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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New public-access source with 3-D information for protein interactions

Dec. 17, 2012 — Researchers have developed a platform that compiles all the atomic data, previously stored in diverse databases, on protein structures and protein interactions for eight organisms of relevance. They apply a singular homology-based modelling procedure.

The scientists Roberto Mosca, Arnaud Ceol and Patrick Aloy provide the international biomedical community with Interactome3D (interactome3d.irbbarcelona.org), an open-access and free web platform developed entirely by the Institute for Research in Biomedicine (IRB Barcelona). Interactome 3D offers for the first time the possibility to anonymously access and add molecular details of protein interactions and to obtain the information in 3D models. For researchers, atomic level details about the reactions are fundamental to unravel the bases of biology, disease development, and the design of experiments and drugs to combat diseases.

Interactome 3D provides reliable information about more than 12,000 protein interactions for eight model organisms, namely the plant Arabidopsis thaliana, the worm Caenorhabditis elegans, the fly Drosophila melanogaster, the bacteria Escherichia coli and Helicobacter pylori, the brewer's yeast Saccharomyces cerevisiae, the mouse Mus musculus, and Homo sapiens. These models are considered the most relevant in biomedical research and genetic studies. The journal Nature Methods presents the research results and accredits the platform on the basis of it high reliability and precision in modelling interactions, which reaches an average of 75%.

Patrick Aloy, ICREA researcher at IRB Barcelona, head of the Structural Bioinformatics and Network Biology Lab, and researcher with the joint IRB Barcelona-BSC programme, explains "we have designed Interactome3D for molecular and cellular biologists. It is a well organized non-technical interface that presents the results in a simple manner. With only a few clicks of the mouse, you can get the information you are looking for and you don't have to be a bioinformatician to navigate around the platform, to look things up or to interpret the results." The post-doctoral fellow Roberto Mosca explains that platform has come about after more than four years of lab experience: "we undertake collaborations with groups around the world that need these data; data that we can now provide automatically." The data included in Interactome3D is updated every six months and the researchers expect to be able to simulate up the 16,000 interaction in the near future. "The tool is continuously growing. We will introduce more information and thus increase the number of interactions covered while maintaining reliability as a key feature," remarks Mosca.

Network biology or the interactome: the key -ome to understand protein function

Thanks to genomes, we now know all the biomolecules present in a given organism. The genome is the same for all the cells but the cells do not use the whole genome. Depending on the cell type, tissue site or functional activities, the cells activate a small part of the genome. The proteomes offer information regarding the proteins activated in a specific cell type and in a given period of time. Both genomes and proteomes "provide us with a very useful list but this list does not indicate the relations," explains Aloy. Network biologists like Mosca, Ceol and Aloy delve into the interactome: that is to say, they want to find out what are the possible interactions of proteosome proteins. "This is the information that we have compiled in Interactome3D," says Aloy. "But there is another thing to consider: the interactome tell us which proteins react with each other, but if you need to know how this occurs or how this affects a mutation in a given protein and its interaction, or how to combat or reinforce a given interaction, you need the molecular details of the interactions. This is the main innovation of Interactome3D, and what is unique to this system is the integration of molecular details of known protein interactions," explains Aloy.

The IRB Barcelona researchers expect Interactome3D to be embraced by the scientific community. "More than five years ago we set up a simpler platform that receives thousands of visits per month. Interactome3D is a much improved tool and we know that there is a need for an application with these characteristics," state the researchers.

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Roberto Mosca, Arnaud Céol, Patrick Aloy. Interactome3D: adding structural details to protein networks. Nature Methods, 2012; DOI: 10.1038/NMETH.2289

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Lignin-based thermoplastic conversion process

Nov. 30, 2012 — Turning lignin, a plant's structural "glue" and a byproduct of the paper and pulp industry, into something considerably more valuable is driving a research effort headed by Amit Naskar of Oak Ridge National Laboratory.

In a cover article published in Green Chemistry, the research team describes a process that ultimately transforms the lignin byproduct into a thermoplastic -- a polymer that becomes pliable above a specific temperature. Researchers accomplished this by reconstructing larger lignin molecules either through a chemical reaction with formaldehyde or by washing with methanol. Through these simple chemical processes, they created a crosslinked rubber-like material that can also be processed like plastics.

"Our work addresses a pathway to utilize lignin as a sustainable, renewable resource material for synthesis of thermoplastics that are recyclable," said Naskar, a member of the Department of Energy laboratory's Material Science and Technology Division.

Instead of using nearly 50 million tons of lignin byproduct produced annually as a low-cost fuel to power paper and pulp mills, the material can be transformed into a lignin-derived high-value plastic. While the lignin byproduct in raw form is worth just pennies a pound as a fuel, the value can potentially increase by a factor of 10 or more after the conversion.

Naskar noted that earlier work on lignin-based plastics utilized material that was available from pulping industries and was a significantly degraded version of native lignin contained in biomass. This decomposition occurs during harsh chemical treatment of biomass.

"Here, however, we attempted to reconstruct larger lignin molecules by a simple crosslinking chemistry and then used it as a substitute for rigid phase in a formulation that behaves like crosslinked rubbers that can also be processed like plastics," Naskar said.

Crosslinking involves building large lignin molecules by combining smaller molecules where formaldehyde helps to bridge the smaller units by chemical bonding. Naskar envisions the process leading to lower cost gaskets, window channels, irrigation hose, dashboards, car seat foam and a number of other plastic-like products.

Other ORNL authors are Tomonori Saito, Rebecca Brown, Marcus Hunt, Deanna Pickel, Joseph Pickel, Jamie Messman, Frederick Baker and Martin Keller. The research was funded by the Laboratory Directed Research and Development program.

