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DOE OSTI2025

Uncovering the True Active Sites in Ni–N–C Catalysts for CO 2 Electroreduction

Understanding and designing active sites in single-atom catalysts (SACs) requires going beyond static models to capture their dynamic evolution under realistic electrochemical conditions. Here, in this work, we develop an integrated theoretical framework that accounts for operational conditions, by combining grand canonical density functional theory (GC-DFT) with machine-learning-accelerated sampling, to uncover structure–activity–stability relationships in Ni–N–C SACs for the CO 2 reduction reaction (CO 2 RR). A library of NiN x C 4–x (x = 0–4) motifs─representing coordination defects likely formed during high-temperature synthesis─was systematically evaluated. Under working conditions, these sites were found to undergo hydrogenation, and NiN 3 C 1_ H 1 was identified as the most probable active site. At reducing potentials, hydrogen adsorbs spontaneously at C–Ni bridge sites rather than Ni top sites, while subsurface hydrogen facilitates bent CO 2 adsorption crucial for activation. High CO 2 RR selectivity toward CO arises from site separation: Ni centers drive CO2RR, while the hydrogen evolution reaction (HER) occurs at the C–Ni bridge or N sites and from thermodynamic suppression of HER at moderate hydrogen coverage. At more negative potentials, a shift in the CO 2 RR rate-determining process (RDP) and Ni out-of-surface displacement induced by coadsorption of H and H 2 O jointly reduce activity and selectivity. Thus, both the high CO2RR selectivity of Ni–N–C catalysts and its reversal with more negative potentials can be rationalized by accounting for hydrogenated surfaces. This highlights the necessity of modeling realistic; in situ conditions. This framework provides generalizable insights into the dynamic behavior of active sites in SACs, offering guidance for the rational design of active and robust catalysts for a wide range of electrochemical reactions.

25 ENERGY STORAGE↗

DOE OSTI2025

Long-Range Allosteric Communication Modulated by Active Site Mn(II) Coordination Drives Catalysis in Xanthobacter autotrophicus Acetone Carboxylase

Acetone carboxylase (AC) from Xanthobacter autotrophicus is a 360 KDa α2β2γ2 heterohexamer that catalyzes the ATP-dependent formation of phosphorylated acetone and bicarbonate intermediates that react at Mn(II) metal active sites to form acetoacetate. Structural models of X. autotrophicus AC (XaAC) with and without nucleotides reveal that the binding and phosphorylation of the two substrates occurs ~40 Å from the Mn(II) active sites where acetoacetate is formed. Based on the crystal structures, a significant conformational change was proposed to open and close a tunnel that facilitates the passage of reaction intermediates between the sites for nucleotide binding and phosphorylation of substrates and Mn(II) sites of acetoacetate formation. We have employed electron paramagnetic resonance (EPR), kinetic assays, and hydrogen/deuterium exchange mass spectrometry (HDX-MS) of poised ligand-bound states and site-specific amino acid variants to complete an in-depth analysis of Mn(II) coordination and allosteric communication throughout the catalytic cycle. In contrast with the established paradigms for carboxylation, our analyses of XaAC suggested a carboxylate shift that couples both local and long-range structural transitions. Shifts in the coordination mode of a single carboxylic acid residue (αE89) mediate both catalysis proximal to a Mn(II) center and communication with an ATP active site in a separate subunit of a 180 kDa α2β2γ2 complex at a distance of 40 Å. This work demonstrates the power of combining structural models from X-ray crystallography with solution-phase spectroscopy and biophysical techniques to elucidate functional aspects of a multi-subunit enzyme.

