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Biological Chemistry

Science Concentrates

August 8, 2005 | A version of this story appeared in Volume 83, Issue 32

Makeup of a bacterial compartment

Credit: © 2005 SCIENCE

Structural details of a bacterial microcompartment called the carboxysome indicate a higher degree of subcellular organization in bacteria than people may think, says Todd O. Yeates of UCLA. Microcompartments are cellular inclusions made of proteins and are known to s equester metabolic processes within a defined space in many bacterial cells. Photosynthetic cyanobacteria, for example, carry out carbon-fixing reactions in carboxysomes. Yeates, with colleague Cheryl A. Kerfeld and others, has obtained crystal structures revealing that certain carboxysomes from cyanobacteria are solid protein shells punctured by tiny pores (Science 2005, 309, 936). The shells are structured and assembled much like viruses--through large numbers of small proteins assembled into crystalline-like layers. They arise from wedge-shaped protein building blocks that form hexamers, which in turn form sheets (shown). Bending sheets into closed shells likely requires pentamers, although "we don't have structures yet of pentagonal subunits," Yeates says. Each hexamer contains a highly charged and narrow pore, suggesting that the compartments control what goes in and out.

Progress in DNA sequencing

Quicker and cheaper methods of sequencing DNA have been revealed by two independent studies. Both the time and cost of DNA sequencing must be reduced for the sequencing of individual genomes for medical purposes to become feasible. Scientists at 454 Life Sciences, in Branford, Conn., say that their method for sequencing large genomes is 100 times faster than conventional ones (Nature, published online July 31, dx.doi.org/10.1038/nature03959). The firm's apparatus can decode a 25 million-base-pair bacterial genome in just four hours with 99% or better accuracy. Its method relies on an in vitro emulsion-based way to isolate and amplify genomic DNA fragments, which are then sequenced via a luminescent pyrosequencing protocol carried out in picoliter wells on a fiber-optic slide. Separately, George M. Church of Harvard Medical School and coworkers report a highly accurate DNA sequencing method that costs ninefold less per base than conventional sequencing (Science, published online Aug. 4, dx.doi.org/10.1126/ science.1117389). After emulsion-based amplification, DNA fragments are analyzed using a fluorescent ligation-based sequencing method and an inexpensive microscope.

New technique applies contacts to a single molecule

A novel method for forming electrical contacts with single organic molecules may potentially facilitate the development of molecular electronic devices, its developers say. Israel Bar-Joseph and coworkers at Weizmann Institute of Science, Rehovot, Israel, prepared a bridged dimer structure consisting of two gold nanoparticles connected by a single dithiolated organic molecule by mixing a solution of the dithiol with a gold colloid (Nature 2005, 436, 677). They isolated dimeric colloidal particles from this mixture by centrifugation. Electrostatic trapping of a dimer between two gold electrodes on a silicon substrate enabled the current-voltage characteristics of the single molecule to be measured. The group used the technique to investigate the electrical conduction through three molecules: 4,4´ -biphenyldithiol (BPD), a fully conjugated molecule, and bis-(4-mercaptophenyl)-ether (BPE) and 1,4-benzenedimethanethiol (BDMT), in which conjugation is broken by an oxygen atom and methylene groups, respectively. "We find that the oxygen in BPE and the methylene groups in BDMT both suppress the electrical conduction relative to that in BPD," the authors note.

Ecstasy affects Parkinson's

In a study to screen potential therapies for Parkinson's disease, researchers at Duke University Medical Center have produced the first strong evidence that amphetamine derivatives such as 3,4-methylenedioxymethamphetamine (MDMA, also known as the street drug Ecstasy, shown) play a direct role in signaling muscles to move (PloS Biol., published online Aug. 1, dx.doi.org/ 10.1371/journal.pbio.0030271). Parkinson's disease is marked by the progressive loss of dopamine neurons and corresponding deterioration of muscle control. The researchers, led by Tatyana D. Sotnikova, used dopamine-free mice, which exhibit severe muscle rigidity and other Parkinson's-like symptoms, to screen more than 70 compounds. They found that high concentrations of amphetamines, MDMA in particular, reversed some of the symptoms via an unknown mechanism that appears to be unrelated to dopamine, serotonin, or norepinephrine neurotransmission. They believe the motion-inducing effect may be mediated by receptors for endogenous amphetamine-like amines such as phenylethylamine.

Easy protein purification

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Large-scale protein purification usually requires a chromatographic separation, which can be expensive and time-consuming. Two independent groups now describe a fast, inexpensive way to purify recombinant proteins using tags called elastin-like polypeptides (ELPs), which are attached to the protein through a self-cleaving linker. When these ELP tags are heated above a transition temperature in the presence of salt, they precipitate, taking the fusion protein with them. Following the separation, the conditions are adjusted so that the linker cleaves itself, liberating the purified protein. The researchers led by Ashutosh Chilkoti of Duke University and Carlos D. M. Filipe of McMaster University, in Hamilton, Ontario, use microfiltration to separate the precipitated proteins from the rest of the mixture (J. Am. Chem. Soc. 2005, 127, 11228). David W. Wood and coworkers at Princeton University use centrifugation instead (Nat. Methods, published online Aug. 2, dx.doi.org/10. 1038/nmeth787).

 

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