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Protein gets in on DNA's origami act
Engineered bacteria make self-assembling tetrahedra.
Practitioners of DNA origami have spent the better part of the past decade folding the molecule into minuscule smiley faces, boxes, letters of the alphabet and dozens of other intricate shapes.
Proteins, on the other hand, have been rather late in joining the origami party — even though nature is adept at moulding them into a dazzling array of functional shapes, including molecular-recognition systems and catalysts.
Now Roman Jerala, a biochemist at the National Institute of Chemistry in Ljubljana, Slovenia, is making up for lost time. He and his colleagues have designed and built a protein that folds itself into a tetrahedron — a pyramid with a triangular base — and he says that the strategy could be used to make a wide range of other shapes. Whereas examples of DNA origami often look pretty, few of these creations have any practical use. Proteins, on the other hand, are much better suited to performing useful tasks, such as delivering drugs, according to Jerala.
Doing the twist
Proteins are long chains of amino acids folded into complicated shapes, and the precise sequence of these building blocks determines the overall structure of the folded molecule. One common structural element in proteins is the coiled coil, in which two or more helices of amino acids twist around each other like the strands of a rope. The helices stick together with the help of a mutual attraction between water-repelling (hydrophobic) amino acids, which run up the inside of the coiled coil.
Jerala reasoned that six coiled coils could be used as the edges of a tetrahedron. So his team worked out the amino-acid sequences of 12 different protein helices that each had unique patterns of hydrophobic regions along their length. This fingerprint ensured that each helix could pair with only one of the others in the set.
Then the researchers joined the 12 helices into a chain, using flexible linkers of four amino acids to act like a hinge between each helix. Genetically modified Escherichia coli bacteria were drafted in to synthesize the protein, which — once purified — folded into tetrahedra measuring just 5 nanometres along each edge (see image above). “It’s a new protein fold that doesn’t exist in nature,” says Jerala. The work is published today in Nature Chemical Biology1.
"This type of assembly has been achieved before using DNA, but it has always been assumed that it would be much harder to do this with proteins because there is no straightforward code that relates sequence to structure, as there is with DNA,” says Dek Woolfson, a biochemist at the University of Bristol, UK.
Woolfson and his colleagues have recently joined coiled coils coming from distinct protein chains to build protein ‘cages’2, but he says that stringing all the components of the coiled coils into a single protein chain, as Jerala has done, is an exciting step because it offers a way to design and produce completely new protein shapes using reprogrammed bacteria.
Jerala says that attaching antibodies to the four vertices of his protein tetrahedron could enable it to target particular cells. Any drugs loaded inside could be released by breaking the tetrahedron apart — by means of a competing protein, a change in pH or a pulse of light hitting a photosensitive linker, he suggests.
Creating such a working system will take many years. For now, Jerala’s team is trying to double the size of the coiled coils in the tetrahedron, and thinking about making other shapes, such as prisms and bipyramids.
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[Time 5]
Article 4
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China earthquake points to future risk sites
But researchers at odds over effects of Ya'an tremor on nearby seismic faults.
The deadly tremor that shook the city of Ya'an in southwestern China last weekend may hint at where future quakes will strike in the region, researchers say. But they disagree on which seismic fault is likely to rupture next.
At 8:02 a.m. local time on 20 April, an earthquake recorded as magnitude 6.6 by the US Geological Survey struck Ya’an in Sichuan province. According to the latest official figures, the death toll has reached 193, with 12,211 people injured and 25 missing
The Ya’an quake was caused by the failure of the southern segment of the Longmenshan fault. In May 2008, a rupture at the northern end of the same fault caused the devastating magnitude-7.9 Wenchuan earthquake that killed around 80,000 people.
The latest quake “is not surprising”, says Liu Qiyuan, a geophysicist at the China Earthquake Administration’s Institute of Geology in Beijing. In the aftermath of the Wenchuan quake, several research groups, including Liu’s, calculated the stress changes in adjacent faults and found that the biggest stress increase was in the southern Longmenshan fault.
“As the stress has been released by the Ya’an quake, the fault is now safe,” says Liu. He predicts that the Xianshuihe and Anninghe faults — which intersect with the southern end of the Longmenshan fault from the west and east, respectively — now pose the greatest seismic hazards.
Both of those faults are very active and have produced several large earthquakes over the past 200 years. Moreover, the Wenchuan quake and the magnitude-6.9 Yushu quake in 2010have added considerable stress in faults, says Liu. With a network of about 300 broadband seismometers in the region, “we are monitoring the crust movement very closely,” he says.
Stresses and strains
However, Mian Liu, a geophysicist at the University of Missouri in Columbia, does not agree. “The kind of stress increase caused by an adjacent fault failure is typically less than a few per cent of the stress that is required to produce a large earthquake,” he says. “It’s not a reliable indicator for seismic hazards.”
By contrast, he adds, analyses of a fault’s seismic moment — a measure of strain energy in the crust that could be used to produce earthquakes — are more useful. “It’s like checking the bank balance by calculating the incomes and the spendings,” Mian Liu says.
The ‘incomes’ depend on how fast the fault moves, which indicates how quickly the strain energy builds up over time. The ‘spendings’ are based on the history of previous ruptures. Such accounting led Mian Liu and his colleagues to predict in 2010 that the southern segment of the Longmenshan fault could rupture and produce quakes of magnitude 7.7 in the next 50 years1. In the event, it took only 3 years. “It seems that nature is in a hurry,” he says.
