalyst to form ethylene.

Theoretical and experimental results indicate that the conversion of methane and the selectivity to produce ethylene are controlled by how strong the sulfur bonds to the catalyst. Using these concepts, the team explored different metal sulfide catalysts to ultimately tune the metal-sulfur bond strength in order to control the conversion of methane to ethylene. Chemical companies consider methane a particularly attractive raw material because of the large reserves of natural gas in the U.S. and other parts of the world.

In 2007, Dow issued a "Methane Challenge," seeking revolutionary chemical processes to facilitate the conversion of methane to ethylene and other useful chemicals. The company received about 100 proposals from universities, institutes and companies around the world. In 2008, the company awarded major research grants to Cardiff University and Northwestern University to advance the quest. Neurock is a member of the Northwestern University team. He is using theoretical methods and high-performance computing to understand the processes that control catalysis and to guide the experimental research at Northwestern.

"The abundance of natural gas, along with the development of new methods to extract it from hidden reserves, offers unique opportunities for the development of catalytic processes that can convert methane to chemicals," Neurock said. "Our finding -- of using sulfur to catalyze the conversion of methane to ethylene -- shows initial promise for the development of new catalytic processes that can potentially take full advantage of these reserves. The research, however, is really just in its infancy."

Neurock's co-investigators on the Nature Chemistry paper are Qingjun Zhu, Staci Wegener, Chao Xie and Tobin Marks of Northwestern University, and U.Va. colleague Obioma Uche. 

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Qingjun Zhu, Staci L. Wegener, Chao Xie, Obioma Uche, Matthew Neurock, Tobin J. Marks. Sulfur as a selective ‘soft’ oxidant for catalytic methane conversion probed by experiment and theory. Nature Chemistry, 2012; DOI: 10.1038/nchem.1527

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Algae can take energy from other plants

Nov. 20, 2012 — Flowers need water and light to grow. Even children learn that plants use sunlight to gather energy from earth and water. Members of Professor Dr. Olaf Kruse's biological research team at Bielefeld University have made a groundbreaking discovery that one plant has another way of doing this. They have confirmed for the first time that a plant, the green alga Chlamydomonas reinhardtii, not only engages in photosynthesis, but also has an alternative source of energy: it can draw it from other plants. This finding could also have a major impact on the future of bioenergy.

The research findings have been released on November 20 in the online journal Nature Communications.

Until now, it was believed that only worms, bacteria, and fungi could digest vegetable cellulose and use it as a source of carbon for their growth and survival. Plants, in contrast, engage in the photosynthesis of carbon dioxide, water, and light. In a series of experiments, Professor Dr. Olaf Kruse and his team cultivated the microscopically small green alga species Chlamydomonas reinhardtii in a low carbon dioxide environment and observed that when faced with such a shortage, these single-cell plants can draw energy from neighbouring vegetable cellulose instead.

The alga secretes enzymes (so-called cellulose enzymes) that 'digest' the cellulose, breaking it down into smaller sugar components. These are then transported into the cells and transformed into a source of energy: the alga can continue to grow.

'This is the first time that such a behaviour has been confirmed in a vegetable organism', says Professor Kruse. 'That algae can digest cellulose contradicts every previous textbook. To a certain extent, what we are seeing is plants eating plants'. Currently, the scientists are studying whether this mechanism can also be found in other types of alga. Preliminary findings indicate that this is the case.

In the future, this 'new' property of algae could also be of interest for bioenergy production. Breaking down vegetable cellulose biologically is one of the most important tasks in this field. Although vast quantities of waste containing cellulose are available from, for example, field crops, it cannot be transformed into biofuels in this form. Cellulose enzymes first have to break down the material and process it. At present, the necessary cellulose enzymes are extracted from fungi that, in turn, require organic material in order to grow. If, in future, cellulose enzymes can be obtained from algae, there would be no more need for the organic material to feed the fungi. Then even when it is confirmed that algae can use alternative nutrients, water and light suffice for them to grow in normal conditions.

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Olga Blifernez-Klassen, Viktor Klassen, Anja Doebbe, Klaudia Kersting, Philipp Grimm, Lutz Wobbe, Olaf Kruse. Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii. Nature Communications, 2012; 3: 1214 DOI: 10.1038/ncomms2210

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New geometries: Researchers create new shapes of artificial microcompartments

Dec. 12, 2012 — n nature, biological functions are often carried out in tiny protective shells known as microcompartments, structures that provide home to enzymes that convert carbon dioxide into energy in plant cells and to viruses that replicate once they enter the cell.

Most of these shells buckle into an icosahedron shape, forming 20 sides that allow for high interface with their surroundings. But some shells -- such as those found in the single-celled Archaea or simple, salt-loving organisms called halophiles -- break into triangles, squares, or non-symmetrical geometries. While these alternate geometries may seem simple, they can be incredibly useful in biology, where low symmetry can translate to higher functionality.

Researchers at Northwestern University have recently developed a method to recreate these shapes in artificial microcompartments created in the lab: by altering the acidity of their surroundings. The findings could lead to designed microreactors that mimic the functions of these cell containers or deliver therapeutic materials to cells at specific targeted locations.

