I doubt many people think about protein folding when shopping for a new video game console, but if you're interested in protein folding and thinking about buying a PlayStation 3 next month, there's an article on CNN.com you should read. Apparently "Sony worked with Stanford University's Folding@home project to harness the PS3's technology to help study how proteins are formed in the human body and how they sometimes form incorrectly."

Folding@home is a distributed computing project, which means you can download a program onto your computer (in this case, your new PS3) that will enable you to donate 'down time' to analyze chunks of data. By dividing the "calculations into smaller packets ... [the computers can] do jobs that would strain the most powerful supercomputers." And since the PS3 has a pretty powerful graphics card, you can apparently "watch the protein as it folds."

Folding@home isn't the only distributed computing project out there: you've probably heard of SETI@home and there are a number of other projects, including Rosetta@home, the Drug Design and Optimization Lab, and fightAIDS@home.

I think this is a great idea: Sony hopes to sell 2 million PS3s in the United States and Japan in 2006 and 6 million worldwide by March, so using gaming consoles in @home projects could dramatically decrease the time needed to do these computations...

Joshua

Joshua Finkelstein (Associate Editor, Nature)

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-Our gung-ho enthusiasm for antidepressants mean that there is a certain amount of Prozac in the water these days. Freshwater mussels are less than pleased, though, since Prozac is making them release their larvae before they are viable. Freshwater mussels are sensitive creatures, and 70 percent of the species native to North America are extinct.

-In an irresistible item, a peculiar bird called the Black-Bone Silky Fowl has been found to be packed with carnosine, which has a rep for anti-aging and other positive health effects. The bird is a staple of Chinese medicine, and has soft white feathers over black flesh and bones.

-Check out the brand new Chemical Structure Lookup Service, hosted at NIH,. http://cactus.nci.nih.gov/cgi-bin/lookup/search

-Fucoxanthin, from brown seaweed, is taken up by the fat. It seems to both reduce adipose tissue and turn the fat a bright orange. Anti-obesity clinical trials are in the works.

-Adrienne Kozlowski, retired chemist, and her husband, have taken up hot air ballooning as a hobby. They say it is a perfect diversion for chemists, because manipulating the balloon is all a matter of mastering the laminar flow of the air.

-Peter Murray Rust, of Cambridge, on the future of Chemical information: "We are going to start mashing, and it is going to amaze the world."

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In the September issue of Nature Chemical Biology, John Silvius wrote about McGill University's interdepartmental graduate program in chemical biology, which was established in 2002 and now has "roughly 30 graduate students, 10 postdoctoral fellows and 30 faculty mentors."

The program involves scientists from the Department of Biochemistry, the Department of Chemistry, and the Department of Pharmacology and Therapeutics, and a "key objective of the program is to maximize opportunities for students with chemistry and life science backgrounds to share and appreciate their sometimes distinct perspectives on the field of chemical biology." Silvius wrote that this is accomplished via seminar discussion meetings, workshops, and an "annual research symposium at which students present their work to other students and faculty mentors."

There are other interdepartmental and multi-institutional graduate programs in chemical biology: for example, there is the Cornell/Rockefeller/Sloan-Kettering Tri-Institutional Training Program in Chemical Biology in New York City (which involves Cornell University, The Rockefeller University, Memorial Sloan-Kettering Cancer Center, and the Weill Medical College of Cornell). Graduate students in the Tri-Institutional Training Program can rotate in (and join) laboratories at any of the institutions and they do not have to teach classes, "enabling them to take an accelerated course schedule (four courses per semester during the first year)." (Although I understand that the program was designed so the students could take a large number of classes, I really enjoyed teaching during graduate school and think it's an important experience for all graduate students. But I'll save that topic for another blog post...)

There's obviously more than one way to train the next generation of chemical biologists, but Silvius believes that

An effective training program in chemical biology must produce graduates who have a distinct sense of intellectual identity yet can work effectively with researchers that are more conventionally trained either in chemistry or in the life sciences alone... Moreover, by promoting constant intermixing of individuals trained in the cultures of chemistry and biology, such a program allows students to be participants in the very type of stimulating, creative ferment that drives the field of chemical biology itself.

