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Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center
Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O 2 -binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme–substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen.
The unique Phe–His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S–C bond cleavage
The 2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) enzyme is the only member of the disulfide oxidoreductase (DSOR) family of enzymes, which are important for reductively cleaving S–S bonds, to have carboxylation activity. 2-KPCC catalyzes the conversion of 2-ketopropyl-coenzyme M to acetoacetate, which is used as a carbon source, in a controlled reaction to exclude protons. A conserved His–Glu motif present in DSORs is key in the protonation step; however, in 2-KPCC, the dyad is substituted by Phe–His. Here, we propose that this difference is important for coupling carboxylation with C–S bond cleavage. We substituted the Phe–His dyad in 2-KPCC to be more DSOR like, replacing the phenylalanine with histidine (F501H) and the histidine with glutamate (H506E), and solved crystal structures of F501H and the double variant F501H_H506E. We found that F501 protects the enolacetone intermediate from protons and that the F501H variant strongly promotes protonation. We also provided evidence for the involvement of the H506 residue in stabilizing the developing charge during the formation of acetoacetate, which acts as a product inhibitor in the WT but not the H506E variant enzymes. Finally, we determined that the F501H substitution promotes a DSOR-like charge transfer interaction with flavin adenine dinucleotide, eliminating the need for cysteine as an internal base. Taken together, these results indicate that the 2-KPCC dyad is responsible for selectively promoting carboxylation and inhibiting protonation in the formation of acetoacetate.
Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a genetic trait that can cause hemolytic anemia. To date, over 150 nonsynonymous mutations have been identified in G6PD, with pathogenic mutations clustering near the dimer and/or tetramer interface and the allosteric NADP + -binding site. Recently, our lab identified a small molecule that activates G6PD variants by stabilizing the allosteric NADP + and dimer complex, suggesting therapeutics that target these regions may improve structural defects. Here, we elucidated the connection between allosteric NADP + binding, oligomerization, and pathogenicity to determine whether oligomer stabilization can be used as a therapeutic strategy for G6PD deficiency (G6PD def ). We first solved the crystal structure for G6PD K403Q , a mutant that mimics the physiological acetylation of wild-type G6PD in erythrocytes and demonstrated that loss of allosteric NADP + binding induces conformational changes in the dimer. These structural changes prevent tetramerization, are unique to Class I variants (the most severe form of G6PD def ), and cause the deactivation and destabilization of G6PD. We also introduced nonnative cysteines at the oligomer interfaces and found that the tetramer complex is more catalytically active and stable than the dimer. Furthermore, stabilizing the dimer and tetramer improved protein stability in clinical variants, regardless of clinical classification, with tetramerization also improving the activity of G6PD K403Q and Class I variants. These findings were validated using enzyme activity and thermostability assays, analytical size-exclusion chromatography (SEC), and SEC coupled with small-angle X-ray scattering (SEC-SAXS). Taken together, our findings suggest a potential therapeutic strategy for G6PD def and provide a foundation for future drug discovery efforts.
A catalytic dyad modulates conformational change in the CO 2 -fixing flavoenzyme 2-ketopropyl coenzyme M oxidoreductase/carboxylase
2-Ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) is a member of the flavin and cysteine disulfide containing oxidoreductase family (DSOR) that catalyzes the unique reaction between atmospheric CO 2 and a ketone/enolate nucleophile to generate acetoacetate. However, the mechanism of this reaction is not well understood. Here, we present evidence that 2-KPCC, in contrast to the well-characterized DSOR enzyme glutathione reductase, undergoes conformational changes during catalysis. Using a suite of biophysical techniques including limited proteolysis, differential scanning fluorimetry, and native mass spectrometry in the presence of substrates and inhibitors, we observed conformational differences between different ligand-bound 2-KPCC species within the catalytic cycle. Analysis of site-specific amino acid variants indicated that 2-KPCC-defining residues, Phe501-His506, within the active site are important for transducing these ligand induced conformational changes. We propose that these conformational changes promote substrate discrimination between H + and CO 2 to favor the metabolically preferred carboxylation product, acetoacetate.
