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Dielectrophoretic Sorting of Membrane Protein Nanocrystals

"Dielectrophoretic Sorting of Membrane Protein Nanocrystals", Bahige G. Abdallah , Tzu-Chiao Chao, Christopher Kupitz, Petra Fromme, and Alexandra Ros, ACS Nano, 2013, 7 (10), pp 9129–9137
DOI: 10.1021/nn403760q

Structure elucidation of large membrane protein complexes is still a considerable challenge, yet is a key factor in drug development and disease combat. Femtosecond nanocrystallography is an emerging technique with which structural information of membrane proteins is obtained without the need to grow large crystals, thus overcoming the experimental riddle faced in traditional crystallography methods. Here, we demonstrate for the first time a microfluidic device capable of sorting membrane protein crystals based on size using dielectrophoresis. We demonstrate the excellent sorting power of this new approach with numerical simulations of selected submicrometer beads in excellent agreement with experimental observations. Crystals from batch crystallization broths of the huge membrane protein complex photosystem I were sorted without further treatment, resulting in a high degree of monodispersity and crystallinity in the 100 nm size range. Microfluidic integration, continuous sorting, and nanometer-sized crystal fractions make this method ideal for direct coupling to femtosecond nanocrystallography.

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Pizzarello: Antarctic meteorites and cosmochemical evolution

Important new findings on the chemistry of ancient asteroid fragments known as Carbonaceous Chondrites have recently been reported. Scientists led by Sandra Pizzarello, a research professor within Arizona State University's Department of Chemistry and Biochemistry, have detected enantiomeric excesses of up to 60 percent of D-allo-isoleucine, a non-protein amino acid. At the time of publication, this fraction exceeded any previously published enantiomeric excesses. The findings offer important insights into the primitive distribution and evolution of organic compounds in the early Solar System and can help constrain models of the physical and chemical processes that were active in the accretionary disk of the nascent sun.
The work has recently been published in the Proceedings of the National Academy of Sciences (PNAS). The paper is titled, "Large enantiomeric excesses in primitive meteorites and the diverse effects of water in cosmochemical evolution", and is co-authored by Pizzarello, Devin L. Schrader, Adam A. Monroe, ASU chemistry graduate student, and Dante S. Lauretta.
One intriguing group of Carbonaceous Chondrites, the remarkably pristine Renazzo-type (CR) chondrites found in Antarctica, contain organic materials and water-soluble molecules such as amino acids and ammonia. Pizzarello et al. analyzed select CR meteorites with different petrographic classifications to assess the abundance and distribution of key organic compounds in the context of aqueous processes and concomitant hydrated mineral phases. According to the authors, several CR compounds such as amino acids and sugar alcohols are fully represented in rocks with no or minimal water exposure, indicating an origin for these compounds that may predate parent body processes.

Carbonaceous meteorites are known to contain organic materials as diverse as kerogen-like macromolecules and simpler soluble compounds. Because some meteoritic compounds are identical to biomolecules and may have molecular traits such as chiral asymmetry, meteorites give insights into the evolution of the biogenic elements ahead of biochemistry.
Several of these CR2 meteorites, provided by the ASU Center for Meteorite Studies and NASA’s Johnson Space Center, have been studied by Pizzarello and coworkers through the years. These studies have shown that the formation of meteoritic compounds span vast cosmic locales from the cold environments of the interstellar molecular clouds to various asteroidal bodies. One question debated by meteoriticists involves whether the water processes known to occur in some asteroids did foster the compounds’ final syntheses from precursors.
However, carbonaceous meteorites are also fragile and Earthlike rocks that, if not actually seen falling, easily go undetected and disappear into the environment. As a result, very few “meteorite falls” in storage exist. Pizzarello was able to obtain and study several carbonaceous meteorites found in Antarctica, where the mean subfreezing temperatures and very dry climate provide an excellent natural curatorial environment until the samples are collected.

"Large enantiomeric excesses in primitive meteorites and the diverse effects of water in cosmochemical evolution" Pizzarello S., Schrader D.L., Monroe A.A. and Lauretta D.S. PNAS www.pnas.org/cgi/doi/10.1073/pnas.1204865109 (2012).

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This illustration by the Mayo Clinic is an example of abnormal bone density in osteoporosis. Scientists at Arizona State University and NASA are developing a new approach to the medical challenge of detecting bone loss by applying a technique that originated in the Earth sciences. Their findings are presented in a paper published in the online Early Edition of the Proceedings of the National Academy of Sciences (PNAS) the week of May 28, 2012.
Image by permission of Mayo Foundation for Medical Education and Research. All rights reserved.

Earlier detection of bone loss may be in future
NASA-funded research at ASU looks to isotope analysis rather than X-ray for measurement

Are your bones getting stronger or weaker? Right now, it’s hard to know. Scientists at Arizona State University and NASA are taking on this medical challenge by developing and applying a technique that originated in the Earth sciences. In a new study, this technique was more sensitive in detecting bone loss than the X-ray method used today, with less risk to patients. Eventually, it may find use in clinical settings, and could pave the way for additional innovative biosignatures to detect disease.

“Osteoporosis, a disease in which bones grow weaker, threatens more than half of Americans over age 50,” explained Ariel Anbar, a professor in ASU’s Department of Chemistry and Biochemistry and the School of Earth and Space Exploration, and senior author of the study.

“Bone loss also occurs in a number of cancers in their advanced stages. By the time these changes can be detected by X-rays, as a loss of bone density, significant damage has already occurred,” Anbar said. “Also, X-rays aren’t risk-free. We think there might be a better way.”

With the new technique, bone loss is detected by carefully analyzing the isotopes of the chemical element calcium that are naturally present in urine. Isotopes are atoms of an element that differ in their masses. Patients do not need to ingest any artificial tracers and are not exposed to any radiation, so there is virtually no risk, the authors noted.

The findings are presented in a paper published in the online Early Edition of the Proceedings of the National Academy of Sciences (PNAS) the week of May 28. It is titled “Rapidly assessing changes in bone mineral balance using natural stable calcium isotopes.”

“The paper suggests an exciting new approach to the problem,” said Rafael Fonseca, chair of the Department of Medicine at the Mayo Clinic in Arizona, and a specialist in the bone-destroying disease multiple myeloma. Fonseca was not associated with the study but is partnering with the ASU team on collaborative research based on the findings.

“Right now, pain is usually the first indication that cancer is affecting bones. If we could detect it earlier by an analysis of urine or blood in high-risk patients, it could significantly improve their care,” Fonseca said.

The new technique makes use of a fact well known to Earth scientists, but seldom used in biomedicine: Different isotopes of a chemical element can react at slightly different rates. When bones form, the lighter isotopes of calcium enter bone a little faster than the heavier isotopes. That difference, called “isotope fractionation,” is the key.

“Instead of isotopes of calcium, think about jelly beans,” explained Jennifer Morgan, lead author of the study. “We all have our favorite. Imagine a huge pile of jelly beans with equal amounts of six different kinds. You get to make your own personal pile, picking out the ones you want. Maybe you pick two black ones for every one of another color because you really like licorice. It’s easy to see that your pile will wind up with more black jelly beans than any other color. Therefore, the ratio of black to red or black to green will be higher in your pile than in the big one. That’s similar to what happens with calcium isotopes when bones form. Bone favors lighter calcium isotopes and picks them over the heavier ones.”

Other factors, especially bone destruction, also come into play, making the human body more complicated than the jelly bean analogy. But 15 years ago, corresponding author Joseph Skulan, now an adjunct professor at ASU, combined all the factors into a mathematical model that predicted that calcium isotope ratios in blood and urine should be extremely sensitive to bone mineral balance.

“Bone is continuously being formed and destroyed,” Skulan explained. “In healthy, active humans, these processes are in balance. But if a disease throws the balance off then you ought to see a shift in the calcium isotope ratios.”

The predicted effect on calcium isotopes is very small, but can be measured using sensitive mass spectrometry methods developed by Morgan as part of her doctoral work with Anbar, Skulan and co-author Gwyneth Gordon, an associate research scientist in the W.M. Keck Foundation Laboratory for Environmental Biogeochemistry at ASU. Co-author Stephen Romaniello, currently a doctoral student with Anbar at ASU, contributed an updated mathematical model.

The new study, funded by NASA, examined calcium isotopes in the urine of a dozen healthy subjects confined to bed (“bed rest”) for 30 days at the University of Texas Medical Branch at Galveston’s Institute for Translational Sciences–Clinical Research Center. Whenever a person lies down, the weight-bearing bones of the body, such as those in the spine and leg, are relieved of their burden, a condition known as “skeletal unloading”. With skeletal unloading, bones start to deteriorate due to increased destruction. Extended periods of bed rest induce bone loss similar to that experienced by osteoporosis patients, and astronauts.

“NASA conducts these studies because astronauts in microgravity experience skeletal unloading and suffer bone loss,” said co-author Scott M. Smith, NASA nutritionist. “It’s one of the major problems in human spaceflight, and we need to find better ways to monitor and counteract it. But the methods used to detect the effects of skeletal unloading in astronauts are also relevant to general medicine.”

Lab analysis of the subjects’ urine samples at ASU revealed that the new technique can detect bone loss after as little as one week of bed rest, long before changes in bone density are detectable by the conventional approach, dual-energy X-ray absorptiometry (DEXA).

Importantly, it is the only method, other than DEXA, that directly measures net bone loss.

“What we really want to know is whether the amount of bone in the body is increasing or decreasing”, said Morgan.

Calcium isotope measurements seem poised to assume an important role in detecting bone disease – in space, and on Earth. The team is working now to evaluate the technique in samples from cancer patients.

“This is a ‘proof-of-concept’ paper,” explained Anbar “We showed that the concept works as expected in healthy people in a well-defined experiment. The next step is to see if it works as expected in patients with bone-altering diseases. That would open the door to clinical applications.”