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Tomonori Saito, Rebecca H. Brown, Marcus A. Hunt, Deanna L. Pickel, Joseph M. Pickel, Jamie M. Messman, Frederick S. Baker, Martin Keller, Amit K. Naskar. Turning renewable resources into value-added polymer: development of lignin-based thermoplastic. Green Chemistry, 2012; 14 (12): 3295 DOI: 10.1039/C2GC35933B

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Synthetic membrane channels built out of DNA: Nanotech structures mimic nature's way of tunneling through cell walls

Nov. 20, 2012 — As reported in the journal Science, physicists at the Technische Universitaet Muenchen (TUM) and the University of Michigan have shown that synthetic membrane channels can be constructed through "DNA nanotechnology." This technique employs DNA molecules as programmable building materials for custom-designed, self-assembling, nanometer-scale structures. The researchers present evidence that their nature-inspired nanostructures may also behave like biological ion channels. Their results could mark a step toward applications of synthetic membrane channels as molecular sensors, antimicrobial agents, and drivers of novel nanodevices.

Over the past three decades, researchers have advanced DNA nanotechnology from an intriguing idea to an emerging technology, with a toolbox of methods and a portfolio of nanometer-scale objects designed to demonstrate its potential. What's new here is the claim that DNA nanotech can be used to mimic one of the most widespread and important nanomachines in nature.

To wall off the insides of cells from the outside world, organisms in all three domains of life use the same kind of barrier: an impermeable membrane made from two layers of lipid molecules. Such membranes can also be found within cells, for example encapsulating the nucleus, and even surrounding many kinds of viruses. And to mediate between the different environments on either side of this universal barrier, nature provides a common type of passageway. Membrane channels are tube-like structures made of proteins, which pierce the barriers and regulate the two-way exchange of material and information between the inside and outside. Now researchers have demonstrated the first artificial membrane channel made entirely of DNA, and its characteristics suggest a number of potential applications. "If you want, for example, to inject something into a cell, you have to find a way to punch a hole into the cell membrane, and this device can do that, at least with model cell membranes," says TUM Prof. Hendrik Dietz, a fellow of the TUM Institute for Advanced Study.

In a shape inspired by a natural channel protein, the DNA-based membrane channel consists of a needle-like stem 42 nanometers long with an internal diameter of just two nanometers, partly sheathed by a barrel-shaped cap. A ring of cholesterol units around the edge of the cap helps the device "dock" to a lipid membrane while the stem sticks through it, forming a channel that appears to function like the real thing. TUM Professor Friedrich Simmel, co-coordinator of the Excellence Cluster Nanosystems Initiative Munich, explains: "We have not tested this yet with living cells, but experiments with lipid vesicles show that our synthetic device will bind to a bilayer lipid membrane in the right orientation, so that the stem both penetrates the membrane and holds at the surface, forming a pore."

Further experiments demonstrated that the resulting pores have electrical conductivity comparable to that of a natural cell wall with ion channels, suggesting that they might be able to act like voltage-controlled gates. The results also suggest that transmembrane current could be tuned by adjusting fine structural details of the synthetic channels. To test one potential application of the DNA nanotech devices, the researchers used them as "nanopores" for several different molecular sensing experiments. These confirmed that it is possible, by observing changes in the electrical characteristics, to record the passage of single molecules through synthetic membrane channels made from DNA. Because this approach allows both geometric and chemical tailoring of the membrane channels, it might offer advantages over two other families of molecular sensors, based on biological and solid-state nanopores respectively.

Other conceivable applications remain to be investigated. One notion is to imitate the action of viruses or phages, breaking through the cell walls of targeted bacteria to kill them. In gene therapy, synthetic membrane channels might be used as nano-needles to inject material into cells. Such channels could also be used in basic studies of cell metabolism. Another idea is to harness the so-called ion flux -- which in cell membranes moves material in and out through the channel -- to drive sophisticated nanodevices inspired by other natural mechanisms. "We might be able to mimic natural ion pumps, transport proteins, and rotary motors like the enzyme responsible for synthesizing ATP," says Dietz. "I love that idea. That's what keeps me running."

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M. Langecker, V. Arnaut, T. G. Martin, J. List, S. Renner, M. Mayer, H. Dietz, F. C. Simmel. Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures. Science, 2012; 338 (6109): 932 DOI: 10.1126/science.1225624

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Complex chemistry within the Martian soil: No definitive detection of organics yet

Dec. 3, 2012 — NASA's Mars Curiosity rover has used its full array of instruments to analyze Martian soil for the first time, and found a complex chemistry within the Martian soil. Water and sulfur and chlorine-containing substances, among other ingredients, showed up in samples Curiosity's arm delivered to an analytical laboratory inside the rover.

Detection of the substances during this early phase of the mission demonstrates the laboratory's capability to analyze diverse soil and rock samples over the next two years. Scientists also have been verifying the capabilities of the rover's instruments.

Curiosity is the first Mars rover able to scoop soil into analytical instruments. The specific soil sample came from a drift of windblown dust and sand called "Rocknest." The site lies in a relatively flat part of Gale Crater still miles away from the rover's main destination on the slope of a mountain called Mount Sharp. The rover's laboratory includes the Sample Analysis at Mars (SAM) suite and the Chemistry and Mineralogy (CheMin) instrument. SAM used three methods to analyze gases given off from the dusty sand when it was heated in a tiny oven. One class of substances SAM checks for is organic compounds -- carbon-containing chemicals that can be ingredients for life.

"We have no definitive detection of Martian organics at this point, but we will keep looking in the diverse environments of Gale Crater," said SAM Principal Investigator Paul Mahaffy of NASA's Goddard Space Flight Center in Greenbelt, Md.

