Ensemble structure of the N-terminal domain (1-267) of FUS in a biomolecular condensate.

Solutions of some proteins phase separate into a condensed state of high protein concentration and a dispersed state of low concentration. Such behavior is observed in living cells for a number of RNA-binding proteins that feature intrinsically disordered domains. It is relevant for cell function via the formation of membraneless organelles and transcriptional condensates. On a basic level, the process can be studied in vitro on protein domains that are necessary and sufficient for liquid-liquid phase separation (LLPS). We have performed distance distribution measurements by electron paramagnetic resonance for 13 sections in an N-terminal domain (NTD) construct of the protein fused in sarcoma (FUS), consisting of the QGSY-rich domain and the RGG1 domain, in the denatured, dispersed, and condensed state. Using 10 distance distribution restraints for ensemble modeling and three such restraints for model validation, we have found that FUS NTD behaves as a random-coil polymer under good-solvent conditions in both the dispersed and condensed state. Conformation distribution in the biomolecular condensate is virtually indistinguishable from the one in an unrestrained ensemble, with the latter one being based on only residue-specific Ramachandran angle distributions. Over its whole length, FUS NTD is slightly more compact in the condensed than in the dispersed state, which is in line with the theory for random coils in good solvent proposed by de Gennes, Daoud, and Jannink. The estimated concentration in the condensate exceeds the overlap concentration resulting from this theory. The QGSY-rich domain is slightly more extended, slightly more hydrated, and has slightly higher propensity for LLPS than the RGG1 domain. Our results support previous suggestions that LLPS of FUS is driven by multiple transient nonspecific hydrogen bonding and π-sp2 interactions.

Active Sites in Cr(III)-Based Ethylene Polymerization Catalysts from Machine-Learning-Supported XAS and EPR Spectroscopy.

The ethylene polymerization Phillips catalyst has been employed for decades and is central to the polymer industry. While Cr(III) alkyl species are proposed to be the propagating sites, there is so far no direct experimental evidence for such proposal. In this work, by coupling Surface organometallic chemistry, EPR spectroscopy, and machine learning-supported XAS studies, we have studied the electronic structure of well-defined silica-supported Cr(III) alkyls and identified the presence of several surface species in high and low-spin states, associated with different coordination environments. Notably, low-spin Cr(III) sites are shown to participate in ethylene polymerization, indicating that similar Cr(III) alkyl species could be involved in the related Phillips catalyst.

Nickel(I)-Phenolate Complexes: The Key to Well-Defined Ni(I) Species.

Phosphine-stabilized monovalent nickel complexes play an important role in catalysis, either as catalytically active species or as decomposition products. Most routes to access these complexes are highly ligand specific or rely on strong reducing agents. Our group recently disclosed a path to access nickel(I)-phenolate complexes from bis(1,5-cyclooctadiene)nickel(0) (Ni(cod)2). Herein, we demonstrate this protocol's broad applicability by ligating a wide range of mono- and bidentate phosphine ligands. We further show the versatility of the phenolate fragment as a precursor to nickel(I)-alkyl or aryl species, which are relevant to Ni catalysis or synthetically useful nickel(I)-chloride and hydride complexes. We also demonstrate that the chloride complex can be synthesized in a one-pot procedure starting from Ni(cod)2 in good yield, making this protocol a valuable alternative to current procedures. Single-crystal X-ray diffraction, IR, and EPR (or NMR) spectroscopy were employed to characterize all of the synthesized nickel complexes.

Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility.

RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.

EPR Study on the Oxidative Degradation of Phenyl Sulfonates, Constituents of Aromatic Hydrocarbon-Based Proton-Exchange Fuel Cell Membranes.