However, the concept extends even beyond bone and calcium, the authors noted. Many diseases may cause subtle changes in element isotope abundances, or in the concentrations of elements. These sorts of signatures have not been systematically explored in the development of biosignatures of cancers and other diseases.

“The concept of inorganic signatures represents a new and exciting approach to diagnosing, treating and monitoring complex diseases such as cancer,” stated Anna Barker, director of Transformative Healthcare Networks and co-director of the Complex Adaptive Systems Initiative in the Office of Knowledge Enterprise Development at ASU. Barker, who came to ASU after being deputy director of the National Cancer Institute, emphasized the simplicity of the approach compared to the challenges of deciphering complex genome-derived data, adding “there is an opportunity to create an entirely new generation of diagnostics for cancer and other diseases.”

The National Aeronautics and Space Administration Human Research Program and specifically the Human Health and Countermeasures Element and the Flight Analogs Project supported this work. Bed rest studies were supported in part by the National Center for Research Resources, National Institutes of Health.

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Written by Jenny Green.

SOURCES:
Ariel Anbar, anbar@asu.edu
Joseph Skulan, hematite3@gmail.com

MEDIA CONTACT:
Carol Hughes, carol.hughes@asu.edu
480-965-6375


Untangling mysteries of spider silk

Using high-energy X-rays provided by Argonne's Advanced Photon Source (APS), scientists peered into the structure of orb spiders’ dragline silk. This is the chief thread that allows them to dangle precipitously off branches and window frames.

"Spider silk has a unique combination of mechanical strength and elasticity that make it one of the toughest materials we know," said Professor Jeff Yarger of Arizona State University, one of the lead researchers of the study.

Paging Peter Parker: Scientists have taken another step closer to producing viable artificial spider silk by zooming-in on the nanoscopic structure of the natural, spider-made stuff, using the brightest X-ray beams in the Western Hemisphere.

And as it turns out, despite the intricate and deliberate patterns woven by common orb spiders, the strongest part of their silk — the threads called dragline silk, which are used to create the scaffolding of the entire web — are mostly made up of extremely random and disordered atoms on the nanoscale, according to the results of a new study by scientists in Arizona and Illinois.

In fact, between 85 and 90 percent of orb spiders’ dragline silk fibers are “amorphous regions,” comprised of random, disorganized atoms, which researchers believe are responsible for providing the silk with its extreme elasticity.

The remaining 15 to 10 percent of the silk is a highly-orderly crystalline lattice structure of atoms which gives the silk its amazing strength — as strong as steel.

See the difference between the orderly regions (multicolored) and random amorphous (blue) in the following image of X-ray data provided by Argonne National Laboratory in Illinois, where the study took place.

“These techniques we develop are getting us closer and closer to know the exact molecular structures within natural spider silk,” said Jeff Yarger, a biochemistry professor at Arizona State University and one of the lead researchers of the study, in an email to TPM.

“This knowledge is required in order to develop synthetic spider silk,” Yarger added.

Scientists have already managed to bioengineer spider silk out of silk worms and goats’ milk, but as Yarger pointed out, they aren’t quite as good as the spider-made silk.

“The problem is that these synthetic silks do not form the correct secondary and tertiary structures that natural spider silk fibers form,” Yarger told TPM.

The thought is that by getting a better view at what makes up real spider silk, scientists will be able to better replicate it on their own.

“Previously scientists had concentrated on the more ordered crystalline regions even though they form a minority of the fiber,” said Chris Benmore, an X-ray scientist on the project, in an email to TPM.

Benmore works specifically at the Advanced Photon Source (APS), the high-powered x-ray facility used to get the new close-up of the spider silk. The APS is a synchrotron facility — a giant particle accelerator measuring over a half-mile around, located at the Argonne National Laboratory in Argonne, Illinois, near Chicago and funded by the Department of Energy.

Scientists from around the country and the globe are allowed to use the x-rays for their own research projects. As Argonne explains, the APS is “open to everyone who has a need for extremely brilliant x-ray photon beams.”

In this case, the APS high-energy X-rays allowed Yarger and his colleagues to achieve an unprecedented level of detail when it came to imaging the amorphous regions of spider silk, zooming in to 10 million times magnification.

“We have recently developed a very powerful high energy x-ray probe at the APS which does not destroy the sample (which is a problem with lower energy x-rays) and provides a detailed insight into both the amorphous and crystalline regions of the spider silk,” Benmore explained.

The results of the X-ray study were published in a paper in the journal Physical Review Letters in late April.

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"Total X-Ray Scattering of Spider Dragline Silk", C. J. Benmore, T. Izdebski, and J. L. Yarger Phys. Rev. Lett. 108, 178102 (2012) – Published April 24, 2012



Redding investigates Photosystem 1

Oxygenic photosynthesis employs two chlorophyll-binding, multisubunit photosystems, PS1 and PS2, to absorb sunlight and convert the energy into charge-separated states, ultimately producing chemical energy in the form of NAPDH and ATP, which are used to drive carbon fixation and other endothermic reactions. Both photosystems funnel excitation energy from a relatively large network of chlorophylls (and other pigments, such as carotenoids) in the antenna toward a much smaller network in the reaction center (RC).

In Photosystem 1 (PS1), phylloquinone (PhQ) acts as a secondary electron acceptor
from chlorophyll ec3 and also as an electron donor to the iron−sulfur cluster FX. PS1 possesses two virtually equivalent branches of electron transfer (ET) cofactors from P700 to FX, and the lifetime of the semiquinone intermediate displays biphasic kinetics, reflecting ET along the two different branches.

PhQ in PS1 serves only as an intermediate in ET and is not normally fully reduced to the quinol form. This is in contrast to PS2, in which plastoquinone (PQ) is doubly reduced to plastoquinol (PQH2) as the terminal electron acceptor. Redding and coworkers purified PS1 particles from the menD1 mutant of Chlamydomonas reinhardtii that cannot synthesize PhQ, resulting in replacement of PhQ by PQ in the quinone-binding pocket. The magnitude of the stable flash-induced P700+ signal of menD1 PS1, but not wild-type PS1, decreased during a train of laser flashes, as it was replaced by a ∼30 ns back-reaction from the preceding radical pair (P700+A0−).

Redding et al. show that this process of photoinactivation is due to double reduction of PQ in the menD1 PS1 and have characterized the process. It is accelerated at lower pH, consistent with a rate-limiting protonation step. Moreover, a point mutation (PsaA-L722T) in the PhQA site that accelerates ET to FX ∼2-fold, likely by weakening the sole H-bond to PhQA, also accelerates the photoinactivation process. The addition of exogenous PhQ can restore activity to photoinactivated PS1 and confer resistance to further photoinactivation. This process also occurs with PS1 purified from the menB PhQ biosynthesis mutant of Synechocystis PCC 6803, demonstrating that it is a general phenomenon in both prokaryotic and eukaryotic PS1.

"Double Reduction of Plastoquinone to Plastoquinol in Photosystem 1", Michael D. McConnell, John B. Cowgill, Patricia L. Baker, Fabrice Rappaport,and Kevin E. Redding, Biochemistry, 2011 Dec 27;50(51):11034-46. Epub 2011 Dec 1.



Hayes & Herckes explore novel fingerprinting technique

Bioaerosols are diverse and complex dispersed particles that are either living or of biological origin. These include viruses, pollen, fungal spores, bacteria, and debris from vertebrates, including humans, and other biota (plants, insects, etc).

These particles range from ~10 nm to 100 μm, and their existence has been recognized for well over a century. Currently, the central topics of bioaerosol studies are health hazards, effects on the atmosphere, terrorism detection, and global climate.

Over the past decade, several studies focused on molecular and isotopic markers that can be used to track bioaerosols, especially for tracing particles released from soils and a variety of agricultural environments. Molecular marker studies have mainly focused on organic marker compounds, for example saccharides, alkanes, and steroids for tracing soil dust and plant bioaerosols.

Beyond these studies, viewing animal and human bioaerosols as an information-rich marker of its source has not been seriously considered. Reasons for this absence are lack of sufficient (bio) analytical capabilities and poor understanding of the biochemical fingerprints likely to be present in this type of debris.

Considering the body of evidence that does exist indicating abundant cellular material and proteins in the atmosphere, this is somewhat surprising—limited analytical capabilities notwithstanding. Even though there is imperfect knowledge of the “dead” and fragmented biological fraction of particles in the atmosphere, the mere existence of this type of debris creates an opportunity for its use in many potential applications.

Living organisms, including humans, constantly release a surprisingly large amount of dead skin cells and fragments into the environment. As analytical capabilities are improved and are focused on the characterization of this fraction (and the living fraction), detailed biochemical information will be found within the aerosol. This has the potential to significantly affect fields ranging from biochemical forensics and biodiversity studies to medical profiling and environmental studies.

"Exploring the feasibility of bioaerosol analysis as a novel fingerprinting technique". Josemar A. Castillo, Sarah J. R. Staton, Thomas J. Taylor, Pierre Herckes and Mark A. Hayes, Anal Bioanal Chem, 2012, 403(1), 15-26, DOI: 10.1007/s00216-012-5725-0


Allen and Williams shine new light on photosynthesis

One of the outstanding questions of early Earth biology is how ancient organisms made the evolutionary transition from anoxygenic (no oxygen produced) to oxygenic (oxygen-producing) photosynthesis. A team of scientists from ASU has moved us significantly closer to understanding this problem. Photo by: stock.xchng

Photosynthesis is one of the fundamental processes of life on Earth. The evolutionary transition from anoxygenic (no oxygen produced) to oxygenic (oxygen-producing) photosynthesis resulted in the critical development of atmospheric oxygen in amounts large enough to allow the evolution of organisms that use oxygen, including plants and mammals.

