Modeling fatty acid delivery from intestinal fatty acid binding protein to a membrane

Abstract

Intestinal fatty acid binding protein (IFABP) interacts with biological membranes and delivers fatty acid (FA) into them via a collisional mechanism. However, the membrane-bound structure of the protein and the pathway of FA transfer are not precisely known. We used molecular dynamics (MD) simulations with an implicit membrane model to determine the optimal orientation of apo- and holo-IFABP (bound with palmitate) on an anionic membrane. In this orientation, the helical portal region, delimited by the alphaII helix and the betaC-betaD and betaE-betaF turns, is oriented toward the membrane whereas the putative beta-strand portal, delimited by the betaB-betaC, betaF-betaG, betaH-betaI turns and the N terminus, is exposed to solvent. Starting from the MD structure of holo-IFABP in the optimal orientation relative to the membrane, we examined the release of palmitate via both pathways. Although the domains can widen enough to allow the passage of palmitate, fatty acid release through the helical portal region incurs smaller conformational changes and a lower energetic cost.

Figure 1.

The crystal structure of apo-IFABP superimposed on four MD structures obtained from simulations in water (A) or the lowest energy MD structure on an anionic membrane (B). The crystal structure of holo-IFABP superimposed on four MD structures from simulations in water (C). The crystal structure is shown in gray. The structures in water are the energy-minimized average structures calculated from the last 1.6 ns of four MD simulations; the MD structure on the membrane is the energy-minimized structure obtained at the end of 2-ns MD simulations.

Figure 2.

The holo-IFABP structure (shown in black) superimposed on the apo-IFABP structure (shown in gray). (A) Crystal structures. (B) Energy-minimized average structures obtained over the last 1.6 ns of four MD simulations in water.

Figure 3.

The optimal orientation of apo-IFABP (A) and of IFABP bound with palmitate (B) relative to an anionic membrane. The structures are obtained at the end of 2-ns MD simulations, after energy minimization. The membrane is depicted by the rectangular box; the upper surface represents the plane of smeared charge (located at z = 16 Å); the lower surface represents the hydrophobic tail/headgroup boundary (located at z = 13 Å).

Figure 4.

The transfer of palmitate from the membrane bound holo-IFABP to the membrane via the helical portal region. The membrane is represented by the rectangle; the upper surface corresponds to the plane of smeared charge; the lower surface is the hydrocarbon/headgroup boundary.

Figure 5.

(A) The distance between the center of mass of IFABP (IFABP_com) and that of palmitate (FA_com) during FA transfer from the holo-IFABP to an anionic membrane through the helical portal region. (B) The change in effective energy of FA during its release, calculated as the difference in the effective energy of the IFABP-FA-membrane complex (W_PMFA) and of the same conformation but with FA transferred to water, away from the membrane and IFABP (W_{PM_FA,H2O}). (C) The RMSD of IFABP from the optimal structure during FA transfer.

Figure 6.

The position of residues with which the carboxyl group of palmitate makes hydrogen bonds as palmitate travels from the center of IFABP toward the helical portal (A) or alternative portal (B). The protein conformations are the energy minimized average structures calculated from MD trajectories for the first 720 ps (A) or the first 6300 ps (B). Hydrogen bonds are calculated for the same time periods.

Figure 7.

The energy-minimized average structure of IFABP from the FA-transfer-through-the-helical-portal-region MD simulation (colored in black) superimposed on the optimal structure (colored in gray). The average structure was calculated between 272 and 292 ps (A), 312 and 335 ps (B), 350 and 404 ps (C), and 450 and 456 ps (D).

Figure 8.

The transfer of palmitate from the membrane bound holo-IFABP to the membrane via the alternative portal region. See the caption of ▶ for the description of the membrane.

Figure 9.

(A) The distance between the center of mass of IFABP (IFABP_com) and that of palmitate (FA_com) during FA release from holo-IFABP through the alternative portal region. (B) The change in effective energy of FA during the release (see the caption of ▶ for details). (C) The RMSD of IFABP from the optimal structure during FA transfer.

Figure 10.

The energy-minimized average structure of IFABP from the FA-transfer-through-the-alternative-portal-region MD simulation (colored in black) superimposed on the optimal structure (colored in gray). The average structure was calculated between 2 and 300 ps (A), 1166 and 1360 ps (B), 1442 and 1486 ps (C), 1580 and 3700 ps (D), 4078 and 4116 ps (E), and 4510 and 6000 ps (F).