A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template.

Primases have a fundamental role in DNA replication. They synthesize a primer that is then extended by DNA polymerases. Archaeoeukaryotic primases require for synthesis a catalytic and an accessory domain, the exact contribution of the latter being unresolved. For the pRN1 archaeal primase, this domain is a 115-amino acid helix bundle domain (HBD). Our structural investigations of this small HBD by liquid- and solid-state nuclear magnetic resonance (NMR) revealed that only the HBD binds the DNA template. DNA binding becomes sequence-specific after a major allosteric change in the HBD, triggered by the binding of two nucleotide triphosphates. The spatial proximity of the two nucleotides and the DNA template in the quaternary structure of the HBD strongly suggests that this small domain brings together the substrates to prepare the first catalytic step of primer synthesis. This efficient mechanism is likely general for all archaeoeukaryotic primases.

The left prefrontal cortex determines relevance at encoding and governs episodic memory formation.

The role hemispheric lateralization in the prefrontal cortex plays for episodic memory formation in general, and for emotionally valenced information in particular, is debated. In a randomized, double-blind, and sham-controlled design, healthy young participants (n = 254) performed 2 runs of encoding to categorize the perceptual, semantic, or emotionally valenced (positive or negative) features of words followed by a free recall and a recognition task. To resolve competing hypotheses about the contribution of each hemisphere, we modulated left or right dorsolateral prefrontal cortex (DLPFC) activity using transcranial direct current stimulation during encoding (1 mA, 20 min). With stimulation of the left DLPFC, but not the right DLPFC, encoding and free recall performance improved particularly for words that were processed semantically. In addition, enhancing left DLPFC activity increased memory formation for positive content while reducing that for negative content. In contrast, promoting right DLPFC activity increased memory formation for negative content. The left DLPFC assesses semantic properties of new memory content at encoding and thus influences how successful new episodic memories are established. Hemispheric laterlization-more active left DLPFC and less active right DLPFC-at the encoding stage shifts the formation of memory traces in favor of positively valenced content.

A pocket-factor-triggered conformational switch in the hepatitis B virus capsid.

Viral hepatitis is growing into an epidemic illness, and it is urgent to neutralize the main culprit, hepatitis B virus (HBV), a small-enveloped retrotranscribing DNA virus. An intriguing observation in HB virion morphogenesis is that capsids with immature genomes are rarely enveloped and secreted. This prompted, in 1982, the postulate that a regulated conformation switch in the capsid triggers envelopment. Using solid-state NMR, we identified a stable alternative conformation of the capsid. The structural variations focus on the hydrophobic pocket of the core protein, a hot spot in capsid-envelope interactions. This structural switch is triggered by specific, high-affinity binding of a pocket factor. The conformational change induced by the binding is reminiscent of a maturation signal. This leads us to formulate the "synergistic double interaction" hypothesis, which explains the regulation of capsid envelopment and indicates a concept for therapeutic interference with HBV envelopment.

Photostability of sennosides and their aglycones in solution.

INTRODUCTION: Sennosides are the main active constituents of the dried leaves and/or pods of Senna alexandrina Mill. that are used as laxatives. A hypothesis is that aglycones are formed during the degradation of sennosides. However, it is unknown, whether this happens under visible light exposure and how photosensitive sennosides behave in solution. OBJECTIVES: Pure anthraquinone glycosides were tested on their behaviour during sample preparation in the lab under visible light exposure in dependence on the instability of the solvent. MATERIALS AND METHODS: Samples before and after exposure were analysed using UHPLC with UV/Vis and MS detection. RESULTS: Under visible light protection, the solutions were stable for 14 days at room temperature whereas a loss of 20%-60% was measured after 1 day of light exposure. The loss of sennosides due to degradation can be as fast as up to 2%-2.5% per hour, which might have a tremendous impact on phytochemical analysis results during the course of an analysis. The formation of aglycones was not observed in the degradation of sennosides and rhein-8-O-glucoside. CONCLUSION: Aglycones could not be found as a result of the forced degradation. The solutions of sennosides clearly need to be protected from light to obtain reliable analytical results, and light protection is a major point for the stability of liquid preparations.

The hypnagogic state: A brief update.

The hypnagogic state refers to a transitional stage between wakefulness and sleep, in which sensory perceptions can be experienced. In this review, we compile and discuss the recent scientific literature on hypnagogia research regarding the future directions proposed by Schacter (1976; Psychological Bulletin, 83, 452). After a short introduction discussing the terminology used in hypnagogia research and the differentiation of hypnagogic states with other related phenomena, we review the reported prevalence of hypnagogic states. Then, we evaluate the six future directions suggested by Schacter and we propose three further future directions. First, a better understanding of the emotional quality of hypnagogic states is needed. Second, a better understanding of why hypnagogic states occur so frequently in the visual and kinaesthetic modalities is needed. Lastly, a better understanding of the purpose of hypnagogic states is needed. In conclusion, research has made great progress in recent years, and we are one step closer to demystifying the hypnagogic state.

