ABSTRACT
A dual-template molecularly imprinted electrochemical sensor was developed for the simultaneous detection of serotonin (5-HT) and glutamate (Glu). First, amino-functionalized reduced graphene oxide (NRGO) was used as the modification material of a GCE to increase its electrical conductivity and specific surface area, using Glu and 5-HT as dual-template molecules and o-phenylenediamine (OPD) with self-polymerization ability as functional monomers. Through self-assembly and electropolymerization, dual-template molecularly imprinted polymers were formed on the electrode. After removing the templates, the specific recognition binding sites were exposed. The amount of NRGO, polymerization parameters, and elution parameters were further optimized to construct a dual-template molecularly imprinted electrochemical sensor, which can specifically recognize double-target molecules Glu and 5-HT. The differential pulse voltammetry (DPV) technique was used to achieve simultaneous detection of Glu and 5-HT based on their distinct electrochemical activities under specific conditions. The sensor showed a good linear relationship for Glu and 5-HT in the range 1 ~ 100 µM, and the detection limits were 0.067 µM and 0.047 µM (S/N = 3), respectively. The sensor has good reproducibility, repeatability, and selectivity. It was successfully utilized to simultaneously detect Glu and 5-HT in mouse serum, offering a more dependable foundation for objectively diagnosing and early warning of depression. Additionally, the double signal sensing strategy also provides a new approach for the simultaneous detection of both electroactive and non-electroactive substances.
Subject(s)
Electrochemical Techniques , Glutamic Acid , Graphite , Limit of Detection , Molecular Imprinting , Phenylenediamines , Serotonin , Serotonin/blood , Serotonin/analysis , Electrochemical Techniques/methods , Electrochemical Techniques/instrumentation , Animals , Glutamic Acid/analysis , Glutamic Acid/blood , Glutamic Acid/chemistry , Graphite/chemistry , Mice , Phenylenediamines/chemistry , Depression/diagnosis , Depression/blood , Electrodes , Biomarkers/blood , Biomarkers/analysis , Reproducibility of ResultsABSTRACT
The negligible cytotoxicity of anion surface-linked dendrons makes glutamic acid-based dendrons a potential candidate for materials and biological applications. Despite the inherent drawbacks of the conventional solution phase synthesis of glutamic acid-based dendrons, there have been no advancements in these protocols. Herein, we demonstrate the first-ever convergent solid phase synthesis of dendrons, up to fourth generation, having glutamic acid branching points produced by preactivation of dicarboxylic acid groups with N-hydroxysuccinimide and simultaneous coupling with amine groups of two growing peptide chains, with excellent yields (30-70%). In addition to the general advantages, such as the easy workup, a final single purification step, and an overall short synthesis duration, the convergent solid phase synthesis allowed us to chemically synthesize glutamic acid branching-based dendrons that cannot be accessed by standard divergent solid phase synthesis. This method has also been validated for its application in synthesizing hard-to-achieve Janus peptide dendrimers in a single stretch on a solid support. Our work corroborates the efficacy of controlled -COOH activation to accomplish an atypical solid phase synthesis of diverse glutamic acid dendrons in a convergent fashion. This is the first example of a Janus peptide dendrimer being synthesized on a solid support, utilizing both convergent and divergent approaches simultaneously.