Curiosity's APXS instrument and the Mars Hand Lens Imager (MAHLI) camera on the rover's arm confirmed Rocknest has chemical-element composition and textural appearance similar to sites visited by earlier NASA Mars rovers Pathfinder, Spirit and Opportunity.

Curiosity's team selected Rocknest as the first scooping site because it has fine sand particles suited for scrubbing interior surfaces of the arm's sample-handling chambers. Sand was vibrated inside the chambers to remove residue from Earth. MAHLI close-up images of Rocknest show a dust-coated crust one or two sand grains thick, covering dark, finer sand.

"Active drifts on Mars look darker on the surface," said MAHLI Principal Investigator Ken Edgett, of Malin Space Science Systems in San Diego."This is an older drift that has had time to be inactive, letting the crust form and dust accumulate on it."

CheMin's examination of Rocknest samples found the composition is about half common volcanic minerals and half non-crystalline materials such as glass. SAM added information about ingredients present in much lower concentrations and about ratios of isotopes. Isotopes are different forms of the same element and can provide clues about environmental changes. The water seen by SAM does not mean the drift was wet. Water molecules bound to grains of sand or dust are not unusual, but the quantity seen was higher than anticipated.

SAM tentatively identified the oxygen and chlorine compound perchlorate. This is a reactive chemical previously found in arctic Martian soil by NASA's Phoenix Lander. Reactions with other chemicals heated in SAM formed chlorinated methane compounds -- one-carbon organics that were detected by the instrument. The chlorine is of Martian origin, but it is possible the carbon may be of Earth origin, carried by Curiosity and detected by SAM's high sensitivity design.

"We used almost every part of our science payload examining this drift," said Curiosity Project Scientist John Grotzinger of the California Institute of Technology in Pasadena. "The synergies of the instruments and richness of the data sets give us great promise for using them at the mission's main science destination on Mount Sharp."

NASA's Mars Science Laboratory Project is using Curiosity to assess whether areas inside Gale Crater ever offered a habitable environment for microbes. NASA's Jet Propulsion Laboratory in Pasadena manages the project for NASA's Science Mission Directorate in Washington.

For more information about Curiosity and other Mars mission, visit: http://www.nasa.gov/mars

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Thin-skinned catalyst for chemical reactions: Yolk-shell nanocrystal structure offers greater selectivity for heterogeneous catalysis

Dec. 13, 2012 — A chemical nanostructure developed by Boston College researchers behaves much like the pores of the skin, serving as a precise control for a typically stubborn method of catalysis that is the workhorse of industrial chemistry.

Scientists have been trying to develop so-called yolk-shell catalysts as a means of imparting greater selectivity on heterogeneous catalysis, a process used in most industrial chemistry, including the manufacture of fine chemicals, petrochemicals and agrochemicals.

Boston College Assistant Professor of Chemistry Chia-Kuang Tsung and his team developed a nanostructure that can regulate chemical reactions thanks to a thin, porous skin capable of precisely filtering molecules based on their size or chemical make-up, the group reported recently in the Journal of the American Chemical Society.

"The idea is to make a smarter catalyst," said Tsung. "To do that, we placed a layer of 'skin' on the surface that can discriminate between which chemical reacts or does not react with the catalyst."

The team started with a nanoscale metallic crystal, then applied a "sacrificial layer" of copper oxide over it, Tsung said. Next, a shell of highly refined material known as a metal-organic framework, or MOF, was applied to the structure. Immediately, the polycrystalline MOF adhered to the cooper oxide, forming and outer layer of porous "skin." At the same time, the MOF began to etch away the copper oxide layer from the surface of the crystal, creating a tiny chamber between the skin and the catalyst where the chemical reaction can take place.

Testing the structure with gases of varying molecular structure, Tsung said the skin proved it could allow ethylene, with the small molecule size, to pass through and reach the catalyst. The gas cyclooctene, with larger molecule size, was effectively blocked from reaching the catalyst. Tests showed the central difference between new method and earlier incarnations of yolk-shell catalysts was the creation of the empty chamber between the skin and catalyst, the researchers reported.

Tsung said the unprecedented level of control is a significant step in the use of unique nanoscale chemical structures in the effort to impart greater selectivity and control on heterogeneous catalysis, a proven process used to create chemicals in nearly all areas outside of pharmaceutical research, which employs homogeneous catalysis.

Scientists have been looking for ways to exert greater selectivity in heterogeneous catalysis in an effort to expand its application and extend "green chemistry" benefits of reduced byproducts and waste, Tsung said.

The key to the nanocrystal is the extremely precise structure of the metal-organic framework, Tsung said, which gives the skin an intricate network of pore-like passages through which select gases or liquids can pass before contacting the catalyst and triggering the desired reaction.

"We can make these pores very precisely, just like your skin or like the membrane surrounding a cell," Tsung said. "We can change their composition and chemical properties in order to accept or reject certain types of reactions. That is a level of control chemists in a variety of fields are eager to see nurtured and refined."

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Chun-Hong Kuo, Yang Tang, Lien-Yang Chou, Brian T. Sneed, Casey N. Brodsky, Zipeng Zhao, Chia-Kuang Tsung. Yolk–Shell Nanocrystal@ZIF-8 Nanostructures for Gas-Phase Heterogeneous Catalysis with Selectivity Control. Journal of the American Chemical Society, 2012; 134 (35): 14345 DOI: 10.1021/ja306869j

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DNA hydrogel flows like liquid but remembers its original shape

Dec. 5, 2012 — A bit reminiscent of the Terminator T-1000, a new material created by Cornell researchers is so soft that it can flow like a liquid and then, strangely, return to its original shape.

Rather than liquid metal, it is a hydrogel, a mesh of organic molecules with many small empty spaces that can absorb water like a sponge. It qualifies as a "metamaterial" with properties not found in nature and may be the first organic metamaterial with mechanical meta-properties.

