Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion.
We provide an atomistic trajectory of ribosome translocation mediated by EF-G. Morphing between high-resolution structures with MMB.
This project aims at providing new insight about RNA translation into protein, focusing on the translocation step induced by Elongation Factor G (EF-G). In the past few years, biologists provided high-resolution structures of key steps of the process. Our goal is to compute a trajectory of the translocation at atomic level using an accurate morphing technique.
Jun 5, 2017
Final trajectory in PDB format, a movie.
Input files for MMB to reproduce the morphs.