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ClpB is a tightly regulated AAA+ disaggregation machine. Each ClpB molecule is composed of a flexibly attached N-terminal domain (NTD), an essential middle domain (MD) that activates the machine by tilting, and two nucleotide-binding domains. The NTD is not well-characterized structurally and is commonly considered to serve as a dispensable substrate-binding domain. Here, we use single-molecule FRET spectroscopy to directly monitor the real-time dynamics of ClpB's NTD and reveal its unexpected autoinhibitory function. We find that the NTD fluctuates on the microsecond time scale, and these dynamics result in steric hindrance that limits the conformational space of the MD to restrict its tilting. This leads to significantly inhibited ATPase and disaggregation activities of ClpB, an effect that is alleviated upon binding of a substrate protein or the cochaperone DnaK. This entropic inhibition mechanism, which is mediated by ultrafast motions of the NTD and is not dependent on any strong interactions, might be common in related ATP-dependent proteases and other multidomain proteins to ensure their fast and reversible activation.

A new mechanism of allostery in proteins, based on charge rather than structure, is reported. We demonstrate that dynamic redistribution of charge within a protein can control its function and affect its interaction with a binding partner. In particular, the association of an antibody with its target protein antigen is studied. Dynamic charge shifting within the antibody during its interaction with the antigen is enabled by its binding to a metallic surface that serves as a source for electrons. The kinetics of antibody-antigen association are enhanced when charge redistribution is allowed, even though charge injection happens at a position far from the antigen binding site. This observation points to charge-reorganization allostery, which should be operative in addition or parallel to other mechanisms of allostery, and may explain some current observations on protein interactions.

Correction: Chemical Senses, Volume 46, 2021, bjab050, https://doi.org/10.1093/chemse/bjab050 Published: 08 December 2021 Recent anecdotal and scientific reports have provided evidence of a link between COVID-19 and chemosensory impairments, such as anosmia. However, these reports have downplayed or failed to distinguish potential effects on taste, ignored chemesthesis, and generally lacked quantitative measurements. Here, we report the development, implementation, and initial results of a multilingual, international questionnaire to assess self-reported quantity and quality of perception in 3 distinct chemosensory modalities (smell, taste, and chemesthesis) before and during COVID-19. In the first 11 days after questionnaire launch, 4039 participants (2913 women, 1118 men, and 8 others, aged 19-79) reported a COVID-19 diagnosis either via laboratory tests or clinical assessment. Importantly, smell, taste, and chemesthetic function were each significantly reduced compared to their status before the disease. Difference scores (maximum possible change +/- 100) revealed a mean reduction of smell (-79.7 +/- 28.7, mean +/- standard deviation), taste (-69.0 +/- 32.6), and chemesthetic (-37.3 +/- 36.2) function during COVID-19. Qualitative changes in olfactory ability (parosmia and phantosmia) were relatively rare and correlated with smell loss. Importantly, perceived nasal obstruction did not account for smell loss. Furthermore, chemosensory impairments were similar between participants in the laboratory test and clinical assessment groups. These results show that COVID-19-associated chemosensory impairment is not limited to smell but also affects taste and chemesthesis.The multimodal impact of COVID-19 and the lack of perceived nasal obstruction suggest that severe acute respiratory syndrome coronavirus strain 2 (SARS-CoV-2) infection may disrupt sensory-neural mechanisms.

The mechanism of acetylene bromoboration in neat boron tribromide was studied carefully by means of experiment and theory. Besides the syn-addition mechanism through a four-center transition state,...

About 97% of lubricant base oils are currently sourced from petroleum and the majority of the rest is produced from vegetable oils. We demonstrate a promising catalytic route to produce base oils from lignocellulosic biomass-derived 2-alkylfurans and ketones via carbon–carbon coupling in neat conditions. Among several homogeneous and heterogeneous acid catalysts tested, a perfluorinated sulfonic acid (Aquivion PW79S) exhibits the best catalytic performance and yields up to 90% renewable furan-containing base oils with the use of a thiol promotor. The effects of the acid strength of the catalysts, molecular size and structure of thiols and ketones, and fraction of thiols are studied. Electronic structure calculations elucidate the reaction pathway and indicate that the thiol reduces the barrier of the rate-determining dehydration step. The structure and properties of base oils can be tuned by using different synthons. These base oils have excellent properties and can be competitive with or surpass the commercial synthetic alkylnaphthalene and furan-containing bio-ester base oils.

Identifying the influence of atomic order on the catalytic reactivity of bimetallic catalysts is essential for their rational design. However, the synthesis of atomically ordered nanostructures und...

Background Acute kidney injury represents a major threat to the transplanted kidney. Nevertheless, these kidneys have the potential to fully recover. Tubular regeneration following acute kidney injury is driven by the regenerative potential of tubular cells originating from a tubular stem cell pool. We investigated urinary sediments of acute kidney injury transplanted patients and compared it to those of non-transplanted patients. Thereby we discovered tubular cell agglomerates, which have not been described in vivo. We hypothesized that these so-called nephrospheres were associated with recovery from acute kidney injury. Methods Urine sediment of 45 kidney-transplanted and 19 non-transplanted individuals was investigated. Nephrospheres were isolated and stained for several molecular markers including aquaporin 1 (AQP1) and calcium sensing receptor (CASR). Nephrospheres were cultured to examine their growth behavior in vitro. In addition, quantitative PCR for CASR, AQP1, and podocin (NPHS2) was performed. Results Nephrospheres were excreted in the urine of 17 kidney-transplant recipients 7 days after onset of acute kidney injury and were detectable over several days until kidney function was recovered to baseline creatinine levels. None were found in the urine of non-transplanted individuals. Nephrospheres were either AQP1+/CASR+ or AQP1−/CASR+ and could be cultured for 27 days. Mitotic cells could still be visualized after 17 days in culture. Quantitative PCR detected AQP1 in both kidney-transplanted and non-transplanted individuals during the phase of creatinine decline. As a limitation qPCR was only performed for the entire urinary sediment. Conclusions Nephrospheres are three dimensional tubular cell agglomerates which appeared in urine of kidney transplant recipients recovering from acute kidney injury. Appearance of nephrospheres in urine was independent of the duration after kidney transplantation. Nephrospheres proliferated in cell culture and kept expressing kidney specific marker. Presence of nephrospheres in urine showed a specificity of 100% and a sensitivity of 60.71% for recovery. Electronic supplementary material The online version of this article (10.1186/s12882-019-1454-3) contains supplementary material, which is available to authorized users.