Hydrogels have already been considered for use in drug delivery -- the spaces can be filled with drugs that release slowly as the gel biodegrades -- and as frameworks for tissue rebuilding. The ability to form a gel into a desired shape further expands the possibilities. For example, a drug-infused gel could be formed to exactly fit the space inside a wound.

Dan Luo, professor of biological and environmental engineering, and colleagues describe their creation in the Dec. 2 issue of the journal Nature Nanotechnology

The new hydrogel is made of synthetic DNA. In addition to being the stuff genes are made of, DNA can serve as a building block for self-assembling materials. Single strands of DNA will lock onto other single stands that have complementary coding, like tiny organic Legos. By synthesizing DNA with carefully arranged complementary sections Luo's research team previously created short stands that link into shapes such as crosses or Y's, which in turn join at the ends to form meshlike structures to form the first successful all-DNA hydrogel. Trying a new approach, they mixed synthetic DNA with enzymes that cause DNA to self-replicate and to extend itself into long chains, to make a hydrogel without DNA linkages.

"During this process they entangle, and the entanglement produces a 3-D network," Luo said. But the result was not what they expected: The hydrogel they made flows like a liquid, but when placed in water returns to the shape of the container in which it was formed.

"This was not by design," Luo said.

Examination under an electron microscope shows that the material is made up of a mass of tiny spherical "bird's nests" of tangled DNA, about 1 micron (millionth of a meter) in diameter, further entangled to one another by longer DNA chains. It behaves something like a mass of rubber bands glued together: It has an inherent shape, but can be stretched and deformed.

Exactly how this works is "still being investigated," the researchers said, but they theorize that the elastic forces holding the shape are so weak that a combination of surface tension and gravity overcomes them; the gel just sags into a loose blob. But when it is immersed in water, surface tension is nearly zero -- there's water inside and out -- and buoyancy cancels gravity.

To demonstrate the effect, the researchers created hydrogels in molds shaped like the letters D, N and A. Poured out of the molds, the gels became amorphous liquids, but in water they morphed back into the letters. As a possible application, the team created a water-actuated switch. They made a short cylindrical gel infused with metal particles placed in an insulated tube between two electrical contacts. In liquid form the gel reaches both ends of the tube and forms a circuit. When water is added, the gel reverts to its shorter form that will not reach both ends. (The experiment is done with distilled water that does not conduct electricity.)

The DNA used in this work has a random sequence, and only occasional cross-linking was observed, Luo said. By designing the DNA to link in particular ways he hopes to be able to tune the properties of the new hydrogel.

The research has been partially supported by the U.S. Department of Agriculture and the Department of Defense.

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Jong Bum Lee, Songming Peng, Dayong Yang, Young Hoon Roh, Hisakage Funabashi, Nokyoung Park, Edward J. Rice, Liwei Chen, Rong Long, Mingming Wu, Dan Luo. A mechanical metamaterial made from a DNA hydrogel. Nature Nanotechnology, 2012; 7 (12): 816 DOI: 10.1038/nnano.2012.211

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Paper-and-scissors technique rocks the nano world: Future nanofluidic devices for batteries, water purification systems

Nov. 14, 2012 — Sometimes simplicity is best. Two Northwestern University researchers have discovered a remarkably easy way to make nanofluidic devices: using paper and scissors. And they can cut a device into any shape and size they want, adding to the method's versatility.

Nanofluidic devices are attractive because their thin channels can transport ions -- and with them a higher than normal electric current -- making the devices promising for use in batteries and new systems for water purification, harvesting energy and DNA sorting.

The "paper-and-scissors" method one day could be used to manufacture large-scale nanofluidic devices without relying on expensive lithography techniques.

The Northwestern duo found that simply stacking up sheets of the inexpensive material graphene oxide creates flexible "paper" with tens of thousands of very useful channels. A tiny gap forms naturally between neighboring sheets, and each gap is a channel through which ions can flow.

Using a pair of regular scissors, the researchers simply cut the paper into a desired shape, which, in the case of their experiments, was a rectangle.

"In a way, we were surprised that these nanochannels actually worked, because creating the device was so easy," said Jiaxing Huang, who conducted the research with postdoctoral fellow Kalyan Raidongia. "No one had thought about the space between sheet-like materials before. Using the space as a flow channel was a wild idea. We ran our experiment at least 10 times to be sure we were right."

Huang is an assistant professor of materials science and engineering and the Morris E. Fine Junior Professor in Materials and Manufacturing in the McCormick School of Engineering and Applied Science.

"Many people have studied graphene oxide papers but mainly for their mechanical properties or for making graphene," Huang said. "Here we show that graphene oxide paper naturally generates numerous nanofluidic ion channels when layered."

The findings are published in the Journal of the American Chemical Society.

To create a working device, the researchers took a pair of scissors and cut a piece of their graphene oxide paper into a centimeter-long rectangle. They then encased the paper in a polymer, drilled holes to expose the ends of the rectangular piece and filled up the holes with an electrolyte solution (a liquid containing ions) to complete the device.

Next they put electrodes at both ends and tested the electrical conductivity of the device. Huang and Raidongia observed higher than normal current, and the device worked whether flat or bent.

The nanochannels have significantly different -- and desirable -- properties from their bulk channel counterparts, Huang said. The nanochannels have a concentrating effect, resulting in an electric current much higher than those in bulk solutions.

Graphene oxide is basically graphene sheets decorated with oxygen-containing groups. It is made from inexpensive graphite powders by chemical reactions known for more than a century.

Scaling up the size of the device is simple. Tens of thousands of sheets or layers create tens of thousands of nanochannels, each channel approximately one nanometer high. There is no limit to the number of layers -- and thus channels -- one can have in a piece of paper.

