Molecules, monthly

While teaching a genetics course at a community college in Knoxville Tennessee last year, Margaret Franzen -- now the program director of the BioMolecular Modeling center at the Milwakee School of Engineering -- had her students close their text books and hit the Web. In order for them to learn the various structural components of proteins, and how those proteins are affected by mutations, each month the students picked a molecule to study from David Goodsell's Web site "Molecule of the Month."

Using the molecular images, which are stylized cartoons in vivid colors of the atoms that make up the protein, the students learned what functions each part of the proteins are responsible for. For example, the hemoglobin molecule -- from May 2003 and possibly the most popular molecule, according to Goodsell -- is animated with motion to show how an oxygen atom binds at heme sites in the hemoglobin. Click on a link, and another image shows a mutation of glutamate 6 to valine on the beta chain of the hemoglobin protein, highlighted in bright green. "Goodsell's work, in addition to having beautiful pictures, has clear, easy-to-understand text accessible to students," Franzen says. "If they were to go to the original research papers they would give up."

At Scripps Research Institute, Goodsell spends most of his time using computational chemistry to design drugs that inhibit HIV infection. But part of his grant money is for creating education images, so for about two hours a month he uses structural information from X-ray crystallography to render drawings and paintings of hundreds of proteins and other molecular components in the Protein Data Bank. "My approach is completely designed to pull in non-technical audiences," Goodsell says. "The whole point of the Molecule of the Month is to be a gateway -- an easy way of going to the Protein Data Bank and not get lost in all the complexity."In 2005 Goodsell and colleagues used his computer-generated graphics to help to study the binding of a new type of HIV protease inhibitor that effectively blocks some forms of feline immunodeficiency virus, as well as HIV in other species. For each mutant form of the virus and potential action, Goodsell must create a new image.

The molecules he picks for the Molecule of the Month are in no particular order; sometimes he takes requests from educators. The challenge is finding a compelling anecdote that goes with each one -either its history of discovery, or unique function in the body. Goodsell's favorite drawing is the ribosome, posted in 2000, which was a long sought-after structure. "It was kind of like a holy grail for so many years," he says. "So much electron microscopy work was done giving tantalizing glimpses [of it], and then, boom -- there it is." In addition to the monthly molecules, Goodsell has illustrated his own books and created posters for high school teachers on cellular machinery. Some of his other popular work includes illustrations of all the molecules packed in living cells. "He is basically giving us information [on]...how unbelievably crowded the cell is," says Felice Frankel, senior research science fellow and head of the Envisioning Science program at Harvard. "Finally we are recognizing it is an extraordinarily complex system, but never thought of it that way because all [other] representations are so simple."While the Molecule of the Month is geared toward educators like Franzen, Goodsell creates his paintings for an even broader audience. Next year he will re-launch his first book, The Machinery of Life, with all new illustrations. With this, non-scientists will have the opportunity to do what many college students now do every month, once Goodsell posts his latest molecule online: explore.Andrea Gawrylewski mail@the-scientist.comImages: Hemoglobin, Ribosome, E. coli (painting). All courtesy of David Goodsell.Links within this article:Margaret Franzen http://www.rpc.msoe.edu/cbm/about/biographies.php#MargaretFranzenDavid Goodsell http://mgl.scripps.edu/people/goodsellMolecule of the Month http://mgl.scripps.edu/people/goodsell/pdbProtein Data Bank http://www.rcsb.org/pdb/home/home.doA. Brik, et al. "1,2,3-triazole as a peptide surrogate in the rapid synthesis of HIV-1 protease inhibitors," Chembiochem, 6:1167-0, Jul 2005. http://www.the-scientist.com/pubmed/15934050Protein Data Bank posters http://www.rcsb.org/pdb/staticA. Gawrylewski, "The bytes behind biology," The Scientist, Aug, 2007. http://www.the-scientist.com/2007/8/1/44/1/Felice Frankel http://web.mit.edu/felicef/David Goodsell paintings, Flickr.com http://www.flickr.com/photos/62496662@N00D. Goodsell, The Machinery of Life, Springer, December 1997. http://tinyurl.com/2jchzq