Fundamental knowledge of the active site requirements for the selective activation of C–O bonds over heterogeneous catalysts is required to design multistep processes for the synthesis of complex chemicals. Here we employ reaction kinetics measurements, extensive catalyst characterization, first principles calculations and microkinetic modelling to reveal metal oxides as a general class of catalysts capable of selectively cleaving C–O bonds with unsaturation at the α position, at a moderate temperature and H2 pressure. Strikingly, metal oxides are considerably more active catalysts than commonly employed VIIIB and IB transition metal catalysts. We identify the normalized Gibbs free energy of oxide formation as both a reactivity and a catalyst stability descriptor and demonstrate the generality of the radical-mediated, reverse Mars–van Krevelen C–O bond activation mechanism on oxygen vacancies, previously established only for RuO2. Importantly, we provide evidence that the substrate plays an equally key role to the catalyst in C–O bond activation. Metal oxides have been identified as a promising class of catalysts for carbon–oxygen bond cleavage in the context of biomass valorization, although the systematic understanding of their reactivity remains elusive. Now, a combination of catalytic screening and first principles calculations provide important insights into this family of catalysts.

Metal-support interactions have been widely utilized for optimizing the catalytic reactivity of oxide-supported Au nanoparticles. Optimized reactivity was mainly detected with small (1-5 nm) oxide-supported Au nanoparticles and correlated to highly reactive sites at the oxide-metal interface. However, catalytically active sites are not necessarily restricted to the interface but reside as well on the Au surface. Uncovering the interconnection between reactive sites located at the interface and those situated at the metal surface is of crucial importance for understanding the reaction mechanism on Au nanoparticles. Herein, high-spatial-resolution IR nanospectroscopy measurements were conducted to map the localized reactivity in hydrogenation reactions on oxide-supported Au particles while using nitro-functionalized ligands as probes molecules. Comparative analysis of the reactivity pattern on single particles supported on various oxides revealed that oxide-dependent reactivity enhancement was not limited to the oxide-metal interface but was detected throughout the Au particle, leading to site-independent reactivity. These results indicate that reactive Au sites on both the oxide-metal interface and metal surface can activate the nitro groups toward hydrogenation reactions. The observed influence of oxide support (TiO2 > SiO2 > Al2O3) on the overall reactivity pattern specified that hydrogen dissociation occurred at the oxide-metal interface, followed by highly efficient intraparticle hydrogen atom diffusion to the interior parts of the Au particle. In contrast to Au particles, the oxide-metal interface had only a minor impact on the reactivity of supported Pt particles in which hydrogen dissociation and nitro group reduction were effectively activated on Pt sites. Single-particle measurements provided insights into the relative reactivity pattern of oxide-supported Au particles, revealing that the less-reactive Au metal sites can activate hydrogenation reactions in the presence of hydrogen atoms that diffuse from the Au/oxide boundary.

AAA+ ring-shaped machines, such as the disaggregation machines ClpB and Hsp104, mediate ATP-driven substrate translocation through their central channel by a set of pore loops. Recent structural studies have suggested a universal hand-over-hand translocation mechanism, in which pore loops are moving rigidly in tandem with their corresponding subunits. However, functional and biophysical studies are in discord with this model. Here, we directly measure the real-time dynamics of the pore loops of ClpB as they function in substrate threading, using single-molecule FRET spectroscopy. All pore loops undergo large-amplitude fluctuations on the microsecond timescale and change their conformation upon interaction with substrate proteins. Conformational dynamics of two of the pore loops strongly correlate with disaggregation activity, suggesting that they are the main contributors to substrate pulling through the central channel. Finally, the pore loops present differential dependence on ATP hydrolysis along the axial channel. This set of findings is rationalized in terms of an ultrafast Brownian-ratchet translocation mechanism, which likely acts in parallel to the much slower hand-over-hand process in ClpB and other AAA+ machines.

ClpB is an ATP-dependent protein disaggregation machine that is activated on demand by co-chaperones and by aggregates caused by heat shock or mutations. The regulation of ClpB’s function is critical, since its persistent activation is toxicin vivo. Each ClpB molecule is composed of an auxiliary N-terminal domain (NTD), an essential regulatory middle domain (MD) that activates the machine by tilting, and two nucleotide-binding domains that are responsible for ATP-fuelled substrate threading. The NTD is generally thought to serve as a substrate-binding domain, which is commonly considered to be dispensable for ClpB’s activity, and is not well-characterized structurally due to its high mobility. Here we use single-molecule FRET spectroscopy to directly monitor the real-time dynamics of ClpB’s NTD and reveal its involvement in novel allosteric interactions. We find that the NTD fluctuates on a microsecond timescale and, unexpectedly, shows little change in conformational dynamics upon binding of a substrate protein. During its fast motion, the NTD makes crucial contacts with the regulatory MD, directly affecting its conformational state and thereby influencing the overall ATPase and unfolding activity of this machine. Moreover, we also show that the NTD mediates signal transduction to the nucleotide-binding domains through conserved residues. The two regulatory pathways revealed here enable the NTD to suppress the MD in the absence of protein substrate, and to limit ATPase and disaggregation activities of ClpB. The use of multiple parallel allosteric pathways involving ultrafast domain motions might be common to AAA+ molecular machines to ensure their fast and reversible activation.

