Methane Oxidation to Methanol

The direct transformation of methane to methanol remains a significant challenge for operation at a larger scale. Central to this challenge is the low reactivity of methane at conditions that can facilitate product recovery. This review discusses the issue through examination of several promising routes to methanol and an evaluation of performance targets that are required to develop the process at scale. We explore the methods currently used, the emergence of active heterogeneous catalysts and their design and reaction mechanisms and provide a critical perspective on future operation. Initial experiments are discussed where identification of gas phase radical chemistry limited further development by this approach. Subsequently, a new class of catalytic materials based on natural systems such as iron or copper containing zeolites were explored at milder conditions. The key issues of these technologies are low methane conversion and often significant overoxidation of products. Despite this, interest remains high in this reaction and the wider appeal of an effective route to key products from C-H activation, particularly with the need to transition to net carbon zero with new routes from renewable methane sources is exciting.

Correction: Heteroleptic iron(II) complexes of chiral 2,6-bis(oxazolin-2-yl)-pyridine (PyBox) and 2,6-bis(thiazolin-2-yl)pyridine ligands - the interplay of two different ligands on the metal ion spin state

Correction for 'Heteroleptic iron(II) complexes of chiral 2,6-bis(oxazolin-2-yl)-pyridine (PyBox) and 2,6-bis(thiazolin-2-yl)pyridine ligands - the interplay of two different ligands on the metal ion spin state' by Namrah Shahid et al., Dalton Trans., 2022, 51, 4262-4274, DOI: 10.1039/d2dt00393g.

A Comparative Assessment Study of Known Small-molecule GPVI Modulators

The GPVI platelet receptor was recently validated as a safe antiplatelet target for the treatment of thrombosis using several peptidic modulators. In contrast, few weakly potent small-molecule GPVI antagonists have been reported. Those that have been published often lack evidence for target engagement, and their biological efficacy cannot be compared because of the natural donor variability associated with the assays implemented. Herein, we present the first side-by-side assessment of the reported GPVI small-molecule modulators. We have characterized their functional activities on platelet activation and aggregation using flow cytometry as well as light transmission and electrical impedance aggregometry. We also utilized microscale thermophoresis (MST) and saturation transfer difference (STD) NMR to validate GPVI binding and have used this along with molecular modeling to suggest potential binding interactions. We conclude that of the compounds examined, losartan and compound 5 are currently the most viable GPVI modulators.

Triggered and monitored drug release from bifunctional hybrid nanocomposites

Polymer-coated carbon dot-containing calcium carbonate nanoparticles are reported as unique nanocomposites capable of encapsulating a chemotherapeutic drug and displaying afterglow behaviour.

Heteroleptic iron(ii) complexes of chiral 2,6-bis(oxazolin-2-yl)-pyridine (PyBox) and 2,6-bis(thiazolin-2-yl)pyridine ligands – the interplay of two different ligands on the metal ion spin sate

The spin-crossover properties of [Fe(LR)L][ClO4]2 (LR = a chiral PyBox {L1R} or ThioPyBox {L2R} derivative) show subtle differences depending on the tridentate ‘L’ co-ligand.

Spin-States of Diastereomeric Iron(II) Complexes of 2,6-Bis(thiazolin-2-yl)pyridine (ThioPyBox) Ligands and a Comparison with the Corresponding PyBox Derivatives

This report investigates homoleptic iron(II) complexes of thiazolinyl analogues of chiral PyBox tridentate ligands: 2,6-bis(4-phenyl-4,5-dihydrothiazol-2-yl)pyridine (L¹Ph), 2,6-bis(4-isopropyl-4,5-dihydrothiazol-2-yl)pyridine (L¹iPr), and 2,6-bis(4-tert-butyl-4,5-dihydrothiazol-2-yl)pyridine (L¹t-Bu). Crystallographic data imply the larger and more flexible thiazolinyl rings reduce steric clashes between the R substituents in homochiral [Fe((R)-L¹R)₂]²⁺ or [Fe((S)-L¹R)₂]²⁺ (R = Ph, iPr, or t-Bu), compared to their PyBox (L²R) analogues. Conversely, the larger heterocyclic S atoms are in close contact with the R substituents in heterochiral [Fe((R)-L¹Ph)((S)-L¹Ph)]²⁺, giving it a more sterically hindered ligand environment than that in [Fe((R)-L²Ph)((S)-L²Ph)]²⁺ (L²Ph = 2,6-bis(4-phenyl-4,5-dihydrooxazol-2-yl)pyridine). Preformed [Fe((R)-L¹Ph)((S)-L¹Ph)]²⁺ and [Fe((R)-L¹iPr)((S)-L¹iPr)]²⁺ do not racemize by ligand redistribution in CD₃CN solution, but homochiral [Fe(L¹iPr)₂]²⁺ and [Fe(L¹t-Bu)₂]²⁺ both undergo partial ligand displacement in that solvent. Homochiral [Fe(L¹Ph)₂]²⁺ and [Fe(L¹iPr)₂]²⁺ exhibit spin-crossover equilibria in CD₃CN, centered at 344 ± 6 K and 277 ± 1 K respectively, while their heterochiral congeners are essentially low-spin within the liquid range of the solvent. These data imply that the diastereomers of [Fe(L¹Ph)₂]²⁺ and [Fe(L¹iPr)₂]²⁺ show a greater difference in their spin-state behaviors than was previous found for [Fe(L²Ph)₂]²⁺. Gas-phase DFT calculations (B86PW91/def2-SVP) of the [Fe(L¹R)₂]²⁺ and [Fe(L²R)₂]²⁺ complexes reproduce most of the observed trends, but they overstabilize the high-spin state of SCO-active [Fe(L¹iPr)₂]²⁺ by ca. 1.5 kcal mol^-1. This might reflect the influence of intramolecular dispersion interactions on the spin states of these compounds. Attempts to model this with the dispersion-corrected functionals B97-D2 or PBE-D3 were less successful than our original protocol, confirming that the spin states of sterically hindered molecules are a challenging computational problem.

