Oxygen Activation in Aromatic Ring Cleaving Salicylate Dioxygenase: Detection of Reaction Intermediates with a Nitro-substituted Substrate Analog.

Cupin dioxygenases such as salicylate 1,2-dioxygense (SDO) perform aromatic C-C bond scission via a 3-His motif tethered iron cofactor. Here, transient kinetics measurements are used to monitor the catalytic cycle of SDO by using a nitro-substituted substrate analog, 3-nitrogentisate. Compared to the natural substrate, the nitro group reduces the enzymatic kcat by 500-fold, thereby facilitating the detection and kinetic characterization of reaction intermediates. Sums and products of reciprocal relaxation times derived from kinetic measurements were found to be linearly dependent on O2 concentration, suggesting reversible formation of two distinct intermediates. Dioxygen binding to the metal cofactor takes place with a forward rate of 5.9×103 M-1 s-1: two orders of magnitude slower than other comparable ring-cleaving dioxygenses. Optical chromophore of the first intermediate is distinct from the in situ generated SDO Fe(III)-O2⋅- complex but closer to the enzyme-substrate precursor.

Calcium Regulates S100A12 Zinc Sequestration by Limiting Structural Variations.

Antimicrobial proteins such as S100A12 and S100A8/A9 are highly expressed and secreted by neutrophils during infection and participate in human immune response by sequestering transition metals. At neutral pH, S100A12 sequesters Zn2+ with nanomolar affinity, which is further enhanced upon calcium binding. We investigated the pH dependence of human S100A12 zinc sequestration by using Co2+ as a surrogate. Apo-S100A12 exhibits strong Co2+ binding between pH 7.0 and 10.0 that progressively diminishes as the pH is decreased to 5.3. Ca2+ -S100A12 can retain nanomolar Co2+ binding up to pH 5.7. NMR spectroscopic measurements revealed that calcium binding does not alter the side-chain protonation of the Co2+ /Zn2+ binding histidine residues. Instead, the calcium-mediated modulation is achieved by restraining pH-dependent conformational changes to EF loop 1, which contains Co2+ /Zn2+ binding Asp25. This calcium-induced enhancement of Co2+ /Zn2+ binding might assist in the promotion of antimicrobial activities in humans by S100 proteins during neutrophil activation under subneutral pH conditions.

Accurate Backbone 13 C and 15 N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter.

Chemical shift tensors obtained from solid-state NMR spectroscopy are very sensitive reporters of structure and dynamics in proteins. While accurate 13 C and 15 N chemical shift tensors are accessible by magic angle spinning (MAS) NMR, their quantum mechanical calculations remain challenging, particularly for 15 N atoms. Here we compare experimentally determined backbone 13 Cα and 15 NH chemical shift tensors by MAS NMR with hybrid quantum mechanics/molecular mechanics/molecular dynamics (MD-QM/MM) calculations for the carbohydrate-binding domain of galectin-3. Excellent agreement between experimental and computed 15 NH chemical shift anisotropy values was obtained using the Amber ff15ipq force field when solvent dynamics was taken into account in the calculation. Our results establish important benchmark conditions for improving the accuracy of chemical shift calculations in proteins and may aid in the validation of protein structure models derived by MAS NMR.

Ca(II) and Zn(II) Cooperate To Modulate the Structure and Self-Assembly of S100A12.

S100A12 is a member of the Ca2+ binding S100 family of proteins that functions within the human innate immune system. Zinc sequestration by S100A12 confers antimicrobial activity when the protein is secreted by neutrophils. Here, we demonstrate that Ca2+ binding to S100A12's EF-hand motifs and Zn2+ binding to its dimeric interface cooperate to induce reversible self-assembly of the protein. Solution and magic angle spinning nuclear magnetic resonance spectroscopy on apo-, Ca2+-, Zn2+-, and Ca2+,Zn2+-S100A12 shows that significant metal binding-induced chemical shift perturbations, indicative of conformational changes, occur throughout the polypeptide chain. These perturbations do not originate from changes in the secondary structure of the protein, which remains largely preserved. While the overall structure of S100A12 is dominated by Ca2+ binding, Zn2+ binding to Ca2+-S100A12 introduces additional structural changes to helix II and the hinge domain (residues 38-53). The hinge domain of S100A12 is involved in the molecular interactions that promote chemotaxis for human monocyte, acute inflammatory responses and generates edema. In Ca2+-S100A12, helix II and the hinge domain participate in binding with the C-type immunoglobulin domain of the receptor for advanced glycation products (RAGE). We discuss how the additional conformational changes introduced to these domains upon Zn2+ binding may also impact the interaction of S100A12 and target proteins such as RAGE.