The thermodynamics of protein folding in bulk solution have been thoroughly investigated for decades. By contrast, measurements of protein substrate stability inside the GroEL/ES chaperonin cage have not been reported. Such measurements require stable encapsulation, that is no escape of the substrate into bulk solution during experiments, and a way to perturb protein stability without affecting the chaperonin system itself. Here, by establishing such conditions, we show that protein stability in the chaperonin cage is reduced dramatically by more than 5 kcal mol−1 compared to that in bulk solution. Given that steric confinement alone is stabilizing, our results indicate that hydrophobic and/or electrostatic effects in the cavity are strongly destabilizing. Our findings are consistent with the iterative annealing mechanism of action proposed for the chaperonin GroEL., eLife digest All cells contain molecules known as proteins that perform many essential roles. Proteins are made of chains of building blocks called amino acids that fold to form the proteins’ three-dimensional structures. Many proteins fold spontaneously into their well-defined and correct structures. However, some proteins fold incorrectly, which prevents them from working properly, and can lead to formation of aggregates that may harm the cell. To prevent such damage, cells have evolved proteins known as molecular chaperones that assist in the folding of other proteins. For example, a molecular chaperone called GroEL is found in a bacterium known as Escherichia coli. This molecular chaperone contains a cavity which prevents target proteins from forming clumps by keeping them away from other proteins. However, it remained unclear precisely how GroEL works and whether enclosing target proteins in its cavity has other effects. Moritella profunda is a bacterium that thrives in cold environments and, as a result, many of its proteins are unstable at room temperature and tend to unfold or fold incorrectly. To study how GroEL works, Korobko et al. used a protein from M. profunda called dihydrofolate reductase as a target protein for the chaperone. A clever trick was then used to determine the folding state of dihydrofolate reductase when inside the chaperone cavity. The experiments revealed that the environment within the cavity of GroEL strongly favors dihydrofolate reductase adopting its unfolded state instead of its folded state. This suggests that GroEL helps dihydrofolate reductase and other incorrectly folded target proteins to unfold, thus providing the proteins another opportunity to fold again correctly. Parkinson’s disease, Alzheimer’s disease and many other diseases are caused by proteins folding incorrectly and forming aggregates. A better understanding of how proteins fold may, therefore, assist in developing new therapies for such diseases. These findings may also help biotechnology researchers develop methods for producing difficult-to-fold proteins on a large scale.

Hana Polachek,1,* Nir Debotton,2,* Valeria Feinshtein,1 Mazal Rubin,1 Zvi Ben-Zvi,1,‡ Gershon Holcberg,3 Riad Agbaria,1 Arik Dahan1 1Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; 2Department of Chemical Engineering, Shenkar College of Engineering and Design, Ramat-Gan, Israel; 3Division of Obstetrics and Gynecology, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel *These authors contributed equally to this work ‡Professor Zvi Ben-Zvi passed away on August 4, 2017 Introduction: Six years after the US Food and Drug Administration approval of the broad-spectrum antibiotic ofloxacin (OFLX), the chiral switching of this racemic mixture resulted in a drug composed of the l-optical isomer levofloxacin (LVFX). Since both fluoroquinolones (FQs) were introduced to the pharmaceutical market, they have been widely prescribed by physicians, with careful administration during pregnancy and breastfeeding. Therefore, the role of the influx and efflux placental transporters in the concentrations of these drugs that permeate through human placental barrier model was investigated in this study. Methods: The contribution of major carriers on the transplacental flux of OFLX and LVFX uptake into choriocarcinoma BeWo cells was evaluated in the presence vs absence of well-known inhibitors. Results: Our results reveal that neither the influx transporters such as organic cation transporters, organic anion transporters, and monocarboxylate transporters nor the efflux transporters such as P-glycoprotein or breast cancer resistance protein significantly affected the transport of OFLX. In contrast, multiple transporters revealed pronounced involvement in the transfer of the levorotatory enantiomer in and out of the invitro placental barrier. These data suggest a non-carrier-mediated mechanism of transport of the racemic mixture, while LVFX is subjected to major influx and efflux passage through the placental brush border membranes. Conclusion: This study provides underlying insights to elucidate the governing factors that influence the flux of these FQs through organ barriers, in view of the controversial safety profile of these drugs in pregnant population. Keywords: drug transport, fluoroquinolones, levofloxacin, ofloxacin, placenta, pregnancy

Vzajemna pozice funkcnich skupin iminu a boronove kyseliny v ortho regioisomeru ((ferrocenylimino)methyl)fenylboronove kyseliny (1a) usnadňuje a významně podporuje vratne molekularni přepinani mezi C=N iminem a COR-NH hemiaminalem. Tyto dva stavy jsou kontrolovatelne elektrochemicky pomoci oxidace/redukce ferrocenylove skupiny a tak je vytvořen jednoduchý dynamický molekularni přepinac pro adici/eliminaci nukleofilu na/z iminu. Výjimecne redoxni chovani 1a v protických primarnich alkoholech je způsobeno interakci obou motivů boronove kyseliny a iminoveho atomu uhliku s molekulou alkoholu. Chovani kyselin 1 je ovlivněno typem rozpoustědla, oxidacnim stavem ferrocenyloveho zbytku a blizkosti skupiny boronove kyseliny. Navic, dalsi rovnovahy zahrnujici větsinu možných interakci skupin iminu a boronove kyseliny s okolim zahrnujici vliv různých O-nukleofilů jsou take detailně popsany s cilem porozumět zakladnim faktorům interakce B-N.

