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Cryo-EMStructuresNote: This page contains background about the sourcing of our atomic coordinates. Feel free to skip ahead to Substitutions and Modifications to begin your experiments. The structures that are the departure point for our Molecular Dynamics (MD) studies are cryo-EM images of five ribosome translocation stages, published by the Korostelev group. Briefly, cryo-EM is a method where an aqueous solution of the macromolecule is frozen, then an electron beam is passed through the sample and picked up by a detector. A computer then takes all of the images of the proteins in solution (in various orientations) and stitches them together to make a 3D structure. The PDBs below can therefore be considered average structures at energy minima along the translocation reaction coordinate. They are resolved at 3.5 - 4.2 angstroms, while for reference a carbon-carbon single bond length is about 1.5 angstroms. Cryo-EM is only sensitive enough to resolve heavy atoms (not hydrogen), and residues that are part of flexible chains can also be problematic. They are sometimes not resolved or they are grown in based on the known amino acid/nucleotide sequence. For these reasons, these static structures have serious limitations in understanding dynamic phenomena, which we overcome using MD. Stage I / 5JUO Understanding PDB Files If you open a PDB file, you will see the coordinates and identifiers for each atom in the system. A sample line: ATOM 265 HO5' U 3 172.950 259.409 225.896 1.00 0.00 H
Continue on to Subsystem Initialization to learn more about the development of Neighborhood 2, or skip ahead to Substitutions and Modifications to begin your experiments. |