Subject(s)
Dendrimers , Glutamic Acid , Peptides , Solid-Phase Synthesis Techniques , Dendrimers/chemistry , Dendrimers/chemical synthesis , Solid-Phase Synthesis Techniques/methods , Peptides/chemistry , Peptides/chemical synthesis , Glutamic Acid/chemistry , Molecular StructureABSTRACT
Human hyaluronidase 1 (HYAL1) and PH20 play vital roles in degrading hyaluronic acids through the substrate-assisted double displacement mechanism. While HYAL1, a lysosomal enzyme, functions optimally under acidic conditions, PH20, a sperm surface hyaluronidase, displays a broader pH range, from acidic to neutral. Our objective was to extend HYAL1's pH range towards neutral pH by introducing repulsive charge-charge interactions involving the catalytic Glu131, increasing its pKa as the proton donor. Substituting individual acidic residues in the ß3-loop (S77D), ß3'-ß3â³ hairpin (T86D and P87E), and at Ala132 (A132D and A132E) enabled HYAL1 to demonstrate enzyme activity at pH 7, with the mutants S77D, P87E, and A132E showing the highest activity in the substrate gel assay. However, double and triple substitutions, including S77D/T86D/A132E as found in the PH20 configuration, did not result in enhanced activity compared to single substitutions. Conversely, PH20 mutants with non-acidic substitutions, such as D94S in the ß3-loop and D103T in the ß3'-ß3â³ hairpin, significantly reduced activity within the pH range of 4 to 7. However, the PH20 mutant E149A, reciprocally substituted compared to A132E in HYAL1, exhibited activity similar to PH20 wild-type (WT) at pH 7. In a turbidimetric assay, HYAL1 mutants with single acidic substitutions exhibited activity similar to that of PH20 WT at pH 7. These results suggest that substituting acidic residues near Glu131 results in HYAL1 activity at neutral pH through electrostatic repulsion. This study highlights the significance of charge-charge interactions in both HYAL1 and PH20 in regulating the pH-dependent activity of hyaluronidases.
Subject(s)
Hyaluronoglucosaminidase , Humans , Amino Acid Substitution , Catalytic Domain , Cell Adhesion Molecules , Glutamic Acid/metabolism , Glutamic Acid/chemistry , Hyaluronic Acid/metabolism , Hyaluronic Acid/chemistry , Hyaluronoglucosaminidase/chemistry , Hyaluronoglucosaminidase/metabolism , Hyaluronoglucosaminidase/genetics , Hydrogen-Ion Concentration , Models, Molecular , MutationABSTRACT
Beta-N-methylamino-l-alanine (BMAA) is a potential neurotoxic nonprotein amino acid, which can reach the human body through the food chain. When BMAA interacts with bicarbonate in the human body, carbamate adducts are produced, which share a high structural similarity with the neurotransmitter glutamate. It is believed that BMAA and its l-carbamate adducts bind in the glutamate binding site of ionotropic glutamate receptor 2 (GluR2). Chronic exposure to BMAA and its adducts could cause neurological illness such as neurodegenerative diseases. However, the mechanism of BMAA action and its carbamate adducts bound to GluR2 has not yet been elucidated. Here, we investigate the binding modes and the affinity of BMAA and its carbamate adducts to GluR2 in comparison to the natural agonist, glutamate, to understand whether these can act as GluR2 modulators. Initially, we perform molecular dynamics simulations of BMAA and its carbamate adducts bound to GluR2 to examine the stability of the ligands in the S1/S2 ligand-binding core of the receptor. In addition, we utilize alchemical free energy calculations to compute the difference in the free energy of binding of the beta-carbamate adduct of BMAA to GluR2 compared to that of glutamate. Our findings indicate that carbamate adducts of BMAA and glutamate remain stable in the binding site of the GluR2 compared to BMAA. Additionally, alchemical free energy results reveal that glutamate and the beta-carbamate adduct of BMAA have comparable binding affinity to the GluR2. These results provide a rationale that BMAA carbamate adducts may be, in fact, the modulators of GluR2 and not BMAA itself.
Subject(s)
Amino Acids, Diamino , Carbamates , Cyanobacteria Toxins , Receptors, AMPA , Receptors, AMPA/metabolism , Receptors, AMPA/chemistry , Amino Acids, Diamino/chemistry , Amino Acids, Diamino/metabolism , Carbamates/chemistry , Carbamates/metabolism , Molecular Dynamics Simulation , Humans , Binding Sites , Protein Binding , Glutamic Acid/metabolism , Glutamic Acid/chemistry , LigandsABSTRACT
L-Glutamic acid (L-Glu) is a basic unit of proteins and also serves as an important neurotransmitter in the central nervous system. Its structural properties are critical for biological functions and selective receptor recognition. Although this molecule has been extensively studied, the low frequency vibrational behavior that is closely related to conformational changes and the intermolecular interactions between L-Glu and its receptors are still unclear. In this study, we acquired the fingerprint spectrum of L-Glu by using air plasma terahertz (THz) time-domain spectroscopy in the 0.5-18 THz range. The low frequency vibrational characteristics of L-Glu were investigated through density functional theory (DFT) calculations. The THz responses of the ligand binding domain of the NMDAR-L-Glu complex were studied by the ONIOM method, with a focus on discussing the normal modes and interactions of ligand L-Glu and water molecules. The results illustrate that THz spectroscopy exhibits a sensitive response to the influence of L-Glu on the structure of the NMDAR. The water molecules in proteins have various strong vibration modes in the THz band, showing specificity, diversity and complexity of vibrational behavior. There is potential for influencing and regulating the structural stability of the NMDAR-L-Glu complex through water molecules.