Phenanthrylene-ethynylidene macrocycles combining electron donor and electron acceptor subunits in their shape-persistent fully conjugated core were synthesized. The donor subunits consisted of two 9,10-dialkoxyphenanthrenes linked either with 1,2-ethynylidene or 2,5-thienylene bridge. The acceptors were 9,10-phenanthroquinone and dibenzoquinoxaline and dibenzophenazines derived from it. Solvatochromic photoluminescence from intramolecular-charge-transfer (ICT) excited state was observed mainly in non-polar solvents. In more polar solvents, the excited states favor non-radiative relaxation. DFT calculated HOMO/LUMO energies of the macrocycles correlate well with spectroscopic and electrochemical data. In the series of substituted dibenzophenazine acceptors a good correlation with Hammett substituent constants σp– was found.

Significance The potential effect of conformational dynamics of enzymes on their chemical steps has been intensely debated recently. We use single-molecule FRET experiments on adenylate kinase (AK) to shed new light on this question. AK closes its domains to bring its two substrate close together for reaction. We show that domain closure takes only microseconds to complete, which is two orders of magnitude faster than the chemical reaction. Nevertheless, active-site mutants that reduce the rate of domain closure also reduce the reaction rate, suggesting a connection between the two phenomena. We propose that ultrafast domain closure is used by enzymes as a mechanism to optimize mutual orientation of substrates, a novel mode of coupling between conformational dynamics and catalysis., The functional cycle of many proteins involves large-scale motions of domains and subunits. The relation between conformational dynamics and the chemical steps of enzymes remains under debate. Here we show that in the presence of substrates, domain motions of an enzyme can take place on the microsecond time scale, yet exert influence on the much-slower chemical step. We study the domain closure reaction of the enzyme adenylate kinase from Escherichia coli while in action (i.e., under turnover conditions), using single-molecule FRET spectroscopy. We find that substrate binding increases dramatically domain closing and opening times, making them as short as ∼15 and ∼45 µs, respectively. These large-scale conformational dynamics are likely the fastest measured to date, and are ∼100–200 times faster than the enzymatic turnover rate. Some active-site mutants are shown to fully or partially prevent the substrate-induced increase in domain closure times, while at the same time they also reduce enzymatic activity, establishing a clear connection between the two phenomena, despite their disparate time scales. Based on these surprising observations, we propose a paradigm for the mode of action of enzymes, in which numerous cycles of conformational rearrangement are required to find a mutual orientation of substrates that is optimal for the chemical reaction.

Along our way towards the advanced saccharide-sensitive probes, three novel electroactive iminoboronate regioisomers of [(ferrocenylimino)methyl]phenylboronic acid have been synthesized. The ortho, meta, and para regioisomers were characterized structurally by NMR, MS, FT-IR, UV/Vis and their electrochemical behavior in aqueous solution was studied using cyclic voltammetry. The obtained results confirmed different behavior of the ortho isomer due to an interaction of boronic acid moiety with the proximate imine group of the iminoferrocenyl residue.

In mango, fruitlet abscission initiates with a decrease in polar auxin transport through the abscission zone (AZ), triggered by ethylene. To explore the molecular components affecting this process, we initially conducted experiments with developing fruitlet explants in which fruitlet drop was induced by ethephon, and monitored the expression patterns of distinct indole-3-acetic acid (IAA)-related genes, comparing control vs. ethephon-treated pericarp and AZ profiles. Over the examined time period (48 h), the accumulation of MiPIN1 and MiLAX2 IAA-efflux and influx genes decreased in both control and treated tissues. Nevertheless, ethephon-treated tissues displayed significantly lower levels of these transcripts within 18–24 h. An opposite pattern was observed for MiLAX3 , which overall exhibited up-regulation in treated fruitlet tissues. Ethephon treatment also induced an early and pronounced down-regulation of five out of six IAA-responsive genes, and a substantial reduction in the accumulation of two IAA-synthesis related transcripts, contrasting with significant up-regulation of Gretchen Hagen3 transcript ( MiGH3.1 ) encoding an IAA–amino synthetase. Furthermore, for both control and treated AZ, the decrease in IAA-carrier transcripts was associated with a decrease in IAA content and an increase in IAA–Asp:IAA ratio, suggesting that fruitlet drop is accompanied by formation of this non-hydrolyzed IAA–amino acid conjugate. Despite these similarities, ethephon-treated AZ displayed a sharper decrease in IAA content and higher IAA–Asp:IAA ratio within 18 h. Lastly, the response of IAA-related genes to exogenous IAA treatment was also examined. Our results are discussed, highlighting the roles that distinct IAA-related genes might assume during mango fruitlet drop.

