(Collaboration with Kevin Sanbonmatsu, Los Alamos)

Using the "Q Machine" supercomputer, Los Alamos computer scientists have created a molecular simulation of the cell's protein-making structure, the ribosome. The project, simulating 2.64 million atoms in motion, is more than six times larger than any biological simulations performed to date. The ribosome is the ancient molecular factory responsible for synthesizing proteins in all organisms. Using the new tool, the Los Alamos team led by Kevin Sanbonmatsu is the first to observe the entire ribosome in motion at atomic detail. This first simulation of the ribosome offers a new method for identifying potential antibiotic targets for such diseases as anthrax. Until now, only static, snapshot structures of the ribosome have been available. Science Daily, 11/01/2005.

Our role in this project is to develop force field for drug molecules, such as antibiotics paramomycin and tetracycline. This information will be used to study on atomic level how the drugs affect the protein-making function of the bacterial ribosome. This can help to identify potential candidates for more efficient and safe new antibiotics.

Figure 9: (on the right) Upper frames: Molecular environment of the decoding center of the ribosome (left) and chemical structure of the antibiotic paramomycin (right).

Lower frame: A computer model of paramomycin (bold) attached to the decoding center of the ribosome.

 

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