To manufacture very massive arrays of channels, one only needs to put more graphene oxide sheets in the paper or to stack up many pieces of paper. A larger device, of course, can handle larger quantities of electrolyte.

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The above story is reprinted from materials provided by Northwestern University. The original article was written by Megan Fellman.

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Kalyan Raidongia, Jiaxing Huang. Nanofluidic Ion Transport through Reconstructed Layered Materials. Journal of the American Chemical Society, 2012; 134 (40): 16528 DOI: 10.1021/ja308167f

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Study fuels insight into conversion of wood to bio-oil

Dec. 14, 2012 — New research from North Carolina State University provides molecular-level insights into how cellulose -- the most common organic compound on Earth and the main structural component of plant cell walls -- breaks down in wood to create "bio-oils" which can be refined into any number of useful products, including liquid transportation fuels to power a car or an airplane.

Using a supercomputer that can perform functions thousands of times faster than a standard desktop computer, NC State chemical and biomolecular engineer Dr. Phillip Westmoreland and doctoral student Vikram Seshadri calculate what's occurring at the molecular level when wood is rapidly heated to high temperatures in the absence of oxygen, a decomposition process known as pyrolysis.

The results, which could help spur more effective and efficient ways of converting farmed and waste wood into useful bio-oils, appear in a feature article on the cover of the Dec. 13 print edition of the Journal of Physical Chemistry A.

Much of the energy that can be extracted from wood exists in the cellulose found in cell walls. Cellulose is a stiff, rodlike substance consisting of chains of a specific type of a simple sugar called glucose. The paper describes a mechanism for how glucose decomposes when heated. The mechanism is somewhat surprising, Westmoreland says, because it reveals how water molecules and even the glucose itself can trigger this decomposition.

"The calculations in the paper show that although the decomposition products and rates differ in glucose and cellulose, the various elementary steps appear to be the same, but altered in their relative importance to each other," Westmoreland says.

Knowing the specifics of the decomposition process will allow researchers to make predictions about the ease of extracting energy from different types of wood from various soil types.

The researchers are now conducting experiments to verify their calculations.

The research was funded by the U.S. Department of Energy. The computations were performed on Pittsburgh Supercomputing Center computers.

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Vikram Seshadri, Phillip R. Westmoreland. Concerted Reactions and Mechanism of Glucose Pyrolysis and Implications for Cellulose Kinetics. The Journal of Physical Chemistry A, 2012; 116 (49): 11997 DOI: 10.1021/jp3085099

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Synthetic biology research: Could fuel for cars or household power supplies be created from naturally-occurring fatty acids?

Dec. 17, 2012 — Writing in PNAS, the researchers have shown that the emerging field of synthetic biology can be used to manipulate hydrocarbon chemicals, found in soaps and shampoos, in cells.

This development, discovered with colleagues at the University of Turku in Finland, could mean fuel for cars or household power supplies could be created from naturally-occurring fatty acids.

The researchers, led by Professor Nick Turner from The University of Manchester, used synthetic biology to hijack the naturally-existing fatty acids and direct those fatty molecules towards the production of ready-to-use fuel and household chemicals.

Hydrocarbon chemicals are everywhere in our daily lives; as fragrance in soap, thickener in shampoo and fuel in the car. Their number of carbons and whether they are acid, aldehyde, alcohol or alkane are important parameters that influence how toxic they are to biological organisms, the potential for fuel and their olfactory perception as aroma compounds.

The breakthrough allows researchers to further explore how to create renewable energy from sustainable sources, and the advance could lead to more innovative ways of sourcing fuel from natural resources.

Synthetic biology is an area of biological research and technology that combines science and engineering for the benefit of society. Significant advances have been made in this field in recent years.

Professor Turner said: "In our laboratories in Manchester we currently work with many different biocatalysts that catalyse a range of chemical reactions -- the key is to match up the correct biocatalyst with the specific product you are trying to make.

"Biocatalysts recognise molecules in the way that a lock recognises a key -- they have to fit perfectly together to work. Sometime we redesign the lock so that if can accept a slightly different key allowing us to make even more interesting products.

"In this example we need to make sure that the fatty acid starting materials would be a perfect match for the biocatalysts that we discovered and developed in our laboratories.

"As with many leading areas of science today, in order to make major breakthroughs it is necessary for two or more laboratories around the world to come together to solve challenging problems."

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M. Kalim Akhtar, Nicholas J. Turner, and Patrik R. Jones. Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities. PNAS, December 17, 2012 DOI: 10.1073/pnas.1216516110

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Research may have important implications for combating diabetes

Dec. 12, 2012 — Research by University of Notre Dame biochemist Anthony S. Serianni is providing new insights that could have important implications for understanding and treating diabetes.

Serianni points out that biological compounds known as dicarbonyl sugars are produced inside the human body from the natural breakdown of the simple sugar, glucose. The formation of these sugars is enhanced in diabetic patients because glucose concentrations in the blood and plasma of diabetics are significantly elevated.

"We investigated, under laboratory conditions that approximate those in the body, the degradation of a specific dicarbonyl sugar called glucosone," Serianni said. "To establish with certainty the chemical fates of the individual carbons of the glucosone molecule during degradation, we replaced some of its carbons with a rare form of carbon (denoted 13C) and applied an analytical technique known as nuclear magnetic resonance (NMR) spectroscopy to observe at the molecular level how the individual 13C carbons behave as degradation occurred."

"We learned that glucosone degrades by an unanticipated reaction pathway that involves a novel rearrangement of the carbon backbone of the molecule, a process we call C1-C2 transposition."

The discovery undermines some prevailing assumptions about how sugars generally undergo degradation.

