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abstracts
We have obtained very detailed information about the internal water molecules in the large internal cavity inside fatty acid binding (FABP) proteins , in the presence of bound fatty acids (FA), by Ultra High Resolution X-Ray Crystallography (UHR) to 0.7 Å and Neutron Protein Crystallography (NPC) to 1.9 Å using a "radically small" (V=0.05 mm3) crystal. These waters form a very well ordered dense cluster of 12 molecules, positioned between the hydrophilic internal wall of the cavity and the fatty acid molecule. This information has been used for a detailed electrostatic analysis based on the charge distribution description modeled in the multipole formalism and on the Atoms in Molecules theory. This information is also being used in molecular dynamics simulations of H-FABP and its complex with FA in order to quantify the energetic contribution of these internal waters to the binding energy. The experiment has been done with oleic acid, coming with the protein expressed in E. Coli. The results have been analyzed in order to understand the interactions between the FA, the internal water and the protein, and in particular the role played by the water molecules in determining the potency and specificity of FA binding to FABPs. The major tool for visualizing the water molecules inside the H-FABP cavity is UHR X-Ray Crystallography combined with NPC. UHR crystallographic structures give the positions of hydrogen and oxygen atoms for well-ordered water molecules. NPC determines hydrogen atom positions, particularly of water molecules which have multiple conformations, leading to the best possible crystallographic model. This model was then complemented by a transferred charge distribution to accurately determine the electrostatic and topological properties in the binding pocket, providing a description of the way water molecules in hydration layer contribute to the binding of ligand, which is essential to understand and model ligand binding.
abstracts
Early neutron crystallography studies replaced hydrogen with deuterium by soaking the crystal in heavy water prior to data collection, which exchanged labile hydrogen atoms (OH, NH, and SH) and solvent molecules only. Carbon bonded hydrogen atoms were not replaced, and their negative scattering density resulted in cancellation in nuclear density maps with resolution worse than 1.8 Å. Furthermore complications arise due to partial exchange, where deuterium is present in some unit cells and hydrogen in others. More recently it has become possible to completely replace hydrogen with deuterium through expression in a deuterated medium, using facilities such as the Deuteration Laboratory (DLAB) in Grenoble. As this is a complex and expensive task, the question arises as to the importance of its use. As well as allowing the study of radically smaller crystals (<0.05mm3), it also has the possibility to avoid the cancellation problems discussed above. We have obtained data from high quality crystals of partially hydrogenated type III antifreeze protein, where methyl protonated valine and leucine residues were incorporated into the perdeuterated protein. This provides an excellent opportunity to assess the effects of negative scattering from hydrogen atoms not only on the visibility of neighbouring carbon atoms but also on water molecules in close vicinity. The observation of these cancellation effects gives a further reason to use full deuteration in neutron protein crystallography.
