Macromolecular Structure and Function

DNA binding of TtgV

DNA binding of TtgV

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Movies, Presentations and Archived News

This page is intended as a repository of movies and presentations that the lab has produced.  In addition, it contains a complete list of news snippets.

Movies

TtgV bound to operator DNA

The multidrug efflux regulator TtgV undergoes dramatic conformational changes upon DNA binding and induces complementary conformational changes in its cognate DNA.  The DNA binding domains of TtgV rotate downwards and the C-terminal domains slide against each other to form the highly asymmetric configuration that is stabilized by DNA binding.  Upon TtgV binding, B-DNA is highly distorted with widened major grooves and narrowed minor grooves, resulting in an overall 60 degree concave bent.

DNA binding morph

Movie illustrating conformational changes upon TtgV binding to DNA.  Interpolation between the bound and unbound structures of TtgV shows that that binding of TtgV to DNA requires bending of DNA and large domain movements in TtgV.

Activator-bound RNA Polymerase

On the left is a cartoon showing the conformational changes during σ54-dependent transcription initiation.  The σ54-RNA polymerase binds to consensus sequences at positions -24 and -12, forming a stable closed complex.  Activator proteins use the energy from ATP hydrolysis to remodel this complex, changing the position of the origin of DNA melting and removing a region of σ54 that causes a physical block to loading of the melted template DNA.

On the right is the cryo-EM reconstruction of σ54–RNA polymerase in complex with the AAA activator PspF.  Cryo-EM reconstructions are generated from a large number of individual 2D images, each of which is assigned an angular position around a theoretical Euler sphere.  Each sphere in the movie represents an individual 2D image used to generate the 3D reconstruction.  (The image was generated using an Euler-plot program provided by Dr. Alessandro Costa, University of Oxford.)

RNA pol activation Euler angles cartoon

Movie illustrating the σ54–activator complex.  Left:  RNA polymerase in green, σ54 in blue, PspF in red, and DNA in orange.  Right:  Surface representation of the complex of RNA polymerase II and σ54.

For more information, please refer to Bose et al., 2008.

σ54 activator PspF

σ54 activators, which are AAA-ATPases, undergo conformational rearrangements in response to the hydrolysis of ATP in the active site.  This causes movements, on the top surface of the activator, of two loops that are responsible for mediating the interaction with σ54-RNA polymerase.

PspF side view PspF top view

Movie illustrating ATP hydrolysis-dependent movements in PspF.  Side and top view of PspF.  The raising and lowering of the two surface loops during the ATP hydrolysis cycle are shown.

For more information, please refer to Rappas et al., 2005.

Conformational changes in p97–p47

Illustration of the nucleotide-dependent conformational changes in the p97–p47 complex.  The AMP–PNP-bound state is shown in blue and the ADP-bound state in orange.  The rendered surfaces were obtained from p97–p47 cryo-EM reconstructions.

p97 top view p97 side view p97 bottom view

Movie illustrating nucleotide-dependent conformational changes in the p97–p47 complex.  Top, side and bottom views of the p97–p47 complex.

For more information, please refer to Beuron et al., 2006.