"Since sugar degradation in the body has important physiological implications, for example by causing changes in protein structure that accompany aging and by producing highly reactive by-products that damage cellular constituents, understanding how these molecules are transformed in the body is essential to understanding spontaneous cellular processes that are not necessarily subject to typical cellular controls," Serianni said.

The research also demonstrates a new role for phosphate as a catalyst in sugar degradation, a role that may be more common in in vitro and in vivo biochemistry than currently appreciated.

The research is a culmination of prior studies that Serianni's research group has conducted on saccharide degradation and rearrangement. In 1982, his group discovered the first stereospecific C1-C2 transposition reaction of saccharides, catalyzed by molybdate ion, that resulted in a process called C2 epimerization. This work led to new and convenient synthetic pathways for the 13C-labeling of saccharides upon which a commercial business as founded.

Serianni's lab has also promoted the use of 13C and other isotopes as tools to investigate new chemical and biochemical reactions, to probe biological metabolism, and to develop new clinical and diagnostic tools and tests.

"In this sense, the glucosone work fits nicely into our overall research mission," Serianni said.

The glucosone research was described in a study that appeared in the Journal of the American Chemical Society and was supported by the National Institute of Diabetes and Digestive and Kidney Disease.

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Journal Reference:

Wenhui Zhang, Anthony S. Serianni. Phosphate-Catalyzed Degradation ofd-Glucosone in Aqueous Solution Is Accompanied by C1–C2 Transposition. Journal of the American Chemical Society, 2012; 134 (28): 11511 DOI: 10.1021/ja3020296

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Need for speed: High-speed measurements of molecular motion in the cell nucleus

Dec. 3, 2012 — Using a new measurement technique, Heidelberg researchers have succeeded in tracking interactions between proteins and DNA in the cell nucleus at a resolution of 1/1000 of a second. They were able to measure the binding of highly specialised protein complexes that specifically change the spatial structure of the genetic information, thereby controlling the readout of the DNA information. The work of Dr. Karsten Rippe and his team was carried out at the BioQuant Center of Heidelberg University and the German Cancer Research Center. Their research has demonstrated that the positioning of nucleosomes -- complexes of DNA and specialised proteins -- is a precisely regulated molecular process. Aberrant regulation can be linked to several types of cancer.

The results of these studies were published in the Proceedings of the National Academy of Sciences.

In the human genome, the DNA strands are wrapped around specific packaging proteins, the histones. Located between these complexes, called nucleosomes, are histone-free DNA sequences that connect the nucleosomes, much like a pearl necklace. "Activating a gene requires freely accessible DNA. If the corresponding DNA is occluded in the nucleosome, the gene is often turned off," explains Dr. Rippe. "Hence, the nucleosome positions determine the readout pattern of the DNA sequence. The free DNA between two nucleosomes is more easily accessible than the DNA sequences in a nucleosome." Molecular machines called chromatin remodelers can use energy to move nucleosomes along the DNA chain. Thus they establish the readout pattern that, along with other factors, determines the active DNA programme of the cell.

Rippe's team of scientists are using fluorescence microscopy to investigate how the chromatin remodelers control the readout of the genetic information. With it they were able to measure that most of the approx. one million chromatin remodelers in the human cell transiently bind to nucleosomes to test whether all the approx. 30 million nucleosomes are at the right position. A new way of measurement was needed to understand how these molecular machines work. "We had to record short binding events at a resolution of 1/1000 of a second and at the same time detect the rare events with a binding time of several seconds or even minutes," says Karsten Rippe. Doctoral student Fabian Erdel came up with an idea that led to "Pixel-wise Photobleaching Profile Evolution Analysis," or 3PEA, which can be used to take such measurements in living cells.

In his experiments, Fabian Erdel used a laser beam to extinguish the artificial fluorescent tag attached to the chromatin remodelers. He noticed that the "bleached" proteins produced a "shadow" when they moved while the image was being recorded. The shape of this shadow depended on how much the movement of the chromatin remodelers slowed down due to binding to nucleosomes. "It was not easy calculating duration times of binding from the shadow image, but it was worth the effort. Our method has exciting new applications because we can use it to measure the binding of proteins in living cells very quickly and precisely," remarks Fabian Erdel.

Using 3PEA measurements, the researchers demonstrated that an individual chromatin remodeler travels through the entire cell nucleus within a single second testing more than 300 nucleosomes -- mostly without becoming active. Only occasionally the molecular machine would bind to a nucleosome for several seconds or even minutes, causing it to shift position on the DNA. Dr. Rippe and his team next want to decode signals that activate the chromatin remodelers at certain locations on the genome.

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F. Erdel, K. Rippe. Quantifying transient binding of ISWI chromatin remodelers in living cells by pixel-wise photobleaching profile evolution analysis. Proceedings of the National Academy of Sciences, 2012; 109 (47): E3221 DOI: 10.1073/pnas.1209579109

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Oil and water: An icy interaction when oil chains are short, but steamy when chains are long

Dec. 3, 2012 — Water transforms into a previously unknown structure in between a liquid and a vapor when in contact with alcohol molecules containing long oily chains, according to Purdue University researchers. However, around short oily chains water is more icelike.

Water plays a huge role in biological processes, from protein folding to membrane formation, and it could be that this transformation is useful in a way not yet understood, said Dor Ben-Amotz, the professor of chemistry who led the research.

Ben-Amotz's research team found that as they examined alcohols with increasingly long carbon chains, the transformation occurred at lower and lower temperatures.

When in contact with a chain seven carbon atoms long, the water molecules became much looser and more vaporlike at a temperature of 140 degrees Fahrenheit, which is about halfway between the melting and boiling points.

"For oils with chains longer than four carbons, or about one nanometer in length, we saw the water transform into a completely new structure as the temperature rose," Ben-Amotz said. "If the trend we saw holds true, then this transformation could be happening at body temperature around important physiological molecules like proteins and phospholipids."