Self-Assembly and Host-Guest Interactions of Pd3L2 Metallo-cryptophanes with Photoisomerizable Ligands

New photoswitchable pyridyl-azo-phenyl-decorated tripodal host ligands (L_az) that belong to the cyclotriveratrylene family have been synthesized, and their photoswitching behavior and crystal structures determined. The latter includes a remarkable 7-fold Borromean-weave entanglement of π-π stacked layers. Trigonal bipyramidal {[Pd(en)]₃(L_az)₂}⁶⁺ metallo-cryptophanes (en = ethylenediamine) were formed from these and a previously known pyridyl-azo-phenyl-decorated tripodal host ligand. These coordination cages dissociate at low concentrations and are less robust to photoswitching of the L_az ligands than were previously reported Ir(III)-linked metallo-cryptophanes with similar ligands, reflecting the greater lability of the Pd-N bonds. The {[Pd(en)]₃(L_az)₂}⁶⁺ cages all act as hosts, binding octyl sulfate anions, or N-[2-(dimethylamino)ethyl]-1,8-naphthalimide in a dimethyl sulfoxide solution.

The effect of tether groups on the spin states of iron(II)/bis[2,6-di(pyrazol-1-yl)pyridine] complexes

The synthesis of six 2,6-di(pyrazol-1-yl)pyridine derivatives bearing dithiolane or carboxylic acid tether groups is described: [2,6-di(pyrazol-1-yl)pyrid-4-yl]methyl (R)-lipoate (L1), 2-[(2,6-di(pyrazol-1-yl)pyridine)-4-carboxamido]ethyl (R)-lipoate (L2), 2-[(2,6-di(pyrazol-1-yl)pyridine)-4-carboxy]ethyl (R)-lipoate (L3), N-([2,6-di(pyrazol-1-yl)pyrid-4-ylsulfanyl]-2-aminoethyl (R)-lipoamide (L4), 2-[(2,6-di(pyrazol-1-yl)pyridine)-4-carboxamido]acetic acid (L5) and 2-[(2,6-di(pyrazol-1-yl)pyridine)-4-carboxamido]propionic acid (L6). The iron(ii) perchlorate complexes of all the new ligands exhibit gradual thermal spin-crossover (SCO) in the solid state above room temperature, except L4 whose complex remains predominantly high-spin. Crystalline [Fe(L6)2][ClO4]2·2MeCN contains three unique cation sites which alternate within hydrogen-bonded chains, and undergo gradual SCO at different temperatures upon warming. The SCO midpoint temperature (T1/2) of the complexes in CD3CN solution ranges between 208-274 K, depending on the functional group linking the tether groups to the pyridyl ring. This could be useful for predicting how these complexes might behave when deposited on gold or silica surfaces.

Influence of ligand substituent conformation on the spin state of an iron(II)/di(pyrazol-1-yl)pyridine complex

The temperature of the solution-phase spin-crossover equilibrium in iron(ii) complexes of 4-alkylsulfanyl-2,6-di{pyrazol-1-yl}pyridine (bppSR) complexes depends strongly on the alkylsulfanyl substituent. DFT calculations imply this reflects the conformation of the alkylsulfanyl groups, which lie perpendicular to the heterocyclic ligand donors in [Fe(bppStBu)2]2+ but are oriented co-planar with the ligand core for smaller SR substituents.

The flexibility of long chain substituents influences spin-crossover in isomorphous lipid bilayer crystals

These two compounds are isomorphous but show different spin-state behaviour on cooling. This may be influenced by the packing of alkyl vs. alkynyl chains in the solid state.

Amylin and beta amyloid proteins interact to form amorphous heterocomplexes with enhanced toxicity in neuronal cells

Human pancreatic islet amyloid polypeptide (hIAPP) and beta amyloid (Aβ) can accumulate in Type 2 diabetes (T2D) and Alzheimer's disease (AD) brains and evidence suggests that interaction between the two amyloidogenic proteins can lead to the formation of heterocomplex aggregates. However, the structure and consequences of the formation of these complexes remains to be determined. The main objective of this study was to characterise the different types and morphology of Aβ-hIAPP heterocomplexes and determine if formation of such complexes exacerbate neurotoxicity. We demonstrate that hIAPP promotes Aβ oligomerization and formation of small oligomer and large aggregate heterocomplexes. Co-oligomerized Aβ42-hIAPP mixtures displayed distinct amorphous structures and a 3-fold increase in neuronal cell death as compared to Aβ and hIAPP alone. However, in contrast to hIAPP, non-amyloidogenic rat amylin (rIAPP) reduced oligomer Aβ-mediated neuronal cell death. rIAPP exhibited reductions in Aβ induced neuronal cell death that was independent of its ability to interact with Aβ and form heterocomplexes; suggesting mediation by other pathways. Our findings reveal distinct effects of IAPP peptides in modulating Aβ aggregation and toxicity and provide new insight into the potential pathogenic effects of Aβ-IAPP hetero-oligomerization and development of IAPP based therapies for AD and T2D.

NMR metabolomics reveals effects of Cryptosporidium infections on host cell metabolome

Background

Cryptosporidium is an important gut microbe whose contributions towards infant and immunocompromise patient mortality rates are steadily increasing. Over the last decade, we have seen the development of various tools and methods for studying Cryptosporidium infection and its interactions with their hosts. One area that is sorely overlooked is the effect infection has on host metabolic processes.

