One area we’ve been putting a lot of attention into is understanding how folding may be different in the cell than say in a test tube. This is a pretty critical area, as we care about the cell more than the test tube, but virtually all folding studies done in science (both experiment and simulation) in our groups and others are
examined in a test tube (in vitro).
In order to understand how folding in the cell may be different, we’ve been examining scenarios which mimic how the cell might be different. We have several projects in progress right now in this direction, but we’ve had results on it over the last 2 years (when we started thinking in these directions). One paper of note is paper #50 (Protein folding under confinement: a role for solvent), where we examine how confinement (found in the cellular environment, such as in chaperones) changes folding. We also looked at this issue in paper #36 (Nanotube confinement denatures protein helices) some time ago, and as time has gone by, we’ve been maturing our methods.
Our most recent work looks directly at atomistic models of parts of the cellular environment (notably a chaperone and the ribosome) to see their effect on folding. Check out this movie below where Del and Jeremy talk about some of their work in this area.