May 11, 2007

2007 Week 19: Related Articles


Knots, Origami, & Water
"Knot" To Be Undone, Researchers Discover Unusual Protein Structure
Researchers funded by the National Institute of General Medical Sciences have determined the structure of a protein with a surprising feature in it: a knot. This is the first time a knot has been found in a protein from the most ancient type of single-celled organism, an archaebacterium, and one of only a few times a knot has been seen in any protein structure.
"It's a surprising and different structure," said NIGMS' John Norvell, Ph.D., director of the Protein Structure Initiative. Protein folding theory previously held that forming a knot was beyond the ability of a protein. Joachimiak suggests that the newly discovered knot may stabilize the amino acid subunits of the protein.

MIT Finds Most Complex Protein Knot Ever Seen
Knots are rare in proteins - less than 1 percent of all proteins have any knots, and most are fairly simple. The researchers analyzed 32,853 proteins, using a computational technique never before applied to proteins at this scale.
Of those that had knots, all were enzymes. Most had a simple three-crossing, or trefoil knot, a few had four crossings, and the most complicated, a five-crossing knot, was initially found in only one protein - ubiquitin hydrolase.
The complicated knot found in ubiquitin hydrolase may prevent it from getting sucked into the proteasome as it works, Mirny said. The researchers hypothesize that proteins with complex knots can't be pulled into the proteasome as easily, and the knots may make it harder for the protein to unfold, which is necessary for degradation.
The same knot is found in ubiquitin hydrolase in humans and in yeast, supporting the theory that there is a connection between the knot and the protein's function. This also seems to suggest that the knot has been "highly preserved throughout evolution," Virnau said.

Since their initial screening, the researchers have discovered five-crossing knots in two other proteins - a brain protein whose overexpression and mutations are linked with cancer and Parkinson's disease, and a protein involved in the HIV replication cycle. They have also found examples of proteins that are closely related and structurally similar except for the presence or absence of a knot.

Origami Helps Scientists Solve Problems
"Origami helps in the study of mathematics and science in many ways," says Martin Kruskal, a mathematician at Rutgers University, "Using origami anyone can become a scientific experimenter with no fuss." Kruskal found that origami is simpler to develop than most scientific theories and a lot easier to apply.

'DNA Origami': Caltech Scientist Creates New Method For Folding Strands Of Dna To Make Microscopic Structures
In a new development in nanotechnology, a researcher at the California Institute of Technology has devised a way of weaving DNA strands into any desired two-dimensional shape or figure, which he calls "DNA origami."
"The construction of custom DNA origami is so simple that the method should make it much easier for scientists from diverse fields to create and study the complex nanostructures they might want," Rothemund explains.
Although Rothemund has hitherto worked on two-dimensional shapes and structures, he says that 3-D assemblies should be no problem. In fact, researchers at other institutions are already using his method to attempt the building of 3-D cages. One biomedical application that Rothemund says could come of this particular effort is the construction of cages that would sequester enzymes until they were ready for use in turning other proteins on or off.

Unexpected Similarities Between Raindrops And Proteins
Raindrops and proteins seem to have a lot in common. This has been shown in a new study by scientists at UmeƄ University in Sweden. The principle behind the formation of raindrops is very similar to how proteins fold. This knowledge is vital to our understanding of neurodegenerative diseases like ALS.

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