Capillarity theory for the fly-casting mechanism.
Biomolecular folding and function are often coupled. During molecular recognition events, one of the binding partners may transiently or partially unfold, allowing more rapid access to a binding site. We describe a simple model for this fly-casting mechanism based on the capillarity approximation and polymer chain statistics. The model shows that fly casting is most effective when the protein unfolding barrier is small and the part of the chain which extends toward the target is relatively rigid. These features are often seen in known examples of fly casting in protein-DNA binding. Simulations of protein-DNA binding based on well-funneled native-topology models with electrostatic forces confirm the trends of the analytical theory.
Trizac
Emmanuel
E
Laboratoire de Physique Théorique et Modéles Statistiques, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8626, Université Paris-Sud, F-91405 Orsay Cedex, France.
Levy
Yaakov
Y
Wolynes
Peter G
PG
D001665:Binding Sites / Q000235:genetics; D002197:Capillary Action; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism*; D008958:Models, Molecular; D011485:Protein Binding; D017510:Protein Folding; D011506:Proteins / Q000378:metabolism*; D055672:Static Electricity
D011506:Proteins; D004247:DNA