“What we saw in our computer calculations wasn’t at all what we expected to see when we began,” said co-lead author and Senior Constellation Professor of Biocomputation and Bioinformatics Angel Garcia. “The mechanism for entrance in the cell was clear in one simulation, but in some instances simulations show one result and you never see that result again. Then we started doing other simulations and it kept happening again and again.”
Garcia and his collaborator, postdoctoral researcher Henry Herce, initially set out to uncover how the peptide interacts with a lipid bilayer that is used to model the cell membrane. A highly efficient biological system, the cell membrane is composed of a lipid bilayer (made up of two monolayers) designed to protect the cell by preventing the influx of material. Each lipid in the bilayer has a polar, or charged, end and a non-polar end. A monolayer of lipids faces the exterior of the cell, with the polar end facing the outside of the cell. Another monolayer is under the first layer, forming the bilayer. The polar end of the lower layer faces the interior of the cell, forming a middle section containing the uncharged halves of both monolayers.
Because charged particles seek each other in order to neutralize themselves and achieve a more stable state, the surface of the polar cell membrane and the positively charged HIV peptide are drawn to one another. But the interior of the bilayer is not charged and forms a strong barrier against the entrance of any charged material.