Expression, purification, and characterization of diacylated Lipo-YcjN from Escherichia coli
YcjN is a putative substrate binding protein expressed from a cluster of genes involved in carbohydrate import and metabolism in Escherichia coli. Here, we determine the crystal structure of YcjN to a resolution of 1.95 Å, revealing that its three-dimensional structure is similar to substrate binding proteins in subcluster D-I, which includes the well-characterized maltose binding protein. Furthermore, we found that recombinant overexpression of YcjN results in the formation of a lipidated form of YcjN that is posttranslationally diacylated at cysteine 21. Comparisons of size-exclusion chromatography profiles and dynamic light scattering measurements of lipidated and nonlipidated YcjN proteins suggest that lipidated YcjN aggregates in solution via its lipid moiety. Additionally, bioinformatic analysis indicates that YcjN-like proteins may exist in both Bacteria and Archaea, potentially in both lipidated and nonlipidated forms. Together, our results provide a better understanding of the aggregation properties of recombinantly expressed bacterial lipoproteins in solution and establish a foundation for future studies that aim to elucidate the role of these proteins in bacterial physiology.
Competitive exchange between divalent metal ions [Cu(II), Zn(II), Ca(II)] and Hg(II) bound to thiols and natural organic matter
Mercuric Hg(II) ion forms exceptionally strong complexes with various organic ligands, particularly thiols and dissolved organic matter (DOM) in natural water. Few studies, however, have experimentally determined whether or not the presence of base cations and transition metal ions, such as Ca(II), Cu(II), and Zn(II), would compete with Hg(II) bound to these ligands, as concentrations of these metal ions are usually orders of magnitude higher than Hg(II) in aquatic systems. Different from previous model predictions, a significant fraction of Hg(II) bound to cysteine (CYS), glutathione (GSH), or DOM was found to be competitively exchanged by Cu(II), but not by Zn(II) or Ca(II). About 20–75% of CYS-bound-Hg(II) [at 2:1 CYS:Hg(II)] and 14–40% of GSH-bound-Hg(II) [at 1:1 GSH:Hg(II)] were exchanged by Cu(II) at concentrations 1–3 orders of magnitude greater than Hg(II). Competitive exchange was also observed between Cu(II) and Hg(II) bound to DOM, albeit to a lower extent, depending on relative abundances of thiol and carboxylate functional groups on DOM and their equilibrium time with Hg(II). When complexed with ethylenediaminetetraacetate (EDTA), most Hg(II) could be exchanged by Cu(II) and Zn(II), as well as Ca(II) at increasing concentrations. Furthermore, these results shed additional light on competitive exchange reactions between Hg(II) and coexisting metal ions and have important implications in Hg(II) chemical speciation and biogeochemical transformation, particularly in contaminated environments containing relatively high concentrations of Hg(II) and metal ions.
Bacterial effectors mimicking ubiquitin-proteasome pathway tweak plant immunity
Plant pathogenic Gram-negative bacteria evade the host plant immune system by secreting Type III (T3E) and Type IV effector (T4E) proteins into the plant cytoplasm. Mostly T3Es are secreted into the plant cells to establish pathogenicity by affecting the vital plant process viz. metabolic pathways, signal transduction and hormonal regulation. Ubiquitin-26S proteasome system (UPS) exists as one of the important pathways in plants to control plant immunity and various cellular processes by employing several enzymes and enzyme components. Pathogenic and non-pathogenic bacteria are found to secrete effectors into plants with structural and/or functional similarity to UPS pathway components like ubiquitin E3 ligases, F-box domains, cysteine proteases, inhibitor of host UPS or its components, etc. The bacterial effectors mimic UPS components and target plant resistance proteins for degradation by proteasomes, thereby taking control over the host cellular activities as a strategy to exert virulence. Thus, the bacterial effectors circumvent plant cellular pathways leading to infection and disease development. Finally, this review highlights known bacterial T3E and T4E proteins that function and interfere with the ubiquitination pathway to regulate the immune system of plants.