Subject(s)
Glutamic Acid , Receptors, N-Methyl-D-Aspartate , Terahertz Spectroscopy , Terahertz Spectroscopy/methods , Glutamic Acid/chemistry , Receptors, N-Methyl-D-Aspartate/chemistry , Receptors, N-Methyl-D-Aspartate/metabolism , Vibration , Water/chemistry , Density Functional Theory , Ligands , Protein BindingABSTRACT
In vivo glutamate sensing has provided valuable insight into the physiology and pathology of the brain. Electrochemical glutamate biosensors, constructed by cross-linking glutamate oxidase onto an electrode and oxidizing H2O2 as a proxy for glutamate, are the gold standard for in vivo glutamate measurements for many applications. While glutamate sensors have been employed ubiquitously for acute measurements, there are almost no reports of long-term, chronic glutamate sensing in vivo, despite demonstrations of glutamate sensors lasting for weeks in vitro. To address this, we utilized a platinum electrode with nanometer-scale roughness (nanoPt) to improve the glutamate sensors' sensitivity and longevity. NanoPt improved the GLU sensitivity by 67.4% and the sensors were stable in vitro for 3 weeks. In vivo, nanoPt glutamate sensors had a measurable signal above a control electrode on the same array for 7 days. We demonstrate the utility of the nanoPt sensors by studying the effect of traumatic brain injury on glutamate in the rat striatum with a flexible electrode array and report measurements of glutamate taken during the injury itself. We also show the flexibility of the nanoPt platform to be applied to other oxidase enzyme-based biosensors by measuring γ-aminobutyric acid in the porcine spinal cord. NanoPt is a simple, effective way to build high sensitivity, robust biosensors harnessing enzymes to detect neurotransmitters in vivo.
Subject(s)
Amino Acid Oxidoreductases , Biosensing Techniques , Glutamic Acid , Biosensing Techniques/instrumentation , Biosensing Techniques/methods , Animals , Glutamic Acid/analysis , Glutamic Acid/chemistry , Rats , Amino Acid Oxidoreductases/chemistry , Amino Acid Oxidoreductases/metabolism , Electrodes , Platinum/chemistry , Swine , Brain Injuries, Traumatic/metabolism , Electrochemical Techniques/methods , Electrochemical Techniques/instrumentation , Hydrogen Peroxide/analysis , Hydrogen Peroxide/metabolism , Hydrogen Peroxide/chemistry , Rats, Sprague-Dawley , Male , ElectroplatingABSTRACT
Amino acids are important chiral compounds in the human body, and are important basic components that make up the human body and play an important role in the human body. Among them, different enantiomers of an amino acid may have different roles, and different types of amino acids can be interconverted. However, the content of D-amino acids is much lower than that of L-amino acids, which is difficult to be detected. At present, many of the potential roles of D-amino acids, such as the conversion of D-amino acids to each other, have not yet been fully revealed. Hence, we synthesized fluorescent probe (R)-5 by condensation of 1,1'-Bi-2-naphthol (BINOL) and 2-(Aminomethyl)pyridine with Schiff base, which can recognize both D-arginine and D-glutamic acid at low concentrations. Meanwhile, (R)-5 can be applied to paper-based sensors for the detection of arginine and glutamate in living cells and for food amino acid detection.
