Quantifying platinum binding on protein-functionalized magnetic microparticles using single particle-ICP-TOF-MS.

This work describes an analytical procedure, single particle-inductively coupled plasma-time-of-flight-mass spectrometry (SP-ICP-TOF-MS), that was developed to determine the platinum binding efficiency of protein-coated magnetic microparticles. SP-ICP-TOF-MS is advantageous due to its ability to quasi-simultaneously detect all nuclides (7Li-242Pu), allowing for both platinum and iron (composition of magnetic microparticles) to be measured concurrently. This method subsequently allows for the differentiation between bound and unbound platinum. The 1 µm magnetic microparticles were fully characterized for their iron concentration, particle concentration, and trace element composition by bulk digestion-ICP-MS and SP-ICP-TOF-MS. The results of both approaches agreed with the certificate values. Using the single particle methodology the platinum loading was quantified to be to 0.18 ± 0.02 fg per particle and 0.32 ± 0.02 fg per particle, for the streptavidin-coated and azurin-coated microparticles, respectively. Both streptavidin-coated and the azurin-coated microparticles had a particle-platinum association of >65%. Platinum bound samples were also analyzed via bulk digestion-based ICP-MS. The bulk ICP-MS results overestimated platinum loading due to free platinum in the samples. This highlights the importance of single particle analysis for a closer inspection of platinum binding performance. The SP-ICP-TOF-MS approach offers advantages over typical bulk digestion methods by eliminating laborious sample preparation, enabling differentiation between bound/unbound platinum in a solution, and quantification of platinum on a particle-by-particle basis. The procedure presented here enables quantification of metal content per particle, which could be broadly implemented for other single particle applications.

Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization.

Customization of deuterated biomolecules is vital for many advanced biological experiments including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating Escherichia coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed, and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of 36 lipid species were quantitatively profiled in 15 different growth conditions, and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.

Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2.

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M-1 s-1, achieves sub-µM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 µM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity.

The factors controlling lignin composition remain unclear. Catechyl (C)-lignin is a homopolymer of caffeyl alcohol with unique properties as a biomaterial and precursor of industrial chemicals. The lignin synthesized in the seed coat of Cleome hassleriana switches from guaiacyl (G)- to C-lignin at around 12 to 14 days after pollination (DAP), associated with a rerouting of the monolignol pathway. Lack of synthesis of caffeyl alcohol limits C-lignin formation before around 12 DAP, but coniferyl alcohol is still synthesized and highly accumulated after 14 DAP. We propose a model in which, during C-lignin biosynthesis, caffeyl alcohol noncompetitively inhibits oxidation of coniferyl alcohol by cell wall laccases, a process that might limit movement of coniferyl alcohol to the apoplast. Developmental changes in both substrate availability and laccase specificity together account for the metabolic fates of G- and C-monolignols in the Cleome seed coat.

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation.

Bacteria and archaea possessing the hgcAB gene pair methylate inorganic mercury (Hg) to form highly toxic methylmercury. HgcA consists of a corrinoid binding domain and a transmembrane domain, and HgcB is a dicluster ferredoxin. However, their detailed structure and function have not been thoroughly characterized. We modeled the HgcAB complex by combining metagenome sequence data mining, coevolution analysis, and Rosetta structure calculations. In addition, we overexpressed HgcA and HgcB in Escherichia coli, confirmed spectroscopically that they bind cobalamin and [4Fe-4S] clusters, respectively, and incorporated these cofactors into the structural model. Surprisingly, the two domains of HgcA do not interact with each other, but HgcB forms extensive contacts with both domains. The model suggests that conserved cysteines in HgcB are involved in shuttling HgII, methylmercury, or both. These findings refine our understanding of the mechanism of Hg methylation and expand the known repertoire of corrinoid methyltransferases in nature.

Hole Hopping through Cytochrome P450.

High-potential iron-oxo species are intermediates in the catalytic cycles of oxygenase enzymes. They can cause heme degradation and irreversible oxidation of nearby amino acids. We have proposed that there are protective mechanisms in which hole hopping from oxidized hemes through tryptophan/tyrosine chains generates a surface-exposed amino-acid oxidant that could be rapidly disarmed by reaction with cellular reductants. In investigations of cytochrome P450BM3, we identified Trp96 as a critical residue that could play such a protective role. This Trp is cation-π paired with Arg398 in 81% of mammalian P450s. Here we report on the effect of the Trp/Arg cation-π interaction on Trp96 formal potentials as well as on electronic coupling strengths between Trp96 and the heme both for wild type cytochrome P450 and selected mutants. Mutation of Arg398 to His, which decreases the Trp96 formal potential, increases Trp-heme electronic coupling; however, surprisingly, the rate of phototriggered electron transfer from a Ru-sensitizer (through Trp96) to the P450BM3 heme was unaffected by the Arg398His mutation. We conclude that Trp96 has moved away from Arg398, suggesting that the protective mechanism for P450s with this Trp-Arg pair is conformationally gated.

Overview and new insights into the thiol reactivity of coordinated NO in {MNO}(6/7/8) (M = Fe, Co) complexes.