Sulfonated aromatic hydrocarbon-based ionomers are potential constituents of next-generation polymer electrolyte fuel cells (PEFCs). Widespread application is currently limited due to their susceptibility to radical-initiated oxidative degradation that, among other intermediates, involves the formation of highly reactive aromatic cation radicals. The intermediates undergo chain cleavage (dealkylation/dearylation) and the loss of protogenic sulfonate groups, all leading to performance loss and eventual membrane failure. Laser flash photolysis experiments indicated that cation radicals can also be formed via direct electron ejection. We aim to establish the major degradation pathway of proton-exchange membranes (PEMs). To this end, we irradiated aqueous solutions of phenyl sulfonate-type model compounds with a Xe arc lamp, thus generating radicals. The radicals were trapped by 5,5-dimethyl-1-pyrroline N-oxide (DMPO), and the formed adducts were observed by electron paramagnetic resonance (EPR). The formed DMPO spin adducts were assigned and relative adduct concentrations were quantified by simulation of the experimental EPR spectra. Through the formation of the DMPO/•SO3 - adduct, we established that desulfonation dominates for monoaromatic phenyl sulfonates. We observed that diaryl ether sulfonates readily undergo homolytic C-O scission that produces DMPO/•aryl adducts. Our results support the notion that polyphenylene sulfonates are the most stable against oxidative attack and effectively transfer electrons from DMPO, forming DMPO/•OH. Our findings help to identify durable moieties that can be used as building blocks in the development of next-generation PEMs.

A complete biomimetic iron-sulfur cubane redox series.

Synthetic iron-sulfur cubanes are models for biological cofactors, which are essential to delineate oxidation states in the more complex enzymatic systems. However, a complete series of [Fe4S4]n complexes spanning all redox states accessible by 1-electron transformations of the individual iron atoms (n = 0-4+) has never been prepared, deterring the methodical comparison of structure and spectroscopic signature. Here, we demonstrate that the use of a bulky arylthiolate ligand promoting the encapsulation of alkali-metal cations in the vicinity of the cubane enables the synthesis of such a series. Characterization by EPR, 57Fe Mössbauer spectroscopy, UV-visible electronic absorption, variable-temperature X-ray diffraction analysis, and cyclic voltammetry reveals key trends for the geometry of the Fe4S4 core as well as for the Mössbauer isomer shift, which both correlate systematically with oxidation state. Furthermore, we confirm the S = 4 electronic ground state of the most reduced member of the series, [Fe4S4]0, and provide electrochemical evidence that it is accessible within 0.82 V from the [Fe4S4]2+ state, highlighting its relevance as a mimic of the nitrogenase iron protein cluster.

Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase.

The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

Characterization of Weak Protein Domain Structure by Spin-Label Distance Distributions.

Function of intrinsically disordered proteins may depend on deviation of their conformational ensemble from that of a random coil. Such deviation may be hard to characterize and quantify, if it is weak. We explored the potential of distance distributions between spin labels, as they can be measured by electron paramagnetic resonance techniques, for aiding such characterization. On the example of the intrinsically disordered N-terminal domain 1-267 of fused in sarcoma (FUS) we examined what such distance distributions can and cannot reveal on the random-coil reference state. On the example of the glycine-rich domain 188-320 of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) we studied whether deviation from a random-coil ensemble can be robustly detected with 19 distance distribution restraints. We discuss limitations imposed by ill-posedness of the conversion of primary data to distance distributions and propose overlap of distance distributions as a fit criterion that can tackle this problem. For testing consistency and size sufficiency of the restraint set, we propose jack-knife resampling. At current desktop computers, our approach is expected to be viable for domains up to 150 residues and for between 10 and 50 distance distribution restraints.

Gradual opening of Smc arms in prokaryotic condensin.

