Electrostatic recognition between superoxide and copper, zinc superoxide dismutase

Interfacial Lithium Cations Catalyze Biomimetic Aerobic Oxygenation via Short-Range Electrostatic Interaction

Enzymes often involve short-range electrostatic interactions in the deliberate microenvironment for accelerating the catalysis. Comparatively, electrostatic interactions from ions in solutions are mostly shielded by solvent or counter-ion shells, creating negligible catalytic effects. Herein, we discovered that the interfacial Li+ cations accumulated on electrodes catalyze the selective water-involved O2 electro-reduction into peroxide anion (OOH-), forming an active side-on Li+-OOH- complex via short-range electrostatic interaction. This complex reduces the O2 reduction energy barrier and increases the nucleophilicity, expediting the aerobic oxygenation of ketones. Aside from trapping active intermediates, Li+ cations also attract the excessive water dipoles to prevent them from quenching the active Li+-OOH- complex. By using probe-assisted quantitative methods, we demonstrated the unique under-coordinative characteristics of interfacial Li+ for interacting with reaction intermediates, and the effective concentration of under-coordinative Li+ on the interface is an order of magnitude higher than in the bulk solution. These analyses provide essential evidences about the intrinsic difference between bulk ions and interfacial ions toward catalysis.

Active binding mechanism to superoxide dismutase and toxicological implication for environmentally prevalent phthalates and their hydrolytic products: Coupling in vitro bioassay with molecular dynamics simulation

Phthalic acid esters (PAEs) are widely used as plasticizers to improve the flexibility and durability of plastics. However, their environmental presence poses risks by inducing oxidative stress and contributing to metabolic syndrome. Despite being linked to various diseases, the mechanisms by which PAEs disrupt antioxidant enzymes, particularly superoxide dismutase (SOD), are not well understood. This study investigated the molecular interactions between PAEs, their metabolites, and SOD using bioassays and theoretical simulations. The results showed that key metabolites, monophthalates (MAEs) and phthalic acid (PA), strongly inhibited SOD activity, with potency increasing as side chain length decreased. In contrast, PAEs caused minor changes in SOD activity. The inhibition resulted from tight binding of MAEs and PA to the residues in the enzyme's bottom cavity. PAEs and metabolites induced significant structural changes in the secondary structures, catalytic channel, and hydrogen bond network, destabilizing the protein and impairing its function. A strong correlation between SOD inhibition and Gibbs free binding energies at Arg141 was observed. Arg141 and allelic residues can serve as biomarkers for early warnings of oxidative stress. This study improves our understanding of oxidative stress mechanisms caused by PAEs and emphasizes the need for better risk management of phthalate exposure.

Theoretical insights into the binding of mono/di-ethyl phthalates to superoxide dismutase and associated structural changes impairing antioxidant activity: A coupled molecular docking and dynamics simulation approach

Phthalic acid esters (PAEs) are plasticizers known to increase oxidative stress by impairing antioxidant defenses, including superoxide dismutase (SOD) activity. Since oxidative stress plays a critical role in disease development, the disruption of SOD function by PAEs presents a significant concern. However, the precise molecular mechanisms underlying the regulation of SOD activity remain unclear. This study investigated how diethyl phthalate (DEP) and its major metabolite, monoethyl phthalate (MEP), affected SOD activity using molecular docking and dynamics simulations. The results revealed that both DEP and MEP bound to SOD through weak hydrophilic interactions and hydrogen bonds with residues Lys9, Thr17, Asn51, Thr52, and Arg141 in the bottom of the enzyme's two subunit cavities. These interactions triggered structural changes, particularly in the electrostatic loop and catalytic channels, destabilizing SOD. DEP and MEP increased the enzyme's radius of gyration and solvent-accessible surface area while disrupting intra-protein interactions. MEP showed a stronger inhibitory effect, significantly altering SOD's conformation. This change correlated with reduced catalytic activity (R2 > 0.9). Consequently, the inhibition of the enzyme is primarily due to the disruption of Arg141's conformation and function, which weakens SOD's antioxidant defense and potentially contributes to diseases related to oxidative damage. These results underscore the health risks posed by PAEs, especially following metabolic transformation, and highlight the importance of addressing their oxidative impact.

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H2O2 and O2. This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1's mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure's unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

Benzimidazole-based mononuclear polypyridyl Cu(II) complexes: DNA binding, cleavage, and in vitro antiproliferative studies

This paper addresses the synthesis, characterization, DNA binding, cleavage, and in vitro antiproliferative activity studies of a series of heteroleptic mononuclear copper(II) complexes [Cu(L)(bpy)](ClO4)2, {1}; [Cu(L)(phen)](ClO4)2, {2}; and [Cu(L)(Mephen)](ClO4)2, {3} derived from different polypyridyl ligands, where in the complex architecture, one 2,6-bis(1-methyl-1H-benzo[d]imidazol-2-yl)pyridine(Mebzimpy) (L) moiety is connected to the central Cu metal in a tridentate fashion and the bidentate co-ligands are 2,2'-bipyridine (bpy), 1,10-phenanthroline (phen) and 2,9-dimethyl-1,10-phenanthroline (Mephen). All the synthesized complexes were characterized using various spectroscopic and analytical methods, along with the single-crystal X-ray diffraction (SCXRD) technique. The complexes crystallize in a penta-coordinated distorted square pyramidal geometry. The redox properties of the complexes were also studied by using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The DNA binding nature of the complexes was investigated utilizing absorbance spectral measurement and fluorescence quenching experiments with ethidium bromide (EB) as a DNA intercalator, employing double-stranded salmon sperm DNA (ss-DNA). Both the binding constant (Kb) and the Stern-Volmer constant (KSV) were found to be in the order of 104. In silico molecular docking analysis confirmed that all the complexes could interact with the minor groove of duplex DNA. The DNA cleaving ability of the complexes was studied by gel electrophoresis using supercoiled plasmid DNA; however, no DNA cleavage was found. DNA-binding polypyridyl complexes are well known to disrupt DNA metabolic pathways and cause cytotoxicity to rapidly growing cancer cells. Hence, cell viability analysis was also carried out with complexes 1-3. It was observed that complexes 2 and 3 prevented the proliferation of the human osteosarcoma cell line U2OS and the triple-negative breast cancer cell line MDA-MB-231. Overall, these findings could be beneficial in the design and development of future antitumor agents.

