Preparation and characterization of MnIIMnIII complexes with relevance to class Ib ribonucleotide reductases
Not Available
Biochemistry & Molecular Biology↗
Engineering topics
Farquhar, Erik R.
Publications and source records attributed to Farquhar, Erik R..
An engineered lactate oxidase based electrochemical sensor for continuous detection of biomarker lactic acid in human sweat and serum
Lactate levels in humans reveal intensity and duration of exertion and provide a critical readout for the severity of life-threatening illnesses such as pediatric sepsis. Using the lactate oxidase enzyme (Lox) from Aerococcus viridians, we demonstrated its functionality for lactate electrochemical sensing in physiological fluids in a lab setting. The structure and dynamics of LOx were validated by crystallography, X-ray scattering, and hydroxyl radical protein footprinting. This provided a validated protein template for understanding and designing an enzyme-based electrochemical sensing elements. Using this template, LOx enzyme variants were generated and compared. Comparison of the variants demonstrates that one exhibits effective lactate sensing at significantly reduced operating voltages. Additionally, we demonstrate that the four hexahistidine-tags on each enzyme tetramer are sufficient for immobilization to create a durable, functional sensor, with no need for a covalent attachment, enabling self-immobilization and eliminating the need for additional immobilization steps. The functionality of the LOx enzyme variants was verified at physiological lactate concentrations in both human serum (0–4 mM) and artificial sweat (0–100 mM) using 3-electrode setups for analysis of the three variants in parallel. Accuracy of measurement in both artificial sweat and human serum were high. Employing a microfluidic flow cell, we successfully monitored varying lactate levels in physiological fluids continuously over a 2h period. Overall, this optimized LOx enzyme, which self-immobilizes onto gold sensing electrodes, facilitates efficient and reliable lactate detection and continuous monitoring at reduced operating voltages suitable for further development towards commercial use.
60 APPLIED LIFE SCIENCES↗
Class Ib Ribonucleotide Reductases: Activation of a Peroxido-Mn II Mn III to Generate a Reactive Oxo-Mn III Mn IV Oxidant
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
In vitro maturation of NiSOD reveals a role for cytoplasmic histidine in processing and metalation
The importance of cellular low molecular weight (LMW) ligands in metalloenzyme maturation is largely unexplored. Maturation of NiSOD requires post-translational N-terminal processing of the proenzyme, SodN, by its cognate protease, SodX. Here we provide evidence for the participation of L-histidine in the protease-dependent maturation of Nickel-dependent Superoxide Dismutase (NiSOD) from Streptomyces coelicolor. Furthermore, in vitro studies using purified proteins cloned from S. coelicolor and overexpressed in E. coli support a model where a ternary complex formed between the substrate (SodN), the protease (SodX) and L-Histidine creates a novel Ni-binding site that is capable of the N-terminal processing of SodN and specifically incorporates Ni into the apo-NiSOD product. Thus, L-Histidine serves many of the functions associated with a metallochaperone or, conversely, eliminates the need for a metallochaperone in NiSOD maturation.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Intact mass spectrometry screening to optimize hydroxyl radical dose for protein footprinting
Hydroxyl radical protein footprinting (HRPF) using synchrotron radiation is a well-validated method to assess protein structure in the native solution state. In this method, X-ray radiolysis of water generates hydroxyl radicals that can react with solvent accessible side chains of proteins, with mass spectrometry used to detect the resulting labeled products. An ideal footprinting dose provides sufficient labeling to measure the structure but not so much as to influence the results. The optimization of hydroxyl radical dose is typically performed using an indirect Alexa488 fluorescence assay sensitive to hydroxyl radical concentration, but full evaluation of the experiment's outcome relies upon bottom-up liquid chromatography mass spectrometry (LC-MS) measurements to directly determine sites and extent of oxidative labeling at the peptide and protein level. A direct evaluation of the extent of labeling to provide direct and absolute measurements of dose and “safe” dose ranges in terms of, for example, average numbers of labels per protein, would provide immediate feedback on experimental outcomes prior to embarking on detailed LC-MS analyses. To this end, we describe an approach to integrate intact MS screening of labeled samples immediately following exposure, along with metrics to quantify the extent of observed labeling from the intact mass spectra. Intact MS results on the model protein lysozyme were evaluated in the context of Alexa488 assay results and a bottom-up LC-MS analysis of the same samples. In conclusion, this approach provides a basis for placing delivered hydroxyl radical dose metrics on firmer technical grounds for synchrotron X-ray footprinting of proteins, with explicit parameters to increase the likelihood of a productive experimental outcome. Further, the method directs approaches to provide absolute and direct dosimetry for all types of labeling for protein footprinting.