Results

Using a ¹H nuclear magnetic resonance approach to metabolomics, we have explored the nature of the mouse gut metabolome as well as providing the first insight into the metabolome of an infected cell line. Statistical analysis and predictive modelling demonstrated new understandings of the effects of a Cryptosporidium infection, while verifying the presence of known metabolic changes. Of note is the potential contribution of host derived taurine to the diarrhoeal aspects of the disease previously attributed to a solely parasite-based alteration of the gut environment, in addition to other metabolites involved with host cell catabolism.

Conclusion

This approach will spearhead our understanding of the Cryptosporidium-host metabolic exchange and provide novel targets for tackling this deadly parasite.

Fully Collapsed Imploded Cryptophanes in Solution and in the Solid State

Cryptophanes with flexible linkers derived from (±)-tris-(4-formyl-phenyl)-cyclotriguaiacylene with either bisoxydi(ethylamine) or bis(aminopropyl)ether were isolated as single crystals, the crystal structures of which showed the proposed, but previously uncharacterised, out-in conformation, in which both cyclotriguaiacylene fragments adopt a crown conformation with one crown sitting inside the other. The usual cage-like out-out conformation of the cryptophanes was observed when crystals were dissolved upon heating, and the molecules collapsed back to the out-in isomers over time. In contrast, a cryptophane also derived from (±)-tris-(4-formyl-phenyl)-cyclotriguaiacylene but with rigid dibenzalhydrazine linkers was isolated as the more usual out-out isomer.

Supramolecular Self-Sorting Networks using Hydrogen-Bonding Motifs

A current objective in supramolecular chemistry is to mimic the transitions between complex self-sorted systems that represent a hallmark of regulatory function in nature. In this work, a self-sorting network, comprising linear hydrogen motifs, was created. Selecting six hydrogen-bonding motifs capable of both high-fidelity and promiscuous molecular recognition gave rise to a complex self-sorting system, which included motifs capable of both narcissistic and social self-sorting. Examination of the interactions between individual components, experimentally and computationally, provided a rationale for the product distribution during each phase of a cascade. This reasoning holds through up to five sequential additions of six building blocks, resulting in the construction of a biomimetic network in which the presence or absence of different components provides multiple unique pathways to distinct self-sorted configurations.

Identity and Activity of 2,4-Dichlorophenoxyacetic Acid Metabolites in Wild Radish ( Raphanus raphanistrum)

Synthetic auxin herbicides, such as 2,4-dichlorophenoxyacetic acid (2,4-D), are widely used for selective control of broadleaf weeds in cereals and transgenic crops. Although the troublesome weed wild radish ( Raphanus raphanistrum) has developed resistance to 2,4-D, no populations have yet displayed an enhanced capacity for metabolic detoxification of the herbicide, with both susceptible and resistant wild radish plants readily metabolizing 2,4-D. Using mass spectrometry and nuclear magnetic resonance, the major 2,4-D metabolite was identified as the glucose ester, and its structure was confirmed by synthesis. As expected, both the endogenous and synthetic compounds retained auxin activity in a bioassay. The lack of detectable 2,4-D hydroxylation in wild radish and the lability of the glucose ester suggest that metabolic 2,4-D resistance is unlikely to develop in this species.

Construction of Fluorescent Analogs to Follow the Uptake and Distribution of Cobalamin (Vitamin B12) in Bacteria, Worms, and Plants

Vitamin B₁₂ is made by only certain prokaryotes yet is required by a number of eukaryotes such as mammals, fish, birds, worms, and Protista, including algae. There is still much to learn about how this nutrient is trafficked across the domains of life. Herein, we describe ways to make a number of different corrin analogs with fluorescent groups attached to the main tetrapyrrole-derived ring. A further range of analogs were also constructed by attaching similar fluorescent groups to the ribose ring of cobalamin, thereby generating a range of complete and incomplete corrinoids to follow uptake in bacteria, worms, and plants. By using these fluorescent derivatives we were able to demonstrate that Mycobacterium tuberculosis is able to acquire both cobyric acid and cobalamin analogs, that Caenorhabditis elegans takes up only the complete corrinoid, and that seedlings of higher plants such as Lepidium sativum are also able to transport B₁₂.

A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch

Orbitides are cyclic ribosomally-synthesized and post-translationally modified peptides (RiPPs) from plants; they consist of standard amino acids arranged in an unbroken chain of peptide bonds. These cyclic peptides are stable and range in size and topologies making them potential scaffolds for peptide drugs; some display valuable biological activities. Recently two orbitides whose sequences were buried in those of seed storage albumin precursors were said to represent the first observable step in the evolution of larger and hydrophilic bicyclic peptides. Here, guided by transcriptome data, we investigated peptide extracts of 40 species specifically for the more hydrophobic orbitides and confirmed 44 peptides by tandem mass spectrometry, as well as obtaining solution structures for four of them by NMR. Acquiring transcriptomes from the phylogenetically important Corymboideae family confirmed the precursor genes for the peptides (called PawS1-Like or PawL1) are confined to the Asteroideae, a subfamily of the huge plant family Asteraceae. To be confined to the Asteroideae indicates these peptides arose during the Eocene epoch around 45 Mya. Unlike other orbitides, all PawL-derived Peptides contain an Asp residue, needed for processing by asparaginyl endopeptidase. This study has revealed what is likely to be a very large new family of orbitides, uniquely buried alongside albumin and processed by asparaginyl endopeptidase.

Wearable embroidered muscle activity sensing device for the human upper leg

Within the last decade, running has become one of the most popular physical activities in the world. Although the benefits of running are numerous, there is a risk of Running Related Injuries (RRIs) of the lower extremities. Electromyography (EMG) techniques have previously been used to study causes of RRIs, but the complexity of this technology limits its use to a laboratory setting. As running is primarily an outdoors activity, this lack of technology acts as a barrier to the study of RRIs in natural environments. This study presents a minimally invasive wearable muscle sensing device consisting of jogging leggings with embroidered surface EMG (sEMG) electrodes capable of recording muscle activity data of the quadriceps group. To test the use of the device, a proof of concept study consisting of N = 2 runners performing a set of 5 km running trials is presented in which the effect of running surfaces on muscle fatigue, a potential cause of RRIs, is evaluated. Results show that muscle fatigue can be analysed from the sEMG data obtained through the wearable device, and that running on soft surfaces (such as sand) may increase the likelihood of suffering from RRIs.

