High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP–oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution
E. I. Howard,
B. Guillot,
M. P. Blakeley,
M. Haertlein,
M. Moulin,
A. Mitschler,
A. Cousido-Siah,
F. Fadel,
W. M. Valsecchi,
Takashi Tomizaki,
T. Petrova,
J. Claudot,
A. Podjarny
Affiliations
E. I. Howard
Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
B. Guillot
CNRS and Université de Lorraine, Laboratoire CRM2, UMR 7036, Vandoeuvre-lès-Nancy, F-54506, France
M. P. Blakeley
Institut Laue–Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
M. Haertlein
ILL–EMBL Deuteration Laboratory, Partnership for Structural Biology, 71 avenue des Martyrs, Grenoble 38000, France
M. Moulin
ILL–EMBL Deuteration Laboratory, Partnership for Structural Biology, 71 avenue des Martyrs, Grenoble 38000, France
A. Mitschler
Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
A. Cousido-Siah
Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
F. Fadel
Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
W. M. Valsecchi
Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
Takashi Tomizaki
Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
T. Petrova
Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290, Russian Federation
J. Claudot
CNRS and Université de Lorraine, Laboratoire CRM2, UMR 7036, Vandoeuvre-lès-Nancy, F-54506, France
A. Podjarny
Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch CEDEX, France
Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H...H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.