Secondary sphere interactions modulate peroxynitrite scavenging by the E2 domain of amyloid precursor protein

Peroxynitrite (ONOO-) is a highly reactive nitrogen species that can cause significant damage to proteins, lipids, and DNA. Various enzymes, including metalloenzymes, play crucial roles in reducing ONOO- concentrations to protect cellular components. While the interaction of ONOO- with heme proteins is well known, the reduction by Cu-containing proteins is less studied. Amyloid precursor protein (APP), implicated in Alzheimer's disease, has an E2 domain that binds copper ions with a dissociation constant of KD ∼ 10-12 M and is proposed to be involved in iron homeostasis, copper trafficking, and oxidative stress response. Our recent studies using EXAFS, UV-Vis, and EPR spectroscopy revealed a previously unidentified labile water ligand in the Cu(II) site of the E2 domain, suggesting reactivity with anionic substrates like ONOO-. Experimental data showed that Cu(I)-E2 reduces ONOO- at a significant rate (1.1 × 105 M-1 s-1), comparable to native peroxynitrite scavengers, while maintaining active site integrity through multiple redox cycles. This study further investigates the mechanism of ONOO- reduction by Cu(I)-E2 using the Griess assay, demonstrating that reduction occurs via single electron transfer, forming nitrite and nitrate. This process aligns with previous findings that Cu(I)-E2 is oxidized to Cu(II)-E2 upon ONOO- reduction. Mutations at Lys435, affecting secondary sphere interactions, revealed that factors beyond electrostatics are involved in substrate recruitment. MD simulations suggest that steric hindrance from a newly formed hydrogen bond also plays a role. Understanding ONOO- reduction by the E2 domain of APP expands our knowledge of copper proteins in mitigating oxidative stress and elucidates their physiological and pathological roles, particularly in Alzheimer's disease.

Neurological Diseases can be Regulated by Phase Separation

Several neurological diseases arise from abnormal protein aggregation within neurones and this is closely regulated by phase separation. One such is motor neurone disease and aberrant aggregation of superoxide dismutase. Again these events are regulated by electrical forces that are examined.

Electron transfer in biological systems

Examples of how metalloproteins feature in electron transfer processes in biological systems are reviewed. Attention is focused on the electron transport chains of cellular respiration and photosynthesis, and on metalloproteins that directly couple electron transfer to a chemical reaction. Brief mention is also made of extracellular electron transport. While covering highlights of the recent and the current literature, this review is aimed primarily at introducing the senior undergraduate and the novice postgraduate student to this important aspect of bioinorganic chemistry.

Outstanding Superoxide Dismutase Catalytic Activity Of Simple Peptide-Based Nickel(II) Complexes

We present here the most active synthetic Ni superoxide dismutase (NiSOD) mimic reported to date. Reactive oxygen species are aggressive compounds, which concentrations are tightly regulated in vivo. Among them, the superoxide anion, O2⋅-, is controlled by superoxide dismutases. Capitalizing on the versatility of the Amino-Terminal CuII- and NiII-binding (ATCUN) peptide motif, we introduced positive charges around the NiII center to favor the interaction with the superoxide radical anion. At physiological pH, the pentapeptide H-Cys-His-Cys-Arg-Arg-NH2 coordinates NiII after the deprotonation of one thiol, two amides, and either the second thiol or the N-terminal ammonium, leading to an equilibrium between the two N3S1 and N2S2 coordination modes. Under catalytic conditions, a kcat value of 8.6(4)×106 L.mol-1.s-1 was measured. Within the first second, the catalyst remained undegraded with quantitative consumption of O2⋅- (completed up to 37 catalytic cycles). An extra arginine (Arg) was introduced at the peptide C-terminus to increase the global charge of the NiII complex from +1 to +2. This had no effect on the catalytic performance, highlighting the critical role of charge distribution in space as a determining factor influencing the reactivity.

Ebselen analogues delay disease onset and its course in fALS by on-target SOD-1 engagement

Amyotrophic lateral sclerosis (ALS) selectively affects motor neurons. SOD1 is the first causative gene to be identified for ALS and accounts for at least 20% of the familial (fALS) and up to 4% of sporadic (sALS) cases globally with some geographical variability. The destabilisation of the SOD1 dimer is a key driving force in fALS and sALS. Protein aggregation resulting from the destabilised SOD1 is arrested by the clinical drug ebselen and its analogues (MR6-8-2 and MR6-26-2) by redeeming the stability of the SOD1 dimer. The in vitro target engagement of these compounds is demonstrated using the bimolecular fluorescence complementation assay with protein-ligand binding directly visualised by co-crystallography in G93A SOD1. MR6-26-2 offers neuroprotection slowing disease onset of SOD1G93A mice by approximately 15 days. It also protected neuromuscular junction from muscle denervation in SOD1G93A mice clearly indicating functional improvement.

Oxidative Stress in Healthy and Pathological Red Blood Cells

Red cell diseases encompass a group of inherited or acquired erythrocyte disorders that affect the structure, function, or production of red blood cells (RBCs). These disorders can lead to various clinical manifestations, including anemia, hemolysis, inflammation, and impaired oxygen-carrying capacity. Oxidative stress, characterized by an imbalance between the production of reactive oxygen species (ROS) and the antioxidant defense mechanisms, plays a significant role in the pathophysiology of red cell diseases. In this review, we discuss the most relevant oxidant species involved in RBC damage, the enzymatic and low molecular weight antioxidant systems that protect RBCs against oxidative injury, and finally, the role of oxidative stress in different red cell diseases, including sickle cell disease, glucose 6-phosphate dehydrogenase deficiency, and pyruvate kinase deficiency, highlighting the underlying mechanisms leading to pathological RBC phenotypes.

Hydrogen sulfide functions as a micro-modulator bound at the copper active site of Cu/Zn-SOD to regulate the catalytic activity of the enzyme

The present study examines whether there is a mechanism beyond the current concept of post-translational modifications to regulate the function of a protein. A small gas molecule, hydrogen sulfide (H₂S), was found to bind at active-site copper of Cu/Zn-SOD using a series of methods including radiolabeled binding assay, X-ray absorption near-edge structure (XANES), and crystallography. Such an H₂S binding enhanced the electrostatic forces to guide the negatively charged substrate superoxide radicals to the catalytic copper ion, changed the geometry and energy of the frontier molecular orbitals of the active site, and subsequently facilitated the transfer of an electron from the superoxide radical to the catalytic copper ion and the breakage of the copper-His61 bridge. The physiological relevance of such an H₂S effect was also examined in both in vitro and in vivo models where the cardioprotective effects of H₂S were dependent on Cu/Zn-SOD.

Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1

Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or β3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades.