Substrate promiscuity and active site differences in gentisate 1,2-dioxygenases: electron paramagnetic resonance study.

Gentisate 1,2-dioxygenases (GDOs) are non-heme iron enzymes that catalyze the oxidation of dihydroxylated aromatic substrate, gentisate (2,5-dihydroxybenzoate). Salicylate 1,2-dioxygenase (SDO), a member of the GDO family, performs the ring scission of monohydroxylated substrates such as salicylate, thereby oxidizing a broader range of substrates compared to GDOs. Although the two types of enzymes share a high degree of sequence similarity, the origin of substrate specificity between SDO and GDOs is not understood. We present electron paramagnetic resonance (EPR) investigation of ferrous-nitrosyl complexes of SDO and a GDO from the bacterium Corynebacterium glutamicum (GDOCg). The EPR spectra of these complexes, which mimic the Fe-substrate-O2 intermediates in the catalytic cycle, show unexpected differences in the substrate binding mode and the coordination geometry of the metal cofactor in the two enzymes. Binding of substrate to the ferrous center increases the symmetry of the Fe(II)-NO complex in SDO, while a reverse trend is observed in GDOCg where substrate ligation reduces the symmetry of the nitrosyl complex. Identical EPR spectra were obtained for the NO derivatives of a variant of GDOCg(A112G), which can oxidize salicylate, and wild-type GDOCg revealing that the A112G mutation does not alter the nature of the Fe-substrate-O2 ternary complex.

Direct detection and characterization of bioinorganic peroxo moieties in a vanadium complex by 17O solid-state NMR and density functional theory.

Electronic and structural properties of short-lived metal-peroxido complexes, which are key intermediates in many enzymatic reactions, are not fully understood. While detected in various enzymes, their catalytic properties remain elusive because of their transient nature, making them difficult to study spectroscopically. We integrated 17O solid-state NMR and density functional theory (DFT) to directly detect and characterize the peroxido ligand in a bioinorganic V(V) complex mimicking intermediates non-heme vanadium haloperoxidases. 17O chemical shift and quadrupolar tensors, measured by solid-state NMR spectroscopy, probe the electronic structure of the peroxido ligand and its interaction with the metal. DFT analysis reveals the unusually large chemical shift anisotropy arising from the metal orbitals contributing towards the magnetic shielding of the ligand. The results illustrate the power of an integrated approach for studies of oxygen centers in enzyme reaction intermediates.

High-spin Mn-oxo complexes and their relevance to the oxygen-evolving complex within photosystem II.

The structural and electronic properties of a series of manganese complexes with terminal oxido ligands are described. The complexes span three different oxidation states at the manganese center (III-V), have similar molecular structures, and contain intramolecular hydrogen-bonding networks surrounding the Mn-oxo unit. Structural studies using X-ray absorption methods indicated that each complex is mononuclear and that oxidation occurs at the manganese centers, which is also supported by electron paramagnetic resonance (EPR) studies. This gives a high-spin Mn(V)-oxo complex and not a Mn(IV)-oxy radical as the most oxidized species. In addition, the EPR findings demonstrated that the Fermi contact term could experimentally substantiate the oxidation states at the manganese centers and the covalency in the metal-ligand bonding. Oxygen-17-labeled samples were used to determine spin density within the Mn-oxo unit, with the greatest delocalization occurring within the Mn(V)-oxo species (0.45 spins on the oxido ligand). The experimental results coupled with density functional theory studies show a large amount of covalency within the Mn-oxo bonds. Finally, these results are examined within the context of possible mechanisms associated with photosynthetic water oxidation; specifically, the possible identity of the proposed high valent Mn-oxo species that is postulated to form during turnover is discussed.