Acquired resistance to oxaliplatin is not directly associated with increased resistance to DNA damage in SK-N-ASrOXALI4000, a newly established oxaliplatin-resistant sub-line of the neuroblastoma cell line SK-N-AS

The formation of acquired drug resistance is a major reason for the failure of anti-cancer therapies after initial response. Here, we introduce a novel model of acquired oxaliplatin resistance, a sub-line of the non-MYCN-amplified neuroblastoma cell line SK-N-AS that was adapted to growth in the presence of 4000 ng/mL oxaliplatin (SK-N-AS^rOXALI⁴⁰⁰⁰). SK-N-AS^rOXALI⁴⁰⁰⁰ cells displayed enhanced chromosomal aberrations compared to SK-N-AS, as indicated by 24-chromosome fluorescence in situ hybridisation. Moreover, SK-N-AS^rOXALI⁴⁰⁰⁰ cells were resistant not only to oxaliplatin but also to the two other commonly used anti-cancer platinum agents cisplatin and carboplatin. SK-N-AS^rOXALI⁴⁰⁰⁰ cells exhibited a stable resistance phenotype that was not affected by culturing the cells for 10 weeks in the absence of oxaliplatin. Interestingly, SK-N-AS^rOXALI⁴⁰⁰⁰ cells showed no cross resistance to gemcitabine and increased sensitivity to doxorubicin and UVC radiation, alternative treatments that like platinum drugs target DNA integrity. Notably, UVC-induced DNA damage is thought to be predominantly repaired by nucleotide excision repair and nucleotide excision repair has been described as the main oxaliplatin-induced DNA damage repair system. SK-N-AS^rOXALI⁴⁰⁰⁰ cells were also more sensitive to lysis by influenza A virus, a candidate for oncolytic therapy, than SK-N-AS cells. In conclusion, we introduce a novel oxaliplatin resistance model. The oxaliplatin resistance mechanisms in SK-N-AS^rOXALI⁴⁰⁰⁰ cells appear to be complex and not to directly depend on enhanced DNA repair capacity. Models of oxaliplatin resistance are of particular relevance since research on platinum drugs has so far predominantly focused on cisplatin and carboplatin.

Inappropriate expression of the translation elongation factor 1A disrupts genome stability and metabolism

The translation elongation factor eEF1A is one of the most abundant proteins found within cells, and its role within protein synthesis is well documented. Levels of eEF1A are tightly controlled, with inappropriate expression linked to oncogenesis. However, the mechanisms by which increased eEF1A expression alters cell behaviour are unknown. Our analyses in yeast suggest that elevation of eEF1A levels leads to stabilisation of the spindle pole body and changes in nuclear organisation. Elevation of the eEF1A2 isoform also leads to altered nuclear morphology in cultured human cells, suggesting a conserved role in maintaining genome stability. Gene expression and metabolomic analyses reveal that the level of eEF1A is crucial for the maintenance of metabolism and amino acid levels in yeast, most likely because of its role in the control of vacuole function. Increased eEF1A2 levels trigger lysosome biogenesis in cultured human cells, also suggesting a conserved role within metabolic control mechanisms. Taken together, our data suggest that the control of eEF1A levels is important for the maintenance of a number of cell functions beyond translation and that its de-regulation might contribute to its oncogenic properties.

Summary: The translation elongation factor eEF1A is elevated in some cancers. We use yeast and human cell models to show that eEF1A elevation leads to genome instability and metabolic alterations that might affect its oncogenic properties.

New links between SOD1 and metabolic dysfunction from a yeast model of amyotrophic lateral sclerosis

A number of genes have been linked to familial forms of the fatal motor neuron disease amyotrophic lateral sclerosis (ALS). Over 150 mutations within the gene encoding superoxide dismutase 1 (SOD1) have been implicated in ALS, but why such mutations lead to ALS-associated cellular dysfunction is unclear. In this study, we identify how ALS-linked SOD1 mutations lead to changes in the cellular health of the yeast Saccharomyces cerevisiae. We find that it is not the accumulation of aggregates but the loss of Sod1 protein stability that drives cellular dysfunction. The toxic effect of Sod1 instability does not correlate with a loss of mitochondrial function or increased production of reactive oxygen species, but instead prevents acidification of the vacuole, perturbs metabolic regulation and promotes senescence. Central to the toxic gain-of-function seen with the SOD1 mutants examined was an inability to regulate amino acid biosynthesis. We also report that leucine supplementation results in an improvement in motor function in a Caenorhabditiselegans model of ALS. Our data suggest that metabolic dysfunction plays an important role in Sod1-mediated toxicity in both the yeast and worm models of ALS.

Summary: In a new yeast model of ALS we have discovered for the first time that mutations in Sod1 can lead to the formation of toxic, soluble proteins that disrupt metabolic regulation.

