Different reaction mechanisms discussed for DFPase

Knowledge about the reaction mechanism of the enzyme DFPase is a crucial prerequisite for successful directed protein engineering because the mechanism determines the orientation of the substrates in the binding pocket of the enzyme for catalytic turnover. Also residues important for the mechanism can be specifically optimized. For DFPase three different mechanisms were discussed in the past.

When the first X-ray structure of DFPase was published in 2001 (Scharff et al., Structure 9 (2001) 493-502) residue H287 was found to be part of the enzyme’s binding pocket. Mutant H287N only retained minimal residual activity and it was therefore concluded that H287 is activating a water molecule for nucleophilic attack on the substrate’s phosphorus atom. The substrate itself is activated by coordination to the catalytic calcium ion via the phosphoryl oxygen (top scheme in the figure). As mutants like H287F ratain almost full catalytic activity this mechanism was refuted.

It was alternatively proposed that the calcium ion in the catalytic binding site of DFPase activates a directly coordinated water molecule (resulting in a coordinated hydroxide species). This hydroxide ion would then act as the nucleophile to attack the phosphorus atom of the substrate that is also coordinated to the calcium ()middle scheme in the figure). This mechanism was refuted based on the neutron diffraction structure of DFPase that clearly reveals the identity of the coordinated water as a water molecule and not as hydroxide. It is important to mention in this context that the neutron data (and the respective X-ray data for joint refinement) were recorded at room temperature, which is the relevant temperature for catalytic activity. The neutron structure is however compatible to a third mechanism, which was proposed based on isotope labeling, mutational studies and the structure of a protein-inhibitor complex.

Special issue of Acta D

This mechanism (Blum et al., JACS 128 (2006) 12750-12757) identifies the calcium coordinating residue D229 as the active nucleophile. Als an intermediate an instable high-energy phospho-enzyme species is generated, which is subsequently hydrolyzed by water, regenerating the enzyme and releasing the product (bottom scheme in the figure).

The results of the neutron diffraction experiments with DFPase as well as the results of mutational and kinetic studies were now related to each other in the journal Acta Cryst. D. The article is part of a special issue with the title “Neutrons in Biology“. Even though all articles of the issue are worth reading one article is especially recommended: Benno P. Schoenborn, who published the first neutron diffraction structure of a protein (myoglobin) at the end of the 1960s, offers a fascinating overview over more than fourty years of history of the use of neutron in biomolecular research in his article “A history of neutrons in biology: the development of neutron protein crystallography at BNL and LANL“.

Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase).
Blum MM, Tomanicek S, John H, Hanson L, Rüterjans H, Schoenborn BP, Langan P, Chen JC.
Acta Crystallogr D Biol Crystallogr. 2010; 66(11):1131-1138.
http://dx.doi.org/10.1107/S0907444910034013

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Abstract:
Diisopropyl fluorophosphatase (DFPase) is a calcium-dependent phosphotriesterase that acts on a variety of highly toxic organophosphorus compounds that act as inhibitors of acetylcholinesterase. The mechanism of DFPase has been probed using a variety of methods, including isotopic labelling, which demonstrated the presence of a phosphoenzyme intermediate in the reaction mechanism. In order to further elucidate the mechanism of DFPase and to ascertain the protonation states of the residues and solvent molecules in the active site, the neutron structure of DFPase was solved at 2.2 Å resolution. The proposed nucleophile Asp229 is deprotonated, while the active-site solvent molecule W33 was identified as water and not hydroxide. These data support a mechanism involving direct nucleophilic attack by Asp229 on the substrate and rule out a mechanism involving metal-assisted water activation. These data also allowed for the re-engineering of DFPase through rational design to bind and productively orient the more toxic S stereoisomers of the nerve agents sarin and cyclosarin, creating a modified enzyme with enhanced overall activity and significantly increased detoxification properties.

Plot of C-α RMSD values between d-DFPase and h-DFPase

Protein structures solved by neutron diffraction have the significant advantage compared to X-ray structures that hydrogen atoms are clearly observable in the nuclear density maps. This allows the determination of protonation states in amino acid side-chains and the orientation of solvent molecules (especially water) in space. This is of special importance for the elucidation of enzyme mechanisms. The disadvantages of neutron diffraction with proteins exist in the small number of powerful neutron sources and dedicated instruments worldwide. Also – neutron flux even at the most powerful sources is small compared to photon flux at X-ray sources. Therefore large protein crystals are required and data collection times can easily be in the region of several weeks. Another problem is the signal to noise ratio. Hydrogen atoms in the crystal are major contributors to this problems because the large incoherent scattering cross section of hydrogen. High values for this incoherent scattering cross section lead to diffuse scattering and negatively influence the signal to noise ratio. Deuterium on the other hand displays a significantly smaller value (2.05 b for deuterium compared with 80.27 b for normal hydrogen; 1 b = 100 fm²). To overcome this problem, crystals grown with hydrogenous protein are normally soaked with deuterated mother liquor (or brought in contact via gas diffusion).

Cover of Acta F with DFPase

Labile hydrogens (e.g. those of water in the solvent of in acidic or basic functional groups in the protein) are exchanged with deuterium. Non-labile hydrogens like those in aliphatic or aromatic C-H bonds are no exchanged. Therefore a significant number of hydrogen atoms remain in the protein. Such a partially exchanged crystal was used for the already published neutron structure of DFPase.

