Suvrajit Maji, Rezvan Shahoei, Klaus Schulten, and Joachim Frank.
Quantitative characterization of domain motions in molecular
machines.
Journal of Physical Chemistry B, 121:3747-3756, 2017.
(PMC: PMC5479934)
MAJI2017
The work of molecular machines such as the ribosome is accompanied by
conformational changes, often characterized by relative motions of their
domains. The method we have developed seeks to quantify these motions in
a general way, facilitating comparisons of results obtained by different
researchers. Typically there are multiple snapshots of a structure in the form
of pdb coordinates resulting from flexible fitting of low-resolution density
maps, from X-ray crystallography, or from molecular dynamics simulation
trajectories. Our objective is to characterize the motion of each domain as a
coordinate transformation using moments of inertia tensor, a method we
developed earlier. What has been missing until now are ancillary tools that
make this task practical, general, and biologically informative. We have
provided a comprehensive solution to this task with a set of tools
implemented on the VMD platform. These tools address the need for
reproducible segmentation of domains, and provide a generalized description
of their motions using principal axes of inertia. Although this methodology has
been specifically developed for studying ribosome motion, it is applicable to
any molecular machine.
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