Look at situation where there are 2 molecules of the sameprotein, which means same primary sequence. In addition they foldat the same time in the same funnel. Each protein, which isrepresented by a marble, is predicted to take a special path as itmoves down the funnel during the folding process. While it folds,it is possible that the two proteins collide on the way down thefunnel, and as a result of this collision, one or both of thoseproteins misfolds (forms a kinetic trap). As with any collision,energy is exchanged between the colliding molecules, and we canassume that the energy changes as a result of the collisioncontribute to potential misfolding. How can one represent howenergy changes (thermodynamic state functions) in the funnel modelas collision has to take place for both proteins to account for theresulting misfolds?