The reactivity of free NO (NO(+), NO(•), and NO(-)) with thiols (RSH) is relatively well understood, and the oxidation state of the NO moiety generally determines the outcome of the reaction. However, NO/RSH interactions are often mediated at metal centers, and the fate of these species when bound to a first-row transition metal (e.g., Fe, Co) deserves further investigation. Some metal-bound NO moieties (particularly NO(+), yielding S-nitrosothiols) have been more thoroughly studied, yet the fate of these species remains highly condition-dependent and, for M-NO(-), an unexplored field. Herein, we present an overview of thiol reactions with metal nitrosyls that result in N-O bond activation, ligand substitution on {MNO} fragments, and/or redox chemistry. We also present our results pertaining to the thiol reactivity of nonheme {FeNO}(7/8) complexes [Fe(LN4(pr))(NO)](-/0) (1 and 2) and the noncorrin {CoNO}(8) complex [Co(LN4(pr))(NO)] (3), an isoelectronic analogue of the {FeNO}(8) complex 1. Among other products, the reaction of 1 with p-ClPhSH affords [Fe2(µ-SPh-p-Cl)2(NO)4](-) (anion of 6), a reduced Roussin's red ester (rRRE), which was characterized by Fourier transform infrared (FTIR), UV-vis, electron paramagnetic resonance (EPR), and X-ray diffraction. Similarly, the reaction of 1 with glutathione in buffer affords the corresponding rRRE, which has also been spectroscopically characterized by EPR and UV-vis. The oxidation states of the metals and nitrosyls both contribute to the complex nature of these interactions, and as such, we discuss the varying product distribution accordingly. These studies shed insight into the products that may form through MNO/RSH interactions that lead to NOx activation and {MNO} redox.

NO2(-) activation and reduction to NO by a nonheme Fe(NO2)2 complex.

The selective reduction of nitrite (NO2(-)) to nitric oxide (NO) is a fundamentally important chemical transformation related to environmental remediation of NOx and mammalian blood flow. We report the synthesis and characterization of two nonheme Fe complexes, [Fe(LN4(Im))(MeCN)2](BF4)2 (1(MeCN)) and [Fe(LN4(Im))(NO2)2] (2), geared toward understanding the NO2(-) to NO conversion. Complex 2 represents the first structurally characterized Fe(II) complex with two axial NO2(-) ligands that functions as a nitrite reduction catalyst.

Synthesis, properties, and reactivity of a series of non-heme {FeNO}(7/8) complexes: implications for Fe-nitroxyl coordination.

The biochemical properties of nitroxyl (HNO/NO(-)) are distinct from nitric oxide (NO). Metal centers, particularly Fe, appear as suitable sites of HNO activity, both for generation and targeting. Furthermore, reduced Fe-NO(-)/Fe-HNO or {FeNO}(8) (Enemark-Feltham notation) species offer unique bonding profiles that are of fundamental importance. Given the unique chemical properties of {FeNO}(8) systems, we describe herein the synthesis and properties of {FeNO}(7) and {FeNO}(8) non-heme complexes containing pyrrole donors that display heme-like properties, namely [Fe(LN(4)(R))(NO)] (R = C(6)H(4) or Ph for 3; and R = 4,5-Cl(2)C(6)H(2) or PhCl for 4) and K[Fe(LN(4)(R))(NO)] (R = Ph for 5; R = PhCl for 6). X-ray crystallography establishes that the Fe-N-O angle is ~155° for 3, which is atypical for low-spin square-pyramidal {FeNO}(7) species. Both 3 and 4 display ν(NO) at ~1700 cm(-1) in the IR and reversible diffusion-controlled cyclic voltammograms (CVs) (E(1/2)=~-1.20 V vs. Fc/Fc(+) (ferrocene/ferrocenium redox couple) in MeCN) suggesting that the {FeNO}(8) compounds 5 and 6 are stable on the CV timescale. Reduction of 3 and 4 with stoichiometric KC(8) provided the {FeNO}(8) compounds 5 and 6 in near quantitative yield, which were characterized by the shift in ν(NO) to 1667 and ~1580 cm(-1), respectively. While the ν(NO) for 6 is consistent with FeNO reduction, the ν(NO) for 5 appears more indicative of ligand-based reduction. Additionally, 5 and 6 engage in HNO-like chemistry in their reactions with ferric porphyrins [Fe(III)(TPP)X] (TPP = tetraphenylporphyrin; X = Cl(-), OTf(-) (trifluoromethanesulfonate anion or CF(3)SO(3)(-))) to form [Fe(TPP)NO] in stoichiometric yield via reductive nitrosylation.

Exploring the intermediates of photochemical CO2 reduction: reaction of Re(dmb)(CO)3 COOH with CO2.

We have investigated the reaction of Re(dmb)(CO)(3)COOH with CO(2) using density functional theory, and propose a mechanism for the production of CO. This mechanism supports the role of Re(dmb)(CO)(3)COOH as a key intermediate in the formation of CO. Our new experimental work supports the proposed scheme.

Metal-free sequential [3 + 2]-dipolar cycloadditions using cyclooctynes and 1,3-dipoles of different reactivity.

Although metal-free cycloadditions of cyclooctynes and azides to give stable 1,2,3-triazoles have found wide utility in chemical biology and material sciences, there is an urgent need for faster and more versatile bioorthogonal reactions. We have found that nitrile oxides and diazocarbonyl derivatives undergo facile 1,3-dipolar cycloadditions with cyclooctynes. Cycloadditions with diazocarbonyl derivatives exhibited similar kinetics as compared to azides, whereas the reaction rates of cycloadditions with nitrile oxides were much faster. Nitrile oxides could conveniently be prepared by direct oxidation of the corresponding oximes with BAIB, and these conditions made it possible to perform oxime formation, oxidation, and cycloaddition as a one-pot procedure. The methodology was employed to functionalize the anomeric center of carbohydrates with various tags. Furthermore, oximes and azides provide an orthogonal pair of functional groups for sequential metal-free click reactions, and this feature makes it possible to multifunctionalize biomolecules and materials by a simple synthetic procedure that does not require toxic metal catalysts.