One of the outstanding questions of the early Earth is how ancient organisms made this transition. A team of scientists from Arizona State University has moved us closer to understanding how this occurred, in a paper recently published in the Proceedings of the National Academy of Sciences. The paper, titled "Light-driven oxygen production from superoxide by manganese-binding bacterial reaction centers," is authored by James Allen, JoAnn Williams, Tien Le Olson, Aaron Tufts, Paul Oyala and Wei-Jen Lee, all from the Department of Chemistry and Biochemistry in ASU's College of Liberal Arts and Sciences.

Plants and algae, as well as cyanobacteria, use photosynthesis to produce oxygen and “fuels,” the latter being oxidizable substances like carbohydrates and hydrogen. There are two pigment-protein complexes that orchestrate the primary reactions of light in oxygenic photosynthesis: photosystem I and photosystem II.

“In photosynthesis, the oxygen is produced at a special metal site containing four manganese and one calcium atom connected together as a metal cluster,” explains professor James Allen. “ This cluster is bound to the protein called photosystem II that provides a carefully controlled environment for the cluster.”

On illumination, two water molecules bound at the cluster are split into molecular oxygen and four protons. Since water molecules are very stable, this process requires that the metal cluster be capable of efficiently performing very energetic reactions.

Allen, Williams and coworkers are trying to understand how a primitive anoxygenic organism that was capable of performing only simple low energy reactions could have evolved into oxygen-producing photosynthesis.

They have been manipulating the reaction center of the purple bacterium Rhodobacter sphaeroides encouraging it to acquire the functions of photosystem II. In the recent publication, they describe how a mononuclear manganese bound to the reaction center has gained some of the functional features of the metal cluster of photosystem II.

Although the mononuclear manganese cannot split water, it can react with reactive oxygen species to produce molecular oxygen. These results suggest that the evolution of photosynthesis might well have proceeded through intermediates that were capable of oxygen production and served until a protein with a bound manganese-calcium cluster evolved.

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Jenny Green, jenny.green@asu.edu
480-965-1430
Department of Chemistry and Biochemistry

"Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers", James P. Allen, Tien L. Olson, Paul Oyala, Wei-Jen Lee, Aaron A. Tufts, and JoAnn C. Williams, Proceedings of the National Academy of Sciences, (2012) Volume 109, pages 2314-2318

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What ruled the world before DNA and RNA?

All living organisms use DNA as the carrier of genetic material and RNA as the messenger molecule directing the expression of genes and creation of proteins. This arrangement has lasted 3.5 billion years. But what came before these life-giving molecules?

These two massive molecules are wonderfully versatile, capable of assembling and replicating themselves while also folding into all the different shapes needed for proper biological functions. Both DNA and RNA work by stringing together lots of different combinations of molecules called nucleotides, and it's the arrangement of these nucleotides that provides all the larger scale genetic information.

Both DNA and RNA are held together by "backbones" that are made of phosphates and sugar. These chemical bonds provide the structure needed to hold together the long chain of nucleotides in a single giant DNA or RNA molecule. In fact, it's these backbones that give the two forms of genetic material their name - the sugar holding together DNA is deoxyribose, hence deoxyribonucleic acid, while RNA contains ribose.
It's these sugars that have led researchers at Arizona State to consider the possibility of a simpler genetic material that ruled the primordial world more than 3.5 billion years ago. Both ribose and deoxyribose are what's known as five-carbon, or pentose, sugars. This simply means that their chemical structure features five carbon atoms.

The problem with pentose sugars is that they don't emerge and combine easily, especially in an ancient Earth that had not yet been transformed by the presence of RNA and DNA. That's a bit of a biological Catch-22: for pentose sugars to emerge, you need a world that's already full of pentose sugars. The way out of this paradox, according to Arizona State researcher John Chaput, is to presuppose an earlier, less complex form of genetic material that could be a bridge between the lifeless prebiotic world and our current, DNA-dominated planet.
The likeliest candidate, according to Chaput, is a molecule called threose nucleic acid, or TNA. Unlike ribose and deoxyribose, threose is a tetrose sugar, meaning it only has four carbon atoms in its molecular structure. From a chemical standpoint, four is a much easier number than five - threose could easily have formed from the combination of a pair of carbon fragments, each featuring two of the necessary atoms.

That's all well and good, but the theory doesn't mean much if TNA can't actually function as a genetic material for simple organisms. The initial experiments on this point are encouraging, as Chaput reports that TNA "can fold into complex shapes that can bind to a desired target with high affinity and specificity." These functional TNA molecules were created from initial random sequences through a process of Darwinian evolution, the same process by which DNA and RNA first emerged as the carriers of genetic material in the real world.

What's more, TNA is able to bond chemically with both DNA and RNA molecules and still function as a source of genetic information. That's crucial because, if TNA really did once provide genetic data for our planet's very earliest organisms, there must have eventually been a transition point from this early molecule to its immediate successor RNA. In this model, TNA serves as a simpler way for basic life to get started in the unforgiving primordial Earth, which was then able to give way to more complex macromolecules that were able to carry out a wider range of biological functions.
Right now, there's no way to prove that Earth was once a world of TNA - indeed, biologists are still struggling to find hard evidence that RNA once served as the primary source of genetic material before the dominance of DNA. The way forward is to demonstrate that synthetic TNA really can provide all the functions required by early lifeforms. If that holds up, TNA could well then become the likeliest explanation for the first origins of life.

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"Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor" Hanyang Yu, Su Zhan and John C.Chaput, Nature Chemistry (2012) doi:10.1038/nchem.1241.
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Molecules as mini-computers

Photochromes are photoswitchable, bistable chromophores which, like transistors, can implement binary logic operations. When several photochromes are combined in one molecule, interactions between them such as energy and electron transfer allow design of simple Boolean logic gates and more complex logic devices with all-photonic inputs and outputs. Selective isomerization of individual photochromes can be achieved using light of different wavelengths, and logic outputs can employ absorption and emission properties at different wavelengths, thus allowing a single molecular species to perform several different functions, even simultaneously. This manuscript reports a molecule consisting of three linked photochromes that can be configured as AND, XOR, INH, half-adder, half-subtractor, multiplexer, demultiplexer, encoder, decoder, keypad lock, and logically reversible transfer gate logic devices, all with a common initial state. The system demonstrates the advantages of light-responsive molecules as multifunctional, reconfigurable nanoscale logic devices that represent an approach to true molecular information processing units.

The beguiling idea that molecules can manipulate and process information using logic, as do electronic computers and human brains, has spawned numerous studies of molecule-based systems that perform not only as simple logic gates but also as more complex devices such as adders and subtractors, multi- plexers/demultiplexers, encoders/decoders, keypad locks, and multivalued logic devices. In recent years, such decision-making molecular systems have been explored in clever applications taking advantage of binary and multivalued information processing for multiparameter chemosensing, pro-drug activation, medical diagnostics, object labeling, data storage, and smart materials and surfaces. Molecular computing, which requires more than a single logic function/device, has been critically discussed in recent years. One of the foremost problems is the physical integration of many logic gates in arrays in order to achieve functional complexity beyond basic logic gates such as AND, OR, NOR, NAND, XOR, INH, etc. This would require efficient wiring (concatenation) of simple logic switches. Only a few proof-of-principle examples of such concatenation are known in the literature. One approach to circumvent this problem is functional integration. This means that a unimolecular system can mimic a complex logic circuit, composed of various logic gates, without the necessity of representing each logic gate by a different structural feature. The complex logic devices mentioned above are examples of this approach. For example, a molecular half-adder is a combination of AND and XOR logic gate functions in the same molecule.

Many of the molecular logic systems that have been described use chemicals as inputs and optical as well as chemical signals as outputs. However, the use of photons for both inputs and outputs offers several advantages. First, due to the physical equality of input and output, i.e., an all-photonic operation, one barrier for the concatenation of logic devices is removed. Also, light does not require physical access, allowing monolithic structures containing many individual logic elements. This is a potential advantage for transferring molecular logic devices from solution operation to the solid phase in the future. Light does not lead to the buildup of waste products, thus in principle allowing nearly infinite cycling of the system (although this has not been achieved yet in practice). Optical input signals can be delivered by remote control and as pulses, even on the subpicosecond time scale, permitting rapid cycling. Importantly, different chromo- phores in the same molecule interact differently with light of different wavelengths. Moreover, a single substance can perform several logic operations with the same set of inputs, depending upon the readout selected, and may be reconfigured for different operations simply by changing the input wavelengths, output wavelengths, or initial state.

This paper reports a photochromic triad acting as a unimolecular, multifunctional, and reconfigurable logic system that performs the functions of the following devices: AND, XOR (exclusive OR), INH (inhibit), half-adder, half-subtractor, multiplexer, demultiplexer, encoder, decoder, keypad lock, and logically reversible transfer gate. Uniquely, all operations use a common initial state, and the majority (including the half-adder and half- subtractor) share the same two inputs, differing only in the choice of the optical output signal. This not only allows parallel logic operations with the same set of inputs but also makes switching (reconfiguration) among the various logic operations extremely rapid and convenient. The thereby achieved level of functional integration through implementation of logic gate arrays without the need of physical gate-to-gate connections is unprecedented. Additionally, the triad can be reset by a universal optical signal, independent of the preceding input combination/logic operation.

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"All-Photonic Multifunctional Molecular Logic Device",  oakim Andrasson, Uwe Pischel, Stephen D. Straight Thomas A. Moore, Ana L. Moore, and Devens Gust, JACS, August 3, 201, Volume 133, Issue 30 Pages 11641-11648.

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Discoveries in breast cancer detection

Joshua LaBaer, M.D., Ph.D., of the Biodesign Institute at Arizona State University, has been selected as one of three finalists for the Phoenix Business Journal's Health Care Hero award in the researcher/innovator category. The annual award honors exemplary performance in the Phoenix health care industry. Award recipients will be announced at a breakfast at the Arizona Biltmore Resort on Aug. 18.

