Molecular Dynamics Simulation of Transmembrane Helix Dissociation

Abstract

In a typical single-molecule force spectroscopy (SMFS) experiment with a transmembrane protein (TM), a protein surface loop or tail is grabbed by the atomic force microscope cantilever and helices unwind as the TM is pulled in a direction perpendicular to the plane of the membrane. This process is unrelated to the insertion of helical segments from the translocon into the bilayer in a direction parallel to the plane of the membrane. We now use molecular dynamics simulations (MD) to consider a SMFS experiment in which TMs are pulled apart in the plane of the lipid bilayer, so that the helix-helix interactions can be studied. Parallel-versus perpendicular-pulling energy. We calculated the work of separating the helices of the glycophorin A dimer in a sodium dodecyl sulfate (SDS) micelle. Pulling perpendicular to the membrane plane requires about four times the work as parallel pulling to separate the helices. Point pulling. Using MD, we pulled Ala 82 of glycophorin A in a direction parallel to the membrane plane. For 150 ps, the two helices separated smoothly, essentially as rigid rods. However, both Ile 76 side chains remain in van der Waals contact, locking the dimer together. Further pulling unfolds the backbone around Ala 82, until the Ile 76 groups separate after 600 ps. Similar results were observed for a two-helix fragment of bacteriorhodopsin in an SDS micelle. Pulling on Ile 52, the helices separate smoothly for 150 ps. However, during this motion, Leu 13 and Leu 61 remain locked in van der Waals contact. We conclude that SMFS of helical membrane proteins pulled in the direction of the membrane plane would provide valuable information about the interactions that stabilize integral membrane proteins. Experimental implementation will require development of tethering groups compatible with bicelles.