Tuesday, December 13, 2011

Making liquid crystals stand tall

Now, researchers led by Takuzo Aida from the University of Tokyo, Hideo Takezoe from the Tokyo Institute of Technology and Masaki Takata from the RIKEN SPring-8 Center in Harima have discovered that aromatic amides with branched, paraffin-like can act as molecular ‘handles’ for electric field alignment1. Furthermore, they succeeded in growing discotic films hundreds of times thicker than before, putting devices that incorporate this technology one step closer to production.

Aida and colleagues were investigating discotic liquid crystals consisting of molecules called corannulene derivatives when they made their finding. Corannulene has a core of five fused hydrocarbon rings surrounded by ten aromatic amides, giving it a bowl-like shape. Despite this compound’s large size, the researchers found that electric fields could uniformly align the columns with hexagonal geometries over a range of temperatures (Fig. 1).

The researchers first postulated that the inner dipole of the curved corannulene core accounted for the field-induced orientations. But when they synthesized a similar discotic liquid crystal containing a flat, non-polar triphenylene core, they observed the same striking field alignment—key evidence that the amide side chains acted as responsive handles that interact with the applied electric field and guide the discotic molecules into place.

Armed with this knowledge, the researchers synthesized several discotic columnar liquid crystals with slightly tweaked handles to optimize this behavior. Nearly all of these entities showed columnar alignment that persisted even after extinguishing the electric field. The team could also break apart the columns and restore the molecules’ random orientations using a simple heating procedure.

Because the column heights depended on applied field strength, the researchers produced millimeter-thick films in any desired orientation by sandwiching their compounds between two large-area electrodes. “Unless conducting discotic columns can be aligned to macroscopic length scales, they will remain impractical,” says Aida. “Therefore, our achievement is quite important for organic electronic device applications.”

More information: Miyajima, D., et al. Electric-field-responsive handle for large-area orientation of discotic liquid-crystalline molecules in millimeter-thick films. Angewandte Chemie International Edition 50, 7865–7869 (2011).

Provided by RIKEN (news : web)

Enzymatic synthesis of pyrrolysine, the mysterious 22nd amino acid

 With few exceptions, all known proteins are using only twenty amino acids. 25 years ago scientists discovered a 21st amino acid, selenocysteine and ten years ago a 22nd, the pyrrolysine. However, how the cell produces the unusual building block remained a mystery. Now researchers at the Technische Universitaet Muenchen have elucidated the structure of an important enzyme in the production of pyrrolysine.

The scientific journal Angewandte Chemie reports on their results in its "Early View" online section.

Proteins are key players in many vital processes in living organisms.. They transport substances, catalyze chemical reactions, pump ions or recognize signaling molecules. The complexity and variety of proteins is tremendous, in the human body alone there are more than 100,000 different proteins at work. But almost all of them are made up of just twenty different amino acids. Only a few highly specialized proteins additionally contain selenocysteine, the very rare 21st amino acid discovered in 1986.

A big surprise was the discovery of a 22nd amino acid in methane-producing archaea of the family Methanosarcinaceae in 2002: pyrrolysine. It is genetically encoded in a similar manner as that of selenocysteine and the other twenty amino acids. The archaea use the unusual amino acid in proteins that they need for energy conversion. Pyrrolysine is located in the catalytic center of the proteins and is essential for their function. The energy generation process of the archaebacteria would not work without pyrrolysine.

In March 2011, scientists at Ohio State University succeeded in deciphering parts of the manufacturing process of pyrrolysine. They proposed a reaction mechanism suggesting that the enzyme PylB catalyzes the first step of pyrrolysine biosynthesis by converting the amino acid lysine to the intermediate product metyhlornithine. Scientists headed by Michael Groll, Professor of Biochemistry at the TUM-Department of Chemistry, could now determine the crystalline structure of PylB by X-ray using structure analysis.

To their great surprise, they caught the enzyme literally "in the act": at the time of crystallization the reaction product, methylornithine, had not left the enzyme. It adhered to a confined space, a kind of "reaction vessel," still in connection with the centers of the enzyme responsible for its creation. "That the product was still present in the enzyme, was something special and a great stroke of luck," says Felix Quitterer, a member of the scientific staff at the Department of Biochemistry and lead author of the publication. "We were not only able to directly detect the methylornithine, but also retroactively reconstruct how it is created from the source amino acid lysine."