Two years ago, LaBaer, a medical oncologist and research scientist, was recruited from Harvard University to serve as the first Piper Chair in Personalized Medicine at ASU's Biodesign Institute. LaBaer leads a multidisciplinary team in a large-scale effort to discover and validate unique molecular fingerprints of disease. These fingerprints, called biomarkers, can provide an early warning for those at risk of major illnesses. LaBaer is co-inventor of a technology that serves as the molecular toolkit for his approach.

LaBaer's recruit to ASU was a boon to the medical and research community, as he is one of the foremost investigators advancing personalized medicine. He is working in a new field of science called proteomics to make major strides in cancer research, as well as diabetes and infectious diseases.

Recently, LaBaer identified a panel of 28 new biomarkers that may aid in the early diagnosis of breast cancer. These biomarkers are important in breast cancer tumor biology and pathology, as well as drug resistance to leading treatments.

"We believe that these biomarkers will lead to the first type of blood tests for the early detection of breast cancer," said LaBaer. "We hope this will lead to catching breast cancer earlier and saving thousands of lives each year."


In addition to early detection, breast cancer care at present falters when patients become resistant to the drugs used to treat the disease. LaBaer's group recently uncovered 30 novel genes involved in tamoxifen drug resistance. They did this by screening genes implicated in the development of breast cancer cells that become resistant to the drug with a robotic system that places human genes into cancer cells to determine if the genes would change the behavior of those cells.

LaBaer's center is home to a unique, worldwide resource for research called DNASU, a gene library of more than 127,000 unique genes made in his lab and contributed from labs elsewhere. These DNA samples represent more than 750 organisms and provide the raw materials for experiments. His lab has made this library into a shared resource to accelerate research. Housed in a million-dollar custom robotic freezer, the gene library is the only one of its kind in the southwestern United State. To date, they have distributed 250,000 plasmid clones to 550 labs in 35 countries.

In addition to his innovations, LaBaer's community impact has been significant. His center has support from the Breast Cancer Research Foundations, the National Cancer Institute, the National Institute for General Medical Sciences, the National Institute for Allergy and Infectious Diseases, and a $35 million philanthropic gift from the Piper Charitable Trust. LaBaer's center has resulted in jobs, opportunities for students, incoming grant dollars, plus the attention that his cutting-edge research brings.

LaBaer earned a BS from UC-Berkeley, and his MD and PhD degrees at UCSF. He is a board certified physician in Internal Medicine and Medical Oncology and has published 106 publications.

LaBaer is the founder of the International Human Proteome Organization and US HUPO. He serves on the NCI Board of Scientific Advisors and co-chair for the Steering Committee for NCI's Early Detection Research Network. He also serves as an associate editor for the Journal of Proteome Research.

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Structural overlay of the activase C-domain(yellow) onto the hexameric assembly of FtsH, a remote homolog (blue)

How do higher plants regulate CO 2 assimilation under heat-stress conditions?

In recent years, interest in understanding the structure and function of Rubisco activase, a motor protein in plants, has intensified, propelled in part by its purported role in modulating the thermotolerance of photosynthesis.

The first X-ray structural information on Rubisco activase has recently been provided by post-doctoral research associate Nathan Henderson and associate professor Rebekka Wachter who work in Arizona State University’s Department of Chemistry and Biochemisty. The work was published online in the Journal of Biological Chemistry in a rapid report format (http://www.jbc.org/content/early/2011/08/31/jbc.C111.289595), and will appear in print later this year.

Rubisco activase is a motor protein thought to play a central role in coordinating the rate of CO 2 fixation with the light reactions of photosynthesis. In spite of intense efforts by a number of researchers, structural information on activase has remained elusive for well over 20 years.

Rubisco is an extremely abundant enzyme responsible for net atmospheric carbon fixation in all photosynthetic organisms. Its catalytic competence plays an important role in heat-related limitations on biomass production. Activase regulates Rubisco activity by sensing the ATP/ADP ratio and redox poise of the chloroplast stroma, and has been linked to the inhibition of net photosynthesis under heat stress conditions.

The activase domain elucidated in the Wachter lab is essential in the specificity of Rubisco recognition, and will therefore serve as a structural framework to test models for the physical interaction between activase and Rubisco.

This long-awaited piece of a highly complex puzzle will accelerate research efforts aimed at understanding the down-regulation of carbon fixation at elevated temperatures, and will allow for structure-guided genetic engineering of activases to identify more thermostable variants.

"Atomic resolution X-ray structure of the substrate recognition domain of higher plant Rubisco activase", J. Nathan Henderson, Agnieszka M. Kuriata, Raimund Fromme, Michael E. Salvucci and Rebekka M. Wachter, JBC, 2011, doi: 10.1074/jbc.C111.289595

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Threading the needle--A rendition of a new nanotechnology-based DNA sequence reader, which is designed to rapidly read a DNA sequence as a single molecule is passed through an atomic-thin nanopore 

Next-generation DNA sequencing technologies

Two Biodesign Institute at Arizona State University researchers have been awarded more than $5 million in funds from the National Institutes of Health (NIH) to pursue the development of a revolutionary, next-generation DNA sequencing device to rapidly sequence a person's complete DNA information, or genome, for $1000 or less.

Biodesign researchers Stuart Lindsay, Ph.D. and Bharath Takulapalli, Ph.D., received the grants from the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, to develop technologies to enable the everyday use of DNA sequencing technologies by biomedical researchers and health care providers.

"Our promising approach, which combines advances in physics, electronics and nanotechnology, eliminates the need for the use of the major cost of sequencing today---namely, the use of chemical reagents---to read an individual's genome," said Lindsay, an ASU Regents' professor and director of the Biodesign Institute's Center for Single Molecule Biophysics.

"We are confident that NHGRI grantees will continue to make major breakthroughs in the development of technologies that will sequence a human genome for $1,000 or less," said NHGRI Director Eric D. Green, M.D, Ph.D. "As genome sequencing costs continue to decline, researchers and clinicians can increase the scale and scope of their studies. We will continue to fund innovations to accelerate what is known about human health and disease."

During the past decade, DNA sequencing costs have fallen dramatically, fueled in large part by tools, technologies and process improvements developed by the Human Genome Project. Since 2004, NHGRI launched major programs to accelerate improvements in sequencing technologies and to drive down the costs. Today, the cost to sequence a human genome using next generation sequencing has dipped below $20,000.

"With advances in a ‘third generation' of DNA sequencing technologies, we're moving closer to the point when researchers and health care providers can routinely and rapidly screen a person's, or large numbers of people's genome using devices that produce highly accurate data," said Jeff Schloss, Ph.D., NHGRI's program director for technology development.

ASU was the only university to receive more than one award. In total, the NHGRI funded nine teams to develop revolutionary technologies that can meet the $1,000 per genome goal. The approaches will integrate biochemistry, chemistry and physics with engineering to develop the third generation of DNA sequencing and analysis technologies.

ASU has received several multi-million awards since the NHGRI program was launched. Lindsay's research team will use a new four-year, $4.1 million NHGRI award to pursue the development of a device that can rapidly read the human genome.

The technology, which Lindsay calls recognition tunneling, reads the DNA sequence as a single DNA molecule is passed through an atomic-thin nanopore like thread through the eye of a needle. The team has developed proof-of-concept for the technology with the ability to distinguish among the 4 individual chemical components of the DNA code (referred as C, G, A, T) and now wants to translate their discoveries into a commercial instrument to optimize the DNA sequencing.

"We are in the midst of making a third generation reader molecule that gives us larger signals with better discrimination between the DNA bases," said Lindsay,  "Another challenge will be to control the speed of the DNA as it passes through the nanopore so that we can read the sequence as rapidly as possible while still getting a precise recognition signal."

Fellow Biodesign researcher Bharath Takulapalli will be pursuing a slightly different, yet parallel approach during his three-year $916,000 NHGRI award. Takulapalli, an electrical engineering expert, will focus on making improvements to both the nanopore sensor and device, with an emphasis on reading the DNA at very high speeds as it passes through a sensing technology based in part on a semiconductor staple called field-effect transistors (FETs). FETs control the flow of electrons in transistors and serve as the basis for modern digital integrated circuits found in  computers and smart phones.

"As Stuart Lindsay mentions, we have to find the sweet spot to control the rate at which DNA travels through the nanopore," said Takulapalli, an assistant research scientist at the institute's Virginia G. Piper Center for Personalized Diagnostics. "We want to ensure a maximum DNA signal with minimal noise." If successful, the approach has the potential to read up to 100,000 DNA bases per second, or a whole genome in a few minutes.

"This is no doubt a daunting task, but if successful, would represent a high payoff breakthrough in DNA sequencing, providing long reads, and a high-throughput at low-cost," said Takulapalli.

Together, the ASU duo hopes to advance the full potential of the technology toward a day when low-cost, DNA sequencing will become a standard part of everyday medical care.

 ###

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Written by Joe Caspermeyer
& Geoff Spencer (NHGRI)
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Angell recognized for pioneering work in ionic liquids

The American Electrochemical Society honored C. Austen Angell, an ASU Regents' professor of chemistry and biochemistry, with the Max Bredig award for his pioneering work on ionic liquids. The award recognizes Angell's years of innovation in the field of molten salts and ionic liquids chemistry.

Angell was presented with the Bredig award on Oct. 13, at an awards banquet during the Electrochemical Society's 218th meeting in Las Vegas.

The Electrochemical Society is the fourth professional society in the U.S. to recognize Angell's work with one of its internationally contested awards. He won the Materials Research Society's David Turnbull award in 2007 and the American Chemical Society's Joel Henry Hildebrand award in 2004. The American Ceramic Society (Glass Division) was the first with its George Morey award in 1990, the year after Angell joined ASU.

