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
B
Y COMBINING ISOTOPIC LA-
beling and mass spectrometry, researchers have devised a way to study how huge cellular macromolecular complexes as^ semble in real time (Nature V 2005,438,628). James R. Williamson, Megan W. T. Talkington, and Gary Siuzdak of Scripps Research Institute demonstrate the power of their technique on the bacterial 30S ribosome. The 30S ribosome is part of the bacterial protein-making machinery and contains a large RNA molecule and 20 different proteins.
CHEMICAL
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 experimental design should allow it to be adapted to a wide range of such complexes," comments Sarah A. Woodson of Johns Hopkins University in an accompanying Nature commentary A clearer picture of how large cellular complexes assemble should improve our understanding of how such complexes evolved and may guide the development of materials that mimic their properties, she adds. To track assembly, the Scripps
BIOLOGY
MODIFYING DNA RAPID TRANSIT An alkynyl AdoMet analog is shown bound to a methyltransferase (blue ribbon structure). The analog's extended group (yellow) is about to be transferred to DNA (gray).
12
C&EN
/
DECEMBER
Chemical strategy provides new way to derivatize DNA sequence specifically
A
NEW TECHNIQUE THAT
makes it possible to add hydrocarbon chains to DNA in a sequence-specific manner has been developed by a collaborative European group. Methylation is a common type of chemical derivatization that nature uses to turn genes on and off in cells and to modify biomolecules for other purposes. In the process, catalyzed by numerous methyltransferases, methyl groups are removed from 5-adenosyl-L-me-
5,
2005
thionine (AdoMet) at its sulfonium position and placed sequencespecifically 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 hydrocarbons, such as ethyl or propyl groups, and then using methyltransferases to catalyze the transfer of those groups. When that is done, however, reaction rates plummet 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.
team introduced isotopically labeled components during a certain time window during complex assembly. They then measured the isotopic ratios of the resulting complexes and their individual protein components by matrix-assisted 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, Williamson and coworkers obtained results allowing them to conclude that, contrary to previous observations, assembly of the 30S ribosome doesn't irreversibly stall under less-than-perfect conditions. "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 evolutionary advantages, Talkington says.—AMANDA YARNELL
Methyltransferases accept and transfer to D N A hydrocarbons of up to five carbon units with a double or triple bond one carbon atom away from AdoMet's sulfonium center. The unsaturated bonds in these systems activate the transferring group, the researchers believe, and thus permit the reactions to proceed rapidly and still sequence-specifically. The DNA derivization approach was developed by Saulius Klimasauskas, 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 organic 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 biomolecules.—STU BORMAN WWW.CEN-0NLINE.ORG