Multi-subunit SMC ATPases control chromosome superstructure apparently by catalyzing a DNA-loop-extrusion reaction. SMC proteins harbor an ABC-type ATPase "head" and a "hinge" dimerization domain connected by a coiled coil "arm." Two arms in a SMC dimer can co-align, thereby forming a rod-shaped particle. Upon ATP binding, SMC heads engage, and arms are thought to separate. Here, we study the shape of Bacillus subtilis Smc-ScpAB by electron-spin resonance spectroscopy. Arm separation is readily detected proximal to the heads in the absence of ligands, and separation near the hinge largely depends on ATP and DNA. Artificial blockage of arm opening eliminates DNA stimulation of ATP hydrolysis but does not prevent basal ATPase activity. We report an arm contact as being important for controlling the transformations. Point mutations at this arm interface eliminated Smc function. We propose that partially open, intermediary conformations provide directionality to SMC DNA translocation by (un)binding suitable DNA substrates.

NMR and EPR reveal a compaction of the RNA-binding protein FUS upon droplet formation.

Many RNA-binding proteins undergo liquid-liquid phase separation, which underlies the formation of membraneless organelles, such as stress granules and P-bodies. Studies of the molecular mechanism of phase separation in vitro are hampered by the coalescence and sedimentation of organelle-sized droplets interacting with glass surfaces. Here, we demonstrate that liquid droplets of fused in sarcoma (FUS)-a protein found in cytoplasmic aggregates of amyotrophic lateral sclerosis and frontotemporal dementia patients-can be stabilized in vitro using an agarose hydrogel that acts as a cytoskeleton mimic. This allows their spectroscopic characterization by liquid-phase NMR and electron paramagnetic resonance spectroscopy. Protein signals from both dispersed and condensed phases can be observed simultaneously, and their respective proportions can be quantified precisely. Furthermore, the agarose hydrogel acts as a cryoprotectant during shock-freezing, which facilitates pulsed electron paramagnetic resonance measurements at cryogenic temperatures. Surprisingly, double electron-electron resonance measurements revealed a compaction of FUS in the condensed phase.

Supramolecular Approach to Electron Paramagnetic Resonance Distance Measurement of Spin-Labeled Proteins.

We demonstrate a host-guest molecular recognition approach to advance double electron-electron resonance (DEER) distance measurements of spin-labeled proteins. We synthesized an iodoacetamide derivative of 2,6-diazaadamantane nitroxide (DZD) spin label that could be doubly incorporated into T4 Lysozyme (T4L) by site-directed spin labeling with efficiency up to 50% per cysteine. The rigidity of the fused ring structure and absence of mobile methyl groups increase the spin echo dephasing time (Tm) at temperatures above 80 K. This enables DEER measurements of distances >4 nm in DZD-labeled T4L in glycerol/water at temperatures up to 150 K with increased sensitivity compared to that of a common spin label such as MTSL. Addition of ß-cyclodextrin reduces the rotational correlation time of the label, slightly increases Tm, and most importantly, narrows (and slightly lengthens) the interspin distance distributions. The distance distributions are in good agreement with simulated distance distributions obtained by rotamer libraries. These results provide a foundation for developing supramolecular recognition to facilitate long-distance DEER measurements at near physiological temperatures.

Molecular and supported Ti(iii)-alkyls: efficient ethylene polymerization driven by the π-character of metal-carbon bonds and back donation from a singly occupied molecular orbital.