Molten salts and ionic liquids are actually the same thing but at different temperatures. They are exotic liquids in which every particle carries an electric charge -like table salt, except they flow like water - even at room temperature in the case of "ionic liquids."

Molten salts are great carriers of electric current, as needed in batteries. If General Electric Company succeeds in its ambitions, molten salts will be central to immense electric power storage facilities of the future in which excess grid energy will be used to convert sodium in the molten salt, quickly and temporarily, to metallic sodium. Such systems are urgently needed to "load-balance" sustainable, but erratic, renewable energy sources and better serve industrial society. The molten salt in the GE system is NaAlCl4, obtained by combining table salt with the chloride of aluminum, AlCl3. NaAlCl4 is a liquid at temperatures above 157 C (315 F).

Angell is best known for his studies on glass-forming liquids and super-cooled water. Working with colleague Jeff Yarger two years ago, he reported in Nature the first successful vitrification (turn into glass-like substance) of a pure metal. Then in a recent paper in Nature Physics (Nov. 28), he and other colleagues showed how the paradoxical behavior of an iron-cobalt alloy could be used to help understand how all these very different glass-formers might relate to one another.

"I've truly enjoyed working with my colleagues to delve into these materials and chronicle their exotic behaviors," Angell said. "It helps, being part of one of the top-five high-impact research chemistry departments in the country."

Skip Derra,
skip.derra@asu.edu 480-965-4823
Media Relations

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Professor Petra Fromme, Director of the Center
NIH FUNDS CENTER AT ARIZONA STATE TO BATTLE INFECTIOUS DISEASES

Arizona State University has been awarded a $7.7 million grant for the next five years from the National Institute of General Medical Sciences, part of the National Institutes of Health, to unravel the structures of membrane proteins that play a key role in protection against infectious diseases.

As part of the Protein Structure Initiative (PSI:Biology), ASU's Department of Chemistry and Biochemistry in the College of Liberal Arts and Sciences will be home to one of nine new national centers for structure determination of membrane proteins. The centers are focused on the discovery of the structure and function of membrane proteins.

Membrane proteins catalyze essential life functions, like respiration, photosynthesis, cell communication, import and export out of a cell and they play an essential role in the host-pathogen interaction.

"The impact of this work on human health and the battle against infectious diseases will be huge," explained Petra Fromme, a professor in chemistry and biochemistry and the director of the new ASU Center for Membrane Proteins and Infectious Diseases (MPID).

The cell membrane surrounds and protects the cell's interior like a skin. The membrane proteins, which are embedded in the membrane, in turn guard all transport in and out of the cell.

For example, when a virus enters the body, it docks to membrane proteins at the cell surface and subsequently tricks the cell into allowing the virus inside, like a Trojan horse. Once in the cell, its genetic information is released and the virus reprograms the human enzymes (or complete cell machinery) to produce thousands of new virus particles.
From top right hand corner in a clockwise direction: structure of the antiviral protein cyanovirin solved by members of the new PSI:Biology Center at ASU. (The research groups of Petra Fromme and Giovanna Ghirlanda). Next are crystals of the cyanobacterial protein plastocyanin followed by a schematic of a virus 

Elucidation of the membrane protein structures involved in docking and cell entry would enable the development of new drugs that specifically block the pathways into the cell. The virus (or the bacterial pathogen) could be"caught" and neutralized before it even starts its destructive actions.

Solving the specific membrane protein structure is like finding out the exact shape of a lock -once that is known, a key that fits the lock and thereby blocks the docking process can be designed, according to Fromme. The discovery of the structure of these key proteins involved in pathogen-human cell interaction will therefore have a huge impact on human health and pave the way for structure-based rationally designed drugs that fight infectious diseases - diseases that kill millions of humans each year worldwide.

Sixty percent of all current drugs are targeted to membrane proteins, yet only three human membrane protein structures are known despite their medical relevance. The centers will develop highly efficient methods for solving the structures of these elusive yet critically important proteins.

"The ASU center is the only one of the new centers focused specifically on membrane proteins from viral and bacterial pathogens," said Ward Smith, Ph.D., PSI director. "By determining these proteins' structures, the center will provide important clues for understanding infectious disease pathways that could point to new ways to treat and prevent infectious diseases."

"A critical step in understanding the complex processes that are catalyzed by membrane proteins is an understanding of their structure, dynamics and function,"said Fromme. Our knowledge of processes catalyzed by membrane proteins suffers greatly from a lack of information concerning their molecular-level structures. While more than 60,000 structures of soluble proteins have been solved only 250 membrane protein structures have been determined to date. The reason why membrane proteins are so intransigent is that they"live" in biological membranes, and so are not soluble in water. This makes them extremely difficult to isolate, purify and, in particular, to crystallize.

"Researchers at the ASU center will target membrane proteins of key viral and bacterial pathogens, their infectious pathways and molecules involved in host defense against the pathogens," Fromme said."This theme is unique and the results and structures determined by the center will be highly relevant for human health worldwide."

Fromme is an expert in protein structure elucidation. Her group has succeeded in crystallizing and solving the structures of two of the most complex and difficult membrane protein structures to be determined so far, photosystems I and II. These photosystems perform the first and most important step of photosynthesis, the conversion of solar energy into chemical energy, making them the source of energy for all higher life forms on Earth.

The ASU center will feature an interdisciplinary team that includes faculty from the Department of Chemistry and Biochemistry, School of Life Sciences, Department of Physics and the Biodesign Institute. International membrane protein expert professor Martin Caffrey, of Trinity College, Dublin, Ireland, also is involved in the center.

Biodesign's Joshua LaBaer, whose PSI:Biology - Materials Repository - http://psimr.asu.edu has a valuable plasmid repository with immediate broadly available access, will play an important role in the work. Having been the first to publish in this area, LaBaer's group has the experience necessary to provide the needed high throughput of protein expression and screening.

"The protein structure initiative is a response to one of the grand challenges of biological and medical sciences today," said William Petuskey, chair of chemistry and biochemistry."Its products will have far reaching impact and we expect that our new center will play a key role in these important advances."

In addition to the ASU center, other awardee institutions include the Scripps Research Institute, La Jolla Calif.; Harvard Medical School, Cambridge, Mass.; University of California - San Francisco; University of Wisconsin, Madison; New York Structural Biology Center, New York City; California Institute of Technology, Pasadena; Hauptman Woodward Medical Institute, Buffalo, N.Y.; and Washington University, St. Louis.

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Source: Petra Fromme, (480) 965-9028

Media contact: Jenny Green, (480) 965-1430; jenny.green@asu.edu

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this is the design for the DNA Möbius strip. Single-stranded viral DNA is used as scaffolding and 164 short segments of DNA are used as staple strands, to create the nanostructure. The Möbius form is composed of eleven double helices, assembled in parallel (left). Each double-helical length contains a twist of 180 degrees along its central axis, before it seamlessly reconnects with itself. The central helix, (seen in red) circles around the length of the strip once. The other helices circle twice, while also twisting around the core helix by 180 degrees before reconnecting to close the Möbius loop. (Center) A small segment of the strip with the details of the helices shown. Scaffold strands are seen in blue and staple strands are different colors. To create the Möbius, 20.5 units like this were used, with the precise folding pattern pre-programmed through the design of appropriate nucleotide base-pairing. (Right) Atomic Force Microscopy image. 

DNA art imitates life: Construction of a nanoscale Mobius strip

The enigmatic Möbius strip has long been an object of fascination, appearing in numerous works of art, most famously a woodcut by the Dutchman M.C. Escher, in which a tribe of ants traverses the form's single, never-ending surface. Scientists at the Biodesign Institute at Arizona State University's and Department of Chemistry and Biochemistry, led by Hao Yan and Yan Liu, have now reproduced the shape on a remarkably tiny scale, joining up braid-like segments of DNA to create Möbius structures measuring just 50 nanometers across-roughly the width of a virus particle.

Eventually, researchers hope to capitalize on the unique material properties of such nano-architectures, applying them to the development of biological and chemical sensing devices, nanolithography, drug delivery mechanisms pared down to the molecular scale and a new breed of nanoelectronics.

The team used a versatile construction method known as DNA origami and in a dramatic extension of the technique, (which they refer to as DNA Kirigami), they cut the resulting Möbius shapes along their length to produce twisted ring structures and interlocking loops known as catenanes. Their work appears in today's advanced online issue of the journal Nature Nanotechnology. Graduate students involved in this work include Dongran Han and Suchetan Pal in the Yan group. 

Their work appears in today's advanced online issue of the journal Nature Nanotechnology. Graduate students involved in this work include Dongran Han and Suchetan Pal in the Yan group. 

Making a Möbius strip in the everyday world is easy. Cut a narrow strip of paper, bring the two ends of the strip close to each other so that they match, but give them a half-twist before fastening the ends together with a piece of scotch tape. The resulting Möbius strip, which has only one surface and one boundary edge, is an example of a topological form. "As nanoarchitects," Yan says, "we strive to create two classes of structure-geometric and topological." Geometric structures in two and three dimensions abound in the natural world, from complex crystal shapes to starfish, and unicellular organisms like diatoms. Yan cites such natural forms as a boundless source of inspiration for human-designed nanostructures.

Topology, a branch of mathematics, describes the spatial properties of shapes that may be twisted, stretched or otherwise deformed to yield new shapes. Such shape deformations may profoundly alter the geometry of an object, as when a donut shape is pinched and stretched into a figure eight, but the surface topology of such forms is unaffected.

