Time Scales of Conformational Gating in a Lipid-Binding Protein

Lipid-binding proteins sequester amphiphilic molecules in a large internal cavity occupied by ∼30 water molecules, some of which are displaced by the ligand. The role of these internal water molecules in lipid binding and release is not understood. We use magnetic relaxation dispersion (MRD) to directly monitor internal-water dynamics in apo and palmitate-bound rat intestinal fatty acid-binding protein (rIFABP). Specifically, we record the water (2)H and (17)O MRD profiles of the apo and holo forms of rIFABP in solution or immobilized by covalent cross-links. A global analysis of this extensive data set identifies three internal-water classes with mean survival times of ∼1 ns, ∼100 ns, and ∼6 μs. We associate the two longer time scales with conformational fluctuations of the gap between β-strands D and E (∼6 μs) and of the portal at the helix-capped end of the β-barrel (∼100 ns). These fluctuations limit the exchange rates of a few highly ordered structural water molecules but not the dissociation rate of the fatty acid. The remaining 90% (apo) or 70% (holo) of cavity waters exchange among internal hydration sites on a time scale of ∼1 ns but exhibit substantial orientational order, particularly in the holo form.