Subject(s)
Arginine , Fluorescent Dyes , Glutamic Acid , Fluorescent Dyes/chemistry , Glutamic Acid/chemistry , Glutamic Acid/analysis , Arginine/chemistry , Arginine/analysis , Humans , Stereoisomerism , Naphthols/chemistryABSTRACT
Kainate receptors, a subclass of ionotropic glutamate receptors, are tetrameric ligand-gated ion channels that mediate excitatory neurotransmission1-4. Kainate receptors modulate neuronal circuits and synaptic plasticity during the development and function of the central nervous system and are implicated in various neurological and psychiatric diseases, including epilepsy, depression, schizophrenia, anxiety and autism5-11. Although structures of kainate receptor domains and subunit assemblies are available12-18, the mechanism of kainate receptor gating remains poorly understood. Here we present cryo-electron microscopy structures of the kainate receptor GluK2 in the presence of the agonist glutamate and the positive allosteric modulators lectin concanavalin A and BPAM344. Concanavalin A and BPAM344 inhibit kainate receptor desensitization and prolong activation by acting as a spacer between the amino-terminal and ligand-binding domains and a stabilizer of the ligand-binding domain dimer interface, respectively. Channel opening involves the kinking of all four pore-forming M3 helices. Our structures reveal the molecular basis of kainate receptor gating, which could guide the development of drugs for treatment of neurological disorders.
Subject(s)
Concanavalin A , Cryoelectron Microscopy , GluK2 Kainate Receptor , Glutamic Acid , Ion Channel Gating , Models, Molecular , Protein Domains , Receptors, Kainic Acid , Receptors, Kainic Acid/chemistry , Receptors, Kainic Acid/metabolism , Receptors, Kainic Acid/ultrastructure , Humans , Glutamic Acid/metabolism , Glutamic Acid/chemistry , Animals , Concanavalin A/chemistry , Concanavalin A/metabolism , Concanavalin A/pharmacology , Ligands , Allosteric Regulation , Binding SitesABSTRACT
The stability of monoclonal antibodies (mAbs) is vital for their therapeutic success. Sorbitol, a common mAb stabilizer used to prevent aggregation, was evaluated for any potential adverse effects on the chemical stability of mAb X. An LC-MS/MS based analysis focusing on the post-translational modifications (PTMs) of mAb X was conducted on samples that had undergone accelerated aging at 40°C. Along with PTMs that are known to affect mAbs' structure function and stability (such as deamidation and oxidation), a novel mAb PTM was discovered, the esterification of glutamic acid by sorbitol. Incubation of mAb X with a 1:1 ratio of unlabeled sorbitol and isotopically labeled sorbitol (13C6) further corroborated that the modification was the consequence of the esterification of glutamic acid by sorbitol. Levels of esterification varied across glutamic acid residues and correlated with incubation time and sorbitol concentration. After 4 weeks of accelerated stability with isotopically labeled sorbitol, it was found that 16% of the total mAb possesses an esterified glutamic acid. No esterification was observed at aspartic acid sites despite the free carboxylic acid side chain. This study unveils a unique modification of mAbs, emphasizing its potential significance for formulation and drug development.
Subject(s)
Antibodies, Monoclonal , Glutamic Acid , Sorbitol , Antibodies, Monoclonal/chemistry , Drug Stability , Esterification , Glutamic Acid/chemistry , Liquid Chromatography-Mass Spectrometry/methods , Protein Processing, Post-Translational , Protein Stability , Sorbitol/chemistry , Tandem Mass Spectrometry/methodsABSTRACT
A small series of copoly(α,l-glutamic acid/dl-allylglycine)s with the same chain length and allylglycine content (â¼10 mol %) but different spatial distribution of allylglycine units was synthesized and subsequently glycosylated via thiol-ene chemistry. Dilute aqueous copolypeptide solutions (0.1 wt %, physiological saline) were analyzed by circular dichroism spectroscopy, dynamic light scattering, and cryogenic transmission electron microscopy. The copolypeptides adopted a random coil or α-helix conformation, depending on solution pH, and the glycosylated residues either distorted or enhanced the folding into an α-helix depending on their location and spatial distribution along the chain. However, regardless of their secondary structure and degree of charging, all partially glycosylated copolypeptides self-assembled into 3D spherical structures, supposedly driven by a hydrophilic effect promoting microphase separation into glucose-rich and glutamate-rich domains.