Nature is also rich in topological structures, Yan notes, including the elegant Möbius. The circulations of earth's warmer and cooler ocean currents for example, describe a Möbius shape. Other topological structures are common to biological systems, particularly in the case of DNA, the 3 billion chemical bases of which are packed by the chromosome inside the cell, using topological structures. "In bacteria, plasmid DNA is wound into a supercoil," Yan explains. "Then the enzymes can come in and cut and reconfigure the topology to relieve the torsion in the supercoil so that all the other cellular machinery can have access to the gene for replication, transcription and so forth."
A Möbius strip cut along its centerline, yields a Kirigami-Ring. 

To form the Möbius strip in the current study, the group relied on properties of self-assembly inherent in DNA. A strand of DNA is formed from combinations of 4 nucleotide bases, adenine (A), thymine (T), cytosine (C) and guanine (G), which follow one another on the strand like necklace beads. These nucleotide beads can bind to each other according to a strict rule: A always pairs with T, C with G. Thus, a second, complementary strand of DNA binds with the first to form the DNA double helix.

In 2006, Paul Rothemund at Cal Tech demonstrated that the process of DNA self-assembly could be used to produce pre-designed 2D nanoarchitectures of astonishing variety. Thus, DNA origami emerged as a powerful tool for nanostructure design. The method relies on a long, single stranded segment of DNA, used as a structural scaffold and guided through base pairing to assume a desired shape. Short, chemically synthesized "staple strands," composed of complementary bases are used to hold the structure in place.

After synthesis and mixing of DNA staples and scaffold strands, the structure is able to self-assemble in a single step. The technique has been used to produce remarkable nanostructures of smiley faces, squares, disks, geographic maps, and even words, at a scale of 100 nm or less. But the creation of topological forms capable of reconfiguration, like those produced by nature, has proven more challenging.

Once the tiny Möbius structures had been created, they were examined with atomic force- and transmission electron microscopy. The startling images confirm that the DNA origami process efficiently produced Escher-like Möbius strips measuring less than a thousandth the width of a human hair. Yan notes that the Möbius forms displayed both right and left handed twists. Imaging permitted the handedness or chirality of each flattened nanostructure to be determined, based on the height differences observed at the overlapping areas.

Next, the team demonstrated the topological flexibility of the Möbius forms produced, using a folding and cutting-or DNA Kirigami-technique. The Möbius can be modified by cutting along the length of the strip at different locations. Cutting a Möbius along its centerline yields a new structure-a looped form containing a twist of 720 degrees or 4 half-twists. The design, which the group calls a Kirigami-Ring is no longer a Möbius as it has two edges and two surfaces. The Möbius may also be cut along its length one-third of the way into its width, producing a Kirigami-Catenane-a Möbius strip interlinked with a supercoiled ring.

To accurately cut the Möbius nanostructures, a technique known as strand displacement was used, in which the DNA staples holding the central helix in place are outfitted with so-called toe-hold strands which protrude from the central helix. A complementary strand binds to the toehold segment, removing the staples and allowing the Möbius to fall open into either the Kirigami-Ring or Kirigami-Catenane.

Again, the successful synthesis of these forms was confirmed through microscopy, with the Kirigami-Ring structures gradually relaxing into figure eights.

Yan stresses that the success of the new study relied heavily on lead author Dongran Han's remarkable sense of three-dimensional space, allowing him to design geometrical and topological structures in his head. "Han and also Pal are particularly brilliant students," Yan says, pointing out that the complex conceptualization of the nanoarchitectures in their research is primarily performed without computer aid. The group hopes in the future to create software capable of simplifying the process.

"We want to push the Origami-Kirigami technology to create more sophisticated structures to demonstrate that we can make any arbitrary shape or topology using self-assembly," Han says.

Having made inroads into sculpture, painting and even literature, (particularly, the novels of French author Alain Robbe-Grillet), topological structures are now poised to influence scientific developments at the tiniest scale.  

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Written by Richard Harth
Biodesign Institute Science Writer
richard.harth@asu.edu 

"Folding and cutting DNA into reconfigurable topological nanostructures", Dongran Han, Suchetan Pal, Yan Liu & Hao Yan, Nature Nanotechnology Year published: (2010) DOI: doi:10.1038/nnano.2010.193

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Thermogladius shockii - new species of archaeon named after Everett Shock

A recent manuscript published in The Archives of Microbiology - http://www.springerlink.com/content/103luh546m231120/ documents the discovery of a hyperthermophilic archaeon in Yellowstone National Park. It is proposed that this archaeon be named in honor of Professor Everett L. Shock who pioneered the integrated geochemical and microbiological investigation into Yellowstone hot springs.
Hot spring in Yellowstone National Park where the archaeon Thermogladius shockii was recently discovered 

Archaea are a group of single-celled microorganisms. Thermogladius shockii has some very interesting features. It lives in temperatures ranging from 64 to 93oC, with an optimum at 84oC (that's 183oF!), over a wide range of pH, and unlike its closest relatives, it is indifferent about sulfur compounds.

Yellowstone National Park has the largest surface expression of terrestrial hydrothermal activity on Earth. Since 1999, Everett Shock has led field expeditions to Yellowstone with the purpose of integrating geochemistry and microbiology of hot spring ecosystems. The success of these trips has depended on the hard work and enthusiasm of graduate students, undergraduates, faculty collaborators and several colleagues from other institutions.

Shock and co-workers have taken a unified approach to scientific sampling at hot springs by collecting material for geochemical, microbiological, and molecular biological analyses simultaneously from the same locations. Once the field and lab data are collected they can be integrated to give a multidimensional view of how hot spring ecosystems work.

Geochemical samples of water, gases, microbial biofilms, sediment and rock yield compositional data for major and trace elements, organic solutes, trace gases, and mineralogy. These data are used in thermodynamic analyses of the supplies of chemical energy from oxidation-reduction reactions that fuel microbial metabolism. The resulting theoretical predictions supply a framework for interpreting isotopic compositions, phylogenetic data and environmental genomic results from co-located biological samples, and guide the search for specific genes.

In turn, new interpretations of molecular biology data are facilitated by the comprehensive sets of geochemical data. This combination of approaches yields novel insights into the structure and function of high-temperature microbial communities, and new ideas about how those communities participate in the geochemical processes of hydrothermal systems.  

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DNA PACKAGING

While efforts to unlock the subtleties of DNA have produced remarkable insights into the code of life, researchers still grapple with fundamental questions. For example, the underlying mechanisms by which human genes are turned on and off—generating essential proteins, determining our physical traits, and sometimes causing disease—remain poorly understood. Marcia Levitus, faculty member in the department of chemistry and biochemistry and Kaushik Gurunathan at the Biodesign Institute at Arizona State University along with their colleagues Hannah S. Tims, and Jonathan Widom of Northwestern University in Evanston, Illinois have been preoccupied with tiny, spool-like entities known as nucleosomes. Their latest insights into how these structures wrap and unwrap, permitting regulatory proteins to access, bind with and act on regions of DNA, recently appeared in the Journal of Molecular Biology. ;Nucleosomes, Levitus explains, are essential components of the genome, acting to regulate access to DNA and protect it from harm. Nucleosome structure permits the entire strand of human DNA, roughly 6 feet in length, to be densely packed into the nucleus of every cell—an area just 10 microns in diameter. This occurs after nucleosomes assemble and fold into higher order structures, culminating in the formation of chromosomes. Each nucleosome (there are roughly 30 million per cell) consists of a 147 base pair segment of DNA. This length of DNA thread is wound 1.67 times around the spool-like protein units, known as histones. The histone complex, together with its windings of DNA, forms the nucleosome core particle. A multitude of proteins must act on regions of the DNA strand, by binding with appropriate target sites. Essential functions rely on these operations, including gene expression, replication and repair of damaged regions of the DNA molecule. But in eukaryotic cells like those of humans, some 75-80 percent of the DNA strand is curled up and hidden in the nucleosomes—inaccessible to protein binding interactions. In earlier work, the group was able to show that nucleosomes are dynamic structures, quite different from the static pictures produced by X-ray crystallography.  Lengths of DNA make themselves available for protein interaction by unwrapping and rewrapping around the histone core. When nucleosomes unwrap, proteins present in sufficient concentration can find their DNA targets and bind with them. In order to observe and characterize the dynamic behavior of nucleosomes, the team relied on a versatile imaging method known as Fluorescence Resonance Energy Transfer or FRET. The technique allows researchers to look at a pair of fluorescent molecules or fluorophores, one of which is attached to the end of the exposed DNA strand, the other, to one of the histones around which the DNA is coiled.

 As Levitus explains, spontaneous unwrapping and rewrapping of DNA changes the distance between fluorophores, signaling that the process has occurred and allowing the group to quantify the frequency and rate of DNA exposure and concealment. “Although FRET has been used for decades to measure molecular distances in biological systems, dynamic biomolecules such as nucleosomes present particular challenges,” notes Levitus. Traditionally, FRET experiments are performed with protein solutions containing  many billions of particles. In the case of nucleosomes however, the dynamic behavior of each particle is crucial and bulk measurements using FRET are not effective. “In simple terms, if one wanted to understand how humans clap, it would be useless to listen to the whole planet clapping at once. Instead, one would listen to a few individuals, and that is exactly what we did with nucleosomes,” Levitus says. The results of initial studies were revealing. For base pair sequences along the nucleosomes’ outer rind, spontaneous DNA unwrapping occurs at a rapid rate— about 4 times per second. This corresponds to a period of only 250 milliseconds during which this region of DNA remains fully wrapped and occluded by the histone complex. Once unwrapped, the DNA remains exposed for 10-50 milliseconds. These findings present a plausible mechanism to allow protein binding with unwrapped DNA in vivo, so long as the binding sites occur near the ends of wrapped nucleosomal DNA. The new study also examines, for the first time, the condition of DNA sequences occurring further along the wound length of nucleosomal DNA, that is, closer to the nucleosome’s center. Here, rates of DNA unwrapping decreased by orders of magnitude.