Engineering Antioxidant Surfaces for Titanium-Based Metallic Biomaterials

Prolonged inflammation induced by orthopedic metallic implants can critically affect the success rates, which can even lead to aseptic loosening and consequent implant failure. In the case of adverse clinical conditions involving osteoporosis, orthopedic trauma and implant corrosion-wear in peri-implant region, the reactive oxygen species (ROS) activity is enhanced which leads to increased oxidative stress. Metallic implant materials (such as titanium and its alloys) can induce increased amount of ROS, thereby critically influencing the healing process. This will consequently affect the bone remodeling process and increase healing time. The current review explores the ROS generation aspects associated with Ti-based metallic biomaterials and the various surface modification strategies developed specifically to improve antioxidant aspects of Ti surfaces. The initial part of this review explores the ROS generation associated with Ti implant materials and the associated ROS metabolism resulting in the formation of superoxide anion, hydroxyl radical and hydrogen peroxide radicals. This is followed by a comprehensive overview of various organic and inorganic coatings/materials for effective antioxidant surfaces and outlook in this research direction. Overall, this review highlights the critical need to consider the aspects of ROS generation as well as oxidative stress while designing an implant material and its effective surface engineering.

Role of charged residues of the "electrostatic loop" of hSOD1 in promotion of aggregation: Implications for the mechanism of ALS-associated mutations under amyloidogenic conditions

Protein misfolding and amyloid formation are hallmarks of numerous diseases, including amyotrophic lateral sclerosis (ALS), in which hSOD1 aggregation is involved in pathogenesis. We used two point mutations in the electrostatic loop, G138E and T137R, to analyze charge distribution under destabilizing circumstances to gain more about how ALS-linked mutations affect SOD1 protein stability or net repulsive charge. We show that protein charge is important in the ALS disease process using bioinformatics and experiments. The MD simulation findings demonstrate that the mutant protein differs significantly from WT SOD1, which is consistent with the experimental evidence. The specific activity of the wild type was 1.61 and 1.48 times higher than that of the G138E and T137R mutants, respectively. Under amyloid induction conditions, the intensity of intrinsic and ANS fluorescence in both mutants reduced. Increasing the content of β-sheet structures in mutants can be attributed to aggregation propensity, which was confirmed using CD polarimetry and FTIR spectroscopy. Our findings show that two ALS-related mutations promote the formation of amyloid-like aggregates at near physiological pH under destabilizing conditions, which were detected using spectroscopic probes such as Congo red and ThT fluorescence, and also further confirmation of amyloid-like species by TEM. Overall, our results provide evidence supporting the notion that negative charge changes combined with other destabilizing factors play an important role in increasing protein aggregation by reducing repulsive negative charges.

Metal manipulators and regulators in human pathogens: A comprehensive review on microbial redox copper metalloenzymes "multicopper oxidases and superoxide dismutases"

The chemistry of metal ions with human pathogens is essential for their survival, energy generation, redox signaling, and niche dominance. To regulate and manipulate the metal ions, various enzymes and metal chelators are present in pathogenic bacteria. Metalloenzymes incorporate transition metal such as iron, zinc, cobalt, and copper in their reaction centers to perform essential metabolic functions; however, iron and copper have gained more importance. Multicopper oxidases have the ability to perform redox reaction on phenolic substrates with the help of copper ions. They have been reported from Enterobacteriaceae, namely Salmonella enterica, Escherichia coli, and Yersinia enterocolitica, but their role in virulence is still poorly understood. Similarly, superoxide dismutases participate in reducing oxidative stress and allow the survival of pathogens. Their role in virulence and survival is well established in Salmonella typhimurium and Mycobacterium tuberculosis. Further, to ensure survival against stress, like metal starvation or metal toxicity, redox metalloenzymes and metal transportation systems of pathogens actively participate in metal homeostasis. Recently, the omics and protein structure biology studies have helped to predict new targets for regulation the colonization potential of the pathogenic strains. The current review is focused on the major roles of redox metalloenzymes, especially MCOs and SODs of human pathogenic bacteria.

Superoxide Anion Chemistry-Its Role at the Core of the Innate Immunity

Classically, superoxide anion O2•- and reactive oxygen species ROS play a dual role. At the physiological balance level, they are a by-product of O2 reduction, necessary for cell signalling, and at the pathological level they are considered harmful, as they can induce disease and apoptosis, necrosis, ferroptosis, pyroptosis and autophagic cell death. This revision focuses on understanding the main characteristics of the superoxide O2•-, its generation pathways, the biomolecules it oxidizes and how it may contribute to their modification and toxicity. The role of superoxide dismutase, the enzyme responsible for the removal of most of the superoxide produced in living organisms, is studied. At the same time, the toxicity induced by superoxide and derived radicals is beneficial in the oxidative death of microbial pathogens, which are subsequently engulfed by specialized immune cells, such as neutrophils or macrophages, during the activation of innate immunity. Ultimately, this review describes in some depth the chemistry related to O2•- and how it is harnessed by the innate immune system to produce lysis of microbial agents.

A Study of the Interface of Gold Nanoparticles Conjugated to Cowpea Fe-Superoxide Dismutase

The iron superoxide dismutase (FeSOD) is a first barrier to defend photosynthetic organisms from superoxide radicals. Although it is broadly present in plants and bacteria, FeSODs are absent in animals. They belong to the same phylogenic family as Mn-containing SODs, which are also highly efficient at detoxifying superoxide radicals. In addition, SODs can react with peroxynitrite, and FeSOD enzyme has already been used to evaluate the anti-nitrative capacity of plant antioxidants. Gold nanoparticles (AuNPs) have been shown to significantly improve the functionality and the efficiency of ligands, providing they are properly assembled. In this work, the characteristics of the recombinant cowpea (Vigna unguiculata) FeSOD (rVuFeSOD) immobilized onto AuNPs were investigated as a function of (1) NP surface chemistry and (2) biofunctionalization methods, either physical adsorption or covalent bonding. The NP surface chemistry was studied by varying the concentration of the ligand molecule 11-mercaptoundecanoic acid (MUA) on the NP surface. The coverage and activity of the protein on AuNPs was determined and correlated to the surface chemistry and the two biofunctionalization methods. rVuFeSOD-AuNPs conjugate stability was monitored through absorption measurements, agarose gel electrophoresis and DLS, enzymatic activity by a colorimetric assay and by in-gel activity assay, and coverage was measured by colorimetric assay. When using physical adsorption, the NP is the most perturbing agent for the activity of the enzyme. In contrast, only the NP coverage was affected by MUA ligand concentration. However, during covalent attachment, both the NP and the concentration of MUA on the surface influenced the enzyme activity, while the coverage of the NP remained constant. The results evidence the importance of the biomolecule and AuNP interaction for the functionality of the hybrid. These strategies can be used to develop electrochemical biosensors for O2•- and for peroxynitrite in biomedical applications.