Saturation capability of short phase modulated pulses facilitates the measurement of longitudinal relaxation times of quadrupolar nuclei.

The ability of various pulse types, which are commonly applied for distance measurements, to saturate or invert quadrupolar spin polarization has been compared by observing their effect on magnetization recovery curves under magic-angle spinning. A selective central transition inversion pulse yields a bi-exponential recovery for a diamagnetic sample with a spin-3/2, consistent with the existence of two processes: the fluctuations of the electric field gradients with identical single (W1) and double (W2) quantum quadrupolar-driven relaxation rates, and spin exchange between the central transition of one spin and satellite transitions of a dipolar-coupled similar spin. Using a phase modulated pulse, developed for distance measurements in quadrupolar spins (Nimerovsky et al., JMR 244, 2014, 107-113) and suggested for achieving the complete saturation of all quadrupolar spin energy levels, a mono-exponential relaxation model fits the data, compatible with elimination of the spin exchange processes. Other pulses such as an adiabatic pulse lasting one-third of a rotor period, and a two-rotor-period long continuous-wave pulse, both used for distance measurements under special experimental conditions, yield good fits to bi-exponential functions with varying coefficients and time constants due to variations in initial conditions. Those values are a measure of the extent of saturation obtained from these pulses. An empirical fit of the recovery curves to a stretched exponential function can provide general recovery times. A stretching parameter very close to unity, as obtained for a phase modulated pulse but not for other cases, suggests that in this case recovery times and longitudinal relaxation times are similar. The results are experimentally demonstrated for compounds containing 11B (spin-3/2) and 51V (spin-7/2). We propose that accurate spin lattice relaxation rates can be measured by a short phase modulated pulse (<1-2ms), similarly to the "true T1" measured by saturation with an asynchronous pulse train (Yesinowski, JMR 252, 2015, 135-144).

Effect of positional isomerism and vanadium substitution on 51V magic angle spinning NMR Spectra Of Wells-Dawson polyoxotungstates.

We examined the positional isomerism and vanadium substitution on the 51V magic angle spinning NMR spectra of potassium salts of vanadium-substituted polyoxotungstates of the Wells-Dawson series. NMR parameters of this class of catalytically active polyoxotungstates effect of are reported. Multiple species, indicative of differences in the local environment at the substitution sites, are observed in solid-state NMR spectra of the di- and tri- substituted complexes in contrast to solution NMR spectra, where single average chemical shift was observed. The quadrupolar and chemical shift anisotropy parameters depend strongly on the position and the degree of the vanadium substitution into the oxoanion core establishing 51V SATRAS NMR spectroscopy as a sensitive probe of the local electronic environment in these catalytically active solids.

5¹V NMR Crystallography of Vanadium Chloroperoxidase and Its Directed Evolution P395D/L241V/T343A Mutant: Protonation Environments of the Active Site.

Vanadium-dependent haloperoxidases (VHPOs) perform two-electron oxidation of halides using hydrogen peroxide. Their mechanism, including the factors determining the substrate specificity and the pH-dependence of the catalytic rates, is poorly understood. The vanadate cofactor in the active site of VHPOs contains "spectroscopically silent" V(V), which does not change oxidation state during the reaction. We employed an NMR crystallography approach based on (51)V magic angle spinning NMR spectroscopy and Density Functional Theory, to gain insights into the structure and coordination environment of the cofactor in the resting state of vanadium-dependent chloroperoxidases (VCPO). The cofactor environments in the wild-type VCPO and its P395D/L241V/T343A mutant exhibiting 5-100-fold improved catalytic activity are examined at various pH values. Optimal sensitivity attained due to the fast MAS probe technologies enabled the assignment of the location and number of protons on the vanadate as a function of pH. The vanadate cofactor changes its protonation from quadruply protonated at pH 6.3 to triply protonated at pH 7.3 to doubly protonated at pH 8.3. In contrast, in the mutant, the vanadate protonation is the same at pH 5.0 and 8.3, and the cofactor is doubly protonated. This methodology to identify the distinct protonation environments of the cofactor, which are also pH-dependent, could help explain the different reactivities of the wild-type and mutant VCPO and their pH-dependence. This study demonstrates that (51)V-based NMR crystallography can be used to derive the detailed coordination environments of vanadium centers in large biological molecules.

