Lipid exchange in crystal-confined Fatty Acid Binding Proteins: X-ray evidence and Molecular Dynamics explanation

Fatty Acid Binding Proteins (FABPs) are responsible for the long-chain fatty acids transport inside the cell. But despite the years since their structure is known and the many stud- ies published, there is no definitive answer about the stages of the lipid entry-exit mechanism. Their structure forms a β - barrel of 10 anti-parallel strands with a cap in a helix–turn–helix motif, and there is some consensus on the role of the so- called portal region, involving the second α -helix from the cap ( α 2), β C– β D and β E- β F turns in fatty acids exchange. To test the idea of a lid that opens, we performed a soaking experiment on an h-FABP crystal in which the cap is part of the packing contacts, and its movement is strongly restricted. Even in these conditions, we observed the replacement of palmitic acid by 2-Bromohexadecanoic acid (Br-palmitic acid). Our MD simulations reveal a two-step lipid entry process: i.- The travel of the lipid head through the cavity in the order of tens of nanoseconds, and ii.- The accommodation of its hy- drophobic tail in hundreds to thousands of nanoseconds. We observed this even in the cases in which the fatty acids en- ter the cavity by their tail. During this process, the fatty acids do not follow a single trajectory, but multiple ones through which they get into the protein cavity. Thanks to the com- plementary views between experiment and simulation, we can give an approach to a mechanistic view of the exchange process.