Florence Tama

TL;DR: A normal mode analysis of 20 proteins in 'open' or 'closed' forms was performed using simple potential and protein models, the quality of the results was found to depend upon the form of the protein studied, normal modes obtained with the open form of a given protein comparing better with the conformational change than those obtaining with the closed form.

TL;DR: Being a fast method, the RTB approach can be useful for normal mode analyses of large systems, paving the way for further developments and applications in contexts for which the normal modes are needed frequently, as for example during molecular dynamics calculations.

TL;DR: The coincidence of these dynamic transitions with the individual normal modes of the ribosome and the good correspondence between these motions and those observed in experiment suggest an underlying principle of nature to exploit the shape of molecular assemblies such as the Ribosome to provide robustness to functionally important motions.

TL;DR: This review describes recent methods based on normal mode analysis that have enabled us to study dynamics on the microsecond timescale for large macromolecules using different levels of coarse graining, from atomically detailed models to those employing only low-resolution structural information.

TL;DR: A cryo-electron microscopy reconstruction of the Escherichia coli PCC, SecYEG, complexed with the ribosome and a nascent chain containing a signal anchor is presented, proposing a model for co-translational protein translocation.