Hsp90 plays a central role in cell homeostasis by assisting folding and maturation of a large variety of clients. It is a homo-dimer, which functions via hydrolysis of ATP-coupled to conformational changes. Hsp90's conformational cycle in the absence of cochaperones is currently postulated as apo-Hsp90 being an ensemble of "open"/"closed" conformations. Upon ATP binding, Hsp90 adopts an active ATP-bound closed conformation where the N-terminal domains, which comprise the ATP binding site, are in close contact. However, there is no consensus regarding the conformation of the ADP-bound Hsp90, which is considered important for client release. In this work, we tracked the conformational states of yeast Hsp90 at various stages of ATP hydrolysis in frozen solutions employing electron paramagnetic resonance (EPR) techniques, particularly double electron-electron resonance (DEER) distance measurements. Using rigid Gd(III) spin labels, we found the C domains to be dimerized with same distance distribution at all hydrolysis states. Then, we substituted the ATPase Mg(II) cofactor with paramagnetic Mn(II) and followed the hydrolysis state using hyperfine spectroscopy and measured the inter-N-domain distance distributions via Mn(II)-Mn(II) DEER. The point character of the Mn(II) spin label allowed us resolve 2 different closed states: The ATP-bound (prehydrolysis) characterized by a distance distribution having a maximum of 4.3 nm, which broadened and shortened, shifting the mean to 3.8 nm at the ADP-bound state (posthydrolysis). This provides experimental evidence to a second closed conformational state of Hsp90 in solution, referred to as "compact." Finally, the so-called high-energy state, trapped by addition of vanadate, was found structurally similar to the posthydrolysis state.

Additive manufacturing of metals is today one of the most growing fields in materials research. Selective laser melting (SLM) allows to produce metal parts with complicated shapes, but the quality of produced material is relatively low (in compare with conventionally produced materials). The main aims of latest studies is to improve materials properties and reach the same or better quality. Presented paper shows the comparison of fatigue behaviour of SLM and conventional material using copper (Cu7.2Ni1.8Si1Cr) and aluminium (AlCu2Mg1.5Ni and AlSi10Mg) alloys. SLM and standard material samples were subjected to bending fatigue tests which were supplemented by acoustic emission (AE) measurement and fractography analysis. The results from AE measurement allows to analyse fatigue process, determine different fatigue stages and compare the results from SLM and standard material in more detail. The results show that the main difference between fatigue behaviour of SLM and standard material is not only in total fatigue life (the SLM material has significantly worse fatigue resistance), but mainly in the length of fatigue stages and in mechanism of crack development. As we expected, the fatigue resistance of SLM is strongly affected by amount of production defects.

Salmon is regarded as an excellent source of nutrients and there are numerous choices in the types of salmon available. In North America, nutritional labelling for fresh seafood is not required. The lack of nutritional information may be confusing to some consumers when selecting a product for specific health benefits. The aim of this study was to examine the nutritional composition of different types of salmon fillets that are commonly available to Canadian consumers, which included different species, wild and farmed, organic, and environmental sustainability certifications. Six types of salmon were analyzed: farmed Atlantic, farmed organic Atlantic, farmed organic Chinook, wild Chinook, wild Pacific (pink), and wild Sockeye. Protein, fat, fatty acids, amino acids, potassium, iron, cholesterol, and mercury were analyzed. Wild Pacific was the most dissimilar salmon type, due to high moisture content (79%), and lowest fat (0.8%) and fatty acid content, compared with all salmon types. Protein and fat were highest wild Sockeye, wild Chinook, and farmed Atlantic salmon. DHA and EPA were highest in wild Sockeye (81 mg/g) and wild Chinook (79 mg/g), and lower in farmed organic Chinook (23 mg/g), farmed Atlantic (20 mg/g), farmed organic Atlantic (16 mg/g), and wild Pacific (10 mg/g). Mercury was highest in farmed organic Chinook (0.3 μg/g) and lowest in farmed Atlantic (38% lower) and farmed organic Atlantic. Considering nutrient profiles as multivariable, PERMANOVA revealed significant differences due to salmon type, and whether it was wild or farmed, organic or non-organic, certified or not certified. Wild Sockeye and Chinook were found to be the most nutrient-dense and have the highest omega-3 content. However, for frequent consumption, farmed Atlantic salmon is an excellent option due to nutrient density, low mercury, affordability, and availability. This study is important as an indicator of the current nutritional status of various salmon products.

Large protein machines are tightly regulated through allosteric communication channels. Here we demonstrate the involvement of ultrafast conformational dynamics in allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins. Each subunit of ClpB contains a unique coiled-coil structure, the middle domain (M domain), proposed as a control element that binds the co-chaperone DnaK. Using single-molecule FRET spectroscopy, we probe the M domain during the chaperone cycle and find it to jump on the microsecond time scale between two states, whose structures are determined. The M-domain jumps are much faster than the overall activity of ClpB, making it an effectively continuous, tunable switch. Indeed, a series of allosteric interactions are found to modulate the dynamics, including binding of nucleotides, DnaK and protein substrates. This mode of dynamic control enables fast cellular adaptation and may be a general mechanism for the regulation of cellular machineries., Large protein machines are tightly regulated through allosteric communication channels. Here authors use single-molecule FRET and demonstrate the involvement of ultrafast conformational dynamics in the allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins.

The boronic acid moiety in the proximity of electron-donating structures in ((ferrocenylimino)methyl)phenylboronic acid 1 significantly improves the reactivity of the molecule. The ortho regioisomer 1a exhibits a two-fold higher affinity to NaCl compared to its meta 1b and para 1c isomers, respectively. Moreover, the double imine bond in 1a was broken by the interaction with NaCl in methanol upon activation by electrochemical oxidation.