This reaction was not only unknown until now, it is also very difficult to catalyze. It is a cluster of four iron and four sulfur atoms in the active site that is the key to the conversion. "This is a really unusual enzymatic reaction. Up to now no chemist in the laboratory is able to synthesize methylornithine in a one-step reaction starting from lysine," says Michael Groll.

The conversion of lysine to methylornithine is helping scientists to understand how archaebacteria can modify an existing system to enable the formation of a tailored amino acid that, when installed in the appropriate protein, catalyzes a very specific reaction. Researchers can use this knowledge to create artificial amino acids for "custom tailored" enzymes with special properties, that could, for example, find applications in industrial biotechnology and medicine.

A more fundamental reason for the high interest in the synthesis of the 22nd amino acid is that scientists are hoping to find new clues to the evolutionary development of the amino acid-canon. Why does the vast complexity of proteins in living organisms descend from only a few natural amino acids, even though the genetic code would be able to encode many more? An answer on this fundamental question has thus far eluded scientists. Selenocysteine and pyrrolysine are exotic exceptions, but knowledge about their development from the standard amino acids helps to come a little closer to the answer.

This research was funded by the Hans-Fischer-Gesellschaft and the King Abdullah University of Science and Technology as well as the Cluster of Excellence Center for Integrated Protein Science Munich. The measurements were performed at the PXI beamline at the Paul Scherrer Institute (Villigen, Switzerland).

Story Source:

The above story is reprinted from materials provided by Technische Universitaet Muenchen.

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

Journal Reference:

Felix Quitterer, Anja List, Wolfgang Eisenreich, Adelbert Bacher, Michael Groll. Kristallstruktur der Methylornithin-Synthase (PylB): Einblicke in die Biosynthese von Pyrrolysin. Angewandte Chemie, 2011; DOI: 10.1002/ange.201106765

New compound defeats drug-resistant bacteria

A particularly ingenious weapon in the bacterial arsenal is the drug efflux pump. These pumps are proteins located in the membranes of bacteria that can recognize and expel drugs that have breached the membranes. In some cases, the bacterial pumps have become so advanced they can recognize and expel drugs with completely different structures and mechanisms.

"This turns out to be a real problem in , especially when a acquires a gene encoding an efflux pump that acts on multiple ," said Jason Sello, assistant professor of chemistry at Brown University. "In the , a bacterium can go from being drug-susceptible to resistant to five or six different drugs by acquiring a single gene."

"That leaves : Make more new and costly antibiotics or find a way around the pump. Sello and his group chose the latter. In a paper published in the journal Bioorganic and Medicinal Chemistry, the team reports it has discovered a new compound of C-capped dipeptides, called BU-005, to circumvent a family of drug-efflux pumps associated with Gram-positive bacteria, which include the dangerous and tuberculosis . Until that discovery, C-capped dipeptides were known to work only against an efflux pump family associated with Gram-negative bacteria.

"If drug efflux pumps are inhibited, then bacteria will be susceptible to drugs again," Sello said. "This approach is of interest because one would have to discover efflux pump inhibitors rather than entirely new kinds of ."

Recently, a company called MPEX Pharmaceuticals discovered that specific C-capped dipeptides could block the efflux pumps of the RND family, which are responsible for much of the in Gram-negative bacteria. One of these compounds developed at MPEX advanced to phase I of an FDA clinical trial. Sello and his co-authors investigated whether C-capped dipeptides could block the pumps of another drug efflux family, called the major facilitator superfamily (MFS), which is associated mostly with Gram-positive bacteria.

The Brown team thought that new and perhaps more potent C-capped dipeptide efflux pump blockers could be discovered. Since it is not possible to predict which C-capped dipeptides would be efflux pump blockers, they synthesized a collection of structurally diverse C-capped dipeptides and screened it for compounds with new or enhanced activities.

Normally, this is a four- to five-step process. Sello's group reduced that to two steps, taking advantage of a technique used in other chemistry practices, known as the Ugi reaction. Using this approach, the team was able to prepare dozens of different C-capped dipeptides. They assessed each compound's ability to block two efflux pumps in the Streptomyces coelicolor, a relative of the human pathogen Mycobacterium tuberculosis and which resists chloramphenicol, one of the oldest antibacterial drugs.