Combined ligand-observe (19)F and protein-observe (15)N,(1)H-HSQC NMR suggests phenylalanine as the key Δ-somatostatin residue recognized by human protein disulfide isomerase

Human protein disulphide isomerase (hPDI) is an endoplasmic reticulum (ER) based isomerase and folding chaperone. Molecular detail of ligand recognition and specificity of hPDI are poorly understood despite the importance of the hPDI for folding secreted proteins and its implication in diseases including cancer and lateral sclerosis. We report a detailed study of specificity, interaction and dissociation constants (K_d) of the peptide-ligand Δ-somatostatin (AGSKNFFWKTFTSS) binding to hPDI using ¹⁹F ligand-observe and ¹⁵N,¹H-HSQC protein-observe NMR methods. Phe residues in Δ-somatostatin are hypothesised as important for recognition by hPDI therefore, step-wise peptide Phe-to-Ala changes were progressively introduced and shown to raise the K_d from 103 + 47 μM until the point where binding was abolished when all Phe residues were modified to Ala. The largest step-changes in K_d involved the F11A peptide modification which implies the C-terminus of Δ-somatostatin is a prime recognition region. Furthermore, this study also validated the combined use of ¹⁹F ligand-observe and complimentary ¹⁵N,¹H-HSQC titrations to monitor interactions from the protein’s perspective. ¹⁹F ligand-observe NMR was ratified as mirroring ¹⁵N protein-observe but highlighted the advantage that ¹⁹F offers improved K_d precision due to higher spectrum resolution and greater chemical environment sensitivity.

The Fanconi Anemia DNA Repair Pathway Is Regulated by an Interaction between Ubiquitin and the E2-like Fold Domain of FANCL

The Fanconi Anemia (FA) DNA repair pathway is essential for the recognition and repair of DNA interstrand crosslinks (ICL). Inefficient repair of these ICL can lead to leukemia and bone marrow failure. A critical step in the pathway is the monoubiquitination of FANCD2 by the RING E3 ligase FANCL. FANCL comprises 3 domains, a RING domain that interacts with E2 conjugating enzymes, a central domain required for substrate interaction, and an N-terminal E2-like fold (ELF) domain. The ELF domain is found in all FANCL homologues, yet the function of the domain remains unknown. We report here that the ELF domain of FANCL is required to mediate a non-covalent interaction between FANCL and ubiquitin. The interaction involves the canonical Ile44 patch on ubiquitin, and a functionally conserved patch on FANCL. We show that the interaction is not necessary for the recognition of the core complex, it does not enhance the interaction between FANCL and Ube2T, and is not required for FANCD2 monoubiquitination in vitro. However, we demonstrate that the ELF domain is required to promote efficient DNA damage-induced FANCD2 monoubiquitination in vertebrate cells, suggesting an important function of ubiquitin binding by FANCL in vivo.

Q2DSTD NMR deciphers epitope-mapping variability for peptide recognition of integrin αvβ6

Integrin αvβ6 is a cell surface arginine-glycine-aspartic acid (RGD)-specific heterodimeric glycoprotein that is only expressed on epithelia during processes of tissue remodelling, including cancer. The specificity and molecular nature of interactions toward this integrin are poorly understood and new insights into such processes are important to cell biologists and pharmaceutical drug discovery. This study demonstrates the application of quantitative two-dimensional saturation transfer (Q2DSTD) NMR to obtain precise details of peptide interactions with integrin αvβ6 and their correlation to specificity for the integrin. This approach highlights subtle but significant differences in ligand contact by three related 21-mer peptides: FMDV2, an αvβ6 specific peptide and DBD1 and LAP2T1 peptides that bind many αv integrins in addition to αvβ6. FMDV2 and DBD1 differ only by the cyclisation of DBD1; a process that removes αvβ6 specificity. Q2DSTD NMR demonstrates these peptides experience significantly different interactions with the integrin; FMDV contacts primarily through four residues: 6Leu, 10Leu, 12Val and 13Leu, whereas DBD1 and LAP2T1 have more widespread contacts across their sequences. Q2DSTD NMR combined two-dimensional STD with quantitation by considering the relaxation of the ligand (CRL) to provide precise ligand contact information. This study also examines the role of CRL in the Q2DSTD process and how quantitation modifies STD data and unravels epitope-mapping variability to provide precise results that differentiate interactions at the atomic level for each peptide.

19F NMR spectroscopy monitors ligand binding to recombinantly fluorine-labelled b'x from human protein disulphide isomerase (hPDI)

We report a protein-observe (19)F NMR-based ligand titration binding study of human PDI b'x with Δ-somatostatin that also emphasises the need to optimise recombinant protein fluorination when using 5- or 6-fluoroindole. This study highlights a recombinant preference for 5-fluoroindole over 6-fluoroindole; most likely due to the influence of fluorine atomic packing within the folded protein structure. Fluorination affords a single (19)F resonance probe to follow displacement of the protein x-linker as ligand is titrated and provides a dissociation constant of 23 ± 4 μM.

New insights into stop codon recognition by eRF1

In eukaryotes, translation termination is performed by eRF1, which recognizes stop codons via its N-terminal domain. Many previous studies based on point mutagenesis, cross-linking experiments or eRF1 chimeras have investigated the mechanism by which the stop signal is decoded by eRF1. Conserved motifs, such as GTS and YxCxxxF, were found to be important for termination efficiency, but the recognition mechanism remains unclear. We characterized a region of the eRF1 N-terminal domain, the P1 pocket, that we had previously shown to be involved in termination efficiency. We performed alanine scanning mutagenesis of this region, and we quantified in vivo readthrough efficiency for each alanine mutant. We identified two residues, arginine 65 and lysine 109, as critical for recognition of the three stop codons. We also demonstrated a role for the serine 33 and serine 70 residues in UGA decoding in vivo. NMR analysis of the alanine mutants revealed that the correct conformation of this region was controlled by the YxCxxxF motif. By combining our genetic data with a structural analysis of eRF1 mutants, we were able to formulate a new model in which the stop codon interacts with eRF1 through the P1 pocket.

Dynamic prions revealed by magic

Prion proteins can be propagated as amyloid fibrils with several different conformational variants. By providing structural information at atomic level for two such variants of a yeast prion, Frederick and colleagues, in this issue of Chemistry & Biology, reveal how conformational flexibility can generate phenotypic diversity.

Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor

Targeting of proteins to bacterial microcompartments (BMCs) is mediated by an 18-amino-acid peptide sequence. Herein, we report the solution structure of the N-terminal targeting peptide (P18) of PduP, the aldehyde dehydrogenase associated with the 1,2-propanediol utilization metabolosome from Citrobacter freundii. The solution structure reveals the peptide to have a well-defined helical conformation along its whole length. Saturation transfer difference and transferred NOE NMR has highlighted the observed interaction surface on the peptide with its main interacting shell protein, PduK. By tagging both a pyruvate decarboxylase and an alcohol dehydrogenase with targeting peptides, it has been possible to direct these enzymes to empty BMCs in vivo and to generate an ethanol bioreactor. Not only are the purified, redesigned BMCs able to transform pyruvate into ethanol efficiently, but the strains containing the modified BMCs produce elevated levels of alcohol.

Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway

In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI) catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding). However, we do not know how PDI distinguishes folded, partly-folded and unfolded protein substrates. As a model intermediate in an oxidative folding pathway, we prepared a two-disulfide mutant of basic pancreatic trypsin inhibitor (BPTI) and showed by NMR that it is partly-folded and highly dynamic. NMR studies show that it binds to PDI at the same site that binds peptide ligands, with rapid binding and dissociation kinetics; surface plasmon resonance shows its interaction with PDI has a K_d of ca. 10⁻⁵ M. For comparison, we characterized the interactions of PDI with native BPTI and fully-unfolded BPTI. Interestingly, PDI does bind native BPTI, but binding is quantitatively weaker than with partly-folded and unfolded BPTI. Hence PDI recognizes and binds substrates via permanently or transiently unfolded regions. This is the first study of PDI's interaction with a partly-folded protein, and the first to analyze this folding catalyst's changing interactions with substrates along an oxidative folding pathway. We have identified key features that make PDI an effective catalyst of oxidative protein folding – differential affinity, rapid ligand exchange and conformational flexibility.

Optimising selective excitation pulses to maximise saturation transfer difference NMR spectroscopy

A simple method is presented that optimizes the STD NMR Gaussian pulse to deliver significant increases in STD amplification factors with minimal perturbation of the ligand. This approach is practically demonstrated using the wheat-germ agglutinin/N-acetyl-D-glucosamine protein-ligand system.

Structural and functional characterization of ScsC, a periplasmic thioredoxin-like protein from Salmonella enterica serovar Typhimurium

AIMS

The prototypical protein disulfide bond (Dsb) formation and protein refolding pathways in the bacterial periplasm involving Dsb proteins have been most comprehensively defined in Escherichia coli. However, genomic analysis has revealed several distinct Dsb-like systems in bacteria, including the pathogen Salmonella enterica serovar Typhimurium. This includes the scsABCD locus, which encodes a system that has been shown via genetic analysis to confer copper tolerance, but whose biochemical properties at the protein level are not defined. The aim of this study was to provide functional insights into the soluble ScsC protein through structural, biochemical, and genetic analyses.

RESULTS

Here we describe the structural and biochemical characterization of ScsC, the soluble DsbA-like component of this system. Our crystal structure of ScsC reveals a similar overall fold to DsbA, although the topology of β-sheets and α-helices in the thioredoxin domains differ. The midpoint reduction potential of the CXXC active site in ScsC was determined to be -132 mV versus normal hydrogen electrode. The reactive site cysteine has a low pKa, typical of the nucleophilic cysteines found in DsbA-like proteins. Deletion of scsC from S. Typhimurium elicits sensitivity to copper (II) ions, suggesting a potential involvement for ScsC in disulfide folding under conditions of copper stress.

INNOVATION AND CONCLUSION

ScsC is a novel disulfide oxidoreductase involved in protection against copper ion toxicity.

Structural definition is important for the propagation of the yeast [PSI+] prion

Prions are propagated in Saccharomyces cerevisiae with remarkable efficiency, yet we know little about the structural basis of sequence variations in the prion protein that support or prohibit propagation of the prion conformation. We show that certain single-amino-acid substitutions in the prion protein Sup35 impact negatively on the maintenance of the associated prion-based [PSI(+)] trait by combining in vivo phenotypic analysis with solution NMR structural studies. A clear correlation is observed between mutationally induced conformational differences in one of the oligopeptide repeats (R2) in the N terminus of Sup35 and the relative ability to propagate [PSI(+)]. Strikingly, substitution of one of a Gly-Gly pair with highly charged residues that significantly increase structural definition of R2 lead to a severe [PSI(+)] propagation defect. These findings offer a molecular explanation for the dominant-negative effects of such psi-no-more (PNM) mutations and demonstrate directly the importance of localized structural definition in prion propagation.

Structural guided scaffold phage display libraries as a source of bio-therapeutics

We have developed a structurally-guided scaffold phage display strategy for identification of ligand mimetic bio-therapeutics. As a proof of concept we used the ligand of integrin αvβ6, a tumour cell surface receptor and a major new target for imaging and therapy of many types of solid cancer. NMR structure analysis showed that RGD-helix structures are optimal for αvβ6 ligand-interaction, so we designed novel algorithms to generate human single chain fragment variable (scFv) libraries with synthetic V_H-CDR3 encoding RGD-helix hairpins with helices of differing pitch, length and amino acid composition. Study of the lead scFv clones D25scFv and D34scFv and their corresponding V_H-CDR3 derived peptides, D25p and D34p, demonstrated: specific binding to recombinant and cellular αvβ6; inhibition of αvβ6-dependent cell and ligand adhesion, αvβ6-dependent cell internalisation; and selective retention by αvβ6-expressing, but not αvβ6-negative, human xenografts. NMR analysis established that both the D25p and D34p retained RGD-helix structures confirming the success of the algorithm. In conclusion, scFv libraries can be engineered based on ligand structural motifs to increase the likelihood of developing powerful bio-therapeutics.

