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Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

High Performance Computing Simulations of tRNA Movement Through the Ribosome

The rate-limiting step of cognate tRNA selection is the movement inside the ribosome of the aminoacyl-tRNA from the A/T state to the A/A state. Large-scale molecular dynamics simulations demonstrate the stereochemical feasibility for accommodation of the tRNA acceptor stem by the ribosome peptidyl transferase center. Flexibility of the acceptor stem, in addition to flexibility of the anticodon stem region, appears to be important for accommodation. Universally conserved bases U2492, C2556, and C2573 constitute a structural gate, causing the 3'-CCA end to pause before entrance into the peptidyl transferase center. Twenty universally conserved bases interact with the tRNA during the accommodation simulation. The system  is the largest simulated to date. We have performed ten microsecond sampling simulations of drugs dissociating from the ribosome. Quicktime Movie

Kevin Y. Sanbonmatsu

Los Alamos National Laboratory

Email: kys@lanl.gov