TCBG Seminar

The Ribosome in Motion: Explicit Solvent Simulation of the 70S Ribosome

Dr. Kevin Y. Sanbonmatsu
Theoretical Biology and Biophysics
Los Alamos National Laboratory
Los Alamos, NM

Monday, February 24, 2003
3:00 pm (CT)
3269 Beckman Institute


We have recently performed an all-atom simulation of the 70S ribosome in explicit solvent based on a newly developed all-atom homology model of the entire ribosome. The simulations were performed on the Los Alamos National Laboratory Q machine using the NAMD molecular dynamics code, requiring approximately two million atoms and 300,000 CPU hours. We are for the first time able to study the stability of hydrogen bonds at critical regions, such as the intersubunit bridges and the tRNA interaction regions, along with the short timescale dynamics of the ribosome as a whole. Preliminary findings will be presented.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.

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