Superoxide Radicals in the Execution of Cell Death

Superoxide is a primary oxygen radical that is produced when an oxygen molecule receives one electron. Superoxide dismutase (SOD) plays a primary role in the cellular defense against an oxidative insult by ROS. However, the resulting hydrogen peroxide is still reactive and, in the presence of free ferrous iron, may produce hydroxyl radicals and exacerbate diseases. Polyunsaturated fatty acids are the preferred target of hydroxyl radicals. Ferroptosis, a type of necrotic cell death induced by lipid peroxides in the presence of free iron, has attracted considerable interest because of its role in the pathogenesis of many diseases. Radical electrons, namely those released from mitochondrial electron transfer complexes, and those produced by enzymatic reactions, such as lipoxygenases, appear to cause lipid peroxidation. While GPX4 is the most potent anti-ferroptotic enzyme that is known to reduce lipid peroxides to alcohols, other antioxidative enzymes are also indirectly involved in protection against ferroptosis. Moreover, several low molecular weight compounds that include α-tocopherol, ascorbate, and nitric oxide also efficiently neutralize radical electrons, thereby suppressing ferroptosis. The removal of radical electrons in the early stages is of primary importance in protecting against ferroptosis and other diseases that are related to oxidative stress.

Four alternative splicing transcripts of intracellular copper/zinc superoxide dismutase 1 in Oxya chinensis

In this study, we obtained four alternative splicing transcripts of intracellular copper/zinc superoxide dismutase 1 (icCuZnSOD1) in Oxya chinensis. OcicCuZnSOD1a has all common characteristics of CuZnSOD family and is a canonical CuZnSOD. OcicCuZnSOD1b is missing a Zn binding site. OcicCuZnSOD1c lacks Zn ion and is a Cu-only SOD. OcicCuZnSOD1d is missing a CuZnSOD conserved sequence and lacks the E-loop, a conserved disulfide bond, and an active site arginine. OcicCuZnSOD1a was the most heat-resistant and OcicCuZnSOD1c was the most unstable at high temperatures above 55 °C. They were stable at a wide pH range, especially in alkaline conditions. The four variants expressed at the throughout developmental stages and had various tissue expression patterns. OcicCuZnSOD1a and OcicCuZnSOD1d were significantly induced by 8.79 mM CuCl₂ and OcicCuZnSOD1b was significantly up-regulated by 14.67 mM CuCl₂. OcicCuZnSOD1a was significantly inhibited by 19.13 mM ZnSO₄ while OcicCuZnSOD1d were significantly induced by 22.61 mM ZnSO₄. Disc diffusion assay showed that the four isoforms of OcicCuZnSOD1 made the killing zones smaller surrounding the CdCl₂-soaked filter discs. However, the reduction ratios of OcicCuZnSOD1a were the highest. These results implied that the four transcripts played roles in defense against CdCl₂-induced oxidative stress while OcicCuZnSOD1a had stronger antioxidant capacity.

A copper-zinc-superoxide dismutase (CuZnSOD) from redlip mullet, Liza haematocheila: Insights to its structural characteristics, immune responses, antioxidant activity, and potent antibacterial properties

Copper-zinc superoxide dismutase (CuZnSOD) is a nuclear-encoded metalloenzyme responsible for scavenging harmful reactive oxygen species (ROS). In this study, the CuZnSOD homolog from redlip mullet (Liza haematochelia) (MuCuZnSOD) was structurally and functionally characterized to evaluate its antioxidant capacity, antibacterial properties, and protective level in various pathogenic stress conditions. Structural characteristics of MuCuZnSOD were evaluated using different bioinformatics tools. Pairwise sequence comparison and evolutionary tree structure revealed that the MuCuZnSOD sequence was closely related to the CuZnSOD sequence of Oplegnathus fasciatus with a 94.2% sequence identity. Sequence alignment analysis indicated that the CuZnSOD domain was well conserved. The highest transcriptional expression of MuCuZnSOD was identified in the blood. Immune challenge with lipopolysaccharide (LPS), Lactococcus garvieae, and polyinosinic-polycytidylic acid (poly I:C) exhibited an increased MuCuZnSOD mRNA expression in the blood and liver. Transfected green fluorescent protein-fused MuCuZnSOD was localized in the cytoplasm. Recombinant MuCuZnSOD (rMuCuZnSOD) was overexpressed in a bacterial system. The rMuCuZnSOD possessed significant antioxidant properties as determined by conventional xanthine oxidase assay. The optimum pH and temperature of rMuCuZnSOD were found to be pH 9 and 25 °C, respectively. rMuCuZnSOD enzyme activity increased in a concentration-dependent manner. Treatment with potassium cyanide highly inhibited the rMuCuZnSOD activity. rMuCuZnSOD possessed a significant peroxidation activity in the presence of HCO₃- ions as demonstrated by the increased viability in cells treated with the enzyme in the presence of hydrogen peroxide. Antibacterial assays showed that rMuCuZnSOD had significant growth-inhibitory effects on both gram-positive and gram-negative bacteria. Collectively, our findings demonstrate that MuCuZnSOD is an essential antioxidant protein, which regulates the host defense mechanisms and innate immunity under oxidative stress.

A pH Switch Controls Zinc Binding in Tomato Copper-Zinc Superoxide Dismutase

Copper-zinc superoxide dismutase (SOD1) is a major antioxidant metalloenzyme that protects cells from oxidative damage by superoxide anions (O2-). Structural, biophysical, and other characteristics have in the past been compiled for mammalian SOD1s and for the highly homologous fungal and bovine SOD1s. Here, we characterize the biophysical properties of a plant SOD1 from tomato chloroplasts and present several of its crystal structures. The most unusual of these structures is a structure at low pH in which tSOD1 harbors zinc in the copper-binding site but contains no metal in the zinc-binding site. The side chain of D83, normally a zinc ligand, adopts an alternate rotameric conformation to form an unusual bidentate hydrogen bond with the side chain of D124, precluding metal binding in the zinc-binding site. This alternate conformation of D83 appears to be responsible for the previously observed pH-dependent loss of zinc from the zinc-binding site of SOD1. Titrations of cobalt into apo tSOD1 at a similar pH support the lack of an intact zinc-binding site. Further characterization of tSOD1 reveals that it is a weaker dimer relative to human SOD1 and that it can be activated in vivo through a copper chaperone for the SOD1-independent mechanism.

Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic

Cu/Zn superoxide dismutase (SOD1) is a frontline antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology. But far from providing a simple demonstration of how disease arises from SOD1 loss-of-function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises current understanding of SOD1 biology from SOD1 genetics through to protein function and stability.

