Supercomputer reveals new details behind drug-processing protein model

Jerome Baudry and Yinglong Miao, who are jointly affiliated with ORNL and the University of Tennessee, have performed simulations to observe the motions of water molecules in a class of enzymes called P450s. Certain types of P450 are responsible for processing a large fraction of drugs taken by humans.

The supercomputer simulations were designed to help interpret ongoing neutron experiments.

"We simulated what happens in this enzyme over a time scale of 0.3 microseconds, which sounds very fast, but from a scientific point of view, it's a relatively long time," Baudry said. "A lot of things happen at this scale that had never been seen before. It's a computational tour de force to be able to follow that many water molecules for that long."

The team's study of the water molecules' movements contributes to a broader understanding of drug processing by P450 enzymes. Because some populations have a slightly different version of the enzymes, scientists hypothesize that mutations could partially explain why people respond differently to the same drug. One possibility is that the mutations might shut down the channels that bring water molecules in and out of the enzyme's active site, where the chemical modification of drugs takes place. This could be investigated by using the computational tools developed for this research.

By simulating how water molecules move in and out of the protein's centrally located active site, the team clarified an apparent contradiction between experimental evidence and theory that had previously puzzled researchers. X-ray crystallography, which provides a static snapshot of the protein, had shown only six water molecules present in the active site, whereas experimental observations indicated a higher number of water molecules would be present in the enzyme.

"We found that even though there can be many water molecules -- up to 12 at a given time that get in and out very quickly -- if you look at the average, those water molecules prefer to be at a certain location that corresponds to what you see in the crystal structure," Miao said. "It's a very dynamic hydration process that we are exploring with a combination of neutron scattering experiments and simulation."

The simulation research is published in Biophysical Journal as "Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process."

Provided by Oak Ridge National Laboratory (news : web)

Details of new type of electric car battery released

After being spun off from parent company A123 Systems last year; the new offspring, 24M has published a paper in Advanced Energy Materials, ending months of speculation about what it has been working on. It was no secret that the new project was to advance work on a new type of battery that A123 had been working on for a couple of years; namely a battery that could be used to replace the lithium-ion batteries currently used in electric cars. Now, with the paper’s release it's clear that the new battery, similar to a flow battery, uses a liquid material to hold the charge, rather than conventional dry fuel cells, and if successful could do away with a lot of the non-charge holding stuff that makes up nearly three quarters of the bulk of current electric car batteries.

Assisted by a grant from the U.S. Advanced Research Projects Agency-Energy (ARPA-E), to help fund research between the new start-up, MIT and Rutgers University, the new battery, based on research done by Yet-Ming Chiang who is both a professor at MIT and founder of A123 Systems and 24M, if successful, would allow for upsizing of car batteries without adding any non-chargeable material, greatly increasing its density, which would in turn, theoretically greatly reduce the cost of the battery pack in an electric vehicle. Current battery packs now constitute up to a third of the total vehicle price.

The new battery, as described in the paper, uses a sludge-like material contained in storage tanks, rather than dry cells; one positively charged, the other negative. To get the charge from the battery, the materials are pumped through channels allowing ions to move freely between the two and eventually to an external circuit. To facilitate the transfer of electrons from the sludge, nanoscale particles that help to form networks that give the electrons a path to follow were developed and added to the sludge mix. In this type of battery, the amount of storage capacity goes up as the tank size is increased, with no additional materials needed, in sharp contrast to lithium batteries.

The battery is not yet ready for prime time though, as a current model of the battery would be bulky and the electrical conductivity, according to Change, is still far below what would be needed in a real world battery in an actual electrical vehicle; research is still ongoing, as he and his team try to figure out how to increase the concentration of the active materials in the sludge.

More information: Semi-Solid Lithium Rechargeable Flow Battery, Advanced Energy Materials, Article first published online: 20 MAY 2011 DOI: 10.1002/aenm.201100152

Abstract
A new kind of flow battery is fueled by semi-solid suspensions of high-energy-density lithium storage compounds that are electrically ‘wired’ by dilute percolating networks of nanoscale conductor particles. Energy densities are an order of magnitude greater than previous flow batteries; new applications in transportation and grid-scale storage may result.

? 2010 PhysOrg.com

Polarized microscopy technique shows new details of how proteins are arranged

Whether you're talking about genes, or neurons, or the workings of a virus, at the most fundamental level, biology is a matter of proteins. So understanding what protein complexes look like and how they operate is the key to figuring out what makes cells tick. By harnessing the unique properties of polarized light, Rockefeller scientists have now developed a new technique that can help deduce the orientation of specific proteins within the cell. By turning their instruments toward the nuclear pore complex, a huge cluster of proteins that serves as a gateway to a cell's nucleus, the scientists say they have filled in the gaps left by other techniques and made important new discoveries about how the complex works.

"Our new technique allows us to measure how components of large protein complexes are arranged in relation to one another," says Sandy Simon, head of the Laboratory of Cellular Biophysics. "This has the potential to give us important new information about how the nuclear pore complex functions, but we believe it can also be applied to other multi-protein complexes such as those involved in DNA transcription, protein synthesis or viral replication."