Biochemistry & Molecular Biology↗

DOE OSTI2023

Pyridine-containing substrate analogs are restricted from accessing the human cytochrome P450 8B1 active site by tryptophan 281

The human oxysterol 12α-hydroxylase cytochrome P450 8B1 (CYP8B1) is a validated drug target for both type 2 diabetes and nonalcoholic fatty liver disease, but effective selective inhibitors are not yet available. Herein, steroidal substrate-mimicking compounds with a pyridine ring appended to the C12 site of metabolism were designed as inhibitors, synthesized, and evaluated in terms of their functional and structural interactions with CYP8B1. While the pyridine nitrogen was intended to coordinate the CYP8B1 active site heme iron, none of these compounds elicited shifts in the CYP8B1 Soret absorbance consistent with this type of interaction. However, when CYP8B1 was cocrystallized with the pyridine-containing compound with the 3-keto-Δ4 steroid backbone most similar to the endogenous substrate, it was apparent that this ligand was bound in a channel leading to the active site, instead of near the heme iron. Inspection of this structure suggested that tryptophan 281 directly above the heme might restrict active site binding of potential inhibitors with this design. This hypothesis was supported when a CYP8B1 W281F mutation did allow all three compounds to coordinate the heme iron as designed. These results indicated that the design of next-generation CYP8B1 inhibitors should be compatible with the low-ceiling tryptophan immediately above the heme iron.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Active Learning-driven Quantitative Synthesis-Structure-Property Relations for Improving Performance and Revealing Active Sites of Nitrogen-Doped Carbon for the Hydrogen Evolution Reaction

While quantitative structure-properties relations (QSPRs) have been developed successfully in multiple fields, catalyst synthesis affects structure and in turn performance, making simple QSPRs inadequate. Furthermore, catalysts often have multiple active sites preventing one from obtaining insights into structure-property relations. Here, we develop a data-driven quantitative synthesis-structure-property relation (QS2PRs) methodology to elucidate correlations between catalyst synthesis conditions, structural properties as well as observed performance and to provide fundamental insights into active sites and a systematic way to optimize practical catalysts. Here, we demonstrate the approach to the synthesis of nitrogen-doped catalysts (NDC) made via pyrolysis for the performance of the electrochemical hydrogen evolution reaction (HER), quantified by the onset potential and the current density. We determine crystallinity, nitrogen species type and fraction, surface area, and pore structure of the NDC’s using XRD, XPS, and BET characterization. We demonstrated that an active learning-based optimization combined with various elementary machine learning tools (regression, principal component analysis, partial least squares) can efficiently identify optimum pyrolysis conditions to tune structural characteristics and performance with concomitant savings in materials and experimental time. Unlike previous reports on the importance of pyridinic or graphitic nitrogen, we discover that the electrochemical performance is not driven by a single catalyst property; rather, it arises from a multivariate influence of nitrogen dopants, pore structure and disorder in the NDC materials. Identification of active sites can help mechanistic understanding and further catalyst improvement.

42 ENGINEERING↗

NASA NTRSDate not supplied

Simulation of Etch Pit Formation in DSMC Through Active Sites in Carbon Fiber Micro-Structures

Erosion of carbon due to oxidation does not occur uniformly but through localized etch pit formation because of active surface sites. In this work we demonstrate a newly developed capability to capture pitting of carbon fiber microstructures such as FiberForm, which is commonly used as the base material for NASA’s spacecraft ablative thermal protection systems (TPS). The simulations are performed at the meso-scale in order to capture the pit formation and growth using direct simulation Monte Carlo (DSMC), specifically using the Stochastic PArallel Rarefied-gas Time-accurate Analyzer (SPARTA) code. Legacy and latest models both assume uniform reactivity of carbon surface sites with oxygen even at the meso-scale level. However, in reality the carbon surface has locally different reaction rates due to the presence of defects at the atomic scale. The defective nature of these sites enhances their reactivity with atmospheric gases compared to the non-defective sites (2-3 orders of magnitude) and are termed as “active sites”. Thus, these sites tend to be the first to react and eventually get removed through the formation of gases such as CO, CO2, and CN. Their removal results in all the neighboring atoms becoming defective, thus leading to chain reaction of localized carbon removal and formation of etch pits. Capturing the formation of pits during the ablation simulation of carbon micro-structures is critical to predicting their structural failure. Recently a detailed surface chemistry framework was developed in SPARTA, capable of incorporating various detailed surface reaction mechanisms. We have implemented the capability of a single surface having multiple site sets with different reactivities within this framework. We have used this feature to model the presence of active sites on carbon surfaces, whose reactivity is orders of magnitude higher than that of the passive sites due to the presence of defects. The active site fraction is a property of surface elements within SPARTA and is directly proportional to the local reactivity of each surface element. By introducing an initial distribution of the active site fraction across the carbon surface and propagating it in a manner that mimics the evolution of real reacting carbon surfaces, we can capture the formation and growth of etch pits as a result of surface consumption reactions such as oxidation.

