pH-dependent reaction triggering in PmHMGR crystals for time-resolved crystallography.

Serial crystallography and time-resolved data collection can readily be employed to investigate the catalytic mechanism of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl (HMG)-coenzyme-A (CoA) reductase (PmHMGR) by changing the environmental conditions in the crystal and so manipulating the reaction rate. This enzyme uses a complex mechanism to convert mevalonate to HMG-CoA using the co-substrate CoA and cofactor NAD+. The multi-step reaction mechanism involves an exchange of bound NAD+ and large conformational changes by a 50-residue subdomain. The enzymatic reaction can be run in both forward and reverse directions in solution and is catalytically active in the crystal for multiple reaction steps. Initially, the enzyme was found to be inactive in the crystal starting with bound mevalonate, CoA, and NAD+. To observe the reaction from this direction, we examined the effects of crystallization buffer constituents and pH on enzyme turnover, discovering a strong inhibition in the crystallization buffer and a controllable increase in enzyme turnover as a function of pH. The inhibition is dependent on ionic concentration of the crystallization precipitant ammonium sulfate but independent of its ionic composition. Crystallographic studies show that the observed inhibition only affects the oxidation of mevalonate but not the subsequent reactions of the intermediate mevaldehyde. Calculations of the pKa values for the enzyme active site residues suggest that the effect of pH on turnover is due to the changing protonation state of His381. We have now exploited the changes in ionic inhibition in combination with the pH-dependent increase in turnover as a novel approach for triggering the PmHMGR reaction in crystals and capturing information about its intermediate states along the reaction pathway.

X-ray Emission Spectroscopy of Single Protein Crystals Yields Insights into Heme Enzyme Intermediates.

Enzyme reactivity is often enhanced by changes in oxidation state, spin state, and metal-ligand covalency of associated metallocofactors. The development of spectroscopic methods for studying these processes coincidentally with structural rearrangements is essential for elucidating metalloenzyme mechanisms. Herein, we demonstrate the feasibility of collecting X-ray emission spectra of metalloenzyme crystals at a third-generation synchrotron source. In particular, we report the development of a von Hamos spectrometer for the collection of Fe Kß emission optimized for analysis of dilute biological samples. We further showcase its application in crystals of the immunosuppressive heme-dependent enzyme indoleamine 2,3-dioxygenase. Spectra from protein crystals in different states were compared with relevant reference compounds. Complementary density functional calculations assessing covalency support our spectroscopic analysis and identify active site conformations that correlate to high- and low-spin states. These experiments validate the suitability of an X-ray emission approach for determining spin states of previously uncharacterized metalloenzyme reaction intermediates.

pHP-Tethered N-Acyl Carbamate: A Photocage for Nicotinamide.

The synthesis of a new photocaged nicotinamide having an N-acyl carbamate linker and a p-hydroxyphenacyl (pHP) chromophore is described. The photophysical and photochemical studies showed an absorption maximum at λ = 330 nm and a quantum yield for release of 11% that are dependent upon both pH and solvent. While the acyl carbamate releases nicotinamide efficiently, a simpler amide linker was inert to photocleavage. This photocaged nicotinamide has significant advantages with respect to quantum yield, absorbance wavelength, rate of release, and solubility that make it the first practical example of a photocaged amide.

Rapid evolution of the Photosystem II electronic structure during water splitting.

Photosynthetic water oxidation is a fundamental process that sustains the biosphere. A Mn4Ca cluster embedded in the photosystem II protein environment is responsible for the production of atmospheric oxygen. Here, time-resolved x-ray emission spectroscopy (XES) was used to observe the process of oxygen formation in real time. These experiments reveal that the oxygen evolution step, initiated by three sequential laser flashes, is accompanied by rapid (within 50 µs) changes to the Mn Kß XES spectrum. However, no oxidation of the Mn4Ca core above the all MnIV state was detected to precede O-O bond formation, and the observed changes were therefore assigned to O-O bond formation dynamics. We propose that O-O bond formation occurs prior to the transfer of the final (4th) electron from the Mn4Ca cluster to the oxidized tyrosine YZ residue. This model resolves the kinetic limitations associated with O-O bond formation, and suggests an evolutionary adaptation to avoid releasing of harmful peroxide species.

Spectroscopic analysis of catalytic water oxidation by [Ru(II)(bpy)(tpy)H2O]2+ suggests that Ru(V)═O is not a rate-limiting intermediate.

Modern chemistry's grand challenge is to significantly improve catalysts for water splitting. Further progress requires detailed spectroscopic and computational characterization of catalytic mechanisms. We analyzed one of the most studied homogeneous single-site Ru catalysts, [Ru(II)(bpy)(tpy)H2O](2+) (where bpy = 2,2'-bipyridine, tpy = 2,2';6',2″-terpyridine). Our results reveal that the [Ru(V)(bpy)(tpy)═O](3+) intermediate, reportedly detected in catalytic mixtures as a rate-limiting intermediate in water activation, is not present as such. Using a combination of electron paramagnetic resonance (EPR) and X-ray absorption spectroscopy, we demonstrate that 95% of the Ru complex in the catalytic steady state is of the form [Ru(IV)(bpy)(tpy)═O](2+). [Ru(V)(bpy)(tpy)═O](3+) was not observed, and according to density functional theory (DFT) analysis, it might be thermodynamically inaccessible at our experimental conditions. A reaction product with unique EPR spectrum was detected in reaction mixtures at about 5% and assigned to Ru(III)-peroxo species with (-OOH or -OO- ligands). We also analyzed the [Ru(II)(bpy)(tpy)Cl](+) catalyst precursor and confirmed that this molecule is not a catalyst and its oxidation past Ru(III) state is impeded by a lack of proton-coupled electron transfer. Ru-Cl exchange with water is required to form active catalysts with the Ru-H2O fragment. [Ru(II)(bpy)(tpy)H2O](2+) is the simplest representative of a larger class of water oxidation catalysts with neutral, nitrogen containing heterocycles. We expect this class of catalysts to work mechanistically in a similar fashion via [Ru(IV)(bpy)(tpy)═O](2+) intermediate unless more electronegative (oxygen containing) ligands are introduced in the Ru coordination sphere, allowing the formation of more oxidized Ru(V) intermediate.

Mechanism of Catalytic Water Oxidation by the Ruthenium Blue Dimer Catalyst: Comparative Study in D2O versus H2O.

Water oxidation is critically important for the development of energy solutions based on the concept of artificial photosynthesis. In order to gain deeper insight into the mechanism of water oxidation, the catalytic cycle for the first designed water oxidation catalyst, cis,cis-[(bpy)2(H2O)RuIIIORuIII(OH2)(bpy)2]4+ (bpy is 2,2-bipyridine) known as the blue dimer (BD), is monitored in D2O by combined application of stopped flow UV-Vis, electron paramagnetic resonance (EPR) and resonance Raman spectroscopy on freeze quenched samples. The results of these studies show that the rate of formation of BD[4,5] by Ce(IV) oxidation of BD[3,4] (numbers in square bracket denote oxidation states of the ruthenium (Ru) centers) in 0.1 M HNO3, as well as further oxidation of BD[4,5] are slower in D2O by 2.1-2.5. Ce(IV) oxidation of BD[4,5] and reaction with H2O result in formation of an intermediate, BD[3,4]', which builds up in reaction mixtures on the minute time scale. Combined results under the conditions of these experiments at pH 1 indicate that oxidation of BD[3,4]' is a rate limiting step in water oxidation with the BD catalyst.