Although researchers have spent years studying the workings of the nuclear pore complex, there is still much that has remained mysterious. One problem is that there is a "resolution gap" between the two techniques primarily used to visualize protein complexes. Electron microscopy can reveal the broad outlines of a large protein complex, but it can't show details. X-ray crystallography, meanwhile, can show minute detail but only of a small piece of the complex; it can't say how the individual pieces fit together. To further complicate matters, both techniques require fixed samples – while they can give you an idea of what something looks like at a moment in time, they can't tell you how its pieces might move.

The new technique was developed by Simon along with postdoc Alexa Mattheyses, graduate student Claire Atkinson and Martin Kampmann, a former a member of Günter Blobel's Laboratory of Cell Biology who is currently at the University of California, San Francisco. It takes advantage of the properties of polarized light to show how specific proteins are aligned in relation to one another. After genetically attaching fluorescent markers to individual components of the nuclear pore complex, the scientists replaced the cell's own copy of the gene that encodes the protein with the new form that has the fluorescent tag. Then, they used customized microscopes to measure the orientation of the waves of light the fluorescently tagged proteins emitted. By combining these measurements with known data about the structure of the complex, the scientists can confirm or deny the accuracy of previously suggested models.

"Our experimental approach to the structure is synergistic with other studies being conducted at Rockefeller, including analysis with X-ray crystallography in Günter's lab and electron microscopy and computer analysis in Mike Rout's lab," says Simon. "By utilizing multiple techniques, we are able to get a more precise picture of these complexes than has ever been possible before."

The scientists used the technique to study nuclear pore complexes in both budding yeast and human cells. In the case of the human cells, their new data shows that multiple copies of a key building block of the nuclear pore complex, the Y-shaped subcomplex, are arranged head-to-tail, rather than like fence posts, confirming a model proposed by Blobel in 2007.

"As a graduate student with Günter Blobel, I determined the three-dimensional structure of the Y-shaped subcomplex using electron microscopy," says Kampmann. "However, it was still a mystery how these 'Y's are arranged. The new technique we have developed reveals the orientation of building blocks in the cell, and we hope that it will eventually enable us to assemble individual crystal structures into a high-resolution map of the entire nuclear pore complex."

Eventually, the scientists say their technique could go even further. Because the proteins' fluorescence can be measured while the cells are still alive, it could give scientists new insights into how protein complexes react to varying environmental conditions, and how their configurations change over time.

"What happens when other proteins pass through the nuclear pore? Does the orientation of the nucleoporins change? With this technique, can find out not only what the pore looks like when it's sitting still, but what happens to it when it's active," Simon says. Their first characterization of the dynamics of the nuclear pore proteins was published recently in The Biophysical Journal.

Provided by Rockefeller University (news : web)

Research into chromosome replication reveals details of heredity dynamics

A novel study from Karolinska Institutet has deepened the understanding of how chromosome replication, one of life's most fundamental processes, works. In a long term perspective these results could eventually lead to novel cancer therapies. The study is presented in the prestigious scientific journal Nature.

By studying DNA replication in yeast cells, researchers at Karolinska Institutet have discovered that a protein complex (Smc5/6) helps to release torsional stress created in the DNA molecule when chromosomes are replicated in preparation for a coming cell division.

"Our study also indicates that the stress can propagate more freely along the DNA in a chromosome than was previously thought," says KI professor Camilla Sjögren, head of the team that conducted the study.

The study therefore sheds more light on the mechanisms behind one of life's most fundamental processes. Since topoisomerases, enzymes known to remove replication-related stress in the DNA are common targets for cancer treatments, the finding might eventually lead to new therapies.

When a fertilised egg develops into a complete organism, or when old cells are replaced by new ones, it is done through cell division. If human daughter cells are to survive and develop normally, they must each obtain a full set of 46 chromosomes, which are made of double-stranded DNA helices. Since the original mother cell started as a cell with 46 chromosomes, these must be duplicated before division take place.

During this process, the DNA double helix is separated so that the replication machinery can reach the individual DNA strands. This prising apart of the strands creates stress in the form of over-twisted DNA in the vicinity of the replication zone. If this stress is not removed, replication can be slowed down or even stopped, and this, in turn, can lead to mutagenesis and/or cell death.

"Several modern cancer treatments attack topoisomerases, but there's a problem in that some cancers become resistant to such therapies," says Professor Sjögren. "Now that we've discovered that also the Smc5/6 complex releases the stress which form during the replication process, our results might trigger the development of drugs that target Smc5/6. This could create another tool for inhibiting tumour growth."

More information: Andreas Kegel, Hanna Betts-Lindroos, Takaharu Kanno, Kristian Jeppsson, Lena Ström, Yuki Katou, Takehiko Itoh, Katsuhiko Shirahige & Camilla Sjögren, Chromosome length influences replication-induced topological stress, Nature, AOP 2 March 2011, DOI: 10.1038/nature09791