Subject(s)
Saline Solution , Saline Solution/chemistry , Glutamic Acid/chemistry , Glycosylation , Circular Dichroism , Solutions , Glycine/chemistry , Hydrogen-Ion ConcentrationABSTRACT
The multidrug efflux transporter EmrE from Escherichia coli requires anionic residues in the substrate binding pocket for coupling drug transport with the proton motive force. Here, we show how protonation of a single membrane embedded glutamate residue (Glu14) within the homodimer of EmrE modulates the structure and dynamics in an allosteric manner using NMR spectroscopy. The structure of EmrE in the Glu14 protonated state displays a partially occluded conformation that is inaccessible for drug binding by the presence of aromatic residues in the binding pocket. Deprotonation of a single Glu14 residue in one monomer induces an equilibrium shift toward the open state by altering its side chain position and that of a nearby tryptophan residue. This structural change promotes an open conformation that facilitates drug binding through a conformational selection mechanism and increases the binding affinity by approximately 2000-fold. The prevalence of proton-coupled exchange in efflux systems suggests a mechanism that may be shared in other antiporters where acid/base chemistry modulates access of drugs to the substrate binding pocket.
Subject(s)
Antiporters , Escherichia coli Proteins , Escherichia coli , Escherichia coli Proteins/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Escherichia coli/metabolism , Escherichia coli/genetics , Antiporters/metabolism , Antiporters/chemistry , Antiporters/genetics , Binding Sites , Protein Binding , Protons , Protein Conformation , Magnetic Resonance Spectroscopy , Glutamic Acid/metabolism , Glutamic Acid/chemistry , Models, MolecularABSTRACT
Phase separation and percolation contribute to phase transitions of multivalent macromolecules. Contributions of percolation are evident through the viscoelasticity of condensates and through the formation of heterogeneous distributions of nano- and mesoscale pre-percolation clusters in sub-saturated solutions. Here, we show that clusters formed in sub-saturated solutions of FET (FUS-EWSR1-TAF15) proteins are affected differently by glutamate versus chloride. These differences on the nanoscale, gleaned using a suite of methods deployed across a wide range of protein concentrations, are prevalent and can be unmasked even though the driving forces for phase separation remain unchanged in glutamate versus chloride. Strikingly, differences in anion-mediated interactions that drive clustering saturate on the micron-scale. Beyond this length scale the system separates into coexisting phases. Overall, we find that sequence-encoded interactions, mediated by solution components, make synergistic and distinct contributions to the formation of pre-percolation clusters in sub-saturated solutions, and to the driving forces for phase separation.
Subject(s)
Phase Transition , Glutamic Acid/chemistry , Chlorides/chemistry , Humans , Solutions , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/chemistry , Phase SeparationABSTRACT
Hydroxyprolines are abundant in nature and widely utilized by many living organisms. Isomerization of trans-4-hydroxy-d-proline (t4D-HP) to generate 2-amino-4-ketopentanoate has been found to need a glycyl radical enzyme HplG, which catalyzes the cleavage of the C-N bond, while dehydration of trans-4-hydroxy-l-proline involves a homologous enzyme of HplG. Herein, molecular dynamics simulations and quantum mechanics/molecular mechanics (QM/MM) calculations are employed to understand the reaction mechanism of HplG. Two possible reaction pathways of HplG have been explored to decipher the origin of its chemoselectivity. The QM/MM calculations reveal that the isomerization proceeds via an initial hydrogen shift from the Cγ site of t4D-HP to a catalytic cysteine radical, followed by cleavage of the Cδ-N bond in t4D-HP to form a radical intermediate that captures a hydrogen atom from the cysteine. Activation of the Cδ-H bond in t4D-HP to bring about dehydration of t4D-HP possesses an extremely high energy barrier, thus rendering the dehydration pathway implausible in HplG. On the basis of the current calculations, conserved residue Glu429 plays a pivotal role in the isomerization pathway: the hydrogen bonding between it and t4D-HP weakens the hydroxyalkyl Cγ-Hγ bond, and it acts as a proton acceptor to trigger the cleavage of the C-N bond in t4D-HP. Our current QM/MM calculations rationalize the origin of the experimentally observed chemoselectivity of HplG and propose an H-bond-assisted bond activation strategy in radical-containing enzymes. These findings have general implications on radical-mediated enzymatic catalysis and expand our understanding of how nature wisely and selectively activates the C-H bond to modulate catalytic selectivity.
