Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography.

Enzymes populate ensembles of structures with intrinsically different catalytic proficiencies that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL) to observe catalysis in a designed mutant (G150T) isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations and formation of the thioimidate catalytic intermediate selects for catalytically competent substates. A prior proposal for active site cysteine charge-coupled conformational changes in ICH is validated by determining structures of the enzyme over a range of pH values. A combination of large molecular dynamics simulations of the enzyme in crystallo and time-resolved electron density maps shows that ionization of the general acid Asp17 during catalysis causes additional conformational changes that propagate across the dimer interface, connecting the two active sites. These ionization-linked changes in the ICH conformational ensemble permit water to enter the active site in a location that is poised for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

µ-Oxo Dimerization Effects on Ground- and Excited-State Properties of a Water-Soluble Iron Porphyrin CO2 Reduction Catalyst.

Iron 5,10,15,20-tetra(para-N,N,N-trimethylanilinium)porphyrin (Fe-p-TMA) is a water-soluble catalyst capable of electrochemical and photochemical CO2 reduction. Although its catalytic ability has been thoroughly investigated, the mechanism and associated intermediates are largely unknown. Previous studies proposed that Fe-p-TMA enters catalytic cycles as a monomeric species. However, we demonstrate herein that, in aqueous solutions, Fe-p-TMA undergoes formation of a µ-oxo porphyrin dimer that exists in equilibrium with its monomeric form. The propensity for µ-oxo formation is highly dependent on the solution pH and ionic strength. Indeed, the µ-oxo form is stabilized in the presence of electrolytes that are key components of catalytically relevant conditions. By leveraging the ability to chemically control and spectrally address both species, we characterize their ground-state electronic structures and excited-state photodynamics. Global fitting of ultrafast transient absorption data reveals two distinct excited-state relaxation pathways: a three-component sequential model consistent with monomeric relaxation and a two-component sequential model for the µ-oxo species. Relaxation of the monomeric species is best described as a ligand-to-metal charge transfer (τ1 = ∼500 fs), an ionic strength-dependent metal-to-ligand charge transfer (τ2 = 2-4 ps), and finally relaxation of a ligand field excited state to the ground state (τ3 = 5 ps). Conversely, excited-state relaxation of the µ-oxo species proceeds via cleavage of an FeIII-O bond to generate transient FeIV═O and FeII porphyrin species (τ1 = 2 ps) that recombine to the ground-state µ-oxo species (τ2 = ∼1 ns). This latter lifetime extends to timescales relevant for chemical reactivity. It is therefore emphasized that further consideration of catalyst speciation and chemical microenvironments is necessary for elucidating the mechanisms of catalytic CO2 reduction reactions.

Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers.

Dinuclear iron centers with a bridging hydroxido or oxido ligand form active sites within a variety of metalloproteins. A key feature of these sites is the ability of the protein to control the structures around the Fe centers, which leads to entatic states that are essential for function. To simulate this controlled environment, artificial proteins have been engineered using biotin-streptavidin (Sav) technology in which Fe complexes from adjacent subunits can assemble to form [FeIII-(µ-OH)-FeIII] cores. The assembly process is promoted by the site-specific localization of the Fe complexes within a subunit through the designed mutation of a tyrosinate side chain to coordinate the Fe centers. An important outcome is that the Sav host can regulate the Fe···Fe separation, which is known to be important for function in natural metalloproteins. Spectroscopic and structural studies from X-ray diffraction methods revealed uncommonly long Fe···Fe separations that change by less than 0.3 Å upon the binding of additional bridging ligands. The structural constraints imposed by the protein host on the di-Fe cores are unique and create examples of active sites having entatic states within engineered artificial metalloproteins.

Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases.

An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S112E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic FeII complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S112E. Two aqua ligands complete the primary coordination sphere of the FeII center with both involved in hydrogen bond networks within Sav. The corresponding FeIII protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The FeIII protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.