DSMC↗

NASA NTRSDate not supplied

DSMC Simulation of Etch Pit Formation Through Active Sites in Carbon Fiber Micro-Structures

DSMC↗

DOE OSTI2023

Dynamically Formed Active Sites on Liquid Boron Oxide for Selective Oxidative Dehydrogenation of Propane

Boron-based catalysts have been shown to be both active and selective for driving the oxidative dehydrogenation of propane (ODHP) without the use of precious metals. This reaction occurs at temperatures that melt the oxide catalyst which challenges our ability to identify the liquid structures of the boron oxide phase under reaction conditions, hindering the understanding of its active sites and reaction mechanism. By combining ab initio molecular dynamics simulation, in-situ Raman characterization, and microkinetic modeling, we propose that the di-coordinated boron sites (BO2) in liquid boron oxide are the active species for O2 activation under reaction conditions. The formed peroxy-like species (>B-O-O-B<) can be viewed as a moderate oxidant for ODHP. The dynamical >B-O* dangling bond originated from >B-O-O-B< site as well as the liquid B2O3 structure itself, plays a critical role in the abstraction of H atoms from propane (C3H7 radical formation). Microkinetic modeling reveals C3H7 radical formation to be the main rate controlling step (~75% degree of rate control) with the dehydration of boron hydroxyls (B-OHs) to recover the di-coordinated boron active sites controlling the remainder of the rate (~25% degree of rate control). Moreover, the activation barriers are found to strongly depend upon the surface B-OH concentration. These findings provide significant insights into the active site and reaction mechanisms on boron-based catalysts for ODHP and underlie the importance of understanding the liquid nature of the catalyst to account for the catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

CeO2 Nanoparticle Doping as a Probe of Active Site Speciation in the Catalytic Hydrolysis of Organophosphates

Organophosphate hydrolysis is important for degrading environmentally harmful compounds and recovering phosphate ions in biological molecules. CeO2 nanocrystals have been well-studied for dephosphorylation via hydrolysis owing to the accessible and tunable distribution of Ce3+ and Ce4+ ions. However, there remains uncertainty in the literature regarding which surface defect properties direct catalytic activity, such as the Ce3+/Ce4+ distribution, oxygen vacancies, faceting, and dopants, and to what degree they contribute to efficient hydrolysis. Trivalent (M3+) dopants serve as a tool for manipulating defects, including the concentration of Ce3+ and oxygen vacancies, thereby influencing the hydrolytic activity of CeO2. Herein, trivalent metal ions (M = Y3+, Cr3+, In3+, and Gd3+) were employed to modulate the active sites on the CeO2 nanocrystal surface, and the effects of each metal dopant on the cerium oxide active sites for organophosphate hydrolysis were investigated. M-doped CeO2 nanoparticles were synthesized via hydrothermal methods, followed by annealing to remove ligands and prime the nanocrystal surface for catalysis. Catalytic performance was evaluated using dimethyl-p¬-nitrophenyl phosphate (DMNP) as a model organophosphate substrate, with degradation monitored over time using UV-visible absorption spectroscopy. Powder X-ray diffraction (PXRD), X-ray photoelectron spectroscopy (XPS), and Raman spectroscopy revealed successful doping of CeO2 in all cases, albeit with distinctive characteristics demonstrating how M3+ dopants affect catalysis. We show that CeO2 exhibits high sensitivity to dopants that generate lattice strain, Ce3+ ions, and oxygen vacancy defects. Consequently, achieving high catalytic efficiency within CeO2 requires a balanced active site ensemble, wherein defects are maintained at optimal concentrations and distributions on the nanocrystal surface.