From a collection of nearly 100 C-capped dipeptides that they prepared and tested, the group discovered BU-005. The new compound excited the researchers because it prevented the MFS efflux pump family from expelling chloramphenicol. Until now, structurally related C-capped dipeptides had only been reported to prevent chloramphenicol expulsion by other drug efflux pump families.

"Our findings that C-capped dipeptides inhibit efflux pumps in both Gram-positive and Gram-negative bacteria should reinvigorate interest in these compounds," Sello said. "Moreover, our simplified synthetic route should make the medicinal chemistry on this class of compounds much simpler."

Two Brown undergraduate students, Daniel Greenwald '12, and Jessica Wroten '11, helped perform the research and are contributing authors on the paper.

Greenwald joined the team in his freshman year, after reaching out to Sello. "This project was the first real immersion I had into chemistry research at an advanced level," said Greenwald, of Madison, Wisc. "It was an amazing opportunity to be able to use the tools of synthetic chemistry to address problems from molecular biology. It was definitely one of the most engaging aspects of my experience at Brown."

Provided by Brown University (news : web)

Making a light-harvesting antenna from scratch

The invention of the solar cell, in 1941, was inspired by a newfound understanding of semiconductors, materials that can use light energy to create -- and ultimately an electrical current.

have almost nothing to do with the biological photosystems in and that use light energy to push electrons across a membrane -- and ultimately create sugars and other .

At the time, nobody understood these complex assemblages of proteins and pigments well enough to exploit their secrets for the design of .

But things have changed.

At Washington University in St. Louis's Photosynthetic Antenna Research Center (PARC) scientists are exploring native biological photosystems, building hybrids that combine natural and synthetic parts, and building fully synthetic analogs of natural systems.

One team has just succeeded in making a crucial photosystem component -- a light-harvesting antenna -- from scratch. The new antenna is modeled on the chlorosome found in green bacteria.

Chlorosomes are giant assemblies of pigment molecules. Perhaps Nature's most spectacular light-harvesting antennae, they allow green bacteria to photosynthesize even in the in ocean deeps.

Dewey Holten, PhD, professor of chemistry in Arts & Sciences, ard collaborator Christine Kirmaier, PhD, research professor of chemistry are part of a team that is trying to make synthetic chlorosomes. Holten and Kirmaier use ultra-fast laser spectroscopy and other analytic techniques to follow the rapid-fire energy transfers in photosynthesis.

His team's latest results, described in a recent issue of New Journal of Chemistry, were highlighted in the editor's blog.


Biological systems that capture the energy in sunlight and convert it to the energy of chemical bonds come in many varieties, but they all have two basic parts: the light harvesting complexes, or antennae, and the reaction center complexes. The antennae consist of many pigment molecules that absorb photons and pass the excitation energy to the reaction centers.

In the reaction centers, the excitation energy sets off a chain of reactions that create ATP, a molecule often called the energy currency of the cell because the energy stored ATP powers most cellular work. Cellular organelles selectively break those bonds in ATP molecules when they need an energy hit for cellular work.

Green bacteria, which live in the lower layers of ponds, lakes and marine environments, and in the surface layers of sediments, have evolved large and efficient light-harvesting antennae very different from those found in plants bathing in sunlight on Earth's surface.

Making a light-harvesting antenna from scratch

Nature provides three starting points for the design of synthetic pigments: porphyrin, chlorin, and bacteriochlorin. Each of these macrocyles has an alternating double-bond pathway (in blue) that gives the molecule its basic electronic properties, including the ability to absorb visible or near infrared light. Hemoglobin is a porphyrin that lends blood its red color; chlorophyll, the pigment in green plants, is a chlorin; and the pigments in purple photosynthetic bacteria are bacteriochlorins. As the color-coded absorption spectra show, the three types of pigments absorb different colors of sunlight (brown). Credit: Holten/WUSTL

The consist of highly organized three-dimensional systems of as many as 250,000 pigment molecules that absorb light and funnel the through a pigment/protein complex called a baseplate to a reaction center, where it triggers chemical reactions that ultimately produce ATP.

In plants and algae (and in the baseplate in the green bacteria) photo pigments are bound to protein scaffolds, which space and orient the pigment molecules in such a way that energy is efficiently transferred between them.

But chlorosomes don't have a protein scaffold. Instead the pigment molecules self -assemble into a structure that supports the rapid migration of excitation energy.

This is intriguing because it suggests chlorosome mimics might be easier to incorporate in the design of solar devices than biomimetics that are made of proteins as well as pigments.

