Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics

Native mass spectra of large, polydisperse biomolecules with repeated subunits, such as lipoprotein Nanodiscs, can often be challenging to analyze by conventional methods. The presence of tens of closely spaced, overlapping peaks in these mass spectra can make charge state, total mass, or subunit mass determinations difficult to measure by traditional methods. Recently, we introduced a Fourier Transform-based algorithm that can be used to deconvolve highly congested mass spectra for polydisperse ion populations with repeated subunits and facilitate identification of the charge states, subunit mass, charge-state-specific, and total mass distributions present in the ion population. Here, we extend this method by investigating the advantages of using overtone peaks in the Fourier spectrum, particularly for mass spectra with low signal-to-noise and poor resolution. This method is illustrated for lipoprotein Nanodisc mass spectra acquired on three common platforms, including the first reported native mass spectrum of empty “large” Nanodiscs assembled with MSP1E3D1 and over 300 noncovalently associated lipids. It is shown that overtone peaks contain nearly identical stoichiometry and charge state information to fundamental peaks but can be significantly better resolved, resulting in more reliable reconstruction of charge-state-specific mass spectra and peak width characterization. We further demonstrate how these parameters can be used to improve results from Bayesian spectral fitting algorithms, such as UniDec.

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Fabrication of Defined Polydopamine Nanostructures by DNA Origami‐Templated Polymerization

A versatile, bottom‐up approach allows the controlled fabrication of polydopamine (PD) nanostructures on DNA origami. PD is a biosynthetic polymer that has been investigated as an adhesive and promising surface coating material. However, the control of dopamine polymerization is challenged by the multistage‐mediated reaction mechanism and diverse chemical structures in PD. DNA origami decorated with multiple horseradish peroxidase‐mimicking DNAzyme motifs was used to control the shape and size of PD formation with nanometer resolution. These fabricated PD nanostructures can serve as “supramolecular glue” for controlling DNA origami conformations. Facile liberation of the PD nanostructures from the DNA origami templates has been achieved in acidic medium. This presented DNA origami‐controlled polymerization of a highly crosslinked polymer provides a unique access towards anisotropic PD architectures with distinct shapes that were retained even in the absence of the DNA origami template.     

New osmium cluster compounds containing the heterocyclic ligand 2,3-bis-(diphenylphosphino)quinoxaline (dppq): Ligand isomerization and crystal structures of dppq, the isomeric clusters Os3(CO)10(dppq), and HOs3(CO)9[μ-2,3-PhP(η-C6H4)(Ph2P)quinoxaline]

Treatment of the labile cluster 1,2-Os₃(CO)₁₀(MeCN)₂ (1) with the diphosphine ligand 2,3-bis(diphenylphosphino)quinoxaline (dppq) at room temperature affords 1,2-Os₃(CO)₁₀(dppq) (2b) as the kinetic product of ligand substitution in 84% yield. 2b isomerizes to the thermodynamically more stable dppq-chelated cluster 1,1-Os₃(CO)₁₀(dppq) (2c) as the sole observable product under CO at temperatures below 358 K. The kinetics for the conversion of 2b → 2c have been investigated by NMR spectroscopy in CDCl₃ over the temperature range 323-353 K, and the reaction was found to exhibit a rate law that is first order in 2b. The calculated activation parameters [ΔH^≠ = 25.4(4) kcal/mol; ΔS^≠ = −3(1) eu] support an intramolecular isomerization scenario, one that involves the migration of phosphine and CO groups about the cluster polyhedron. The disposition of the dppq ligand in the isomeric Os₃(CO)₁₀(dppq) clusters has been established by X-ray crystallography and ³¹P NMR spectroscopy. Photolysis of 2c at 366 nm leads to CO loss and ortho metalation of one of the aryl groups on the Ph₂P moiety to furnish the hydride cluster HOs₃(CO)₉[μ-PhP(η¹-C₆H₄)(Ph₂P)quinoxaline] (3). The isomerization behavior exhibited by 2b follows that of related diphosphine-substituted Os₃ clusters prepared by us.     

Synthesis of a 7-azaindole by chichibabin cyclization: reversible base-mediated dimerization of 3-picolines

The lithium diisopropylamide (LDA)-mediated condensation of 2-fluoro-3-picoline and benzonitrile to form 2-phenyl-7-azaindole via a Chichibabin cyclization is described. Facile dimerization of the picoline via a 1,4-addition of the incipient benzyllithium to the picoline starting material and fast 1,2-addition of LDA to benzonitrile cause the reaction to be complex. Both adducts are shown to reenter the reaction coordinate to produce the desired 7-azaindole. The solution structures of the key intermediates and the underlying reaction mechanisms are studied by a combination of IR and NMR spectroscopies.     