Miura-Stempel, Emily L.↗

DOE OSTI2021

Identification and quantification of distinct active sites in Hf-Beta zeolites for transfer hydrogenation catalysis

Despite the significant progress made in characterizing different framework heteroatom sites that exist in Lewis acidic zeolites with probe molecule adsorption and spectroscopy, methods to reliably quantify site counts remain indefinite and have been primarily limited to Sn and Ti Lewis acid sites. Here, methods to quantify framework Lewis acidic Hf 4+ sites in zeolite Beta (Hf-Beta) with two Lewis base titrants (pyridine, deuterated acetonitrile) were developed using infrared (IR) spectroscopy. Lewis acid site counts for Hf-Beta zeolites were validated by measuring integrated molar extinction coefficients (IMECs; ε, cm μmol –1 ) on Sn-Beta zeolites using identical Lewis base titrants to benchmark site counts with established literature procedures to quantify Lewis acid sites in Beta zeolites from IR spectra. Highlighting the importance of benchmarking active site counts against well-established experimental protocols, IMECs of CD 3 CN bound to open (ε(Sn; 2316 cm –1 ): 1.80 ± 0.25) and closed (ε(Sn; 2308 cm –1 ): 3.76 ± 0.33) Sn sites were ~1.8x larger than those previously reported while total Lewis acid site counts agreed with those measured by pyridine (ε(Sn; 1451 cm –1 ): 1.58 ± 0.16) on six different Sn-Beta zeolites. IMECs measured for IR peaks reflecting pyridine bound to Lewis acidic Hf sites (ε(Hf; 1448 cm –1 ): 1.54 ± 0.21) and CD 3 CN bound to open (ε(Hf; 2313 cm –1 ): 2.40 ± 0.22) and closed (ε(Hf; 2307 cm –1 ): 3.55 ± 0.41) Hf sites, gave similar counts for the total number of Lewis acidic sites across six Hf-Beta zeolites (Si/Hf = 100–413). Consistent with previous reports with Sn-Beta catalysts where open Sn sites are responsible for catalytic turnover, apparent first and zero-order MPVO rate constants (0.01–1 M cyclohexanone in 2-butanol; per total Hf, 373 K) correlated with the total number of open Hf sites, per total Hf, but not with the total number of closed Hf sites or total Lewis acid site counts. Measured initial MPVO rates (0.1 M cyclohexanone in 2-butanol, per open Hf, 373 K) were ~25x higher on hydrophobic Hf-Beta-F than on hydrophilic Hf-Beta-OH zeolites. Overall, the apparent first-order MPVO rate constants (2-butanol solvent, per open Hf, 373 K) were ~6x higher on Hf-Beta-F than on Hf-Beta-OH zeolites. The characterization methods reported here enable normalization of MPVO turnover rates on Sn- and Hf-Beta zeolites by their number of open sites. Finally, this enables performing quantitative rate comparisons across Lewis acid zeolites of varying active site identity, solvation, and pore topology used in liquid-phase catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate C $\bar{β}$ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRSDate not supplied

Simulation of etch pit formation through active sites in carbon fiber micro-structures

Erosion of carbon due to oxidation does not occur uniformly but through localized etch pit formation as a result of active surface sites. In this work we demonstrate a newly developed capability to capture pitting of carbon fiber microstructures such as FiberForm, which is commonly used as the base material for NASA’s spacecraft ablative thermal protection systems (TPS). The simulations are performed at the meso-scale in order to capture the pit formation and growth using direct simulation Monte Carlo (DSMC), specifically using the Stochastic PArallel Rarefied-gas Time-accurate Analyzer (SPARTA) code. Legacy and latest models both assume uniform reactivity of carbon surface sites with oxygen even at the meso-scale level. However, in reality the carbon surface has locally different reaction rates due to the presence of defects at the atomic scale. The defective nature of these sites enhances their reactivity with atmospheric gases compared to the non-defective sites (2-3 orders of magnitude) and are termed as “active sites”. Thus, these sites tend to be the first to react and eventually get removed through the formation of gasses such as CO, CO2, and CN. Their removal results in all the neighboring atoms becoming defective, thus leading to chain reaction of localized carbon removal and formation of etch pits. Capturing the formation of pits during the ablation simulation of carbon micro-structures is critical to predicting their structural failure. Recently a detailed surface chemistry framework was developed in SPARTA, capable of incorporating various reaction mechanisms such as adsorption, desorption, Eley-Rideal (ER) and Langmuir-Hinshelwood (LH) mechanisms. We have implemented the capability of a single surface having multiple site sets with different reactivities within this framework. We have used this feature to model the presence of active sites on carbon surfaces, whose reactivity is orders of magnitude higher than that of the passive sites due to the presence of defects. The active site fraction is a property of surface elements within SPARTA and is directly proportional to the local reactivity of each surface element. By introducing an initial distribution of the active site fraction across the carbon surface and propagating it in a manner that mimics the evolution of real reacting carbon surfaces, we can capture the formation and growth of etch pits as a result of surface consumption reactions such as oxidation.