While Ti(iii) alkyl species are the proposed active sites in Ziegler-Natta ethylene polymerization catalysts, the corresponding well-defined homogeneous catalysts are not known. We report that well-defined neutral ß-diiminato Ti(iii) alkyl species, namely [Ti(nacnac)(CH2 t Bu)2] and its alumina-grafted derivative [(AlsO)Ti(nacnac)(CH2 t Bu)], are active towards ethylene polymerization at moderate pressures and temperatures and possess an electron configuration well-adapted to insertion of ethylene. Advanced EPR spectroscopy showed that ethylene insertion into a Ti(iii)-C bond takes place during polymerization from Ti(nacnac)(CH2 t Bu)2. A combination of pulsed EPR spectroscopy and DFT calculations, based on a crystal structure of [Ti(nacnac)(CH2 t Bu)2], enabled us to reveal details about the structure and electronic configurations of both molecular and surface-grafted species. For both compounds, the α-agostic C-H interaction, which involves the singly occupied molecular orbital, indicates a π character of the metal-carbon bond; this π character is enhanced upon ethylene coordination, leading to a nearly barrier-less C2H4 insertion into Ti(iii)-C bonds after this first step. During coordination, back donation from the SOMO to the π*(C2H4) occurs, leading to stabilization of π-ethylene complexes and to a significant lowering of the overall energy of the C2H4 insertion transition state. In d1 alkyl complexes, ethylene insertion follows an original "augmented" Cossee-Arlman mechanism that involves the delocalization of unpaired electrons between the SOMO, π*(C2H4) and σ*(Ti-C) in the transition state, which further favors ethylene insertion. All these factors facilitate ethylene polymerization on Ti(iii) neutral alkyl species and make d1 alkyl complexes potentially more effective polymerization catalysts than their d0 analogues.

gem-Diethyl Pyrroline Nitroxide Spin Labels: Synthesis, EPR Characterization, Rotamer Libraries and Biocompatibility.

Invited for this month's cover picture is the group of Professor Enrica Bordignon at the Ruhr University Bochum. The cover picture shows an artistic view of E. coli cells and two spin-labeled recombinantly produced proteins, which can be inserted into the cells for EPR studies. The primary sequence of the proteins is schematically shown with the one-letter amino acid code, and cysteine residues are functionalized with the two new gem diethyl nitroxide spin labels designed to better sustain the reducing cellular environment. Read the full text of their Full Paper at 10.1002/open.201900119.

Comparison of Free Radical Levels in the Aerosol from Conventional Cigarettes, Electronic Cigarettes, and Heat-Not-Burn Tobacco Products.

Aerosols from electronic cigarettes and heat-not-burn tobacco products have been found to contain lower levels of almost all compounds from the list of Harmful and Potentially Harmful Constituents known to be present in tobacco products and tobacco smoke than smoke from conventional cigarettes. Free radicals, which also pose potential health risks, are not considered in this list, and their levels in the different product types have not yet been compared under standardized conditions. We compared the type and quantity of free radicals in mainstream aerosol of 3R4F research cigarettes, two types of electronic cigarettes, and a heat-not-burn tobacco product. Free radicals and NO in the gas phases were separately spin trapped and quantified by electron paramagnetic resonance (EPR) spectroscopy by using a smoking machine for aerosol generation and a flow-through cell to enhance reproducibility of the quantification. Particulate matter was separated by a Cambridge filter and extracted, and persistent radicals were quantified by EPR spectroscopy. Levels of organic radicals for electronic cigarettes and the heat-not-burn product, as measured with the PBN spin trap, did not exceed 1% of the level observed for conventional cigarettes and were close to the radical level observed in air blanks. The radicals found in the smoke of conventional cigarettes were oxygen centered, most probably alkoxy radicals, whereas a signal for carbon-centered radicals near the detection limit was observed in aerosol from the heat-not-burn product and electronic cigarettes. The NO level in aerosol produced by electronic cigarettes was below our detection limit, whereas for the heat-not-burn product, it reached about 7% of the level observed for whole smoke from 3R4F cigarettes. Persistent radicals in particulate matter could be quantified only for 3R4F cigarettes. Aerosols from vaping and heat-not-burn tobacco products have much lower free radical levels than cigarette smoke, however, the toxicological implications of this finding are as yet unknown.

Comparison of the functional properties of trimeric and monomeric CaiT of Escherichia coli.