Synthetic pigments

The goal of the work described in the latest journal article was to see whether synthesized pigment molecules could be induced to self-assemble. The process by which the pigments align and bond is not well understood.

"The structure of the pigment assemblies in chlorosomes is the subject of intense debate," Holten says, "and there are several competing models for it."

Given this uncertainty, the scientists wanted to study many variations of a pigment molecule to see what favored and what blocked assembly.

A chemist wishing to design pigments that mimic those found in photosynthetic organisms first builds one of three molecular frameworks. All three are macrocycles, or giant rings: porphyrin, chlorin and bacteriochlorin.

"One of the members of our team, Jon Lindsey can synthesize analogs of all three pigment types from scratch," says Holten. (Lindsey, PhD, is Glaxo Professor of Chemistry at North Carolina State University.)

Making a light-harvesting antenna from scratch

The absorption spectrum of a synthetic pigment in a polar solvent (magenta) that prevents the pigment molecules from forming assemblies differs substantially from the absorption spectrum of the pigment in a nonpolar solvent (blue). The difference shows that the pigments have the ?hooks? they need to link up properly in solution. Credit: Holten/WUSTL

In the past, chemists making photo pigments have usually started with porphyrins, which are the easiest of the three types of macrocycles to synthesize. But Lindsey also has developed the means to synthesize chlorins, the basis for the pigments found in the chlorosomes of green bacteria. The chlorins push the absorption to the red end of the visible spectrum, an area of the spectrum scientists would like to be able to harvest for energy.

Key to pigment self-assembly are the metal atoms and hydroxyl (OH) and carbonyl (C=O) groups in the pigment molecules.

Doctoral student Olga Mass and coworkers in Lindsey's lab synthesized 30 different chlorins, systematically adding or removing chemical groups thought to be important for self-assembly but also attaching peripheral chemical groups that take up space and might make it harder for the molecules to stack or that shift around the distributions of electrons so that the molecules might stack more easily.

Testing for aggregation

The powdered pigments were carefully packaged and shipped by Fed Ex (because the Post Office won't ship chemicals) to Holten's lab at WUSTL and to David Bocian's lab at the University of California at Riverside.

Scientists in both labs made up green-tinctured solutions of each of the 30 molecules in small test tubes and then poked and prodded the solutions by means of analytical techniques to see whether the pigment had aggregated and, if so, how much had formed the assemblies.

Holten's lab studied their absorption of light and their fluorescence (which indicated the presence of monomers, since assemblies don't normally fluoresce) and Bocian's lab studied their vibrational properties, which are determined by the network of bonds in the molecule or pigment aggregate as a whole.

In one crucial test Joseph Springer, a PhD student in Holten's lab, compared the absorption spectrum of a pigment in a polar solvent that would prevent it from self-assembling to the spectrum of the pigment in a nonpolar solvent that would allow the molecules to interact with one another and form assemblies.

"You can see them aggregate," Springer says. "A pigment that is totally in solution is clear, but colored a brilliant green. When it aggregates, the solution becomes a duller green and you can see tiny flecks in the liquid."

The absorption spectra indicated that some pigments formed extensive assemblies and that the steric and electronic properties of the molecules predicted the degree to which they would assemble.

Up next

Although this project focused on self-assembly, the PARC scientists already have taken the next step toward a practical solar device.

"With Pratim Biswas, PhD, the Lucy and Stanley Lopata Professor and chair of the Department of Energy, Environmental & Chemical Engineering, we've since demonstrated that we can get the pigments to self-assemble on surfaces, which is the next step in using them to design solar devices," says Holten.

"We're not trying to make a more efficient solar cell in the next six months," Holten cautions. "Our goal instead is to develop fundamental understanding so that we can enable the next generation of more efficient solar powered devices."

Biomimicry hasn't always worked. Engineers often point out early flying machines that attempted to mimic birds didn't work and that flying machines stayed aloft only when nventors abandoned biological models and came up with their own designs.

But there is nothing predestined or inevitable about this. As biological knowledge has exploded in the past 50 years, mimicking nature has become a smarter strategy. Biomimetic or biohybrid designs already have solved significant engineering problems in other areas and promise to greatly improve the design of solar powered devices as well.

After all, Nature has had billions of years to experiment with ways to harness the energy in sunlight for useful work.

Provided by Washington University in St. Louis (news : web)