Phenothiazine as novel human superoxide dismutase modulators: discovery, optimization, and biological evaluation

Superoxide dismutases (SODs) are regarded as important antioxidants for protecting cells against damage arising from oxidative stress. Much research is focused on finding new chemicals with an ability to boost human SOD activity. In the research described herein a structure-based approach was used to identify new human Cu-Zn superoxide dismutase (SOD1) modulators based on previously reported plasmodium falciparum iron SOD inhibitors using induced fit docking and molecular dynamic (MD) protocols. The compound with the highest docking binding energy was selected for further structure simplification followed by structural similarity and MD in order to find a new activator/inhibitor scaffold of the SOD1 enzyme. According to the docking survey of the mentioned series, 1,4-bis(3-(1,4,8-trichloro-10Hphenothiazin-10-yl) propyl) piperazine (DS88) was the top scoring compound interacting with the SOD1 active site channel. Following structure simplification and similarity search, the most promising scaffold which is closely related to the phenothiazine antipsychotic class, was identified. Compared with the normal blood SOD1 activity, the percent of O₂ production increased with trifluoperazine, while it decreased with the chlorpromazine. The molecular dynamic investigation shows that trifluoperazine exerts its SOD1 activating effect by stabilizing electrostatic loop while chlorpromazine employs SOD1 inhibition activity through repositioning of the electrostatic loop and increasing its distance from the catalytic metal site which diminished substrate specificity and catalytic activity of the SOD1 enzyme. The results identified the preferred region, orientation, and types of interaction for each activator or inhibitor compound.

Common Signal Transduction Molecules Activated by Bacterial Entry into a Host Cell and by Reactive Oxygen Species

Significance: An increasing number of pathogens are acquiring resistance to antibiotics. Efficient antimicrobial drug regimens are important even for the most advanced therapies, which range from cutting-edge invasive clinical protocols, such as robotic surgeries, to the treatment of harmless bacterial diseases and to minor scratches to the skin. Therefore, there is an urgent need to survey alternative antimicrobial drugs that can reinforce or replace existing antibiotics. Recent Advances: Bacterial proteins that are critical for energy metabolism, promising novel anticancer thiourea derivatives, and the use of synthetic molecules that increase the sensitivity of currently used antibiotics are among the recently discovered antimicrobial drugs. Critical Issues: In the development of new drugs, serious consideration should be given to the previous bacterial evolutionary selection caused by antibiotics, by the high proliferation rate of bacteria, and by the simple prokaryotic structure of bacteria. Future Directions: The survey of drug targets has mainly focused on bacterial proteins, although host signaling molecules involved in the treatment of various pathologies may have unknown antimicrobial characteristics. Recent data have suggested that small molecule inhibitors might enhance the effect of antibiotics, for example, by limiting bacterial entry into host cells. Phagocytosis, the mechanism by which host cells internalize pathogens through β-actin cytoskeletal rearrangement, induces calcium signaling, small GTPase activation, and phosphorylation of the phosphatidylinositol 3-kinase-serine/threonine-specific protein kinase B pathway. Antioxid. Redox Signal. 34, 486-503.

Looking Back at the Early Stages of Redox Biology

The beginnings of redox biology are recalled with special emphasis on formation, metabolism and function of reactive oxygen and nitrogen species in mammalian systems. The review covers the early history of heme peroxidases and the metabolism of hydrogen peroxide, the discovery of selenium as integral part of glutathione peroxidases, which expanded the scope of the field to other hydroperoxides including lipid hydroperoxides, the discovery of superoxide dismutases and superoxide radicals in biological systems and their role in host defense, tissue damage, metabolic regulation and signaling, the identification of the endothelial-derived relaxing factor as the nitrogen monoxide radical (more commonly named nitric oxide) and its physiological and pathological implications. The article highlights the perception of hydrogen peroxide and other hydroperoxides as signaling molecules, which marks the beginning of the flourishing fields of redox regulation and redox signaling. Final comments describe the development of the redox language. In the 18th and 19th century, it was highly individualized and hard to translate into modern terminology. In the 20th century, the redox language co-developed with the chemical terminology and became clearer. More recently, the introduction and inflationary use of poorly defined terms has unfortunately impaired the understanding of redox events in biological systems.

SOD1, more than just an antioxidant

During cellular respiration, radicals, such as superoxide, are produced, and in a large concentration, they may cause cell damage. To combat this threat, the cell employs the enzyme Cu/Zn Superoxide Dismutase (SOD1), which converts the radical superoxide into molecular oxygen and hydrogen peroxide, through redox reactions. Although this is its main function, recent studies have shown that the SOD1 has other functions that deviates from its original one including activation of nuclear gene transcription or as an RNA binding protein. This comprehensive review looks at the most important aspects of human SOD1 (hSOD1), including the structure, properties, and characteristics as well as transcriptional and post-translational modifications (PTM) that the enzyme can receive and their effects, and its many functions. We also discuss the strategies currently used to analyze it to better understand its participation in diseases linked to hSOD1 including Amyotrophic Lateral Sclerosis (ALS), cancer, and Parkinson.

Gastric healing effect of p-coumaric acid isolated from Baccharis dracunculifolia DC on animal model

The p-coumaric acid is a phenolic compound present in large quantities in the extract of Baccharis dracunculifolia DC, a Brazilian medicinal plant used to treat gastric ulcer. Given the necessity for finding new chemical components capable of accelerating gastric healing, in this study, the effects of the p-coumaric acid were evaluated in the acetic acid-induced ulcer model in rats, where histological, inflammatory, and oxidative parameters were analyzed. The healing property was also evaluated in the scratch assay on fibroblast cells (L929) and the cytotoxicity of p-coumaric acid was assessed in both L929 and human gastric adenocarcinoma (AGS) cells by MTT assay. The treatment with p-coumaric acid (10 mg/kg, p.o.) for 7 days, twice a day, decreased by 44.6% the acetic acid-induced gastric ulcer compared with the vehicle-treated group. The vehicle control-treated group showed a larger extension of the ulcer base and an extensive damage into the mucosa and submucosa layers, which were mitigated by the treatment with p-coumaric acid. This beneficial effect was also associated with increased levels of mucin and reduced glutathione, decreased amount of lipid hydroperoxides, and increased superoxide dismutase and catalase activities without interfering with the activity of myeloperoxidase in the gastric tissue. The compound promoted the restructuring of the cell monolayer in the scratch test and did not show toxicity in the L929 cell line, while reduced the viability of the AGS, a lineage of human gastric adenocarcinoma. Thus, p-coumaric acid may be considered a natural source for the treatment of gastric ulcers, by reinforcing protective factors of gastric mucosa and by accelerating gastric healing.

