Multi-drug resistant bacteria present an increasing problem in US hospitals. To design new antibiotics that are effective against these bacteria, it is important to understand drug-target interactions and the targets themselves. We will study a major antibiotic target: the ribosome. Many ribosome antibiotics interfere with the process of decoding by the ribosome ("tRNA selection"). The rate-limiting step of decoding is accommodation, where the tRNA moves from a partially bound state (A/T state) to its fully bound position (A/A state) inside the ribosome. Structural biology techniques have determined the structure of the ribosome before and after accommodation. Kinetics experiments have determined accommodation rates. It is difficult, however, to study the process of accommodation in atomic detail experimentally. Molecular dynamics simulations have been used to study protein folding. However, until recently, the size of the ribosome has made simulations of ribosome conformational changes computationally prohibitive. In our preliminary data, we have combined the high performance computing resources at Los Alamos National Laboratory with all-atom reduced-model potentials to study accommodation of tRNA into the ribosome (Whitford, et al., RNA Journal, 2010). Here, we will use large-scale molecular simulation to study key features of accommodation, including the effect of the elongation factor EF-Tu, the effect of antibiotics and the fidelity mechanism. We will also combine molecular dynamics diffusion calculations together with measured kinetic rates to estimate accommodation barrier heights that correspond to these measured rates.

Public Health Relevance

Supercomputers will be used to simulate a major antibiotic target (the ribosome) in atomic detail. Understanding how antibiotics work will help lay the foundation for developing new drugs to combat resistant bacteria, a critical problem in US hospitals. Results will be validated against single molecule fluorescence experiments and structural biology experiments.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function D Study Section (MSFD)
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Preusch, Peter C
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Los Alamos National Lab
Los Alamos
United States
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Kaushal, Prem S; Sharma, Manjuli R; Booth, Timothy M et al. (2014) Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proc Natl Acad Sci U S A 111:7284-9
Budkevich, Tatyana V; Giesebrecht, Jan; Behrmann, Elmar et al. (2014) Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Cell 158:121-31
Whitford, Paul C; Sanbonmatsu, Karissa Y (2013) Simulating movement of tRNA through the ribosome during hybrid-state formation. J Chem Phys 139:121919
Whitford, Paul C; Blanchard, Scott C; Cate, Jamie H D et al. (2013) Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comput Biol 9:e1003003
Ahmed, Aqeel; Whitford, Paul C; Sanbonmatsu, Karissa Y et al. (2012) Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. J Struct Biol 177:561-70
Zhang, Zhiyong; Sanbonmatsu, Karissa Y; Voth, Gregory A (2011) Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. J Am Chem Soc 133:16828-38
Whitford, Paul C; Ahmed, Aqeel; Yu, Yanan et al. (2011) Excited states of ribosome translocation revealed through integrative molecular modeling. Proc Natl Acad Sci U S A 108:18943-8
Whitford, Paul C; Geggier, Peter; Altman, Roger B et al. (2010) Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA 16:1196-204
Noel, Jeffrey K; Whitford, Paul C; Sanbonmatsu, Karissa Y et al. (2010) SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res 38:W657-61
Whitford, Paul C; Onuchic, Jose N; Sanbonmatsu, Karissa Y (2010) Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. J Am Chem Soc 132:13170-1

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