Domain motions of Argonaute,the catalytic engine of RNA interference |
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| Authors: | Dengming Ming Michael E Wall Kevin Y Sanbonmatsu |
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| Affiliation: | (1) Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, , Los Alamos, USA;(2) Bioscience Division, Los Alamos National Laboratory, , Los Alamos, USA;(3) Los Alamos National Laboratory, Center for Nonlinear Studies, Los Alamos, USA;(4) Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, , Los Alamos, USA |
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| Abstract: | Background The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field. |
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