title: Hydrodynamic effects on the relative rotational velocity of associating proteins.
abstract: Hydrodynamic steering effects on the barnase-barstar association were studied through the analysis of the relative rotational velocity of the proteins. We considered the two proteins approaching each other in response to their electrostatic attraction and employed a method that accounts for the long-range and many-body character of the hydrodynamic interactions, as well as the complicated shapes of the proteins. Hydrodynamic steering effects were clearly seen when attractive forces were applied to the geometric centers of the proteins (resulting in zero torques) and the attraction acted along the line that connects centers of geometry of proteins in their crystallographic complex. When we rotated barstar relative to barnase around this line by an angle in the range from -90° to 60°, the rotational velocity arising solely from hydrodynamic interactions restored the orientation of the proteins in the crystal structure. However, because, in reality, both electrostatic forces and torques act on the proteins and these forces and torques depend on the protein-protein distance and the relative orientation of the binding partners, we also investigated more realistic situations employing continuum electrostatics calculations based on atomistic protein models. Overall, we conclude that hydrodynamic interactions aid barnase and barstar in assuming a proper relative orientation upon complex formation.
authors: Centre of New Technologies, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, 02-89 Warsaw, Poland. mdlugosz@cent.uw.edu.pl
authors: Maciej
authors: M
authors: Długosz
authors: Jan M
authors: JM
authors: Antosiewicz
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D057446:Hydrodynamics; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012260:Ribonucleases / Q000737:chemistry* / Q000378:metabolism*; D012399:Rotation; D055672:Static Electricity
chemical_list: D001426:Bacterial Proteins; C057438:barstar protein, Bacillus amyloliquefaciens; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease