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NEWS OF THE WEEK ASSEMBLY LINE Twenty different proteins must bind to ribosomal RNA (gray) to assemble the 30S ribosome. Here, these proteins are colored according to their binding rates: red (fastest), orange, green, blue, and purple (slowest). BIOPHYSICAL CHEMISTRY TRACKING CELLULAR MACHINE ASSEMBLY Technique observes how parts of a macromolecular complex bind in real time RAPID TRANSIT An alkynyl AdoMet analog is shown bound to a methyl- transferase (blue ribbon structure). The analog's extended group (yellow) is about to be transferred to DNA (gray). B Y COMBINING ISOTOPIC LA- beling and mass spectrome- try, researchers have devised a way to study how huge cellular macromolecular complexes as- ^ semble in real time (Nature V 2005,438,628). James R. William- son, Megan W. T. Talkington, and Gary Siuzdak of Scripps Research In- stitute demonstrate the power of their technique on the bac- terial 30S ribosome. The 30S ribosome is part of the bacte- rial protein-making machinery and contains a large RNA mol- ecule and 20 different proteins. Using their technique, the team measured the rates at which 17 of the 20 proteins bind to the RNA during 30S ribosome assembly. "The elegance of their experi- mental design should allow it to be adapted to a wide range of such complexes," comments Sarah A. Woodson of Johns Hopkins Uni- versity in an accompanying Nature commentary A clearer picture of how large cellular complexes as- semble should improve our under- standing of how such complexes evolved and may guide the devel- opment of materials that mimic their properties, she adds. To track assembly, the Scripps team introduced isotopically la- beled components during a certain time window during complex as- sembly. They then measured the isotopic ratios of the resulting complexes and their individual protein components by matrix-as- sisted laser desorption ionization mass spectrometry. By varying the length of the isotopic "pulse," the researchers were able to calculate the rates at which each protein binds to the complex. By repeating the experiment at different temperatures, Wil- liamson and coworkers obtained results allowing them to con- clude that, contrary to previous observations, assembly of the 30S ribosome doesn't irreversibly stall under less-than-perfect con- ditions. "This suggests that the assembly of key macromolecular complexes such as the ribosome might proceed via an energetic landscape of multiple pathways," a situation that might have evo- lutionary advantages, Talkington says.—AMANDA YARNELL CHEMICAL BIOLOGY MODIFYING DNA Chemical strategy provides new way to derivatize DNA sequence specifically A NEW TECHNIQUE THAT makes it possible to add hy- drocarbon chains to DNA in a sequence-specific manner has been developed by a collaborative European group. Methylation is a common type of chemical de- rivatization that nature uses to turn genes on and off in cells and to modify biomolecules for other purposes. In the process, cata- lyzed by numerous methyltransferas- es, methyl groups are removed from 5-adenosyl-L-me- thionine (AdoMet) at its sulfonium position and placed sequence- specifically in DNA, RNA, and proteins. To derivatize such biomolecules with greater versatility for a range of functional studies, researchers have tried replacing AdoMet's methyl group with larger hydro- carbons, such as ethyl or propyl groups, and then using methyl- transferases to catalyze the trans- fer of those groups. When that is done, however, reaction rates plum- met to impractically low levels. Now, a collaborative team has discovered a clever chemical end run around this problem: Alkyl groups may not work, but some alkenyl and alkynyl groups do. Methyltransferases accept and transfer to DNA hydrocarbons of up to five carbon units with a double or triple bond one carbon atom away from AdoMet's sul- fonium center. The unsaturated bonds in these systems activate the transferring group, the researchers believe, and thus permit the reac- tions to proceed rapidly and still sequence-specifically. The DNA derivization approach was developed by Saulius Klima- sauskas, Howard Hughes Medical Institute international research scholar and head of the Laboratory of Biological DNA Modification at the Institute of Biotechnology, Vilnius, Lithuania; professor of or- ganic chemistry Elmar Weinhold of R W T H Aachen University, in Germany; and coworkers (Nat. Chem. Biol., published online Nov. 27, dx.doi.org/10.1038/nchem bio754). They believe the technique should also work for derivatizing RNA, proteins, and other biomol- ecules.—STU BORMAN 12 C&EN / DECEMBER 5, 2005 WWW.CEN-0NLINE.ORG