Hypnagogic states are quite common: Self-reported prevalence, modalities, and gender differences.

The hypnagogic state refers to the transitional phase between wakefulness and sleep during which vivid experiences occur. In this questionnaire study, we assessed the self-reported prevalence of hypnagogic states considering the frequency of experiences in different modalities. We also assessed the emotional quality and the vividness of the experiences. Moreover, we compared hypnagogic states to other phenomena, such as dreams, sleep paralysis, imagination, and extra-sensory perception in these measures. Hypnagogic states were reported by 80.2 % of 4456 participants and were more prevalent in women than men. Experiences were most often kinaesthetic and visual, and less often auditory, tactile, and olfactory or gustatory. Hypnagogic states were less prevalent than dreams and characterized by different modality profiles. However, they were similar to dreams in their emotional quality, the irritation they caused, and in their vividness. In conclusion, hypnagogic states are quite common.

Tony W. Keller (1937-2023).

Tony Keller, a pioneer in the field of Nuclear Magnetic Resonance (NMR) spectroscopy, passed away on October 27, 2023, at the age of 86 in Spiez, Switzerland. His work and vision were essential to the development and commercialization of NMR spectrometers for many areas of scientific research.

Probing a Hydrogen-π Interaction Involving a Trapped Water Molecule in the Solid State.

The detection and characterization of trapped water molecules in chemical entities and biomacromolecules remains a challenging task for solid materials. We herein present proton-detected solid-state Nuclear Magnetic Resonance (NMR) experiments at 100 kHz magic-angle spinning and at high static magnetic-field strengths (28.2 T) enabling the detection of a single water molecule fixed in the calix[4]arene cavity of a lanthanide complex by a combination of three types of non-covalent interactions. The water proton resonances are detected at a chemical-shift value close to zero ppm, which we further confirm by quantum-chemical calculations. Density Functional Theory calculations pinpoint to the sensitivity of the proton chemical-shift value for hydrogen-π interactions. Our study highlights how proton-detected solid-state NMR is turning into the method-of-choice in probing weak non-covalent interactions driving a whole branch of molecular-recognition events in chemistry and biology.

Solid-State NMR Reveals Asymmetric ATP Hydrolysis in the Multidrug ABC Transporter BmrA.

The detailed mechanism of ATP hydrolysis in ATP-binding cassette (ABC) transporters is still not fully understood. Here, we employed 31P solid-state NMR to probe the conformational changes and dynamics during the catalytic cycle by locking the multidrug ABC transporter BmrA in prehydrolytic, transition, and posthydrolytic states, using a combination of mutants and ATP analogues. The 31P spectra reveal that ATP binds strongly in the prehydrolytic state to both ATP-binding sites as inferred from the analysis of the nonhydrolytic E504A mutant. In the transition state of wild-type BmrA, the symmetry of the dimer is broken and only a single site is tightly bound to ADP:Mg2+:vanadate, while the second site is more 'open' allowing exchange with the nucleotides in the solvent. In the posthydrolytic state, weak binding, as characterized by chemical exchange with free ADP and by asymmetric 31P-31P two-dimensional (2D) correlation spectra, is observed for both sites. Revisiting the 13C spectra in light of these findings confirms the conformational nonequivalence of the two nucleotide-binding sites in the transition state. Our results show that following ATP binding, the symmetry of the ATP-binding sites of BmrA is lost in the ATP-hydrolysis step, but is then recovered in the posthydrolytic ADP-bound state.

Response-category conflict improves target memory in a flanker paradigm.

Previous studies have shown that cognitive control demands and long-term memory interact in several ways. For example, trial-unique Stroop entities which consist of two perceptually distinct stimulus dimensions can enhance subsequent memory. In the present study, we investigated whether this effect generalises to a flanker paradigm. In the study phase, 60 participants had to classify target pictures which were flanked by pictures that were either congruent or incongruent to the target with regard to the response categories, thus manipulating response-category conflict. Then we assessed recognition memory. The results showed that the response-category conflict enhanced subsequent memory for incongruent targets, implying an up-regulation of top-down control that fostered memory encoding. The results demonstrate that the beneficial memory effect of a response-category conflict generalises to a flanker task.

Fast Magic-Angle-Spinning NMR Reveals the Evasive Hepatitis†B Virus Capsid C-Terminal Domain.