Measuring protein reduction potentials using 15N HSQC NMR spectroscopy

NMR spectroscopy was used to measure reduction potentials of four redox proteins by following multiple ¹⁵N HSQC protein resonances across a titration series using mixtures of oxidised and reduced glutathione. Results for PDI a, PDI ab and DsbA agree with the literature and our result for ERp18 confirms this protein as an oxidoreductase of comparable or greater reducing strength than PDI a.

Characterization of the enzyme CbiH60 involved in anaerobic ring contraction of the cobalamin (vitamin B12) biosynthetic pathway

The anaerobic pathway for the biosynthesis of cobalamin (vitamin B(12)) has remained poorly characterized because of the sensitivity of the pathway intermediates to oxygen and the low activity of enzymes. One of the major bottlenecks in the anaerobic pathway is the ring contraction step, which has not been observed previously with a purified enzyme system. The Gram-positive aerobic bacterium Bacillus megaterium has a complete anaerobic pathway that contains an unusual ring contraction enzyme, CbiH(60), that harbors a C-terminal extension with sequence similarity to the nitrite/sulfite reductase family. To improve solubility, the enzyme was homologously produced in the host B. megaterium DSM319. CbiH(60) was characterized by electron paramagnetic resonance and shown to contain a [4Fe-4S] center. Assays with purified recombinant CbiH(60) demonstrate that the enzyme converts both cobalt-precorrin-3 and cobalt factor III into the ring-contracted product cobalt-precorrin-4 in high yields, with the latter transformation dependent upon DTT and an intact Fe-S center. Furthermore, the ring contraction process was shown not to involve a change in the oxidation state of the central cobalt ion of the macrocycle.

An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis

The biosynthesis of many vitamins and coenzymes has often proved difficult to elucidate due to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B₁₂) pathway in E. coli, and by His-tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly-bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalysed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, has been identified, which can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling.

NMR relaxation and structural elucidation of peptides in the presence and absence of trifluoroethanol illuminates the critical molecular nature of integrin αvβ6 ligand specificity

Integrin αvβ6 is an important emerging target for both imaging and therapy of cancer that requires specific ligands based on Arg-Gly-Asp (RGD) peptides. There remains little correlation between integrin-RGD ligand specificity despite studies suggesting an RGD-turn-helix ligand motif is required. Here, we describe the application of ¹⁵N NMR relaxation analyses and structure determination of αvβ6 peptide ligands in the presence and absence of trifluoroethanol (TFE) to identify their critical molecular nature that influences specificity, interaction and function. Two linear peptides; one known to demonstrate αvβ6 specificity (FMDV2) and the other based on a natural RGD ligand (LAP2), were compared to two additional peptides based on FMDV2 but cyclised in different positions using a disulphide bond (DBD1 and DBD2). The cyclic adaptation in DBD1 produces a significant alteration in backbone dynamic properties when compared to FMDV2; a potential driver for the loss in αvβ6 specificity by DBD1. The importance of ligand dynamics are highlighted through a comprehensive reduced spectral density and ModelFree analysis of peptide ¹⁵N NMR relaxation data and suggest αvβ6 specificity requires the formation of a structurally rigid helix preceded by a RGD motif exhibiting slow internal motion. Additional observations include the effect of TFE/water viscosity on global NMR dynamics and the advantages of using spectral density NMR relaxation data to estimate correlation times and motional time regimes for peptides in solution.

One-bond and two-bond J couplings help annotate protein secondary-structure motifs: J-coupling indexing applied to human endoplasmic reticulum protein ERp18

NMR coupling constants, both direct one-bond ((1)J) and geminal two-bond ((2)J), are employed to analyze the protein secondary structure of human oxidized ERp18. Coupling constants collected and evaluated for the 18 kDa protein comprise 1268 values of (1)J(CαHα), (1)J(CαCβ), (1)J(CαC'), (1)J(C'N'), (1)J(N'Cα), (1)J(N') (HN), (2)J(CαN'), (2)J(HNCα), (2)J(C'HN), and (2)J(HαC'). Comparison with (1)J and (2)J data from reference proteins and pattern analysis on a per-residue basis permitted main-chain ϕ,ψ torsion-angle combinations of many of the 149 amino-acid residues in ERp18 to be narrowed to particular secondary-structure motifs. J-coupling indexing is here being developed on statistical criteria and used to devise a ternary grid for interpreting patterns of relative values of J. To account for the influence of the varying substituent pattern in different amino-acid sidechains, a table of residue-type specific threshold values was compiled for discriminating small, medium, and large categories of J. For the 15-residue insertion that distinguishes the ERp18 fold from that of thioredoxin, the J-coupling data hint at a succession of five isolated Type-I β turns at progressively shorter sequence intervals, in agreement with the crystal structure.

The ligand-binding b' domain of human protein disulphide-isomerase mediates homodimerization

Purified preparations of the recombinant b'x domain fragment of human protein-disulphide isomerase (PDI), which are homogeneous by mass spectrometry and sodium dodecyl sulfate polyacrylamide gel electrophoresis, comprise more than one species when analyzed by ion-exchange chromatography and nondenaturing polyacrylamide gel electrophoresis. These species were resolved and shown to be monomer and dimer by analytical ultracentrifugation and analytical size-exclusion chromatography. Spectroscopic properties indicate that the monomeric species corresponds to the "capped" conformation observed in the x-ray structure of the I272A mutant of b'x (Nguyen, Wallis, Howard, Haapalainen, Salo, Saaranen, Sidhu, Wierenga, Freedman, Ruddock, and Williamson, J Mol Biol 2008;383:1144-1155) in which the x region binds to a hydrophobic patch on the surface of the b' domain; conversely, the dimeric species has an "open" or "uncapped" conformation in which the x region does not bind to this surface. The larger bb'x fragment of human PDI shows very similar behavior to b'x and can be resolved into a capped monomeric species and an uncapped dimer. Preparations of recombinant b' domain of human PDI and of the bb' domain pair are found exclusively as dimers. Full-length PDI is known to comprise a mixture of monomeric and dimeric species, whereas the isolated a, b, and a' domains of PDI are found exclusively as monomers. These results show that the b' domain of human PDI tends to form homodimers--both in isolation and in other contexts--and that this tendency is moderated by the adjacent x region, which can bind to a surface patch on the b' domain.