Organic compounds alter the preference and rates of heavy metal adsorption on ferrihydrite
The availability of heavy metals in terrestrial environments is largely controlled by their interactions with minerals and organic matter, with iron minerals having a particularly strong role in heavy metal fate. Because soil organic matter contains a variety of compounds that differ in their chemical properties, the underlying impact organic matter-soil mineral associations bestow on heavy metal binding is still unresolved. Here, we systematically examine the binding of Cd, Zn and Ni by a suite of organic-ferrihydrite assemblages, chosen to account for various compound chemistries within soil organic matter. We posited that organic compound functionality would dictate the extent of association with the organic-ferrihydrite assemblages. Increased heavy metal binding to the assemblages was observed and attributed to the introduction of additional binding sites by the organic functional groups with differing metal affinities. Furthermore, the relative increase depended on the metal's Lewis acidity and followed the order Cd > Zn > Ni, whereas the reverse order was obtained for metal binding by pristine ferrihydrite (Ni > Zn > Cd). Citric acid-, aspartic acid- and cysteine-ferrihydrite assemblages also enhanced the metal binding rate. X-ray absorption spectroscopy revealed that the organic coating contributed significantly to Zn binding by the assemblages, despite relatively low organic surface coverage. Our findings provide valuable information on the nature of heavy metal-organic-mineral interactions and metal adsorption processes regulating their bioavailability and transport.
Metabolic modulation: Pneumocystis phosphoglucomutase is a target influencing host recognition
Herein, this manuscript explores the significance of the phosphoglucomutase (PGM) enzyme in Pneumocystis spp., focusing on its role in fungal surface mannoprotein formation. Through expression of the Pneumocystis murina Pmpgm2 in a Saccharomyces cerevisiae pgm2Δ strain, we demonstrate restoration of binding to the mannose receptor (MR) and macrophages to wildtype yeast levels in this complemented strain. Gas Chromatography-Mass Spectroscopy (GC-MS) confirmed reduced mannose content in the pgm2Δ yeast strain compared to the wild-type and complemented Pmpgm2 cDNA-expressing strains. This study underscores fungal PGM function in dolichol glucosyl phosphate biosynthesis, crucial for proper cell wall mannoprotein formation. Furthermore, highlighting the conservation of targetable cysteine residues across fungal pathogens, PGM inhibition maybe a potential therapeutic strategy against a broad spectrum of fungal infections.
Evaluation of two inoculation routes of an adenovirus-mediated viral protein inhibitor in a Crimean-Congo hemorrhagic fever mouse model
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne nairovirus with a wide geographic spread that can cause severe and lethal disease. No specific medical countermeasures are approved to combat this illness. The CCHFV L protein contains an ovarian tumor (OTU) domain with a cysteine protease thought to modulate cellular immune responses by removing ubiquitin and ISG15 post-translational modifications from host and viral proteins. Viral deubiquitinases like CCHFV OTU are attractive drug targets, as blocking their activity may enhance cellular immune responses to infection, and potentially inhibit viral replication itself. We previously demonstrated that the engineered ubiquitin variant CC4 is a potent inhibitor of CCHFV replication in vitro. A major challenge of the therapeutic use of small protein inhibitors such as CC4 is their requirement for intracellular delivery, e.g., by viral vectors. In this study, we examined the feasibility of in vivo CC4 delivery by a replication-deficient recombinant adenovirus (Ad-CC4) in a lethal CCHFV mouse model. Since the liver is a primary target of CCHFV infection, we aimed to optimize delivery to this organ by comparing intravenous (tail vein) and intraperitoneal injection of Ad-CC4. While tail vein injection is a traditional route for adenovirus delivery, in our hands intraperitoneal injection resulted in higher and more widespread levels of adenovirus genome in tissues, including, as intended, the liver. However, despite promising in vitro results, neither route of in vivo CC4 treatment resulted in protection from a lethal CCHFV infection.