Magic angle spinning NMR spectroscopy: a versatile technique for structural and dynamic analysis of solid-phase systems.

Magic Angle Spinning (MAS) NMR spectroscopy is a powerful method for analysis of a broad range of systems, including inorganic materials, pharmaceuticals, and biomacromolecules. The recent developments in MAS NMR instrumentation and methodologies opened new vistas to atomic-level characterization of a plethora of chemical environments previously inaccessible to analysis, with unprecedented sensitivity and resolution.

NMR crystallography of an oxovanadium(V) complex by an approach combining multinuclear magic angle spinning NMR, DFT, and spin dynamics simulations.

Bioinorganic vanadium(V) solids are often challenging for structural analysis. Here, we explore an NMR crystallography approach involving multinuclear (13) C/(51) V solid-state NMR spectroscopy, density functional theory (DFT), and spin dynamics numerical simulations, for the spectral assignment and the 3D structural analysis of an isotopically unmodified oxovanadium(V) complex, containing 17 crystallographically inequivalent (13) C sites. In particular, we report the first NMR determination of C-V distances. So far, the NMR observation of (13) C-(51) V proximities has been precluded by the specification of commercial NMR probes, which cannot be tuned simultaneously to the close Larmor frequencies of these isotopes (100.6 and 105.2 MHz for (13) C and (51) V, respectively, at 9.4 T). By combining DFT calculations and (13) C-(51) V NMR experiments, we propose a complete assignment of the (13) C spectrum of this oxovanadium(V) complex. Furthermore, we show how (13) C-(51) V distances can be quantitatively estimated.

RF inhomogeneity and how it controls CPMAS.

In this report we discuss the effect of radiofrequency field (RF) inhomogeneity on cross-polarization (CP) under magic-angle spinning (MAS) by reviewing the dependence of the CP-detected signal intensity as a function of the position in the sample space. We introduce a power-function model to quantify the position-dependent RF-amplitude profile. The applicability of this model is experimentally verified by nutation spectra obtained by direct signal detection, as well as by CPMAS signal detection, in two commercial MAS probes with different degrees of RF inhomogeneity. A conclusion is that substantial sections of a totally filled rotor, even in a probe with rather good homogeneity, do not contribute at all to the detected spectra. The consequence is that in CPMAS-based recoupling experiments, such as the CP-with-variable-contact-time (CPVC), spatial selectivity of the Hartmann-Hahn matching condition overcomes complications that could be caused by RF inhomogeneity permitting determination of accurate spectral parameters even in cases with high inhomogeneity.

A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids.

Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN-symmetry based experiments, from which the principal components of the 1H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U-13C,15N-labeled histdine demonstrating that 1H chemical shift tensors can be reliably determined for the 1H15N and 1H13C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1H(C) and 1H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids.

Current treatments for the management of homozygous familial hypercholesterolemia: a systematic review and commentary.