Examination of SOD1 aggregation modulators and their effect on SOD1 enzymatic activity as a proxy for potential toxicity

Small-molecule inhibitors of abnormal protein self-assembly are promising candidates for developing therapy against proteinopathies. Such compounds have been examined primarily as inhibitors of amyloid β-protein (Aβ), whereas testing of inhibitors of other amyloidogenic proteins has lagged behind. An important issue with screening compound libraries is that although an inhibitor suitable for therapy must be both effective and nontoxic, typical screening focuses on efficacy, whereas safety typically is tested at a later stage using cells and/or animals. In addition, typical thioflavin T (ThT)-fluorescence-based screens use the final fluorescence value as a readout, potentially missing important kinetic information. Here, we examined potential inhibitors of superoxide dismutase 1 (SOD1) using ThT-fluorescence including the different phases of fluorescence change and added a parallel screen of SOD1 activity as a potential proxy for compound toxicity. Some compounds previously reported to inhibit other amyloidogenic proteins also inhibited SOD1 aggregation at low micromolar concentrations, whereas others were ineffective. Analysis of the lag phase and exponential slope added important information that could help exclude false-positive or false-negative results. SOD1 was highly resistant to inhibition of its activity, and therefore, did not have the necessary sensitivity to serve as a proxy for examining potential toxicity.

Complete Charge Regulation by a Redox Enzyme Upon Single Electron Transfer

The degree by which metalloproteins partially regulate net charge (Z) upon electron transfer (ET) was recently measured for the first time using "protein charge ladders" of azurin, cytochrome c, and myoglobin [Angew. Chem. Int. Ed. 2018, 57(19), 5364-5368; Angew. Chem. 2018, 130, 5462-5466]. Here, we show that Cu, Zn superoxide dismutase (SOD1) is unique among proteins in its ability to resist changes in net charge upon single ET (e.g., ΔZ_ET(SOD1) =0.05±0.08 per electron, compared to ΔZ_ET(Cyt-c) =1.19±0.02). This total regulation of net charge by SOD1 is attributed to the protonation of the bridging histidine upon copper reduction, yielding redox centers that are isoelectric at both copper oxidation states. Charge regulation by SOD1 would prevent long range coulombic perturbations to residue pK_a 's upon ET at copper, allowing SOD1's "electrostatic loop" to attract superoxide with equal affinity (at both redox states of copper) during diffusion-limited reduction and oxidation of superoxide.

Copper/Zinc Superoxide Dismutase from the Crocodile Icefish Chionodraco hamatus: Antioxidant Defense at Constant Sub-Zero Temperature

In the present study, we describe the purification and molecular characterization of Cu,Zn superoxide dismutase (SOD) from Chionodraco hamatus, an Antarctic teleost widely distributed in many areas of the Ross Sea that plays a pivotal role in the Antarctic food chain. The primary sequence was obtained using biochemical and molecular biology approaches and compared with Cu,Zn SODs from other organisms. Multiple sequence alignment using the amino acid sequence revealed that Cu,Zn SOD showed considerable sequence similarity with its orthologues from various vertebrate species, but also some specific substitutions directly linked to cold adaptation. Phylogenetic analyses presented the monophyletic status of Antartic Teleostei among the Perciformes, confirming the erratic differentiation of these proteins and concurring with the theory of the "unclock-like" behavior of Cu,Zn SOD evolution. Expression of C. hamatus Cu,Zn SOD at both the mRNA and protein levels were analyzed in various tissues, highlighting the regulation of gene expression related to environmental stress conditions and also animal physiology. The data presented are the first on the antioxidant enzymes of a fish belonging to the Channichthyidae family and represent an important starting point in understanding the antioxidant systems of these organisms that are subject to constant risk of oxidative stress.

The biophysics of superoxide dismutase-1 and amyotrophic lateral sclerosis

Few proteins have come under such intense scrutiny as superoxide dismutase-1 (SOD1). For almost a century, scientists have dissected its form, function and then later its malfunction in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). We now know SOD1 is a zinc and copper metalloenzyme that clears superoxide as part of our antioxidant defence and respiratory regulation systems. The possibility of reduced structural integrity was suggested by the first crystal structures of human SOD1 even before deleterious mutations in the sod1 gene were linked to the ALS. This concept evolved in the intervening years as an impressive array of biophysical studies examined the characteristics of mutant SOD1 in great detail. We now recognise how ALS-related mutations perturb the SOD1 maturation processes, reduce its ability to fold and reduce its thermal stability and half-life. Mutant SOD1 is therefore predisposed to monomerisation, non-canonical self-interactions, the formation of small misfolded oligomers and ultimately accumulation in the tell-tale insoluble inclusions found within the neurons of ALS patients. We have also seen that several post-translational modifications could push wild-type SOD1 down this toxic pathway. Recently we have come to view ALS as a prion-like disease where both the symptoms, and indeed SOD1 misfolding itself, are transmitted to neighbouring cells. This raises the possibility of intervention after the initial disease presentation. Several small-molecule and biologic-based strategies have been devised which directly target the SOD1 molecule to change the behaviour thought to be responsible for ALS. Here we provide a comprehensive review of the many biophysical advances that sculpted our view of SOD1 biology and the recent work that aims to apply this knowledge for therapeutic outcomes in ALS.

Nanosecond pulsed electric signals can affect electrostatic environment of proteins below the threshold of conformational effects: The case study of SOD1 with a molecular simulation study

Electric fields can be a powerful tool to interact with enzymes or proteins, with an intriguing perspective to allow protein manipulation. Recently, researchers have focused the interest on intracellular enzyme modifications triggered by the application of nanosecond pulsed electric fields. These findings were also supported by theoretical predictions from molecular dynamics simulations focussing on significant variations in protein secondary structures. In this work, a theoretical study utilizing molecular dynamics simulations is proposed to explore effects of electric fields of high intensity and very short nanosecond duration applied to the superoxide dismutase (Cu/Zn-SOD or SOD-1), an important enzyme involved in the cellular antioxidant defence mechanism. The effects of 100-nanosecond pulsed electric fields, with intensities ranging from 108 to 7x108 V/m, on a single SOD1 enzyme are presented. We demonstrated that the lowest intensity of 108 V/m, although not inducing structural changes, can produce electrostatic modifications on the reaction centre of the enzyme, as apparent from the dipolar response and the electric field distribution of the protein active site. Electric pulses above 5x108 V/m produced a fast transition between the folded and a partially denatured state, as inferred by the secondary structures analysis. Finally, for the highest field intensity used (7x108 V/m), a not reversible transition toward an unfolded state was observed.

Mechanisms of SOD1 regulation by post-translational modifications

SOD1 is commonly known for its ROS scavenging activity, but recent work has uncovered additional roles in modulating metabolism, maintaining redox balance, and regulating transcription. This new paradigm of expanded SOD1 function raises questions regarding the regulation of SOD1 and the cellular partitioning of its biological roles. Despite decades of research on SOD1, much of which focuses on its pathogenic role in amyotrophic lateral sclerosis, relatively little is known about its regulation by post-translational modifications (PTMs). However, over the last decade, advancements in mass spectrometry have led to a boom in PTM discovery across the proteome, which has also revealed new mechanisms of SOD1 regulation by PTMs and an array of SOD1 PTMs with high likelihood of biological function. In this review, we address emerging mechanisms of SOD1 regulation by post-translational modifications, many of which begin to shed light on how the various functions of SOD1 are regulated within the cell.