Subject(s)
Cysteine , Glutamic Acid , Molecular Dynamics Simulation , Quantum Theory , Cysteine/chemistry , Cysteine/metabolism , Glutamic Acid/chemistry , Glutamic Acid/metabolism , Free Radicals/chemistry , Free Radicals/metabolism , Hydrogen BondingABSTRACT
Neurotransmitter ligands electrically excite neurons by activating ionotropic glutamate receptor (iGluR) ion channels. Knowledge of the iGluR amino acid residues that dominate ligand-induced activation would enable the prediction of function from sequence. We therefore explored the molecular determinants of activity in rat N-methyl-D-aspartate (NMDA)-type iGluRs (NMDA receptors), complex heteromeric iGluRs comprising two glycine-binding GluN1 and two glutamate-binding GluN2 subunits, using amino acid sequence analysis, mutagenesis, and electrophysiology. We find that a broadly conserved aspartate residue controls both ligand potency and channel activity, to the extent that certain substitutions at this position bypass the need for ligand binding in GluN1 subunits, generating NMDA receptors activated solely by glutamate. Furthermore, we identify a homomeric iGluR from the placozoan Trichoplax adhaerens that has utilized native mutations of this crucial residue to evolve into a leak channel that is inhibited by neurotransmitter binding, pointing to a dominant role of this residue throughout the iGluR superfamily.
Subject(s)
Hydrophobic and Hydrophilic Interactions , Animals , Rats , Ligands , Binding Sites , Amino Acid Sequence , Protein Binding , Receptors, N-Methyl-D-Aspartate/metabolism , Receptors, N-Methyl-D-Aspartate/chemistry , Receptors, N-Methyl-D-Aspartate/genetics , Receptors, Ionotropic Glutamate/metabolism , Receptors, Ionotropic Glutamate/chemistry , Receptors, Ionotropic Glutamate/genetics , Glutamic Acid/metabolism , Glutamic Acid/chemistry , Models, Molecular , Humans , Amino Acid Substitution , Protein Domains , HEK293 Cells , Glycine/metabolism , Glycine/chemistryABSTRACT
Carboncarbon (C-C) bonds serve as the fundamental structural backbone of organic molecules. As a critical CC bond forming enzyme, α-oxoamine synthase is responsible for the synthesis of α-amino ketones by performing the condensation reaction between amino acids and acyl-CoAs. We previously identified an α-oxoamine synthase (AOS), named as Alb29, involved in albogrisin biosynthesis in Streptomyces albogriseolus MGR072. This enzyme belongs to the α-oxoamine synthase family, a subfamily under the pyridoxal 5'-phosphate (PLP) dependent enzyme superfamily. In this study, we report the crystal structures of Alb29 bound to PLP and L-Glu, which provide the atomic-level structural insights into the substrate recognition by Alb29. We discover that Alb29 can catalyze the amino transformation from L-Gln to L-Glu, besides the condensation of L-Glu with ß-methylcrotonyl coenzyme A. Subsequent structural analysis has revealed that one flexible loop in Alb29 plays an important role in both amino transformation and condensation. Based on the crystal structure of the S87G mutant in the loop region, we capture two distinct conformations of the flexible loop in the active site, compared with the wild-type Alb29. Our study offers valuable insights into the catalytic mechanism underlying substrate recognition of Alb29.