AIMS: Homozygous familial hypercholesterolemia (HoFH) is a rare disorder characterized by markedly elevated circulating low-density lipoprotein cholesterol (LDL-C) from birth. This review aimed to critically evaluate treatments for HoFH with respect to their efficacy, safety, accessibility, overall context and position within the treatment pathway. METHODS: A mixed-methods review was undertaken to systematically identify and characterize primary interventional studies on HoFH, with a focus on LDL-C reduction as the primary outcome. Interventions assessed were ezetimibe, proprotein convertase subtilisin/kexin type 9 inhibitors (PCSK9i), lomitapide, evinacumab, with or without LDL apheresis. RESULTS: Twenty-six seminal studies reporting unique patient data were identified. Four studies were randomized controlled trials (RCTs) with the remainder being single-arm trials or observational registries. Data extracted were heterogeneous and not suitable for meta-analyses. Two RCTs, assessed at being low risk of bias, demonstrated PCSK9i were safe and moderately effective. An RCT demonstrated evinacumab was safe and effective in all HoFH subgroups. Lomitapide was reported to be efficacious in a single-arm trial, but issues with adverse events, tolerability, and adherence were identified. An RCT on ezetimibe showed it was moderately effective when combined with a statin. LDL apheresis was reported as effective, but its evidence base was at very high risk of bias. All interventions lowered LDL-C, but the magnitude of this, and certainty in the supporting evidence, varied. CONCLUSION: In practice, multiple treatments are required to treat HoFH. The sequencing of these should be made on an individualized basis, with consideration made to the benefits of each intervention.

Homozygous familial hypercholesterolaemia (HoFH) is a rare genetic disorder that results in elevated cholesterol levels, which can cause premature cardiovascular events such as heart attacks and stroke. We performed a literature review to systematically identify and analyse studies reporting on newer treatments for HoFH which lower cholesterol levels, focussing on the overall advantages and disadvantages of each treatment. We identified 26 studies, including clinical trials and observational research, reporting on the interventions ezetimibe, proprotein convertase subtilisin/kexin type 9 inhibitors (PCSK9i), lomitapide, evinacumab, and LDL apheresis. While all treatments showed promise in reducing cholesterol levels, none were sufficient to effectively treat HoFH on their own, and often the confidence in the results were limited by the methodological weaknesses of the studies. The evidence suggests that management of HoFH requires an individualized approach, with consideration given to the efficacy, safety, tolerability and accessibility of each treatment.

Proton Transfer via Arginine with Suppressed pKa Mediates Catalysis by Gentisate and Salicylate Dioxygenase.

Gentisate and salicylate 1,2-dioxygenases (GDO and SDO) facilitate aerobic degradation of aromatic rings by inserting both atoms of dioxygen into their substrates, thereby participating in global carbon cycling. The role of acid-base catalysts in the reaction cycles of these enzymes is debatable. We present evidence of the participation of a proton shuffler during catalysis by GDO and SDO. The pH dependence of Michaelis-Menten parameters demonstrates that a single proton transfer is mandatory for the catalysis. Measurements at variable temperatures and pHs were used to determine the standard enthalpy of ionization (ΔHion°) of 51 kJ/mol for the proton transfer event. Although the observed apparent pKa in the range of 6.0-7.0 for substrates of both enzymes is highly suggestive of a histidine residue, ΔHion° establishes an arginine residue as the likely proton source, providing phylogenetic relevance for this strictly conserved residue in the GDO family. We propose that the atypical 3-histidine ferrous binding scaffold of GDOs contributes to the suppression of arginine pKa and provides support for this argument by employing a 2-histidine-1-carboxylate variant of the enzyme that exhibits elevated pKa. A reaction mechanism considering the role of the proton source in stabilizing key reaction intermediates is proposed.

Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins.

Structure and functions of S100 proteins are regulated by two distinct calcium binding EF hand motifs. In this work, we used solution-state NMR spectroscopy to investigate the cooperativity between the two calcium binding sites and map the allosteric changes at the target binding site. To parse the contribution of the individual calcium binding events, variants of S100A12 were designed to selectively bind calcium to either the EF-I (N63A) or EF-II (E31A) loop, respectively. Detailed analysis of the backbone chemical shifts for wildtype protein and its mutants indicates that calcium binding to the canonical EF-II loop is the principal trigger for the conformational switch between 'closed' apo to the 'open' Ca2+ -bound conformation of the protein. Elimination of binding in S100-specific EF-I loop has limited impact on the calcium binding affinity of the EF-II loop and the concomitant structural rearrangement. In contrast, deletion of binding in the EF-II loop significantly attenuates calcium affinity in the EF-I loop and the structure adopts a 'closed' apo-like conformation. Analysis of experimental amide nitrogen (15 N) relaxation rates (R1 , R2 , and 15 N-{1 H} NOE) and molecular dynamics (MD) simulations demonstrate that the calcium bound state is relatively floppy with pico-nanosecond motions induced in functionally relevant domains responsible for target recognition such as the hinge domain and the C-terminal residues. Experimental relaxation studies combined with MD simulations show that while calcium binding in the EF-I loop alone does not induce significant motions in the polypeptide chain, EF-I regulates fluctuations in the polypeptide in the presence of bound calcium in the EF-II loop. These results offer novel insights into the dynamic regulation of target recognition by calcium binding and unravels the role of cooperativity between the two calcium binding events in S100A12.