"If you want to design a very clever capsule, you don't make a sphere. But perhaps you shouldn't make an icosahedron, either," said Monica Olvera de la Cruz, Lawyer Taylor Professor of Materials Science and Engineering, Chemistry, and (by courtesy) Chemical and Biological Engineering at Northwestern's McCormick School of Engineering and one of the paper's authors. "What we are beginning to realize is maybe these lower symmetries are smarter."

To create the new shell geometries, the researchers co-assembled oppositely charged lipids with variable degrees of ionization and externally modified the surrounding electrolyte. The resulting geometries include fully faceted regular and irregular polyhedral, such as square and triangular shapes, and mixed Janus-like vesicles with faceted and curved domains that resembled cellular shapes and shapes of halophilic organisms.

The research was conducted by three McCormick faculty members: Olvera de la Cruz, Lawyer Taylor Professor of Materials Science and Engineering, Professor of Chemistry, and (by courtesy) Chemical and Biological Engineering; Michael J. Bedzyk, professor of materials science and engineering and (by courtesy) physics and astronomy; and Samuel I. Stupp, Board of Trustees Professor of Materials Science and Engineering, Chemistry, and Medicine.

Other authors of the paper include lead co-authors Cheuk-Yui Leung, Liam C. Palmer, and Bao Fu Qiao; Sumit Kewalramani, Rastko Sknepnek, Christina J. Newcomb, and Megan A. Greenfield, all of Northwestern; and Graziano Vernizzi of Siena College.

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Cheuk-Yui Leung, Liam C. Palmer, Bao Fu Qiao, Sumit Kewalramani, Rastko Sknepnek, Christina J. Newcomb, Megan A. Greenfield, Graziano Vernizzi, Samuel I. Stupp, Michael J. Bedzyk, Monica Olvera de la Cruz. Molecular Crystallization Controlled by pH Regulates Mesoscopic Membrane Morphology. ACS Nano, 2012; : 121203090056009 DOI: 10.1021/nn304321w

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Ultra-short laser pulses control chemical processes

Dec. 12, 2012 — Chemical reactions occur so quickly that it is completely impossible to observe their progress or to control them using conventional methods. However, new developments in electrical engineering and quantum technology enable us to achieve a more exact understanding and improved control of the behaviour of atoms and molecules. At the TU Vienna, scientists have succeeded in influencing the splitting of large molecules with up to ten atoms using ultra-short laser pulses.

The flash of light which splits molecules Splitting a molecule is an example of an elemental chemical reaction. The splitting of molecular bonds with a laser pulse is relatively simple. It is much more difficult, however, to influence the splitting of a specific bond in a controlled manner, i.e. to initiate it in a controlled manner or to suppress it. In order to achieve this, the complex processes must be altered at an atomic level. This is carried out at the Institute for Photonics at the TU Vienna using specially-shaped laser pulses, with a duration of only a few femtoseconds. One femtosecond (10-15 seconds) is one millionth of a billionth of a second.

Fast electrons, slow atomic nuclei

One carbon atom has a mass around 22,000 times greater than an electron. It is therefore also relatively inert and cannot be moved easily from its position. A laser pulse can therefore change the movement of the small, light electrons much more rapidly than that of the atomic nuclei: One electron can be extracted from the molecule, then reversed using the laser pulse field and collided again with the molecule. During this collision, the electron can subsequently extract a second electron from the molecule. A doubly charged molecule remains, which can then split into two singly charged fragments under certain circumstances.

"Usually, it takes several femtoseconds for the atomic nuclei to reach a sufficient distance from one another and the molecule to split into two pieces," explains Markus Kitzler from the Institute of Photonics at the TU Vienna. The collision of the electron with the molecule only lasts several hundred attoseconds (10-18 seconds). "We therefore have to deal with two separate timescales," explains Kitzler. "Our specially shaped ultra-short laser pulses affect rapidly-moving electrons. The fact that the state of the electrons is changed by the collision also sets the large, slow atomic nuclei into motion." Using this technique, the TU research team have for the first time been able to show that specific elemental chemical reactions using various hydrocarbon molecules can also be initiated or suppressed in a controlled manner, if the movement of the atomic nuclei are influenced indirectly by the much quicker electrons. The exact shape of the laser pulse is crucial in this process.

The role of electron movement for chemistry

In order to be able to interpret the experimental data correctly and understand what actually happens during these incredibly rapid processes at atomic and electronic level, theoretical calculations and computer simulations are required. This has also been carried out at the TU Vienna -- at the Institute for Theoretical Physics, which collaborates with the Institute for Photonics on attosecond projects. Using this method, we can do more than simply observe whether and how a molecule splits. "The experiments and simulations show how the sequence of chemical processes can also be affected in a targeted manner using precise control of the laser pulse," explains Katharina Doblhoff-Dier from the Institute of Theoretical Physics.

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Xinhua Xie, Katharina Doblhoff-Dier, Stefan Roither, Markus Schöffler, Daniil Kartashov, Huailiang Xu, Tim Rathje, Gerhard Paulus, Andrius Baltuška, Stefanie Gräfe, Markus Kitzler. Attosecond-Recollision-Controlled Selective Fragmentation of Polyatomic Molecules. Physical Review Letters, 2012; 109 (24) DOI: 10.1103/PhysRevLett.109.243001

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