A controlled photorelease of alkynoic acids from the meso-methyl BODIPY photoremovable protecting group facilitates their subsequent efficient decarboxylation to give terminal alkynes for a CuI-catalyzed azide/alkyne cycloaddition. The quantum efficiencies of the photochemical step and the kinetics of the click reaction step are reported.

Complete crush or cut severance of sciatic nerve axons in rats and other mammals produces immediate loss of axonal continuity. Loss of locomotor functions subserved by those axons is restored only after months, if ever, by outgrowths regenerating at ∼1 mm/day from the proximal stumps of severed axonal segments. The distal stump of a severed axon typically begins to degenerate in 1–3 days. We recently developed a polyethylene glycol (PEG) fusion technology, consisting of sequential exposure of severed axonal ends to hypotonic Ca2+-free saline, methylene blue, PEG in distilled water, and finally Ca2+-containing isotonic saline. This study examines factors that affect the PEG fusion restoration of axonal continuity within minutes, as measured by conduction of action potentials and diffusion of an intracellular fluorescent dye across the lesion site of rat sciatic nerves completely cut or crush severed in the midthigh. Also examined are factors that affect the longer-term PEG fusion restoration of lost behavioral functions within days to weeks, as measured by the sciatic functional index. We report that exposure of cut-severed axonal ends to Ca2+-containing saline prior to PEG fusion and stretch/tension of proximal or distal axonal segments of cut-severed axons decrease PEG fusion success. Conversely, trimming cut-severed ends in Ca2+-free saline just prior to PEG fusion increases PEG fusion success. PEG fusion prevents or retards the Wallerian degeneration of cut-severed axons, as assessed by measures of axon diameter and G ratio. PEG fusion may produce a paradigm shift in the treatment of peripheral nerve injuries. © 2016 Wiley Periodicals, Inc.

Shape-persistent macrocycles (SPMs) represent innovative molecular building blocks for the development of highly organised supramolecular architectures with application in nanotechnology, chemistry, catalysis and optoelectronics. Systematic mass spectrometric characterisation of SPMs and their collision-activated decay is not available to date. Characterization of alkoxy-decorated SPMs was performed by matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOFMS) and collision-induced dissociation (CID). Laser excitation of SPMs leads to the formation of stable cation radicals which show characteristic fragmentation patterns. All the product ions formed were identified. Photoelectrons generated during the MALDI process and full-ring conjugation were found to be fundamental for the formation of molecular cation radicals and their stabilisation, respectively. Formation of supramolecular aggregates of SPMs by - stacking was proven. SPMs are suitable motifs for the preparation of novel fullerene-based donor-acceptor systems. Alkoxy-decorated SPMs represent promising electron-donating building blocks that can be exploited in electronics and optoelectronics for the development of robust and highly efficient laser-activated supramolecular switches.

Ligand binding to a protein can stabilize it significantly against unfolding. The variation of the folding free energy, ΔΔG0, due to ligand binding can be derived from a simple reaction scheme involving exclusive binding to the native state. One obtains the following expression: , where Kd is the ligand dissociation constant and L is its concentration, R is the universal gas constant and T is the temperature. This expression has been shown to correctly describe experimental results on multiple proteins. In the current work we studied the effect of ligand binding on the stability of the multi-domain protein adenylate kinase from E. coli (AKE). Unfolding experiments were conducted using single-molecule FRET spectroscopy, which allowed us to directly obtain the fraction of unfolded protein in a model-free way from FRET efficiency histograms. Surprisingly, it was found that the effect of two inhibitors (Ap5A and AMPPNP) and a substrate (AMP) on the stability of AKE was much smaller than expected based on Kd values obtained independently using microscale thermophoresis. To shed light on this issue, we measured the Kd for Ap5A over a range of chemical denaturant concentrations where the protein is still folded. It was found that Kd increases dramatically over this range, likely due to the population of folding intermediates, whose binding to the ligand is much weaker than that of the native state. We propose that binding to folding intermediates may dominate the effect of ligands on the stability of multi-domain proteins, and could therefore have a strong impact on protein homeostasis in vivo.

Restoration of neuronal functions by outgrowths regenerating at ∼1 mm/day from the proximal stumps of severed peripheral nerves takes many weeks or months, if it occurs at all, especially after ablation of nerve segments. Distal segments of severed axons typically degenerate in 1-3 days. This study shows that Wallerian degeneration can be prevented or retarded, and lost behavioral function can be restored, following ablation of 0.5-1-cm segments of rat sciatic nerves in host animals. This is achieved by using 0.8-1.1-cm microsutured donor allografts treated with bioengineered solutions varying in ionic and polyethylene glycol (PEG) concentrations (modified PEG-fusion procedure), being careful not to stretch any portion of donor or host sciatic nerves. The data show that PEG fusion permanently restores axonal continuity within minutes, as initially assessed by action potential conduction and intracellular diffusion of dye. Behavioral functions mediated by the sciatic nerve are largely restored within 2-4 weeks, as measured by the sciatic functional index. Increased restoration of sciatic behavioral functions after ablating 0.5-1-cm segments is associated with greater numbers of viable myelinated axons within and distal to PEG-fused allografts. Many such viable myelinated axons are almost certainly spared from Wallerian degeneration by PEG fusion. PEG fusion of donor allografts may produce a paradigm shift in the treatment of peripheral nerve injuries.

A series of macrocycles consisting of 9,10-substituted phenanthrenes connected by butadiynylene linkers in positions 3 and 6 has been described as well as their transformation into the corresponding phenanthrylene-thienylene macrocycles. Structure and properties of the macrocycles, such as self-association in solution and optical and electrochemical properties, were studied and reported in a comparative manner with respect to the effects of the different sizes and shapes of the macrocycles and the character and length of their side chains.