DSMC↗

DOE OSTI2023

Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

β-Lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This has created a major public health crisis. The use of β-lactamase inhibitors has proven useful in restoring the activity of β-lactam antibiotics, yet, effective clinically approved inhibitors against class B metallo-β-lactamases are not available. L1, a class B3 enzyme expressed by Stenotrophomonas maltophilia , is a significant contributor to the β-lactam resistance displayed by this opportunistic pathogen. Structurally, L1 is a tetramer with two elongated loops, α3-β7 and β12-α5, present around the active site of each monomer. Residues in these two loops influence substrate/inhibitor binding. To study how the conformational changes of the elongated loops affect the active site in each monomer, enhanced sampling molecular dynamics simulations were performed, Markov State Models were built, and convolutional variational autoencoder-based deep learning was applied. The key identified residues (D150a, H151, P225, Y227, and R236) were mutated and the activity of the generated L1 variants was evaluated in cell-based experiments. The results demonstrate that there are extremely significant gating interactions between α3-β7 and β12-α5 loops. Taken together, the gating interactions with the conformational changes of the key residues play an important role in the structural remodeling of the active site. These observations offer insights into the potential for novel drug development exploiting these gating interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

An Active‐Site Sulfonate Group Creates a Fast Water Oxidation Electrocatalyst That Exhibits High Activity in Acid

Abstract The storage of solar energy in chemical bonds will depend on pH‐universal catalysts that are not only impervious to acid, but actually thrive in it. Whereas other homogeneous water oxidation catalysts are less active in acid, we report a catalyst that maintained high electrocatalytic turnover frequency at pH values as low as 1.1 and 0.43 ( k cat =1501±608 s −1 and 831±254 s −1 , respectively). Moreover, current densities, related to catalytic reaction rates, ranged from 15 to 50 mA cm −2 mM −1 comparable to those reported for state‐of‐the‐art heterogeneous catalysts and 30 to 100 times greater than those measured for two prominent literature homogeneous catalysts at pH 1.1 and 0.43. The catalyst also exhibited excellent durability when a chemical oxidant was used (Ce IV , 7400 turnovers, TOF 0.88 s −1 ). Preliminary computational studies suggest that the unusual active‐site sulfonate group acts a proton relay even in strong acid, as intended.

Nash, Aaron G.↗

DOE OSTI2020

An Active–Site Sulfonate Group Creates a Fast Water Oxidation Electrocatalyst That Exhibits High Activity in Acid

The storage of solar energy in chemical bonds will depend on pH–universal catalysts that are not only impervious to acid, but actually thrive in it. Whereas other homogeneous water oxidation catalysts are less active in acid, we report a catalyst that maintained high electrocatalytic turnover frequency at pH values as low as 1.1 and 0.43 (k cat = 1501±608 s –1 and 831±254 s –1 , respectively). Moreover, current densities, related to catalytic reaction rates, ranged from 15 to 50 mA cm –2 mM –1 comparable to those reported for state–of–the–art heterogeneous catalysts and 30 to 100 times greater than those measured for two prominent literature homogeneous catalysts at pH 1.1 and 0.43. The catalyst also exhibited excellent durability when a chemical oxidant was used (Ce IV , 7400 turnovers, TOF 0.88 s –1 ). Here, preliminary computational studies suggest that the unusual active–site sulfonate group acts a proton relay even in strong acid, as intended.