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Written by: Richard Harth

 

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Biological Nanowires expedite future fuel production

Scientists in the UK and US, including researchers at Arizona State University, have been awarded $10.3 million to improve the photosynthetic process as a means of producing renewable fuel.

This award will permit four transatlantic teams, one directed by ASU's Assistant Professor Anne Jones in the department of chemistry and biochemistry, to investigate methods to overcome the limited efficiency of photosynthesis. This will lead to ways of significantly increasing the yield of important crops for food production or sustainable bioenergy. Ensuring a stable energy supply is the central challenge of the 21st century.

The funding has been awarded by the US National Science Foundation (NSF) and the UK Biotechnology and Biological Sciences Research Council (BBSRC) in an unusual program designed to co-opt some of the best minds from the USA and UK to explore this important problem. Although photosynthesis is nature's means for capturing the sun's energy in plants, algae and other organisms, it has intrinsic limitations for major energy production.

"The project represents a radical approach to augment and surpass photosynthetic strategies observed in nature by engineering

modular division of labor through electrical connectivity," says Jones who is also from the College of Liberal Arts and Sciences and the Center for Bioenergy and Photosynthesis at ASU.

"A simple analogy is a power plant unconnected to the distribution grid. Unconnected, excess energy goes to waste, and this is what currently happens in photosynthetic organisms when they are overwhelmed with light. However, engineering of transmission lines allows energy to be utilized and stored elsewhere. In this project, we will set up conductive transmission lines between the photosynthetic apparatus in one species and the fuel-producing metabolism of a second species to funnel excess energy directly into fuel production."

The strategy is to create a trans-cellular, plug-and-play platform that allows the team to shunt electrons from photosynthetic source cells to independently engineered fuel production modules along biological nanowires. "Photosynthesis is essential for life on Earth," says Joann Roskoski, NSF's Acting Assistant Director for Biological Sciences. "By providing food and generating oxygen, it has made our planet hospitable for life. This process is also critical in addressing the food and fuel challenges of the future. For decades, NSF has invested in photosynthesis research projects that range from biophysical studies to ecosystem analyses at a macroscale. The Ideas Lab in photosynthesis was an opportunity to stimulate and support different types of projects than what we have in our portfolio in order to address a critical bottleneck to enhancing the photosynthetic process."

"This is hugely ambitious research, but if the scientists we are supporting can achieve their aims it will be a profound achievement," explains Professor Janet Allen, Director of Research at BBSRC.

Other members of Jones's team in the US are John Golbeck from Penn State University, David Kramer from Michigan State University and Ichiro Matsumura from Emory University School of Medicine. Lee Cronin, from the University of Glasgow, Scotland, will direct the British part of the team including also Travis Bayer at Imperial College London and Thomas Bibby from the University of Southampton.

This project integrates diverse disciplines to address a critical limitation in the efficiency of photosynthesis, and along the way will advance both fundamental and applied knowledge in the areas of synthetic biology, inorganic and biosynthetic chemistry, protein engineering, electron transfer, energy storage, photosynthetic physiology and integration of novel traits into organisms.

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Source: Anne Jones, (480) 965-0356; anne.katherine.jones@asu.edu

Media contact: Jenny Green, (480) 965-1430; jenny.green@asu.edu

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Herckes group recently publishes with cover in the Annals of Occupational Hygiene

The Herckes group has participated in a study on firefighter exposure to polyaromatic hydrocarbons (PAHs) during prescribed burns. The collaborative effort between the three Arizona Universities (ASU, UA and NAU) investigated PAH concentrations in smoke during prescribed burns in Northern Arizona and monitored PAH metabolites in participating firefighters. The Herckes group contributed the analysis of PAHs in smoke. Results showed that PAH concentrations in fine particulate matter are twice as important during smoldering of the fires than during the ignition stage. While PAH concentrations in inhalable particles were high, the PAH metabolites in the firefighters did not show any significant increase between pre and post exposure. The results of the study have been published in the Annals of Occupational Hygiene (including the cover).

"Occupational PAH Exposures during Prescribed Pile Burns", M. S. Robinson, T. R. Anthony, S. R. Littau, P. Herckes, X. Nelson, G. S. Poplin and J. L. Burgess, Annals of Occupational Hygiene 2008 52(6):497-508; doi:10.1093/annhyg/men027.

Link to abstract

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Peter Williams, Professor of Chemistry and Biochemistry, PI on the award  

Powerful analytical instrument coming to ASU for NanoSIMS studies, Peter Williams PI

The National Science Foundation's Major Research and Instrumentation (MRI) Program recently funded a $3.7 million NanoSIMS imaging mass spectrometer for 13 ASU scientists and a large number of collaborators working on diverse topics involving both soft (biological) and hard materials (e.g. minerals).

This nano-scale imaging Secondary Ion Mass Spectrometer will produce chemical and isotopic images of samples ranging from bacteria to meteorites, with the ability to visualize features smaller than 50 nanometers (less than one-thousandth the width of a human hair). It will be used to trace details of metabolism in bacteria performing such roles as nitrogen fixation, pollutant cleanup or generation of biofuels, and to probe issues relating to the origin of life. Studies of microscopic atmospheric aerosol particles will advance our understanding of Earth's climate and global warming.

Measurements in tiny grains in meteorites will cast light on the early history of the solar system, while determination of the precise chemistry of tiny crystals that form in the last few hours before volcanic eruptions will allow ASU scientists to correlate time-resolved magma chemistry with external seismographic data to improve predictability of these catastrophic events.

"The NanoSIMS brings to ASU the capability for chemical and isotopic analysis, and imaging, at nanometer scales. It is one of only seven such instruments in the U.S.," stated Peter Williams, professor in the department of chemistry and biochemistry and principal investigator on the award. "The instrument will support an exceptionally diverse range of research areas. Initially these will include astrochemistry, astrobiology, vulcanology, climate science, environmental microbiology, bioenergy research, biosensors and nanoparticle-cell interactions, but the instrument will be a resource that will be accessible to the entire ASU research community."

In fact many undergraduate and graduate students will use the equipment in their research projects and will be trained in imaging science at the state of the art.

Williams has worked in the SIMS field since 1974. At ASU in 1984 he acquired an early ion microscope and began a research program split between theoretical studies of ion emission and sputtering, developments in analytical methodology and instrumental design, and applications of SIMS to wide-ranging analytical problems in areas such as semiconductor materials and, in particular geochemistry. Since 1985, Professor Richard Hervig of the School of Earth and Space Exploration (one of 12 co-PIs) and Williams have collaborated in building an open analytical facility, with local, national and international collaborations.

Professor James Anderson (co-PI), a research scientist in the Ira A. Fulton Schools of Engineering, will measure isotope ratios in submicron aerosol particles to determine the origins and chemistry of these particles that nucleate water droplets in clouds and so affect global climate.

Willem Vermaas (co-PI), professor in the School of Life Sciences, will utilize the NanoSIMS to study lipid biogenesis in bacteria to improve their value in biofuel production.

The ASU NanoSIMS instrument will enable co-PIs Professors Ariel Anbar and Everett Shock, both in the department of chemistry and biochemistry and the School of Earth and Space Exploration, and Regents' Professor James Elser (School of Life Sciences) to probe the metabolic pathways and mechanisms of element uptake and transfer in the ecosystems where biogeochemical cycles first evolved. A major component of this work is the drive to understand life's origin on the Earth, by studying the biology and ecology of terrestrial microbes, particularly extremophiles. Scientists have discovered an astonishing diversity of microbial metabolisms in the past 30 years, transforming our concept of "habitability." Hydrothermal ecosystems are the longest continuously occupied habitats on Earth. The microbes living there conduct every step of the complex element cycles that form the foundation of biogeochemistry. There is reason to believe that some of these organisms - extremophiles - may closely resemble some of the earliest-evolving life forms on Earth. Connections are being made to the relatively new discipline of astrobiology that explores the possibility of life beyond the Earth.

Research Professor Lynda Williams (co-PI), in the School of Earth and Space Exploration in the College of Liberal Arts and Sciences will use the new instrument to study nanoparticle-cell interactions involved in the healing action of medicinal clays.

Other co-PIs in the project include Meenakshi Wadhwa, Director of the Center for Meteorite Studies, Professors Paul Westerhoff and Nongjian Tao, Regents' Professor Bruce Rittman and Assistant Professor Jonathan Posner all from the Ira A. Fulton Schools of Engineering.

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Protein dynamics & photosynthesis - Woodbury & Matyushov

Protein dynamics to optimize and control bacterial photosynthesis

David N. LeBard, Daniel R. Martin, Su Lin, Neal W. Woodbury and Dmitry V. Matyushov

Bacterial photosynthesis is optimized and controlled by tuning time-scales of protein relaxation to rates of electron transfer.

Proteins function by sampling conformational sub-states within a given fold. How this configurational flexibility and the associated protein dynamics affect the rates of chemical reactions are open questions. The difficulty in exploring this issue arises in part from the need to identify the relevant nuclear modes affecting the reaction rate for each characteristic time-scale of the reaction. Proteins as reaction media display a hierarchy of such nuclear modes, of increasingly collective character, that produce both a broad spectrum of static fluctuations and a broad spectrum of relaxation times. In order to understand the effect of protein dynamics on reaction rates, we have chosen to study a sub-nanosecond electron transfer reaction between the bacteriopheophytin and primary quinone cofactors of the photosynthetic
bacterial reaction center. We show that dynamics affects the activation barrier of the reaction through a dynamical restriction of the configurational space sampled by the protein–water solvent on the reaction
time-scale. The modes which become dynamically arrested on the reaction time-scale of hundreds of picoseconds are related to elastic motions of the protein that are strongly coupled to the hydration
layer of water. Several mechanistic consequences for protein electron transfer emerge from this picture. Importantly, energy parameters used to define the activation barrier of electron transfer reactions lose
their direct connection to equilibrium thermodynamics and become dependent in a very direct way on the relative magnitudes of the reaction and nuclear reorganization time-scales. As a result, the
energetics of protein electron transfer need to be defined on each specific reaction time-scale. This perspective offers a mechanism to optimize protein electron transfer by tuning the reaction rate to the
relaxation spectrum of the reaction coordinate.