To achieve full deuteration of the protein it has to be grown in fully deuterated media. We now report the X-ray structure of fully deuterated DFPase in a new publication in the journal Acta Cryst. F. The structure (solved at room temperature at a resolution of 2.1 Å) shows that full deuteration leads to practically no changes in the protein structure. But even though a very large crystal of d-DFPase was grown (> 2mm³) it did not diffract neutrons beyond very low resolution. An explanation for this unexpected result can be found either in the differences in data aquisition (cross section of the neutron beam compared to the X-ray beam used) or can be based on crystallographic parameters. The scattering characteristics of successful neutron experiments and associated X-ray data are presented in tabulated form and can serve as a guidance for future neutron experiments.

X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): Perdeuteration of proteins for neutron diffraction.
Blum MM, Tomanicek S, John H, Hanson L, Rüterjans H, Schoenborn BP, Langan P, Chen JC.
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2010; 66(4):379-385.
http://dx.doi.org/10.1107/S1744309110004318

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Abstract:
The signal-to-noise ratio is one of the limiting factors in neutron macromolecular crystallography. Protein perdeuteration, which replaces all H atoms with deuterium, is a method of improving the signal-to-noise ratio of neutron crystallography experiments by reducing the incoherent scattering of the hydrogen isotope. Detailed analyses of perdeuterated and hydrogenated structures are necessary in order to evaluate the utility of perdeuterated crystals for neutron diffraction studies. The room-temperature X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase) is reported at 2.1 Å resolution. Comparison with an independently refined hydrogenated room-temperature structure of DFPase revealed no major systematic differences, although the crystals of perdeuterated DFPase did not diffract neutrons. The lack of diffraction is examined with respect to data-collection and crystallographic parameters. The diffraction characteristics of successful neutron structure determinations are presented as a guideline for future neutron diffraction studies of macromolecules. X-ray diffraction to beyond 2.0 Å resolution appears to be a strong predictor of successful neutron structures.

Im the past year the number of entries in the Protein Data Base (PDB) has exceeded the number of 50.000. Most of these structure have been determined by X-ray crystallography, a smaller part by Nuclear Magnetic Resonance (NMR). Compared with this, the number of published neutron diffraction structures of proteins is tiny. Even though the first neutron structure of a protein was already solved in 1969 by Benno Schoenborn (sperm whale myoglobin, the same protein that John Kendrew used to determine the first X-ray structure of a protein ten years earlier) only about 20 proteins were characterized by neutron diffraction up to the present day.

Compared to X-ray diffraction the use of neutrons has a clear advantage. While hydrogen atoms are normally invisible in X-ray structures they become visible with neutrons. Knowing the location of hydrogen atoms means that protonation states of amino acid sidechains are known and that the orientation of water molecules can be determined. This is especially important for the understanding of enzyme machanisms. But why are there so few neutron structures? The reason is the very low flux of even modern neutron sources compared to the photon flux in modern synchrotrons used for X-ray crystallography. Therefore large crystals are required and long measurement time are necessary. Also the number of experimental stations dedicated for bio-macromolecules is limited. Currently only three sources allow the work on proteins (one in the USA, one in France and one in Japan).

The determination of the neutron diffraction structure of the enzyme diisopropyl fluorophosphatase (DFPase) was carried out at the spallation neutron source at Los Alamos National Laboratory (LANL) with one of the smallest crystals ever used for protein neutron crystallography. The volume of the crystal was 0.43 mm³. To record a complete data set about one month of beam time was required. The pulsed spallation source in Los Alamos also allowed the use of time-of-flight (TOF) techniques. The structure was deposited in the PDB under accession code 3BYC.

Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.
Blum MM, Mustyakimov M, Rüterjans H, Kehe K, Schoenborn BP, Langan P, Chen JC.
Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):713-8.
http://dx.doi.org/10.1073/pnas.0807842106

Abstract:
Hydrogen atoms constitute about half of all atoms in proteins and play a critical role in enzyme mechanisms and macromolecular and solvent structure. Hydrogen atom positions can readily be determined by neutron diffraction, and as such, neutron diffraction is an invaluable tool for elucidating molecular mechanisms. Joint refinement of neutron and X-ray diffraction data can lead to improved models compared with the use of neutron data alone and has now been incorporated into modern, maximum-likelihood based crystallographic refinement programs like CNS. Joint refinement has been applied to neutron and X-ray diffraction data collected on crystals of diisopropyl fluorophosphatase (DFPase), a calcium-dependent phosphotriesterase capable of detoxifying organophosphorus nerve agents. Neutron omit maps reveal a number of important features pertaining to the mechanism of DFPase. Solvent molecule W33, coordinating the catalytic calcium, is a water molecule in a strained coordination environment, and not a hydroxide. The smallest Ca-O-H angle is 53°, well beyond the smallest angles previously observed. Residue Asp-229, is deprotonated, supporting a mechanism involving nucleophilic attack by Asp-229, and excluding water activation by the catalytic calcium. The extended network of hydrogen bonding interactions in the central water filled tunnel of DFPase is revealed, showing that internal solvent molecules form an important, integrated part of the overall structure.