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

Department of Chemistry, City College of New York/ CUNY, New York, New York 10031, USA

(RECEIVED April 12, 2007; FINAL REVISION June 11, 2007; ACCEPTED June 12, 2007)

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 II helix and the C-D and E-F turns, is oriented toward the membrane whereas the putative -strand portal, delimited by the B-C, F-G, H-I 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.

Keywords: molecular dynamics simulation; implicit membrane; fatty acid binding protein; palmitate; fatty acid exit site; free energy of binding

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.072875307.

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