Research 2 | Beckstein Lab

Bor1p is a secondary transporter in yeast that is responsible for boron transport, likely powered by the proton gradient across the cell membrane. By combining cryo-electron microscopy and MD simulations we could generate models of Bor1p in inward facing and outward facing conformation, which suggest rigid body movements of the core domain relative to the gate domain, consistent with a rocking-bundle transport mechanism.

We studied the process of sodium/proton antiport in the NapA transporter. Through a combination of X-ray crystallography, biochemistry and computer simulations we could show that the antiporter undergoes a large conformational transition that resembles a *elevator*-like movement whereby a single domain moves up- and down through the membrane and carries a sodium ion with it.

Transition pathways in high dimensional spaces, such as the ones produced by advanced algorithms to sample large conformational changes in macromolecules, are difficult to analyze quantitatively. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA is implemented in the MDAnalysis library.