59 BASIC BIOLOGICAL SCIENCES↗
Aromatic and aliphatic hydrocarbon hydroxylation via a formally Ni IV =O oxidant
The reaction of (NMe 4 ) 2 [Ni II (L Ph )(OAc)] (1[OAc], L Ph = 2,2',2''-nitrilo-tris-(N-phenylacetamide); OAc = acetate) with 3-chloroperoxybenzoic acid (m-CPBA) resulted in the formation of a self-hydroxylated Ni III -phenolate complex, 2, where one of the phenyl groups of L Ph underwent hydroxylation. 2 was characterised by UV-Vis, EPR, and XAS spectroscopies and ESI-MS. 2 decayed to yield a previously characterised Ni II -phenolate complex, 3. We postulate that self-hydroxylation was mediated by a formally Ni IV =O oxidant, formed from the reaction of 1[OAc] with m-CPBA, which undergoes electrophilic aromatic substitution to yield 2. This is supported by an analysis of the kinetic and thermodynamic properties of the reaction of 1[OAc] with m-CPBA. Addition of exogenous hydrocarbon substrates intercepted the self-hydroxylation process, producing hydroxylated products, providing further support for the formally Ni IV =O entity. This study demonstrates that the reaction between Ni II salts and m-CPBA can lead to potent metal-based oxidants, in contrast to recent studies demonstrating carboxyl radical is a radical free-chain reaction initiator in Ni II /m-CPBA hydrocarbon oxidation catalysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Synthesis and Characterization of a Masked Terminal Nickel-Oxide Complex
In exploring terminal nickel-oxo complexes, postulated to be the active oxidant in natural and non-natural oxidation reactions, we report the synthesis of the pseudo-trigonal bipyramidal Ni II complexes (K)[Ni II (L Ph )(DMF)] (1[DMF]) and (NMe 4 ) 2 [Ni II (L Ph )(OAc)] (1[OAc]) (L Ph =2,2’,2’’-nitrilo-tris-(N-phenylacetamide); DMF=N,N-dimethylformamide; - OAc=acetate). Both complexes were characterized using NMR, FTIR, ESI-MS, and X-ray crystallography, showing the L Ph ligand to bind in a tetradentate fashion, together with an ancillary donor. The reaction of 1[OAc] with peroxyphenyl acetic acid (PPAA) resulted in the formation of [(L Ph )Ni III -O-H∙∙∙OAc] 2- , 2, that displays many of the characteristics of a terminal Ni=O species. 2 was characterized by UV-Vis, EPR, and XAS spectroscopies and ESI-MS. 2 decayed to yield a Ni II -phenolate complex 3 (through aromatic electrophilic substitution) that was characterized by NMR, FTIR, ESI-MS, and X-ray crystallography. 2 was capable of hydroxylation of hydrocarbons and epoxidation of olefins, as well as oxygen atom transfer oxidation of phosphines at exceptional rates. While the oxo-wall remains standing, this complex represents an excellent example of a masked metal-oxide that displays all of the properties expected of the ever elusive terminal M=O beyond the oxo-wall.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins
X-ray radiolytic labeling uses broadband X-rays for in situ hydroxyl radical labeling to map protein interactions and conformation. High flux density beams are essential to overcome radical scavengers. However, conventional sample delivery environments, such as capillary flow, limit the use of a fully unattenuated focused broadband beam. An alternative is to use a liquid jet, and we have previously demonstrated that use of this form of sample delivery can increase labeling by tenfold at an unfocused X-ray source. Here we report the first use of a liquid jet for automated inline quantitative fluorescence dosage characterization and sample exposure at a high flux density microfocused synchrotron beamline. Our approach enables exposure times in single-digit microseconds while retaining a high level of side-chain labeling. This development significantly boosts the method’s overall effectiveness and efficiency, generates high-quality data, and opens up the arena for high throughput and ultrafast time-resolved in situ hydroxyl radical labeling.
59 BASIC BIOLOGICAL SCIENCES↗
In vitro functional analysis of gRNA sites regulating assembly of hepatitis B virus
The roles of RNA sequence/structure motifs, Packaging Signals (PSs), for regulating assembly of an HBV genome transcript have been investigated in an efficient in vitro assay containing only core protein (Cp) and RNA. Variants of three conserved PSs, within the genome of a strain not used previously, preventing correct presentation of a Cp-recognition loop motif are differentially deleterious for assembly of nucleocapsid-like particles (NCPs). Cryo-electron microscopy reconstruction of the T = 4 NCPs formed with the wild-type gRNA transcript, reveal that the interior of the Cp shell is in contact with lower resolution density, potentially encompassing the arginine-rich protein domains and gRNA. Symmetry relaxation followed by asymmetric reconstruction reveal that such contacts are made at every symmetry axis. We infer from their regulation of assembly that some of these contacts would involve gRNA PSs, and confirmed this by X-ray RNA footprinting. Mutation of the ε stem-loop in the gRNA, where polymerase binds in vivo, produces a poor RNA assembly substrate with Cp alone, largely due to alterations in its conformation. The results show that RNA PSs regulate assembly of HBV genomic transcripts in vitro, and therefore may play similar roles in vivo, in concert with other molecular factors.
99 GENERAL AND MISCELLANEOUS↗
Formation of cobalt–oxygen intermediates by dioxygen activation at a mononuclear nonheme cobalt( ii ) center
The present study represents the first example showing the generation of Co( ii )-alkylperoxide and Co( iv )-oxo intermediates by employing dioxygen as an oxidant.
Malik, Deesha D.↗
New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting
Synchrotron X-ray footprinting (XF) is a growing structural biology technique that leverages radiation-induced chemical modifications via X-ray radiolysis of water to produce hydroxyl radicals that probe changes in macromolecular structure and dynamics in solution states of interest. The X-ray Footprinting of Biological Materials (XFP) beamline at the National Synchrotron Light Source II provides the structural biology community with access to instrumentation and expert support in the XF method, and is also a platform for development of new technological capabilities in this field. Hee, the design and implementation of a new high-throughput endstation device based around use of a 96-well PCR plate form factor and supporting diagnostic instrumentation for synchrotron XF is described. This development enables a pipeline for rapid comprehensive screening of the influence of sample chemistry on hydroxyl radical dose using a convenient fluorescent assay, illustrated here with a study of 26 organic compounds. The new high-throughput endstation device and sample evaluation pipeline now available at the XFP beamline provide the worldwide structural biology community with a robust resource for carrying out well optimized synchrotron XF studies of challenging biological systems with complex sample compositions.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase
Abstract not provided
Daruwalla, Anahita↗