Water responds very sensitively in its structure to small changes, he said.

"Water's versatility is what makes it so special," he said. "For instance, the surfaces of proteins have both oily and charged regions; and water changes itself to accommodate these very different components and everything in between. We are learning more about exactly how it does this."

The researchers found that water molecules interacting with the oil always formed a more ordered, icelike structure at lower temperatures, while the bulk of the water remained liquid. This ice-like structure would melt away as the temperatures increased and in longer molecules a new structure would appear, he said.

A paper detailing the National Science Foundation-funded work is published in the current issue of Nature and is also highlighted in a news and views article in the same issue. In addition to Ben-Amotz, co-authors include Purdue graduate student Joel Davis and postdoctoral fellows Kamil Gierszal and Ping Wang.

The team's observations add to a more than 70-year debate over the interaction of oil and water, with some studies suggesting that water forms little icebergs around the oil molecules, while others point to a more disordered, vaporlike water structure.

"This question was really up for grabs until we introduced an experimental method that could see these subtle changes in water structure," Ben-Amotz said. "Surprisingly, we found that both sides are right, and it depends on the size of the oil."

The challenge of the experiment was that the team needed to see the very small number of water molecules that are in contact with the oil chains in the presence of a very large number of other water molecules.

The team combined Raman scattering and multivariate curve resolution to create an analysis method capable of managing an unprecedented signal-to-noise ratio of 10,000-to-1.

"Most people never take a spectrum with a signal-to-noise ratio greater than 100-to-1, but if we performed this experiment that way we wouldn't see anything," Ben-Amotz said. "We needed to have a higher signal-to-noise ratio because we were looking for a needle in a mountain-sized haystack."

Raman scattering involves shooting a beam of light containing photons into a sample. As the photons hit molecules within the sample, they lose or gain energy. Such measurements create a spectrum of peaks that reveal the vibrational motions of the molecules present in the sample. Shifts in the peaks' shapes can show changes in the strength of bonds between water molecules and whether the molecules are becoming more or less ordered.

"With Raman scattering the bulk of the water creates a mountainous peak in the spectrum that buries everything else," Ben-Amotz said. "Multivariate curve resolution lets us see small changes in water structure under that mountain. As is often the case in science, the key was combining two already established techniques in a new way."

Davis said the team next plans to explore the effects of changes in pH and ionic charges on this transformation with the goal of making the experiments more relevant to proteins and biological systems.

"We are trying to better understand the driving forces of the behavior of proteins and cell membranes that are critical to our health," he said. "The role of water is an important piece of the puzzle."

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The above story is reprinted from materials provided by Purdue University. The original article was written by Elizabeth K. Gardner.

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Journal Reference:

Joel G. Davis, Kamil P. Gierszal, Ping Wang, Dor Ben-Amotz. Water structural transformation at molecular hydrophobic interfaces. Nature, 2012; 491 (7425): 582 DOI: 10.1038/nature11570

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Rules devised for building ideal protein molecules from scratch

Nov. 28, 2012 — By following certain rules, scientists can prepare architectural plans for building ideal protein molecules not found in the real world. Based on these computer renditions, previously non-existent proteins can be produced from scratch in the lab. The principles to make this happen appear this month in Nature magazine.

The lead authors are Dr. Nobuyasu Koga and Dr. Rie Tatsumi-Koga, a husband-and-wife scientific team in Dr. David Baker's lab at the University of Washington Protein Design Institute.

The project benefited from hundreds of thousands of computer enthusiasts around the world who adopted Rosetta@home for simulating designed proteins.

Protein molecules start as an unstable, high energy chain of amino acids. This chain then begins folding into various shapes to try to achieve a stable, low energy state. The end result is its distinctive molecular structure. Rosetta@home volunteers helped the project team to plot this energy landscape from protein structure predictions.

"The structural options become fewer as the interactions that stabilize the protein selectively favor one folding pattern over others," explained Koga.

"This decline in conformation options to eventually achieve a unique, ordered structure is called a funnel-shaped energy landscape," he said, drawing a tornado-like figure on a whiteboard. The researchers came up with guidelines for robustly generating this type of energy landscape.

According to Tatsumi-Koga, these rules require the interactions among the residues in the protein's amino acid chain to consistently favor the same folded conformation in forming its molecular shape. This is made possible, for example, by defining whether a specific unit will form a "right-handed" orientation or its mirror image, and disfavor others.

The researchers, she said, synthesized the proteins they had originally designed and tested "in silico" (on the computer) and physically characterized them through "in vitro" (laboratory test tube) experiments.

They also compared the molecular structures of the computer models with these laboratory-derived proteins to see how well they matched.

Koga stressed that the project looked strictly at protein structure. He smiled as he said his group was striving toward a "platonic ideal," a reference to Plato's theory of perfect forms.

In our imperfect material world, proteins are not always optimized for their stability, but can be beset by bulges, kinks, strains, and improperly buried parts. Many diseases arise from protein malformations.

During this project, the researchers achieved a library of five ideal structures, but since filing their report have added several more.

To make them accessible to other scientists, the designs have been deposited in the Research Collaboratory for Structural Bioinformatics and the lab analysis of their chemical structure was put in the Biological Magnetic Resonance Database.

The team was not attempting to create specific new proteins that could carry out particular activities.

However, their design principles and methods, according to their report, should allow the ready creation of a wide range of robust, stable, building blocks for the next generation of engineered functional proteins.

Such proteins would be custom-made for the task, instead of repurposed from proteins with unrelated functions. The hope is that engineered proteins will be useful for drug and vaccine development, especially for formidable viruses like HIV or rapidly changing ones, like the flu.

Proteins designed to exact specifications might also prove therapeutically useful in cleaving mutated genes, and for speeding up chemical reactions important in industry and environmental reclamation.

