The translation machinery is the center of protein synthesis and is present in hundreds to thousands of copies in every cell. The translational pathway requires a large number of macromolecular RNA:protein complexes to ensure its proper function. While the individual components and reactions involved in the pathway have been well studied, an integrated picture resolved both spatially and temporally, progressing from molecules to an entire cell is still missing. This research project is designed to extend our knowledge of the function and evolution of translation to higher levels of organization and scale. On the molecular level, the specific goals of the research are to study communication pathways in the RNA:protein complexes that set the genetic code. Interaction pathways that lead to evolution of specificity and editing in the aminoacyl-tRNA syntheses and communication within the ribosome will be studied using network properties and free energy surfaces obtained from molecular dynamics simulations. The folding/assembly landscape of the ribosomal small subunit will be computationally examined using all-atom and knowledge-based GO potentials. These simulations will be carried out simultaneously with folding experiments on the same systems. To study the kinetics of translation and the folding of DNA in the crowded environment of the cell, stochastic simulations of transcription/translation processes will be carried out using the GPU-based Lattice Microbe program. The 3D lattice models are based upon spatial and temporal information obtained from single molecule, proteomics, and cryo-electron tomography data from intact cells. Hypotheses about how the process of translation occurs at a cellular scale will be tested and extended using systems biology approaches.
All of the visualization, simulation, and analysis tools to enable the study of macromolecular RNA:protein assemblies will be made publicly available and updated through the MultiSeq and Network View extensions to the popular VMD biomolecular analysis software. Updates to the hybrid MD-Go and metadynamics free energy modules will be implemented into the molecular dynamics program NAMD that is available on all the NSF Supercomputer facilities. In addition any new analysis tools and results will be incorporated into a series of tutorials for teaching computational biology that will be available online. The PI's research group will continue to participate in the NSF sponsored Graduate Teaching Fellows program to help high school teachers prepare state-of-the-art scientific curriculum for their classrooms. The Lattice Microbe method allows stochastic simulations of complex cellular processes and reactions. All cell simulations software will be made publicly available. As with the other computational biophysics techniques developed by the principal investigator, tutorials and users guides will be developed to assist other researchers in using the methodology in their own studies. This project is jointly supported by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences, the Physics of Living Systems Program in the Physics Division and by the Chemical Theory, Models and Computational Methods Program in the Chemistry Division.