Solution structure and dynamics of ERp18, a small endoplasmic reticulum resident oxidoreductase

Here we report the solution structure of oxidized ERp18 as determined using NMR spectroscopy. ERp18 is the smallest member of the protein disulfide isomerase (PDI) family of proteins to contain a Cys-Xxx-Xxx-Cys active site motif. It is an 18 kDa endoplasmic reticulum resident protein with unknown function although sequence similarity to individual domains of the thiol-disulfide oxidoreductase PDI suggests ERp18 may have a similar structure and function. Like the catalytic domains of PDI, ERp18 adopts a thioredoxin fold with a thioredoxin-like active site located at the N-terminus of a long kinked helix that spans the length of the protein. Comparison of backbone chemical shifts for oxidized and reduced ERp18 shows the majority of residues possess the same backbone conformation in both states, with differences limited to the active site and regions in close proximity. S(2) order parameters from NMR backbone dynamics were found to be 0.81 for oxidized and 0.91 for reduced ERp18, and these observations, in combination with amide hydrogen exchange rates, imply a more rigid and compact backbone for the reduced structure. These observations support a putative role for ERp18 within the cell as an oxidase, introducing disulfide bonds to substrate proteins, providing structural confirmation of ERp18's role as a thiol-disulfide oxidoreductase.

Variation in protein C(alpha)-related one-bond J couplings

Four types of polypeptide (1)J(C alpha X) couplings are examined, involving the main-chain carbon C(alpha) and either of four possible substituents. A total 3105 values of (1)J(C alpha H alpha), (1)J(C alpha C beta), (1)J(C alpha C'), and (1)J(C alpha N') were collected from six proteins, averaging 143.4 +/- 3.3, 34.9 +/- 2.5, 52.6 +/- 0.9, and 10.7 +/- 1.2 Hz, respectively. Analysis of variances (ANOVA) reveals a variety of factors impacting on (1)J and ranks their relative statistical significance and importance to biomolecular NMR structure refinement. Accordingly, the spread in the (1)J values is attributed, in equal proportions, to amino-acid specific substituent patterns and to polypeptide-chain geometry, specifically torsions phi, psi, and chi(1) circumjacent to C(alpha). The (1)J coupling constants correlate with protein secondary structure. For alpha-helical phi, psi combinations, (1)J(C alpha H alpha) is elevated by more than one standard deviation (147.8 Hz), while both (1)J(C alpha N') and (1)J(C alpha C beta) fall short of their grand means (9.5 and 33.7 Hz). Rare positive phi torsion angles in proteins exhibit concomitant small (1)J(C alpha H alpha) and (1)J(C alpha N') (138.4 and 9.6 Hz) and large (1)J(C alpha C beta) (39.9 Hz) values. The (1)J(C alpha N') coupling varies monotonously over the phi torsion range typical of beta-sheet secondary structure and is largest (13.3 Hz) for phi around -160 degrees. All four coupling types depend on psi and thus help determine a torsion that is notoriously difficult to assess by traditional approaches using (3)J. Influences on (1)J stemming from protein secondary structure and other factors, such as amino-acid composition, are largely independent.

Dynamic characterisation of the netrin-like domain of human type 1 procollagen C-proteinase enhancer and comparison to the N-terminal domain of tissue inhibitor of metalloproteinases (TIMP)

The backbone mobility of the C-terminal domain of procollagen C-proteinase enhancer (NTR PCOLCE1), part of a connective tissue glycoprotein, was determined using 15N NMR spectroscopy. NTR PCOLCE1 has been shown to be a netrin-like domain and adopts an OB-fold such as that found in the N-terminal domain of tissue inhibitors of metalloproteinases-1 (N-TIMP-1), N-TIMP-2, the laminin-binding domain of agrin and the C-terminal domain of complement protein C5. NMR relaxation dynamics of NTR PCOLCE1 highlight conformational flexibility in the N-terminus, strand A and the proximal CD loop. This region in N-TIMP is known to be essential for inhibitory activity against the matrix metalloproteinases and suggests that this region is of equal importance for NTR PCOLCE1, although the specific functional activity of the NTR PCOLCE1 domain is still unknown. Dynamics observed within the structural core of NTR PCOLCE1 that are not observed in N-TIMP molecules suggest that although the two domains have a similar architecture, the NTR PCOLCE1 domain will show different thermodynamic properties on binding and hence the target molecule could be somewhat different from that observed for the TIMPs. ModelFree order parameters show that NTR PCOLCE1 has more flexibility than both N-TIMP-1 and N-TIMP-2.

Poly-N-acetylglucosamine and poly(glycerol phosphate) teichoic acid identification from staphylococcal biofilm extracts using excitation sculptured TOCSY NMR

We report the successful application of selective excitation sculptured TOCSY NMR (SXS-TOCSY) to identify individual solution components from a heterogeneous system using selectively acquired (1)H NMR spin system patterns. SXS-TOCSY application is illustrated by detection of the simultaneous presence of poly-beta-(1,6)-N-acetylglucosamine (PNAG) and poly(glycerol phosphate) teichoic acid (TA) carbohydrate polymer components in crude biofilm extracts from Staphylococcus epidermidis without the need for further sample purification and component separation. Biofilms are implicated in the barriers for resistance of microbes toward antibiotics and immune responses, therefore efficient rapid detection and quantification of key components are important to assist in the design of a clinical infection response.