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The above story is reprinted from materials provided by University of Washington. The original article was written by Leila Gray.

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Journal Reference:

Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, Rong Xiao, Thomas B. Acton, Gaetano T. Montelione, David Baker. Principles for designing ideal protein structures. Nature, 2012; 491 (7423): 222 DOI: 10.1038/nature11600

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Curiosity shakes, bakes, and tastes Mars with SAM

Dec. 3, 2012 — NASA's Curiosity rover analyzed its first solid sample of Mars in Nov. with a variety of instruments, including the Sample Analysis at Mars (SAM) instrument suite. Developed at NASA's Goddard Space Flight Center in Greenbelt, Md., SAM is a portable chemistry lab tucked inside the Curiosity rover. SAM examines the chemistry of samples it ingests, checking particularly for chemistry relevant to whether an environment can support or could have supported life.

The sample of Martian soil came from the patch of windblown material called "Rocknest," which had provided a sample previously for mineralogical analysis by Curiosity's Chemistry and Mineralogy (CheMin) instrument. CheMin also received a new sample from the same Rocknest scoop that fed SAM. SAM has previously analyzed samples of the Martian atmosphere.

SAM can get a solid sample of Mars from either a drill or a scoop attached to the end of Curiosity's robotic arm. Since Rocknest is essentially a pile of loose soil, the scoop was used this time.

"This is the first time we've analyzed a solid sample using all three instruments that comprise SAM," said Paul Mahaffy, SAM Principal Investigator at NASA Goddard. "We also cleaned Curiosity's sample manipulation system and successfully tested our ability to move the sample from the manipulation system through the instrument suite."

A complex choreography was required to get the sample inside SAM for analysis, according to Mahaffy. First, since the scoop might still have had contamination from Earth, the first three scoops were shaken, run through a sieve, then dumped right back on the surface with the idea that they would carry away any contaminants with them. A sieved portion of the fourth scoop -- just a few thousandths of a gram -- was then delivered to SAM. A cover that protects SAM from accidentally ingesting windblown material was opened, and Curiosity's arm positioned the sample over SAM's inlet funnels. Before the sample was dropped, SAM turned on its inlet funnel vibrators, which move the sample into a tiny quartz cup. After the sample dropped, the vibrator was turned off, the cover was closed, and the cup, which is on a carousel holding 74 sample cups, was lowered and moved to one of two ovens.

After the sample was baked to release its gases, SAM's three instruments "digested" them and gave Curiosity its first "taste" of Mars. A basic three-step process will be used to analyze future samples as well:

Separate the molecules:

Gas from the sample first travels to the Gas Chromatograph (GC) instrument. The purpose of this instrument is to sort out all the different molecules in the sample, and tell how much of each kind there is. It accomplishes this by using a stream of helium gas to push the sample down a long, narrow tube (which is wound into a coil to save space). Helium is used because it is inert, meaning it won't react with and change any of the sample molecules. The inside of the tube is coated with a thin film. As molecules travel through the tube, they stick for a bit on the film, and the heavier the molecule, the longer it sticks. Thus, the lighter molecules emerge from the tube first, followed by the middleweight molecules, with the heaviest molecules bringing up the rear.

Identify the molecules:

Since molecules of different weights emerge from the tube of the gas chromatograph at different times, the GC can send groups of different weights, one at a time, to SAM's next instrument, which will determine exactly what kind of molecule makes up each of the groups. This is the Quadrupole Mass Spectrometer (QMS) instrument. It fires high-speed electrons at the molecules, breaking them up into fragments and giving the molecules and their fragments an electric charge. These molecules and their fragments with an electric charge can be moved by electric fields. The QMS uses both direct current and alternating current fields to sort the electrically charged molecules and fragments based on their weight (mass). Molecules and fragments of different mass are counted by a detector at different times to generate a mass spectrum, which is a pattern that uniquely identifies molecules.

Identify the volatiles and determine the isotopes:

After the QMS identifies the molecules, the sample is directed into the Tunable Laser Spectrometer (TLS), which can identify and analyze certain volatile molecules, like methane and carbon dioxide. The sample enters a chamber with precisely positioned mirrors at both ends. A laser is fired through a tiny hole in one of the mirrors. As the laser light bounces between the mirrors, it illuminates the sample. Different molecules will absorb certain colors (frequencies) of light, so the TLS identifies the molecules by which colors of the laser are blocked (since the laser is tunable, it can be adjusted to shine in a range of colors).

The TLS can also identify isotopes the same way. Isotopes are versions of an element that are a little bit heavier because their nucleus contains more neutrons. For example, carbon 13 is an atom of carbon with an extra neutron, so it is a heavier version of the more common carbon 12. Occasionally, a carbon 13 will take the place of a carbon 12 in an organic molecule. This is important since life prefers to use the lighter isotopes, because chemical reactions with them require less energy. So if we measure the isotopes of carbon in a material and discover that there is more light carbon relative to heavy carbon than would be found randomly, we might guess that we are seeing the effects of life.

Finally, since volatile molecules are found in the atmosphere as well as in soil and rock, samples of the Martian air can be sent directly to the TLS without going through SAM's other instruments.

SAM was developed at NASA Goddard, but with significant elements provided by industry, university, and NASA partners. NASA's Jet Propulsion Laboratory, a division of the California Institute of Technology, Pasadena, manages the Curiosity/Mars Science Laboratory Project for NASA's Science Mission Directorate, Washington. JPL designed and built the rover.

For more information about SAM, refer to the "SAM I am" site at: http://ssed.gsfc.nasa.gov/sam/samiam.html

For more information about the Curiosity rover, visit: http://www.nasa.gov/msl and http://mars.jpl.nasa.gov/msl

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