The Electron Microscopy Data Bank (EMDB) is a rapidly growing repository for
the dissemination of structural data from single-particle reconstructions of
supramolecular protein assemblies including motors, chaperones, cytoskeletal
assemblies, and viral capsids. While the static structure of these assemblies
provides essential insight into their biological function, their conformational
dynamics and mechanics provide additional important information regarding the
mechanism of their biological function. Here, we present an unsupervised
computational framework to analyze and store for public access the
conformational dynamics of supramolecular protein assemblies deposited in the
EMDB. Conformational dynamics are analyzed using normal mode analysis in the
finite element framework, which is used to compute equilibrium thermal
fluctuations, cross-correlations in molecular motions, and strain energy
distributions for 452 of the 681 entries stored in the EMDB at present. Results
for the viral capsid of hepatitis B, ribosome-bound termination factor RF2, and
GroEL are presented in detail and validated with all-atom based models. The
conformational dynamics of protein assemblies in the EMDB may be useful in the
interpretation of their biological function, as well as in the classification
and refinement of EM-based structures.Comment: Associated online data bank available at:
http://lcbb.mit.edu/~em-nmdb