Secondary transporters exist as monomers, dimers or higher state oligomers. The significance of the oligomeric state is only partially understood. Here, the significance of the trimeric state of the L-carnitine/γ-butyrobetaine antiporter CaiT of Escherichia coli was investigated. Amino acids important for trimer stability were identified and experimentally verified. Among others, CaiT-D288A and -D288R proved to be mostly monomeric in detergent solution and after reconstitution into proteoliposomes, as shown by blue native gel electrophoresis, gel filtration, and determination of intermolecular distances. CaiT-D288A was fully functional with kinetic parameters similar to the trimeric wild-type. Significant differences in amount and stability in the cell membrane between monomeric and trimeric CaiT were not observed. Contrary to trimeric CaiT, addition of substrate had no or only a minor effect on the tryptophan fluorescence of monomeric CaiT. The results suggest that physical contacts between protomers are important for the substrate-induced changes in protein fluorescence and the underlying conformational alterations.

Spin labelling for integrative structure modelling: a case study of the polypyrimidine-tract binding protein 1 domains in complexes with short RNAs.

A combined method, employing NMR and EPR spectroscopies, has demonstrated its strength in solving structures of protein/RNA and other types of biomolecular complexes. This method works particularly well when the large biomolecular complex consists of a limited number of rigid building blocks, such as RNA-binding protein domains (RBDs). A variety of spin labels is available for such studies, allowing for conventional as well as spectroscopically orthogonal double electron-electron resonance (DEER) measurements in EPR. In this work, we compare different types of nitroxide-based and Gd(iii)-based spin labels attached to isolated RBDs of the polypyrimidine-tract binding protein 1 (PTBP1) and to short RNA fragments. In particular, we demonstrate experiments on spectroscopically orthogonal labelled RBD/RNA complexes. For all experiments we analyse spin labelling, DEER method performance, resulting distance distributions, and their consistency with the predictions from the spin label rotamers analysis. This work provides a set of intra-domain calibration DEER data, which can serve as a basis to start structure determination of the full length PTBP1 complex with an RNA derived from encephalomycarditis virus (EMCV) internal ribosomal entry site (IRES). For a series of tested labelling sites, we discuss their particular advantages and drawbacks in such a structure determination approach.

Orthogonal Tyrosine and Cysteine Site-Directed Spin Labeling for Dipolar Pulse EPR Spectroscopy on Proteins.

Site-directed spin labeling of native tyrosine residues in isolated domains of the protein PTBP1, using a Mannich-type reaction, was combined with conventional spin labeling of cysteine residues. Double electron-electron resonance (DEER) EPR measurements were performed for both the nitroxide-nitroxide and Gd(III)-nitroxide label combinations within the same protein molecule. For the prediction of distance distributions from a structure model, rotamer libraries were generated for the two linker forms of the tyrosine-reactive isoindoline-based nitroxide radical Nox. Only moderate differences exist between the spatial spin distributions for the two linker forms of Nox. This strongly simplifies DEER data analysis, in particular, if only mean distances need to be predicted.

Solid-state NMR and EPR Spectroscopy of Mn2+ -Substituted ATP-Fueled Protein Engines.

Paramagnetic metal ions deliver structural information both in EPR and solid-state NMR experiments, offering a profitable synergetic approach to study bio-macromolecules. We demonstrate the spectral consequences of Mg2+ / Mn2+ substitution and the resulting information contents for two different ATP:Mg2+ -fueled protein engines, a DnaB helicase from Helicobacter pylori active in the bacterial replisome, and the ABC transporter BmrA, a bacterial efflux pump. We show that, while EPR spectra report on metal binding and provide information on the geometry of the metal centers in the proteins, paramagnetic relaxation enhancements identified in the NMR spectra can be used to localize residues at the binding site. Protein engines are ubiquitous and the methods described herein should be applicable in a broad context.

Copper is a Cofactor of the Formylglycine-Generating Enzyme.

Formylglycine-generating enzyme (FGE) is an O2 -utilizing oxidase that converts specific cysteine residues of client proteins to formylglycine. We show that CuI is an integral cofactor of this enzyme and binds with high affinity (KD =of 10-17 m) to a pair of active-site cysteines. These findings establish FGE as a novel type of copper enzyme.