Income and Household Material Hardship in Children With Medical Complexity.

BACKGROUND AND OBJECTIVES: Household economic hardship negatively impacts child health but may not be adequately captured by income. We sought to determine the prevalence of household material hardship (HMH), a measure of household economic hardship, and to examine the relationship between household poverty and material hardship in a population of children with medical complexity. METHODS: We conducted a cross-sectional survey study of parents of children with medical complexity receiving primary care at a tertiary children's hospital. Our main predictor was household income as a percentage of the federal poverty limit (FPL): <50% FPL, 51% to 100% FPL, and >100% FPL. Our outcome was HMH measured as food, housing, and energy insecurity. We performed logistic regression models to calculate adjusted odds ratios of having ≥1 HMH, adjusted for patient and clinical characteristics from surveys and the Pediatric Health Information System. RESULTS: At least 1 material hardship was present in 40.9% of participants and 28.2% of the highest FPL group. Families with incomes <50% FPL and 51% to 100% FPL had ∼75% higher odds of having ≥1 material hardship compared with those with >100% FPL (<50% FPL: odds ratio 1.74 [95% confidence interval: 1.11-2.73], P = .02; 51% to 100% FPL: 1.73 [95% confidence interval: 1.09-2.73], P = .02). CONCLUSIONS: Poverty underestimated household economic hardship. Although households with incomes <100% FPL had higher odds of having ≥1 material hardship, one-quarter of families in the highest FPL group also had ≥1 material hardship.

Characterization of monomeric Mn(II/III/IV)-hydroxo complexes from X- and Q-band dual mode electron paramagnetic resonance (EPR) spectroscopy.

Manganese-hydroxo species have been implicated in C-H bond activation performed by metalloenzymes, but the electronic properties of many of these intermediates are not well characterized. The present work presents a detailed characterization of three Mn(n)-OH complexes (where n = II, III, and IV) of the tris[(N'-tert-butylureaylato)-N-ethylene]aminato ([H3buea](3-)) ligand using X- and Q-band dual mode electron paramagnetic resonance (EPR). Quantitative simulations for the [Mn(II)H3buea(OH)](2-) complex demonstrated the ability to characterize similar Mn(II) species commonly present in the resting states of manganese-containing enzymes. The spin states of the Mn(III) and Mn(IV) complexes determined from EPR spectroscopy are S = 2 and 3/2, respectively, as expected for the C3 symmetry imposed by the [H3buea](3-) ligand. Simulations of the spectra indicated the constant presence of two Mn(IV) species in solutions of [Mn(IV)H3buea(OH)] complex. The simulations of perpendicular- and parallel-mode EPR spectra allow determination of zero-field splitting and hyperfine parameters for all complexes. For the Mn(III) and Mn(IV) complexes, density functional theory calculations are used to determine the isotropic Mn hyperfine values, to compare the excited electronic state energies, and to give theoretical estimates of the zero-field energy.

Pediatric Renal Rickets at a Tertiary Center.

We report clinical and etiological profile of 19 children (10 males) with renal rickets managed in the years 2021-2022. Median (IQR) age of presentation was 60 (18-96) months. The commonest cause was renal tubular acidosis (n=8). Genetic analysis revealed the diagnosis in 83% subjects (5 out of 6 tested).