Facet-dependent electron transfer induces distinct arsenic reallocations on hematite
The interfacial electron transfer (ET) between electron shuttling compounds and iron (Fe) oxyhydroxides plays a crucial role in the reductive dissolution of Fe minerals and the fate of surface-bound arsenic (As). However, the impact of exposed facets of highly crystalline hematite on reductive dissolution and As immobilization is poorly understood. In this study, we systematically investigated the interfacial processes of the electron shuttling compound cysteine (Cys) on various facets of hematite and the reallocations of surface-bound As(III) or As(V) on the respective surfaces. Our results demonstrate that the ET process between Cys and hematite generates Fe(II) and leads to reductive dissolution, with more Fe(II) generated on {001} facets of exposed hematite nanoplates (HNPs). Reductive dissolution of hematite leads to significantly enhanced As(V) reallocations on hematite. Nevertheless, upon the addition of Cys, a raipd release of As(III) can be halted by its prompt re-adsorption, leaving the extent of As(III) immobilization on hematite unchanged throughout the course of reductive dissolution. This is due to that Fe(II) can form new precipitates with As(V), a process that is facet-dependent and influenced by water chemistry. Electrochemical analysis reveals that HNPs exhibit higher conductivity and ET ability, which is beneficial for reductive dissolution and As reallocations on hematite. In conclusion, these findings highlight the facet-dependent reallocations of As(III) and As(V) facilitated by electron shuttling compounds and have implications for the biogeochemical processes of As in soil and subsurface environments.
Probing Nanoscale Chemical Environments of Zinc in Diatoms
Diatoms impact the biogeochemical cycling of zinc (Zn) due to elevated cellular Zn levels over other phytoplankton, and their strong biological uptake of Zn in the Southern Ocean sets the global distribution of Zn in ocean water columns. Past studies have revealed the abundance and spatial distribution of Zn in individual diatoms, while others have shown diverse Zn chemical species in whole-cell aggregates. However, intracellular and intercellular variations in Zn chemical forms remained unknown. For the first time, we applied a synchrotron X-ray nanoprobe to cultured diatoms (Phaeodactylum tricornutum and Chaetoceros muelleri) and resolved spatial heterogeneities of Zn chemistry. The result shows the partitioning of Zn between intracellular contents (soft parts) and frustules (mainly in the intracellular contents for P. tricornutum and similar Zn concentrations in the intracellular contents and frustules for C. muelleri). We found multiple Zn chemical species unevenly distributed within individual cells, where Zn–phosphoryl complexes were the most abundant followed by cysteine, histidine, biogenic silica, and carboxyl complexes. Cellular Zn species varied between individual organisms and were influenced by Zn availability. To our knowledge, this work presents the first X-ray measurements of trace metal speciation at sub-100 nm resolution in biological samples in their natural state. In conclusion, this research improves our ability to examine the biogeochemistry of Zn on the nanoscale and can help us understand the role of Zn in plankton growth and the Zn cycle in ocean waters.
Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization
Enhancing the thermostability of enzymes without impacting their catalytic function represents an important yet challenging goal in protein engineering and biocatalysis. We recently introduced a novel method for enzyme thermostabilization that relies on the computationally guided installation of genetically encoded thioether “staples” into a protein via cysteine alkylation with the noncanonical amino acid O-2-bromoethyl tyrosine (O2beY). Here, we demonstrate the functionality of an expanded set of electrophilic amino acids featuring chloroacetamido, acrylamido, and vinylsulfonamido side-chain groups for protein stapling using this strategy. Using a myoglobin-based cyclopropanase as a model enzyme, our studies show that covalent stapling with pchloroacetamido-phenylalanine (pCaaF) provides higher stapling efficiency and enhanced stability (thermodynamic and kinetic) compared to the other stapled variants and the parent protein. Interestingly, molecular simulations of conformational flexibility of the cross-links show that the pCaaF staple allows fewer energetically feasible conformers than the other staples, and this property may be a broader indicator of stability enhancement. Using this strategy, pCaaF-stapled variants with significantly enhanced stability against thermal denaturation (ΔT m ' = +27 °C) and temperature-induced heme loss (ΔT 50 = +30 °C) were obtained while maintaining high levels of catalytic activity and stereoselectivity. Crystallographic analyses of singly and doubly stapled variants provide key insights into the structural basis for stabilization, which includes both direct interactions of the staples with protein residues and indirect interactions through adjacent residues involved in heme binding. This work expands the toolbox of protein stapling strategies available for protein stabilization.
Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds
Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.
Improved Protein Semi-Synthesis Enables Biophysical Studies of Thioamide Destabilization of β-Sheet Interactions
Abstract Thioamides are natural post-translational modifications of the peptide backbone and can be introduced synthetically to probe protein folding or functionalize peptides for translational applications. In this work, we demonstrate that thioamide-containing peptides with C-terminal thioesters can be efficiently generated using Knorr pyrazole activation and used in subsequent native chemical ligation reactions to generate thioamide-containing proteins. We compare this method to acyl azide activation and find that both routes provide similar yields. We also investigate ultrasound-mediated desulfurization of the ligation site cysteine for potential advantages over chemical radical initiators. Scaling up our syntheses allows us to study thioamide perturbations to the β-sheet region of the B1 domain of protein G (GB1) as well as β-strand interactions in amyloid fibrils of the Parkinson’s disease protein α-synuclein. In both contexts, we observe dramatic destabilization of the β-sheet networks, manifested in decreased GB1 thermal stability and altered folding and slowed aggregation of α-synuclein. These findings illustrate the impact that a single atom substitution can have on cooperative hydrogen-bonding networks and prompt future study of both systems.
Precision Loading and Delivery of Molecular Cargo by Size-Controlled Coacervation of Gold Nanoparticles Functionalized with Elastin-like Peptides
Thermoresponsive elastin-like peptides (ELPs) have been extensively investigated in biotechnology and medicine, but little attention has been paid to the process by which coacervation causes ELP-decorated particles to aggregate. Here, using gold nanoparticles (AuNPs) functionalized with a cysteine-terminated 96-repeat of the VPGVG sequence (V96-Cys), we show that the size of the clusters that reversibly form above the ELP transition temperature can be finely controlled in the 250 to 930 nm range by specifying the concentration of free V96-Cys in solution and using AuNPs of different sizes. We further find that the localized surface plasmon resonance peak of the embedded AuNPs progressively red-shifts with cluster size, likely due to an increase in particle–particle contacts. We exploit this fine control over size to homogeneously load precise amounts of the dye Nile Red and the antibiotic Tetracycline into clusters of different hydrodynamic diameters and deliver cargos near-quantitatively by deconstructing the aggregates below the ELP transition temperature. Beyond establishing a key role for free ELPs in the agglomeration of ELP-functionalized particles, our results provide a path for the thermally controlled delivery of precise quantities of molecular cargo. This capability might prove useful in combination photothermal therapies and theranostic applications, and to trigger spatially and temporally uniform responses from biological, electronic, or optical systems.
Mercury Reduction, Uptake, and Species Transformation by Freshwater Alga Chlorella vulgaris under Sunlit and Dark Conditions
As a major entry point of mercury (Hg) to aquatic food webs, algae play an important role in taking up and transforming Hg species in aquatic ecosystems. However, little is known how and to what extent Hg reduction, uptake, and species transformations are mediated by algal cells and their exudates, algal organic matter (AOM), under either sunlit or dark conditions. In this study, using Chlorella vulgaris (CV) as one of the most prevalent freshwater model algal species, we show that solar irradiation could enhance the reduction of mercuric Hg(II) to elemental Hg(0) by both CV cells and AOM. AOM reduced more Hg(II) than algal cells themselves due to cell surface adsorption and uptake of Hg(II) inside the cells under solar irradiation. Synchrotron radiation X-ray absorption near-edge spectroscopy (SR-XANES) analyses indicate that sunlight facilitated the transformation of Hg to less bioavailable species, such as β-HgS and Hg-phytochelatins, compared to Hg(Cysteine) 2 -like species formed in algal cells in the dark. These findings highlight important functional roles and potential mechanisms of algae in Hg reduction and immobilization under varying lighting conditions and how these processes may modulate Hg cycling and bioavailability in the aquatic environment.