Sortin1-hypersensitive mutants link vacuolar-trafficking defects and flavonoid metabolism in Arabidopsis vegetative tissues

Sortin1 is a chemical genetic-hit molecule that causes specific mislocalization of plant and yeast-soluble and membrane vacuolar markers. To better understand its mode of action, we designed a Sortin1-hypersensitive screen and identified several Sortin1-hypersensitive and flavonoid-defective mutants. Mechanistically, Sortin1 mimics the effect of the glutathione inhibitor buthionine sulfoximine and alters the vacuolar accumulation of flavonoids, likely blocking their transport through vacuole-localized ABC transporters. Structure-activity relationship studies conducted in Arabidopsis revealed the structural requirements for Sortin1 bioactivity and demonstrated that overlapping Sortin1 substructures can be used to discriminate between vacuolar-flavonoid accumulations and vacuolar-biogenesis defects. We conclude that Sortin1 is a valuable probe for dissecting novel links among flavonoid transport, vacuolar integrity, and the trafficking of vacuolar targeted cargoes in Arabidopsis.     

Environmental DNA-encoded antibiotics fasamycins A and B inhibit FabF in type II fatty acid biosynthesis

In a recent study of polyketide biosynthetic gene clusters cloned directly from soil, we isolated two antibiotics, fasamycins A and B, which showed activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. To identify the target of the fasamycins, mutants with elevated fasamycin A minimum inhibitory concentrations were selected from a wild-type culture of E. faecalis OG1RF. Next-generation sequencing of these mutants, in conjunction with in vitro biochemical assays, showed that the fasamycins inhibit FabF of type II fatty acid biosynthesis (FASII). Candidate gene overexpression studies also showed that fasamycin resistance is conferred by fabF overexpression. On the basis of comparisons with known FASII inhibitors and in silico docking studies, the chloro-gem-dimethyl-anthracenone substructure seen in the fasamycins is predicted to represent a naturally occurring FabF-specific antibiotic pharmacophore. Optimization of this pharmacophore should yield FabF-specific antibiotics with increased potencies and differing spectra of activity. This study demonstrates that culture-independent antibiotic discovery methods have the potential to provide access to novel metabolites with modes of action that differ from those of antibiotics currently in clinical use.     

Ammonium hexafluorosilicate salts

The preparation and characterization of the ammonium hexafluorosilicate salts, 2[R]⁺ [SiF₆]²⁻ (where R=piperidinium (2), methylammonium (3), quinolinium (4), acridinium (5), 2,2,6,6-tetramethylpiperidinium (6), and propylammonium (7)) is described.The salts were prepared from the reaction of the corresponding alkylammonium fluoride with silica gel. The compounds were characterized by NMR, IR, mass spectrometry and in the case of 1 (piperidinium fluoride), 2-4 by X-ray crystallography. Compounds 1-3 crystallize in the orthorhombic crystal system (space groups Iba2, Fdd2, and Pnnm, respectively), with Z=8, 14, and 4, respectively. Compound 4 crystallizes in the triclinic space group P-1, with Z=2. Compounds 1-4 exhibit hydrogen bonding.     

AAK1 identified as an inhibitor of neuregulin-1/ErbB4-dependent neurotrophic factor signaling using integrative chemical genomics and proteomics

Target identification remains challenging for the field of chemical biology. We describe an integrative chemical genomic and proteomic approach combining the use of differentially active analogs of small molecule probes with stable isotope labeling by amino acids in cell culture-mediated affinity enrichment, followed by subsequent testing of candidate targets using RNA interference-mediated gene silencing. We applied this approach to characterizing the natural product K252a and its ability to potentiate neuregulin-1 (Nrg1)/ErbB4 (v-erb-a erythroblastic leukemia viral oncogene homolog 4)-dependent neurotrophic factor signaling and neuritogenesis. We show that AAK1 (adaptor-associated kinase 1) is a relevant target of K252a, and that the loss of?AAK1?alters ErbB4 trafficking and expression levels,?providing evidence for a previously unrecognized role for AAK1 in Nrg1-mediated neurotrophic?factor signaling. Similar strategies should lead to the discovery of novel targets for therapeutic development.