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The March issue of Journal of Natural Products is a special issue in Honor of Professor G.Robert Pettit

Gordon M. Cragg, Guest Editor, Richard G. Powell, Associate Editor, and Sheo B. Singh, Guest Editor: It is an honor and a pleasure for us to serve as Guest Editors of this issue of the Journal of Natural Products dedicated to Professor George Robert (Bob) Pettit. We wish to express our sincere thanks to Bob’s former students, postdoctoral fellows, visiting scientists, and his many colleagues from the former Cancer Research Institute at Arizona State University and institutions worldwide, for submitting such a diverse set of excellent manuscripts for this issue. Their generosity in terms of time and effort is greatly appreciated and provides well-deserved recognition of the many outstanding contributions that Bob has made to the field of natural products science and anticancer drug discovery over the past five decades.

Bob Pettit was born on June 8, 1929, in Long Branch, New Jersey. He gained his B.S. in chemistry at Washington State University in 1952 and proceeded to Wayne State University, where he completed his M.S. in heterocyclic chemistry in 1954 and his Ph.D. in steroid chemistry in 1956, both under the direction of Professor Carl Djerassi. Bob remembers the Djerassi group of the mid-1950s as an exciting and diverse group of talented young scientists from many parts of the world, including Australia, India, Israel, New Zealand, and the United Kingdom, who proceeded to prominent positions in academia, government, and industry. These included Albert Bowers and John Zderic, who later became CEO and Vice President of Syntex, respectively. In 1956, Bob moved to Norwich Eaton Pharmaceuticals (now Proctor and Gamble) as Senior Research Chemist, and in 1957 he transferred to the University of Maine as Assistant Professor, rising through the ranks to become Full Professor in 1965. After a period as Visiting Professor at Stanford University, he accepted a full Professorship in the Chemistry Department at Arizona State University in late 1965. From 1974 to 1975 he served as Director of the Cancer Research Laboratory, and in 1975 he became the Director of the newly established Cancer Research Institute. Since 1986 he has also occupied the position of Dalton Professor of Cancer Research and Medicinal Chemistry. full story from the Journal of Natural Products.

"Special Issue in Honor of Professor George Robert Pettit",Gordon M. Cragg, Guest Editor, Richard G. Powell, Associate Editor, and Sheo B. Singh, Guest Editor, J. Nat. Prod., 71 (3), 297–299, 2008. 10.1021/np700714j

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Too cool to follow the law- Angell & Richert

This recent study suggests viscous materials do not follow standard laws below a sub-melting point threshold.

So-called glass-formers are a class of highly viscous liquid materials that have the consistency of honey and turn into brittle glass once cooled to sufficiently low temperatures. Zhen Chen, C. Austen Angell and Ranko Richert from Arizona State University, have elucidated the behavior of these materials as they are on the verge of turning into glass in an article recently published in the European Physical Journal E. Although scientists do not yet thoroughly understand their behavior when approaching the glassy state, this new study, which relies on an additional type of dynamic measurement, clearly shows that they do not behave like more simple fluids, referred to as “activated” fluids. This is contrary to recent reports.

Typically, the dynamics of materials are described using a formula called the Arrhenius law, which is well known for chemical reaction rates. It states that a very simple law regulates how temperature affects characteristics such as viscosity and relaxation times –i.e., delay in returning to equilibrium after the
material has been subjected to a perturbation. The authors used a so-called "residuals" analysis to show that Arrhenius type dynamics is not a common behaviour at temperatures between a sub-melting point threshold, called the crossover temperature, which occurs at a dynamic transition point, and the glass transition temperature, where the liquid becomes a glassy solid.

Zhen Chen and co-authors came to this conclusion by analysing not only the material’s viscosity but also more precise data on the dielectric relaxation time available within the same temperature range. This gave them a more exact account of relaxation dynamic properties in highly viscous materials. The study revealed the need for greater precision in the viscosity data of glass-former materials to avoid masking its actual behavior from data treatment and graphical representation.

Reference:
1. Z. Chen et al. (2012). On the dynamics of liquids in their viscous regime approaching the glass transition. European Physical Journal E 35: 65; DOI 10.1140/epje/i2012-12065-2

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Ghirlanda designs protein modules…

Giovanna Ghirlanda from ASU's Department of Chemistry and Biochemistry along with colleagues S. Banu Ozkan from the department of physics and Claudio J. Margulis from the Department of Chemistry and Biochemistry at the University of Iowa have received a NSF grant entitled: Collaborative Research: A General Approach to the Design of Tailor-Made Glycan Recognition Protein Modules.

This collaboration brings together one experimentalist, namely Ghirlanda, and two computational chemists to address protein-carbohydrate interactions.  Protein-carbohydrate interactions play an important role in several biological processes, such as cell growth and differentiation, signal transduction, apoptosis, and fertilization. From a molecular recognition perspective, glycans are challenging ligands, in that they differ from each other simply by the point of attachment to each other, or by the position of single hydroxyl groups. Further, glycan based biopolymers are flexible and highly hydrated.

The objective of this project is to understand at the molecular level protein-glycan interactions in a model system, and to use this knowledge to develop novel glycan recognition proteins through an integrated computational and experimental strategy. Starting from a natural glycan binding protein, cyanovirin, we will explore the sequence space that supports high-affinity binding to the target glycan in parallel, utilizing directed evolution on the experimental side, and fast docking methods as well as explicit solvent molecular dynamics simulations on the computational side.  

"We chose Cyanovirin as model system because the protein shows remarkable and unique specificity for the oligomannoses attached to the surface of the viral envelope glycoprotein gp120 of HIV, resulting in potent antiviral activity," explains Ghirlanda. The Ghirlanda lab has recently  discovered the molecular mechanism of action of cyanovirin, which involves multivalent interactions with gp120. With this grant, the researchers will be able to rationally design improved antiviral proteins.

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Chen studies RNA-protein binding

Telomerase is a specialized reverse transcriptase containing an intrinsic telomerase RNA (TR) which provides the template for telo- meric DNA synthesis. Distinct from conventional reverse transcrip- tases, telomerase has evolved a unique TR-binding domain (TRBD) in the catalytic telomerase reverse transcriptase (TERT) protein, integral for ribonucleoprotein assembly. Two structural elements in the vertebrate TR, the pseudoknot and CR4/5, bind TERT inde- pendently and are essential for telomerase enzymatic activity. However, the details of the TR–TERT interaction have remained elusive. In this study, we employed a photoaffinity cross-linking approach to map the CR4/5-TRBD RNA–protein binding interface by identifying RNA and protein residues in close proximity. Photo- reactive 5-iodouridines were incorporated into the medaka CR4/5 RNA fragment and UV cross-linked to the medaka TRBD protein fragment. The cross-linking RNA residues were identified by alka- line partial hydrolysis and cross-linked protein residues were iden- tified by mass spectrometry. Three CR4/5 RNA residues (U182, U187, and U205) were found cross-linking to TRBD amino acids Tyr503, Phe355, and Trp477, respectively. This CR4/5 binding pocket is distinct and separate from the previously proposed T pocket in the Tetrahymena TRBD. Based on homologous structural models, our cross-linking data position the essential loop L6.1 adjacent to the TERT C-terminal extension domain. We thus propose that stem-loop 6.1 facilitates proper TERT folding by interacting with both TRBD and C-terminal extension. Revealing the telomerase CR4/5-TRBD binding interface with single-residue resolution pro- vides important insights into telomerase ribonucleoprotein archi- tecture and the function of the essential CR4/5 domain.

www.pnas.org/cgi/doi/10.1073/pnas.1100270108

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No extraordinary effects from microwave and mobile phone heating

Study quantifies effects of electric field-induced versus conventional heating

The effect of microwave heating and cell phone radiation on sample material is no different than a temperature increase, according to scientists from the Department of Chemistry and Biochemistry, Arizona State University, in Tempe, as published in a recent issue of EPJ B¹. Abidah Khalife, Ullas Pathak and Ranko Richert attempted for the first time to systematically quantify the difference between microwave-induced heating and conventional heating using a hotplate or an oil-bath, with thin liquid glycerol samples. The authors measured molecular mobility and reactivity changes induced by electric fields in these samples, which can be gauged by what is known as configurational temperature.

By conducting experiments at varying field frequencies and sample thicknesses, they realised that thin samples exposed to low-frequency electric field heating can have a considerably higher mobility and reactivity than samples exposed to standard heating, even if they are at the exact same sample temperature. They also found that at frequencies exceeding several megahertz and for samples thicker than one millimetre, the type of heating used does not have a significant impact on the level of molecular mobility and reactivity, which is mainly dependent on the sample temperature. In effect, the configurational temperatures will only be marginally higher than the real measurable temperature. Previous studies were mostly fundamental in nature and did not establish a connection between microwaves and mobile phone heating effects. These findings imply that for heating with microwave or cell phone radiation operating in the gigahertz frequency range, no other effect than a temperature increase should be expected. Since the results are based on averaged temperatures, future work will be required to quantify local overheating, which can, for example, occur in biological tissue subjected to a microwave field, and better assess the risks linked to using both microwaves and mobile phones.

Reference 1. Khalife A, Pathak U, and Richert R (2011). Heating liquid dielectrics by time dependent fields. European Physical Journal B (EPJ B). 83, 429 – 435, DOI 10.1140/epjb/e2011-20599-5

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