14 SOLAR ENERGY↗

DOE OSTI2024

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

One of the seven natural CO 2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO 2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

bacterial metabolism↗

DOE OSTI2022

An active site loop toggles between conformations to control antibiotic hydrolysis and inhibition potency for CTX-M β-lactamase drug-resistance enzymes

Abstract β-lactamases inactivate β-lactam antibiotics leading to drug resistance. Consequently, inhibitors of β-lactamases can combat this resistance, and the β-lactamase inhibitory protein (BLIP) is a naturally occurring inhibitor. The widespread CTX-M-14 and CTX-M-15 β-lactamases have an 83% sequence identity. In this study, we show that BLIP weakly inhibits CTX-M-14 but potently inhibits CTX-M-15. The structure of the BLIP/CTX-M-15 complex reveals that binding is associated with a conformational change of an active site loop of β-lactamase. Surprisingly, the loop structure in the complex is similar to that in a drug-resistant variant (N106S) of CTX-M-14. We hypothesized that the pre-established favorable loop conformation of the N106S mutant would facilitate binding. The N106S substitution results in a ~100- and 10-fold increase in BLIP inhibition potency for CTX-M-14 and CTX-M-15, respectively. Thus, this indicates that an active site loop in β-lactamase toggles between conformations that control antibiotic hydrolysis and inhibitor susceptibility. These findings highlight the role of accessible active site conformations in controlling enzyme activity and inhibitor susceptibility as well as the influence of mutations in selectively stabilizing discrete conformations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Formation of open ruthenium branched structures with highly exposed active sites for oxygen evolution reaction electrocatalysis

The formation of exposed active sites that have high activity and stability for oxygen evolution reaction (OER) catalysis is a significant opportunity for improving water electrolysers. Low-index facets surface Ru can achieve both high activity and stability for OER. Here, we present a new catalyst design where low-index faceted Ru branches are grown off the corners of Pt nanocubes, forming open Ru branched nanoparticles. This open branched structure, exposing low-index facets on its length-tunable branch, enables a high electrochemically active surface area (ECSA), achieving high activity and stability for OER. This design strategy and synthetic control provide a principle for achieving high-performance OER nanocatalysts.

Xiao, Sa [The University of New South Wales, Sydne↗

DOE OSTI2020

A missense variant remote from the active site impairs stability of human phosphoglucomutase 1

Abstract Missense variants of human phosphoglucomutase 1 (PGM1) cause the inherited metabolic disease known as PGM1 deficiency. This condition is categorised as both a glycogen storage disease and a congenital disorder of glycosylation. Approximately 20 missense variants of PGM1 are linked to PGM1 deficiency, and biochemical studies have suggested that they fall into two general categories: those affecting the active site and catalytic efficiency, and those that appear to impair protein folding and/or stability. In this study, we characterise a novel variant of Arg422, a residue distal from the active site of PGM1 and the site of a previously identified disease‐related variant (Arg422Trp). In prior studies, the R422W variant was found to produce insoluble protein in a recombinant expression system, precluding further in vitro characterisation. Here we investigate an alternative variant of this residue, Arg422Gln, which is amenable to experimental characterisation presumably due to its more conservative physicochemical substitution. Biochemical, crystallographic, and computational studies of R422Q establish that this variant causes only minor changes in catalytic efficiency and 3D structure, but is nonetheless dramatically reduced in stability. Unexpectedly, binding of a substrate analog is found to further destabilise the protein, in contrast to its stabilising effect on wild‐type PGM1 and several other missense variants. This work establishes Arg422 as a lynchpin residue for the stability of PGM1 and supports the impairment of protein stability as a pathomechanism for variants that cause PGM1 deficiency. Synopsis Biochemical and structural studies of a missense variant far from the active site of human PGM1 identify a residue with a key role in enzyme stability.

Stiers, Kyle M.↗