Far positioned ALS associated mutants of Cu/Zn SOD forms partially metallated, destabilized misfolding intermediates

Loss of stability of proteins is associated with their misfolding and aggregation which results in disease. Despite of the higher stability of Cu/Zn superoxide dismutase (SOD1), the point mutations destabilize its structure, results in oligomerization and the aggregation of SOD1 which is closely associated with the motor neuron disorder, amyotrophic lateral sclerosis. In the present study, we analyzed the role of two SOD1 mutants V14G and E100G which are located far away from the metal sites, dimer interface and disulfide region. The SOD1 mutants were recombinantly produced and their activity, structure and stability were investigated using biochemical methods, CD and DSC methods. In comparison with wild-type SOD1, the mutants exhibited reduced activity and the CD data showed comparable secondary structures composition. However, the stability studies using chemical and thermal denaturation methods showed the mutants are destabilized. Interestingly, our DSC data strongly suggested the destabilization of the mutants is due to the partial metalation of Cu/Zn ions. This observation emphasizes that although the mutations V14G and E100G are located away from the metal sites, they could affect the metal binding similar to metal binding region mutants, which are more susceptible to misfold and aggregate.

Superoxide dismutase transcellular shuttle constructed from dendritic MOF and charge reversible protein derivatives

The development of molecular biology has led to the identification of protein-based therapeutics as an intriguing approach for the treatment of a wide range of diseases. To manufacture transcellular protein delivery shuttles, we attempted charge reversal chemistry on native proteins [e.g., superoxide dismutase (SOD): an enzyme capable of scavenging detrimental reactive oxygen species] by the selective conversion of the positively charged amino residues of native SOD to conjugated negatively charged citraconic moieties, eliciting overall negatively charged polyelectrolytes for the subsequent electrostatic self-assembly with cationic metal-organic framework (MOF) derivatives into protein delivery systems. Please note that the charge conversion was reversible, restoring the original amino groups in intracellular acidic endosome compartments (pH 5), which afforded facile charge reversible functions to reclaim the active SOD in the cell interior. In particular, the strategic manufacture of dendritic MOF supramolecular architectures as transcellular shuttles for the aforementioned charge-reversible SOD derivatives is noteworthy. The MOF was surface-functionalized with several polycationic segments, thus contributing to the hyper-charged architecture for the easy accommodation of the negatively charged SOD derivatives. Consequently, the SOD derivatives managed to internalize into cells by hitchhiking via endocytosis of the positively charged MOF. Once they resided in the acidic endosomes, the charge reversal of the SOD derivatives could occur smoothly and result in reduced interactions between the charged-reversed SOD and MOF, leading to the release of active SOD. Simultaneously, the dendritic MOF due to protein release presented a highly positive-charged architecture to provoke endosome membrane disruption, consequently spurring the translocation of SOD to the cytosol for the execution of its enzymatic activities. Herein, the intracellular ROS level of the activated macrophages was validated to be markedly suppressed by our proposed transcellular SOD shuttles, thereby indicating their wide availability to diverse functional proteins for biomedical applications.

What Are We Missing by Not Measuring the Net Charge of Proteins?

The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials-including contributions from tightly bound metal, solvent, buffer, and cosolvent ions-and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pK_a . Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein-its mass-one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pK_a values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔG_z ) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔG_z contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=-2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool-the "protein charge ladder"-and used it to begin to answer these basic questions.

Lactobacillus reuteri DSM 17938 Protects against Gastric Damage Induced by Ethanol Administration in Mice: Role of TRPV1/Substance P Axis

This study aimed to evaluate the effect of Lactobacillus reuteri DSM 17938 (DSM) on ethanol-induced gastric injury, and if its possible mechanism of action is related to inhibiting the transient receptor potential vanilloid type 1 (TRPV1). We evaluated the effect of supplementing 10⁸ CFU•g body wt^-1•day^-1 of DSM on ethanol-induced gastric injury. DSM significantly reduced the ulcer area (1.940 ± 1.121 mm²) with 3 days of pretreatment. The effects of DSM supplementation were reversed by Resiniferatoxin (RTX), TRPV1 agonist (3 nmol/kg p.o.). Substance P (SP) (1 μmol/L per 20 g) plus 50% ethanol resulted in hemorrhagic lesions, and DSM supplementation did not reverse the lesion area induced by administering SP. TRPV1 staining intensity was lower, SP, malondialdehyde (MDA) and nitrite levels were reduced, and restored normal levels of antioxidant parameters (glutathione and superoxide dismutase) in the gastric mucosa in mice treated with DSM. In conclusion, DSM exhibited gastroprotective activity through decreased expression of TRPV1 receptor and decreasing SP levels, with a consequent reduction of oxidative stress.

Carcinogenesis and Reactive Oxygen Species Signaling: Interaction of the NADPH Oxidase NOX1-5 and Superoxide Dismutase 1-3 Signal Transduction Pathways

SIGNIFICANCE

Reduction/oxidation (redox) balance could be defined as an even distribution of reduction and oxidation complementary processes and their reaction end products. There is a consensus that aberrant levels of reactive oxygen species (ROS), commonly observed in cancer, stimulate primary cell immortalization and progression of carcinogenesis. However, the mechanism how different ROS regulate redox balance is not completely understood. Recent Advances: In the current review, we have summarized the main signaling cascades inducing NADPH oxidase NOX1-5 and superoxide dismutase (SOD) 1-3 expression and their connection to cell proliferation, immortalization, transformation, and CD34+ cell differentiation in thyroid, colon, lung, breast, and hematological cancers.

CRITICAL ISSUES

Interestingly, many of the signaling pathways activating redox enzymes or mediating the effect of ROS are common, such as pathways initiated from G protein-coupled receptors and tyrosine kinase receptors involving protein kinase A, phospholipase C, calcium, and small GTPase signaling molecules.

FUTURE DIRECTIONS

The clarification of interaction of signal transduction pathways could explain how cells regulate redox balance and may even provide means to inhibit the accumulation of harmful levels of ROS in human pathologies.