1,3-Diethynylbicyclo[1.1.1]pentane (DEBCP) has been found to be a valuable molecular building block mostly for the synthesis of extended, rigid, rod-like molecules. With its straightforward linear geometry, DEBCP can be used as a nonconjugated alternative to more frequently used pi-conjugated, rod-like building blocks. Examples of reactions that introduce DEBCP into larger structures are (1) the reaction of DEBCP lithium acetylides with electrophiles such as TMSCl, CO2, and Ph2PCl, (2) Sonogashira–Hagihara cross-coupling reactions with aryl or heteroaryl iodides or bromides, and (3) umpolung reactions that afford the corresponding dibromo and diiodo derivatives of DEBCP, which then successfully react with tert-C-cuprates derived from p- and m-dicarbadodecaboranes or bicyclopentanes. These umpolung reactions afforded a new class of molecular rods that combine carborane or bicyclo[1.1.1]pentane cages with ethynylene linkers. Many of the DEBCP derivatives were studied by single-crystal X-ray diffraction. They form well-organized arrays of molecular rotors, the DEBCP units, and so can be considered as examples of artificial molecular-size machines.

To determine the role of BCRP in nitrofurantoin (NF) transport in JAr cells and the possible contribution of OATP2B1, P-gp and MRPs to this transport. Cells were incubated with various BCRP, P-gp, MRPs, organic anion transporting polypeptide (OAT) and OATP2B1 inhibitors for 15 min, followed by incubation for 30 min with NF, with or without the inhibitors mentioned earlier. NF cytotoxicity was examined using neutral red (NR) assay. Intracellular NF levels were analyzed by HPLC. NR assay showed that incubation conditions with NF (as carried out in our experiments) were not cytotoxic. Incubation with specific inhibitors of BCRP (FTC, Chrysin and Novobiocin), showed a significant increase in NF accumulation in the cells. Inhibitors of OATP2B1 (EGCG and BSP) had no influence on NF accumulation. Specific inhibitors of P-gp and MRPs (Verapamil and Indomethacin, respectively) also had no influence on NF accumulation in JAr cells. NF is probably a specific substrate of BCRP, and BCRP has a major active role in NF transport in JAr cells. For the first time, we showed, that P-gp, MRPs, and the OATP2B1, probably have a negligible contribution to NF transport in JAr cells.

The reduction of a series of alpha-cyanostilbenes with SmI(2) was studied in THF in the presence of various proton donors. No reaction occurred in the presence of the alcohols TFE, i-PrOH and t-BuOH. In the presence of MeOH, water and ethylene glycol the reactions occurred; however in the presence of water and ethylene glycol they were too fast for kinetic determinations (tau(1/2) < 1 ms). Reactions with MeOH were first order in SmI(2) and first order in the substrate. The order in MeOH varies as a function of its concentration and the plot of log k vs log [MeOH] is sigmoidal. Comparison of the kinetic isotope effect and the incorporation isotope effect suggests that, counterintuitively, protonation of the radical anion takes place on the carbon beta to the cyano group. It is concluded that proton donors that form complexes with SmI(2) expand the range of substrates that can be reduced by SmI(2). This is due to their proximity to the radical anion as it is formed. This short-lived radical anion cannot be efficiently trapped by a proton donor from the bulk medium. A protocol is herein suggested as to when proton donors which complex to SmI(2), e.g. MeOH, water and ethyleneglycol should be used, and when it is recommended to use noncomplexing proton donors, e.g. TFE, i-PrOH and t-BuOH, to induce reaction.

We investigated the effectiveness of lanreotide for the treatment of active acromegaly in a retrospectively multicenter case series including 53 patients (24 male, 29 female; mean age at diagnosis, 49.5 +/- 13.9 years) with acromegaly treated with lanreotide in nine different centers. Mean tumor diameter was 20 +/- 13 mm; mean basal levels of growth hormone (GH) and insulin-like growth factor I (IGF-I) were 21.3 +/- 26.3 and 579 +/- 177 mug/l, respectively. The primary mode of treatment was surgery in 70% of patients. Twenty-nine patients received only lanreotide (Prolonged Release, Autogel), whereas 24 subjects were also treated with octreotide at another treatment stage. Primary therapy with lanreotide was administered in five patients. Maximal monthly dose of lanreotide Autogel (n = 44) was 60 mg in 45%, 90 mg in 26%, 120 mg in 21% and 180 mg in 8%. During 36 months of lanreotide treatment, mean IGF-I levels decreased from 443 +/- 238 to 276 +/- 147 mug/l (P0.001), and mean GH levels, from 5.2 +/- 6.4 to 3.2 +/- 3.0 mug/l (P0.001). IGF-I levels normalized in 51% of patients and decreased by50% towards normal in 32%; the normalization rate was higher in women (65%) than men (33%, P = 0.04). Safe random GH levels (/=2 mug/l) were achieved in 49% of patients. Both IGF-I normalization and safe GH levels were reached in 32% of the cohort. Lanreotide is an effective treatment for active acromegaly. Female sex was associated with higher rates of IGF-I normalization.

