April 1st/2006

Decoding the Decoder

Molecular simulation of the ribosome

By Katharine Miller, Managing Editor

The ribosome (large subunit in white and small subunit in cyan) uses the transfer RNA molecules (incoming in red; outgoing in yellow) to read the genetic information from the messenger RNA (green) to produce protein. For visualization purposes, the top portion of the ribosome is cut away. Courtesy of LANL. Inside a cell, the ribosome deciphers genetic codes to produce proteins at unfathomable speeds. Now, researchers at Los Alamos National Laboratory (LANL) have simulated this complex nano-machine in action. With 2.6 million atoms moving at once, it’s the largest molecular simulation ever attempted by a factor of six. The work by Kevin Sanbonmatsu, PhD, a computational structural biologist, and his colleagues at LANL revealed some new details about the essential translating molecule, transfer RNA: it must be flexible in two places for decoding to occur. The simulation also identified a new structural gate, which may act as a control mechanism for selecting the proper transfer RNA.