Dear all, I would like to visualize the interface of a protein-protein complex. The complex formation is modulated by a ligand that upon binding alters the overall structure of one protein, which then in turn forms the complex with the second protein (structure of the complex is known). Ligand binding does not seem to induce a discrete conformational switch, rather a subtle alteration of the contact interface. The isolated structure of the first protein without the ligand is known as well.
In addition to depicting the structural difference in conventional ways I was thinking to draw some kind of stretched out topology map of the surface that is interacting - first the surface from the isolated protein, then the surface as it is found in the complex and then maybe some kind of difference map... Does anybody have some suggestions how to do this? I would prefer to do some kind of stretched out surface (basically a rectangle of the region of interest) and show "mountains and valleys" and their change, but not sure if this is feasible. Thanks for any advice! Best wishes, Tobias. -- ___________________________________________ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Wolfgang-Pauli-Str. 10, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax: +41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___________________________________________