If you are a graduate student in (or a recent graduate of) an interdepartmental or multi-institutional graduate program in chemical biology, I'd be interested in hearing your thoughts about your program/your experiences. Why did you choose an interdepartmental or multi-institutional graduate program, instead of a Department of Chemistry & Chemical Biology? (And for those of you who did their graduate work in a Department of Chemistry & Chemical Biology, why didn't you choose an interdepartmental or multi-institutional graduate program?) For those of you working on the interface of other disciplines (for example, biophysics, chemical physics, bionanotechnology, etc.) did your graduate program meet your (scientific) needs/expectations? If not, what could they have done to make it easier for you to pursue interdisciplinary research?

Joshua

Joshua Finkelstein (Associate Editor, Nature)

Posted by Joshua Finkelstein at 10:31 AM | Permalink | Comments (4) | TrackBacks (0)

Chemical & Engineering News published a brief news story today on Ashworth et al., which appeared in the June 1st issue of Nature. In that paper, the authors showed that computational protein design could be used to alter the specificity of the homing endonuclease I-MsoI. The redesigned enzyme was highly active and it cleaved the new recognition sequence about 10,000 times more effectively (in vitro) than the wild-type enzyme.

Earlier this year, David Liu's laboratory demonstrated that it was possible to use directed evolution to modify the specificity of another homing endonuclease (I-SceI), but Ashworth et al. is the first paper in which computational protein design was successfully used to modify the specificity of a homing endonuclease.

The authors say that "the method should be generalizable to any protein–DNA interface redesign problem: for example, the reprogramming of transcription factor binding specificity" and they believe that "[t]he use and refinement of the computational modelling and design strategies described here should ... [enable them to design] novel proteins [that are] able to recognize and cleave any desired DNA site with high specificity for targeted genomics applications."

Joshua

Joshua Finkelstein (Associate Editor, Nature)

Posted by Joshua Finkelstein at 01:54 PM | Permalink | Comments (0) | TrackBacks (0)

As the world prepares to go football crazy later this summer (come on England!), Christopher Ewels from the Institute of Materials in Nantes, France, has been contemplating (in Nano Letters) the world's smallest football: buckminsterfullerene - C60.

Buckminsterfullerene, subject of the 1996 Nobel Prize in Chemistry, is a spherical cage of 60 carbon atoms - an Archimedean solid comprised of 12 pentagonal and 20 hexagonal faces which are stitched together to form a truncated icosahedron. C60 is unique in that it is the smallest fullerene that obeys the Isolated Pentagon Rule - i.e., each pentagon is completely surrounded by hexagons such that no two pentagons share an edge. Neighbouring pentagons in carbon networks are energetically unfavourable as they strain the system and disrupt the C=C bonding pattern. If you take a 4 panel section of C60 - two hexagons that share a common edge and the two pentagons that are linked by it - and rotate this grouping 90 degrees (the same effect as a Stone-Wales rotation), a less symmetric fullerene structure is obtained, which now has two pairs of edge-sharing pentagons. Calculations have shown that this isomer is a whopping 1.6 eV (~37 kcal/mol) less stable than Buckminsterfullerene!

Substitute one of the carbon atoms on each of the shared pentagon edges for nitrogen (i.e., C58N2), however, and it's a whole new ball game. In this case, the isomer with paired pentagons is 0.54 eV (~12.5 kcal/mol) more stable than the icosahedral structure. This result suggests that there may be a whole new family of stable azafullerenes that contain a lot fewer than 60 atoms and that nitrogen substitution into nanotube and thin-film structures may have dramatic structural consequences.

It appears that azafullerenes are in a league of their own and it may just a matter of time before such structures are made and isolated - at which point this exercise in fantasy football will become a reality.

Stuart

Stuart Cantrill (Associate Editor, Nature Nanotechnology)

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