Exploiting the vulnerable active site of a copper-only superoxide dismutase to disrupt fungal pathogenesis

Copper-only superoxide dismutases (SODs) represent a new class of SOD enzymes that are exclusively extracellular and unique to fungi and oomycetes. These SODs are essential for virulence of fungal pathogens in pulmonary and disseminated infections, and we show here an additional role for copper-only SODs in promoting survival of fungal biofilms. The opportunistic fungal pathogen Candida albicans expresses three copper-only SODs, and deletion of one of them, SOD5, eradicated candidal biofilms on venous catheters in a rodent model. Fungal copper-only SODs harbor an irregular active site that, unlike their Cu,Zn-SOD counterparts, contains a copper co-factor unusually open to solvent and lacks zinc for stabilizing copper binding, making fungal copper-only SODs highly vulnerable to metal chelators. We found that unlike mammalian Cu,Zn-SOD1, C. albicans SOD5 indeed rapidly loses its copper to metal chelators such as EDTA, and binding constants for Cu(II) predict that copper-only SOD5 has a much lower affinity for copper than does Cu,Zn-SOD1. We screened compounds with a variety of indications and identified several metal-binding compounds, including the ionophore pyrithione zinc (PZ), that effectively inhibit C. albicans SOD5 but not mammalian Cu,Zn-SOD1. We observed that PZ both acts as an ionophore that promotes uptake of toxic metals and inhibits copper-only SODs. The pros and cons of a vulnerable active site for copper-only SODs and the possible exploitation of this vulnerability in antifungal drug design are discussed.

Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase

Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO2 and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO2 binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn2+ coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, critical features of ligand binding, position, and metal ion cofactor geometry required for all downstream events can be engineered with small numbers of mutations to provide insights into fundamental underpinnings of protein-ligand recognition. Through structural and computational knowledge, the combination of designed and random mutations aids in the robust design of predetermined changes to ligand binding and activity to engineer protein function.

Perspectives on Structural Molecular Biology Visualization: From Past to Present

Visualization has been a key technology in the progress of structural molecular biology for as long as the field has existed. This perspective describes the nature of the visualization process in structural studies, how it has evolved over the years, and its relationship to the changes in technology that have supported and driven it. It focuses on how technical advances have changed the way we look at and interact with molecular structure, and how structural biology has fostered and challenged that technology.

Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins

Human gut Bacteroides use surface-exposed lipoproteins to bind and metabolize complex polysaccharides. Although vitamins and other nutrients are also essential for commensal fitness, much less is known about how commensal bacteria compete with each other or the host for these critical resources. Unlike in Escherichia coli, transport loci for vitamin B₁₂ (cobalamin) and other corrinoids in human gut Bacteroides are replete with conserved genes encoding proteins whose functions are unknown. Here we report that one of these proteins, BtuG, is a surface-exposed lipoprotein that is essential for efficient B₁₂ transport in B. thetaiotaomicron. BtuG binds B₁₂ with femtomolar affinity and can remove B₁₂ from intrinsic factor, a critical B₁₂ transport protein in humans. Our studies suggest that Bacteroides use surface-exposed lipoproteins not only for capturing polysaccharides, but also to acquire key vitamins in the gut.

Eating is the first step in an hours-long process that extracts the nutrients we need to live. It not only nourishes us, but also a vast community of bacteria in our gut called the microbiota. The gut microbiota acts like an extension of our immune system and helps us stay healthy in many ways. For example, it blocks pathogens from making us sick. But too many gut bacteria in the wrong parts of our intestines can be harmful.

Some people are prone to developing a dangerous overgrowth of bacteria in their small intestine where most of our dietary nutrients get absorbed. This overgrowth can lead to many problems including vitamin B12 deficiency even when they eat plenty of it. To understand why, scientists must learn how microbes affect our ability to absorb nutrients from food and how the microbes themselves capture nutrients like vitamin B12 as they pass through our digestive tract.

Now, Wexler et al. show that some gut microbes may be able to pirate vitamin B12 from us as it passes through the digestive tract. Wexler et al. showed that a protein called BtuG on the surface of a type of gut bacteria called Bacteriodes grabs onto vitamin B12 with extraordinary strength. In fact, these bacterial proteins bind to vitamin B12 so strongly that they can even pry it away from our own vitamin B12 collecting protein.

When Bacteriodes with and without BtuG were placed in mice with no gut bacteria of their own, bacteria with BtuG rapidly outcompeted those lacking the protein. The experiments suggest that competition for vitamin B12 among microbes has favored bacteria that are better at capturing the nutrient. More studies are needed to learn whether BtuG contributes to vitamin B12 deficiencies in humans with gut bacteria overgrowth and determine the best ways to combat such deficiencies.

Two metalloenzymes from rockfish (Sebastes schligellii): Deciphering their potential involvement in redox homeostasis against oxidative stress

Disturbance in the balance between pro-oxidants and anti-oxidants result oxidative stress in aerobic organisms. However, oxidative stress can be inhibited by enzymatic and non-enzymatic defense mechanisms. Superoxide dismutases (SODs) are well-known scavengers of superoxide radicals, and they protect cells by detoxifying hazardous reactive oxygen species. Here, we have identified and characterized two different SODs, CuZnSOD and MnSOD, from black rockfish (RfCuZnSOD and RfMnSOD, respectively). In silico analysis revealed the well-conserved molecular structures comprising all essential properties of CuZnSOD and MnSOD. Phylogenetic analysis revealed that both RfCuZnSOD and RfMnSOD cladded with their fish counterparts. The recombinant RfSOD proteins demonstrated their potential superoxide scavenging abilities through a xanthine oxidase assay. The optimum temperature and pH conditions for both rRfSODs were 25 °C and pH 8, respectively. Moreover, the potential peroxidation function of rRfCuZnSOD was observed in the presence of HCO₃^-. The highest peroxidation activity was observed at 100 μg/mL of rRfCuZnSOD using the MTT cell viability assay and flow cytometry. The analogous tissue-specific expression profile indicated ubiquitous expression of both RfCuZnSOD and RfMnSOD in selected tissues of healthy juvenile rockfish. An immune challenge experiment illustrated the altered expression profiles of both RfCuZnSOD and RfMnSOD against lipopolysaccharide, Streptococcus iniae, and polyinosinic-polycytidylic acid (poly I:C). Collectively, these results strengthen the general understanding of the structural and functional characteristics of SODs within the host defense system.

Engineering enzyme microenvironments for enhanced biocatalysis

Protein engineering provides a means to alter protein structure leading to new functions. Much work has focused on the engineering of enzyme active sites to enhance catalytic activity, however there is an increasing trend towards engineering other aspects of biocatalysts as these efforts can also lead to useful improvements. This tutorial discusses recent advances in engineering an enzyme's local chemical and physical environment, with the goal of enhancing enzyme reaction kinetics, substrate selectivity, and activity in harsh conditions (e.g., low or high pH). By introducing stimuli-responsiveness to these enzyme modifications, dynamic control of activity also becomes possible. These new biomolecular and protein engineering techniques are separate and independent from traditional active site engineering and can therefore be applied synergistically to create new biocatalyst technologies with novel functions.