Subject(s)
Glutamic Acid , Substrate Specificity , Glutamic Acid/chemistry , Models, Molecular , Streptomyces/enzymology , Crystallography, X-Ray , Catalytic Domain , Protein Conformation , Pyridoxal Phosphate/metabolism , Pyridoxal Phosphate/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Structure-Activity RelationshipABSTRACT
Artificial nanozymes (enzyme-mimics), specifically metallic nanomaterials, have garnered significant attention recently due to their reduced preparation cost and enhanced stability in a wide range of environments. The present investigation highlights, for the first time, a straightforward green synthesis of biogenic platinum nanoparticles (PtNPs) from a natural resource, namely Prunella vulgaris (Pr). To demonstrate the effectiveness of the phytochemical extract as an effective reducing agent, the PtNPs were characterized by various techniques such as UV-vis spectroscopy, High-resolution Transmission electron microscopy (HR-TEM), zeta-potential analysis, Fourier-transform infrared spectroscopy (FTIR), and Energy dispersive spectroscopy (EDS). The formation of PtNPs with narrow size distribution was verified. Surface decoration of PtNPs was demonstrated with multitudinous functional groups springing from the herbal extract. To demonstrate their use as viable nanozymes, the peroxidase-like activity of Pr/PtNPs was evaluated through a colorimetric assay. Highly sensitive visual detection of H2O2 with discrete linear ranges and a low detection limit of 3.43 µM was demonstrated. Additionally, peroxidase-like catalytic activity was leveraged to develop a colorimetric platform to quantify glutamate biomarker levels with a high degree of selectivity, the limit of detection (LOD) being 7.00 µM. The 2,2-Diphenyl-1-picrylhydrazyl (DPPH) test was used to explore the scavenging nature of the PtNPs via the degradation of DPPH. Overall, the colorimetric assay developed using the Pr/PtNP nanozymes in this work could be used in a broad spectrum of applications, ranging from biomedicine and food science to environmental monitoring.
Subject(s)
Antioxidants , Glutamic Acid , Hydrogen Peroxide , Metal Nanoparticles , Platinum , Prunella , Platinum/chemistry , Metal Nanoparticles/chemistry , Hydrogen Peroxide/chemistry , Hydrogen Peroxide/analysis , Antioxidants/chemistry , Antioxidants/analysis , Antioxidants/pharmacology , Prunella/chemistry , Glutamic Acid/analysis , Glutamic Acid/chemistry , Plant Extracts/chemistryABSTRACT
Na+/H+ antiporters facilitate the exchange of Na+ for H+ across the cytoplasmic membrane in prokaryotic and eukaryotic cells. These transporters are crucial to maintain the homeostasis of sodium ions, consequently pH, and volume of the cells. Therefore, sodium/proton antiporters are considered promising therapeutic targets in humans. The Na+/H+ antiporter in Escherichia coli (Ec-NhaA), a prototype of cation-proton antiporter (CPA) family, transports two protons and one sodium (or Li+) in opposite direction. Previous mutagenesis experiments on Ec-NhaA have proposed Asp164, Asp163, and Asp133 amino acids with the significant implication in functional and structural integrity and create site for ion-binding. However, the mechanism and the sites for the binding of the two protons remain unknown and controversial which could be critical for pH regulation. In this study, we have explored the role of Glu78 in the regulation of pH by Ec-NhaA. Although we have created various mutants, E78C has shown a considerable effect on the stoichiometry of NhaA and presented comparable phenotypes. The ITC experiment has shown the binding of ~ 5 protons in response to the transport of one lithium ion. The phenotype analysis on selective medium showed a significant expression compared to WT Ec-NhaA. This represents the importance of Glu78 in transporting the H+ across the membrane where a single mutation with Cys amino acid alters the number of H+ significantly maintaining the activity of the protein.