1,3-Dipolar cycloaddition reactions of dihydro-3-methylene-2(3H)-furanone (tulipalin A) with various benzonitrile(p-X-benzylide) ylides prefer formation of exo-cycloadducts in the extent corresponding to an increasing electron donor character of the substituent X in the para-position of the benzylide phenyl ring of the 1,3-dipolar reagent. The substituent effect on diastereoselectivity of the 1,3-DC reaction is rationalized in terms of CH/pi interaction between the dipole and the dipolarophile in an exo-transition state. The determining role of such an interaction is demonstrated by the correlation of the observed diastereoselectivities with substituent Hammett sigma constants, which shows a small negative rho value. A certain contribution of CO/pi interaction between the lactone carbonyl and the substituted phenyl ring to mediation of the substituent effect is also discussed. The energy profiles of both reaction pathways were analyzed using DFT and RI-MP2 theoretical approaches. Calculated energy and structural differences between located transition states are consistent with reaction diastereoselectivities.

A cocrystal of gabapentin and oxalic acid has been prepared employing a strategy based on a hydrogen-bonded synthon described by the graph set notation R42(8). High throughput techniques and solvent drop grinding were used along with traditional crystallization methods, including crystallization in aqueous solutions at various pH. A number of new solid forms have been detected. The cocrystal of gabapentin and oxalic acid was fully characterized including single crystal structure analysis, which revealed the R42(8) synthon.

Background: Platelet-derived growth factor (PDGF)-AA isoform and its receptor, PDGF-α receptor (PDGFRA) regulate tooth development and growth. We investigated the expression of both proteins in ameloblastomas, to contribute the understanding of the potential role of the PDGF/PDGFR system in this odontogenic neoplasm. Method: Twenty-nine specimens of ameloblastoma were analyzed for PDGF-AA and PDGFRA expression using immunohistochemistry. The proliferation activity was investigated with the MIB-1 antibody. Additionally, capillary sequencing of genomic DNA was performed to search for mutations in therapeutically relevant exons 12 and 18 of the PDGFRA gene. Results: PDGF-AA and PDGFRA expression were detectable in all cases with the exception of one tumor. However, protein expression levels did neither correlate with each other nor with MIB-1 expression. Unicystic ameloblastomas did not differ from solid tumors with regard to PDGF-AA, PDGFRA, and MIB-1 expression. One tumor revealed a somatic mutation of exon 12 of the PDGFRA gene. Conclusion: PDGF-AA and PDGFRA proteins are regularly expressed in variable levels in ameloblastomas, and somatic mutations of exon 12 and exon 18 of the PDGFRA gene are rare findings.

The crystal chemistry of oxalic acid has been studied since 1880, including 37 published structure determinations of the two anhydrous forms (alpha, beta) and the dihydrate, the latest in 2000. In attempts to cocrystallize asparagine or glutamine with oxalic acid, utilizing the particular hydrogen bond synthon R(4)(2)(8), we unexpectedly obtained two previously unreported sesquihydrates of oxalic acid. Form 1 is orthorhombic, Pnma, and the unit cell is a = 11.231(2) A, b = 12.330(2) A, c = 6.908(1) A. Form 2 crystallizes in the triclinic crystal system in space group P, and the unit cell is a = 6.337(2) A; b = 7.247(3) A, c = 10.571(4)A, alpha = 94.34(1) degrees, beta = 100.244(9) degrees, gamma = 97.67(1) degrees. Both of the new hydrate forms of oxalic acid utilized the R(4)(2)(8) hydrogen bonded synthon.

The objective of this research was to evaluate the effect of 2 levels of somatic cell counts (SCC) in raw milk on Prato cheese composition, protein and fat recovery, cheese yield, and ripening. A 2 x 6 factorial design with 3 replications was performed in this study: 2 levels of SCC and 6 levels of storage time. Initially, 2 groups of dairy cows were selected to obtain low (200,000 cells/ mL) and high (600,000 cells/mL) SCC in milks that were used to manufacture 2 vats of cheese: 1) low SCC and 2) high SCC. Milk, whey, and cheese compositions were evaluated; clotting time was measured; and cheese yield, protein recovery, and fat recovery were calculated. The cheeses were evaluated after 5, 12, 19, 26, 33, and 40 d of ripening according to pH, moisture, pH 4.6 soluble nitrogen, 12% trichloroacetic acid soluble nitrogen as a percentage of total nitrogen, and firmness. High-SCC milk presented significantly higher total protein and nonprotein nitrogen and lower true protein and casein concentrations than did low-SCC milk, indicating an increased whey protein content and a higher level of proteolysis. Although the pH of the milk was not affected by the somatic cell level, the cheese obtained from high-SCC milk presented significantly higher pH values during manufacture and a higher clotting time. No significant differences in cheese yield and protein recovery were observed for these levels of milk somatic cells. The cheese from high-SCC milk was higher in moisture and had a higher level of proteolysis during ripening, which could compromise the typical sensory quality of the product.

Organic salts are generally the preferred crystal form of active pharmaceutical ingredients because of their higher solubilities and/or increased degree of crystallinity. The potential number of suitable organic salts is limited to the counterions specified by the food and drug association (FDA) as GRAS (generally regarded as safe). A recently suggested alternative to the common inorganic salts is the preparation of cocrystals or organic salts, some of which have been shown to improve therapeutic utility while reducing side effects. Candidates for cocrystal formation with a particular structural motif for achieving desired physical properties are chosen on the basis of their ability to utilize known intermolecular interactions in forming those crystals. Because hydrogen bonds are among the strongest and most preferentially directional intermolecular interactions, they have been the leading candidates for the interactions to be utilized in forming cocrystals, although other interactions have also been suggested. Particular preference in the development of the strategy for cocrystal formation utilizing hydrogen bonds has traditionally been based on the tendency of carboxylic acids and amides to form the homoor heterointermolecular synthons described in Etter6s graph-set notation as