“This doesn’t mean that the Longmenshan fault is now safe,” says Mian Liu. Based on seismic measurements, he notes that last week's quake in Ya'an didn’t rupture the entire southern segment, but instead released only one-third of its accumulated energy. “The 60-kilometre intact stretch between the Ya’an and Wenchuan quakes is likely to rupture in the next few decades,” he says. “It’s still able to cause earthquakes of magnitude 6 to 7.”
By comparison, Mian Liu thinks that the Xianshuihe and Anninghe faults are less risky because, although the crust movement has generated a lot of strain energy, they have ‘spent’ a lot in the past, he says.
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Part II: Obstacle
Article 5
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World's Longest-Running Plant Monitoring Program Now Digitized
Researchers at the University of Arizona's Tumamoc Hill have digitized 106 years of growth data on individual plants, making the information available for study by people all over the world. Knowing how plants respond to changing conditions over many decades provides new insights into how ecosystems behave.
The permanent research plots on Tumamoc Hill represent the world's longest-running study that monitors individual plants, said co-author Larry Venable, director of research at Tumamoc Hill. Some of the plots date from 1906 -- and the birth, growth and death of the individual plants on those plots have been periodically recorded ever since.
The century-long searchable archive is unique and invaluable, said Venable, a UA professor of ecology and evolutionary biology who has been studying plants on Tumamoc since 1982. "You can see the ebb and flow of climate, and you can see the ebb and flow of vegetation," he said. Lead author Susana Rodriguez-Buritica said, "Long-term data sets have a special place in ecology." The records have allowed scientists to estimate life spans for desert perennials, some of which are very long-lived, Venable said.
In addition, data from the plots on Tumamoc Hill reveal changes in the Sonoran Desert and have been important to key advances in the science of ecology. For example, the Tumamoc plant censuses helped overturn the long-standing idea that plant communities progress through a series of steps to a stable collection of species known as a climax community. "The desert wasn't progressing toward a climax community," he said. Instead of being in synch, each species and plot was changing to its own rhythm.
Rodriguez-Buritica, a postdoctoral research associate in the UA department of ecology and evolutionary biology, Venable and their co-authors Helen Raichle and Robert H. Webb of the U.S. Geological Survey and Raymond M. Turner, formerly of USGS, have published a description of their data in the Ecological Society of America's journal Ecology and archived the data set with the society athttp://www.esapubs.org/archive/ecol/E094/083/.
The title of their paper is, "One hundred and six years of population and community dynamics of Sonoran Desert Laboratory perennials." The National Science Foundation, the USGS and the U.S. National Park Service funded the archiving.
Landmark research on the physiology and ecology of desert plants has been conducted on Tumamoc Hill ever since the Carnegie Institution of Washington established the Desert Laboratory there in 1903 to study how plants cope with living in the desert.
The first permanent plots, generally 33 feet by 33 feet (10 meters by 10 meters), were established in 1906 by Volney Spalding; nine of his original plots remain to this day. Additional plots were established by Forrest Shreve in the 1910s and 1920s. Two more plots were added in 2010. Currently, there are 21 plots.
For every perennial plant within each plot, the ecologists recorded the species, the area the plant covered and its location. Even seedlings were identified and mapped. In addition to the written records, repeated photographs of the plots have been taken since 1906. Those photographs are in the Desert Laboratory Collection of Repeat Photography at the USGS in Tucson, Ariz.
Over the years, botanists and ecologists have helped census and re-census the plots. Co-author Turner took over the work when he came to the UA as a botany professor in 1957, continued while a botanist for USGS and continues to do in retirement. In 1993, co-author Webb took up the project and is keeping the censuses going.
Sorting through data recorded from 2012 back to 1906 was a huge challenge, said Rodriguez-Buritica. She had something to build on: Janice Bowers of USGS had begun to archive the records but retired before finishing. Initially, Rodriguez-Buritica and Venable thought a year would do it -- but the task ended up taking much longer. The records were in several places -- some at the library or in storage at Tumamoc and some in the UA library's Special Collections. One of the challenges Rodriguez-Buritica faced is that methods of collecting and recording information about plants have changed over time.
Spalding, who established the very first plots in 1906, worked long before the age of computers -- he recorded his observations in a small notebook. Ecologists continued to record their field observations in paper notebooks and created maps on graph paper well into the latter part of the 20th century.
All those paper records had to be digitized.
Only in the last 20 years have scientists been pinpointing plant locations and other observations directly onto a map within their computers by using GPS and GIS technology.
Upon reviewing and checking the data, Rodriguez-Buritica realized that she needed to standardize the information collected over a century so that other scientists could analyze it. Her expertise in applied statistics and spatial ecology was perfect for the job. She also computerized the series of maps created over time so new investigators could see all the plant location maps created since 1906. By putting all the information into a standardized digital format and making it easily accessible on the Web, Rodriguez-Buritica, Venable and their colleagues have ensured that other researchers can build on and expand this unique data set. Tumamoc Hill is one of the birthplaces of plant ecology, Venable said. "In the first half of the 20th century, all the great plant ecologists either worked here or came though here," he said. "Plant ecologists from the Desert Lab were key in founding the Ecological Society of America and its flagship journal, Ecology. It is satisfying to see the project come full circle and be permanently archived 100 years later by the journal that these researchers started."
The Desert Lab and Tumamoc Hill have been designated as a National Environmental Study Site, a National Historic Landmark, an Arizona State Scientific and Educational Natural Area and are on the National Register of Historic Places.
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