Subject(s)
Escherichia coli Proteins , Escherichia coli , Glutamic Acid , Mutagenesis, Site-Directed , Sodium-Hydrogen Exchangers , Escherichia coli Proteins/genetics , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Glutamic Acid/metabolism , Glutamic Acid/chemistry , Sodium-Hydrogen Exchangers/genetics , Sodium-Hydrogen Exchangers/chemistry , Sodium-Hydrogen Exchangers/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Hydrogen-Ion Concentration , Ion Exchange , Models, MolecularABSTRACT
The identification of the coproporphyrin-dependent heme biosynthetic pathway, which is used almost exclusively by monoderm bacteria in 2015 by Dailey et al. triggered studies aimed at investigating the enzymes involved in this pathway that were originally assigned to the protoporphyrin-dependent heme biosynthetic pathway. Here, we revisit the active site of coproporphyrin ferrochelatase by a biophysical and biochemical investigation using the physiological substrate coproporphyrin III, which in contrast to the previously used substrate protoporphyrin IX has four propionate substituents and no vinyl groups. In particular, we have compared the reactivity of wild-type coproporphyrin ferrochelatase from the firmicute Listeria monocytogenes with those of variants, namely, His182Ala (H182A) and Glu263Gln (E263Q), involving two key active site residues. Interestingly, both variants are active only toward the physiological substrate coproporphyrin III but inactive toward protoporphyrin IX. In addition, E263 exchange impairs the final oxidation step from ferrous coproheme to ferric coproheme. The characteristics of the active site in the context of the residues involved and the substrate binding properties are discussed here using structural and functional means, providing a further contribution to the deciphering of this enigmatic reaction mechanism.
Subject(s)
Catalytic Domain , Coproporphyrins , Ferrochelatase , Glutamic Acid , Histidine , Protoporphyrins , Ferrochelatase/metabolism , Ferrochelatase/chemistry , Ferrochelatase/genetics , Coproporphyrins/metabolism , Coproporphyrins/chemistry , Protoporphyrins/metabolism , Protoporphyrins/chemistry , Histidine/metabolism , Histidine/chemistry , Histidine/genetics , Glutamic Acid/metabolism , Glutamic Acid/chemistry , Glutamic Acid/genetics , Heme/metabolism , Heme/chemistry , Substrate Specificity , Models, Molecular , Oxidation-Reduction , Kinetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , CatalysisABSTRACT
Dye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type DyPs. First, we did site saturation mutagenesis of this residue, replacing it with all possible amino acids in bacterial DyPs from Bacillus subtilis (BsDyP) and from Kitasatospora aureofaciens (KaDyP1), the latter being characterized here for the first time. We screened the resulting libraries of variants for activity towards ABTS and identified variants with increased catalytic efficiency. The selected variants were purified and characterized for activity and stability. We furthermore used Molecular Dynamics simulations to rationalize the increased catalytic efficiency and found that the main reason is the electron channeling becoming easier from surface-exposed tryptophans. Based on our findings, we also propose that this glutamate could work as a pH switch in the wild-type enzyme, preventing intracellular damage.
Subject(s)
Bacillus subtilis , Coloring Agents , Glutamic Acid , Peroxidases , Glutamic Acid/chemistry , Glutamic Acid/metabolism , Coloring Agents/chemistry , Coloring Agents/metabolism , Bacillus subtilis/enzymology , Peroxidases/chemistry , Peroxidases/metabolism , Peroxidases/genetics , Molecular Dynamics Simulation , Protein Engineering , Mutagenesis, Site-DirectedABSTRACT
The biological significance of self-assembled protein filament networks and their unique mechanical properties have sparked interest in the development of synthetic filament networks that mimic these attributes. Building on the recent advancement of autoaccelerated ring-opening polymerization of amino acid N-carboxyanhydrides (NCAs), this study strategically explores a series of random copolymers comprising multiple amino acids, aiming to elucidate the core principles governing gelation pathways of these purpose-designed copolypeptides. Utilizing glutamate (Glu) as the primary component of copolypeptides, two targeted pathways were pursued: first, achieving a fast fibrillation rate with lower interaction potential using serine (Ser) as a comonomer, facilitating the creation of homogeneous fibril networks; and second, creating more rigid networks of fibril clusters by incorporating alanine (Ala) and valine (Val) as comonomers. The selection of amino acids played a pivotal role in steering both the morphology of fibril superstructures and their assembly kinetics, subsequently determining their potential to form sample-spanning networks. Importantly, the viscoelastic properties of the resulting supramolecular hydrogels can be tailored according to the specific copolypeptide composition through modulations in filament densities and lengths. The findings enhance our understanding of directed self-assembly in high molecular weight synthetic copolypeptides, offering valuable insights for the development of synthetic fibrous networks and biomimetic supramolecular materials with custom-designed properties.