Experimentally determined protein structures often feature missing domains. One example is the C-terminal domain (CTD) of the hepatitis B virus capsid protein, a functionally central part of this assembly, crucial in regulating nucleic-acid interactions, cellular trafficking, nuclear import, particle assembly and maturation. However, its structure remained elusive to all current techniques, including NMR. Here we show that the recently developed proton-detected fast magic-angle-spinning solid-state NMR at >100 kHz MAS allows one to detect this domain and unveil its structural and dynamic behavior. We describe the experimental framework used and compare the domain's behavior in different capsid states. The developed approaches extend solid-state NMR observations to residues characterized by large-amplitude motion on the microsecond timescale, and shall allow one to shed light on other flexible protein domains still lacking their structural and dynamic characterization.

Emerging Structural Understanding of Amyloid Fibrils by Solid-State NMR.

Amyloid structures at atomic resolution have remained elusive mainly because of their extensive polymorphism and because their polymeric properties have hampered structural studies by classical approaches. Progress in sample preparation, as well as solid-state NMR methods, recently enabled the determination of high-resolution 3D structures of fibrils such as the amyloid-ß fibril, which is involved in Alzheimer's disease. Notably, the simultaneous but independent structure determination of Aß1-42, a peptide that forms fibrillar deposits in the brain of Alzheimer patients, by two independent laboratories, which yielded virtually identical results, has highlighted how structures can be obtained that allow further functional investigation.

How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution?

The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments-where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution-seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the "detector" analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion.

Biomolecular solid-state NMR spectroscopy at 1200 MHz: the gain in resolution.

Progress in NMR in general and in biomolecular applications in particular is driven by increasing magnetic-field strengths leading to improved resolution and sensitivity of the NMR spectra. Recently, persistent superconducting magnets at a magnetic field strength (magnetic induction) of 28.2 T corresponding to 1200 MHz proton resonance frequency became commercially available. We present here a collection of high-field NMR spectra of a variety of proteins, including molecular machines, membrane proteins, viral capsids, fibrils and large molecular assemblies. We show this large panel in order to provide an overview over a range of representative systems under study, rather than a single best performing model system. We discuss both carbon-13 and proton-detected experiments, and show that in 13C spectra substantially higher numbers of peaks can be resolved compared to 850 MHz while for 1H spectra the most impressive increase in resolution is observed for aliphatic side-chain resonances.

Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase.

Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg2+ cofactor with Mn2+ or Co2+ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF4 - and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies. 31 P PCSs induced in the Co2+ -containing sample are then used to localize the DNA phosphate groups on the Co2+ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.

Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR.

Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)-Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 kHz after sedimentation, exploiting very fast spinning of the nondeuterated soluble 42 kDa receptor construct to obtain resolved proton-detected 2D and 3D NMR spectra. FcRn plays a crucial role in regulation of IgG and serum albumin catabolism. It is a clinically validated drug target for the treatment of autoimmune diseases caused by pathogenic antibodies via the inhibition of its interaction with IgG. We herein present the discovery of a small molecule that binds into a conserved cavity of the heterodimeric, extracellular domain composed of an α-chain and ß2-microglobulin (ß2m) (FcRnECD, 373 residues). X-ray crystallography was used alongside NMR at 100 kHz MAS with sedimented soluble protein to explore possibilities for refining the compound as an allosteric modulator. Proton-detected MAS NMR experiments on fully protonated [13C,15N]-labeled FcRnECD yielded ligand-induced chemical-shift perturbations (CSPs) for residues in the binding pocket and allosteric changes close to the interface of the two receptor heterodimers present in the asymmetric unit as well as potentially in the albumin interaction site. X-ray structures with and without ligand suggest the need for an optimized ligand to displace the α-chain with respect to ß2m, both of which participate in the FcRnECD-IgG interaction site. Our investigation establishes a method to characterize structurally small molecule binding to nondeuterated large proteins by NMR, even in their glycosylated form, which may prove highly valuable for structure-based drug discovery campaigns.

HPTLC Fingerprint Authentication of Selected Sideritis spp. Using a Pharmacognostic Approach.

The genus Sideritis (Lamiaceae) comprises around 150 species, of which many are popular herbal remedies in Mediterranean folk medicine. Already mentioned by Dioscorides and Theophrastus, the "ironwort" or "Greek mountain tea" has been receiving increased attention in recent years. A European Union herbal monograph and assessment report (HMPC) has been issued, covering the species Sideritis scardica, S. clandestina, S. raeseri, and S. syriaca. This study presents results of a first pharmacognostic examination of the botanical and phytochemical differences among and between these emerging commercial species, and other, less studied species. An HPTLC method is proposed for normal phase separation of the species; this means applying two mobile phases on silica plates and subsequent derivatization with natural product reagent (NP/PEG) for visualization of phenolic compounds and anisaldehyde for a broader detection. With the help of selected reference compounds, a system suitability test was established for proper chromatographic separation. The method was applied to specimens from botanical gardens and commercial raw material in order to test its suitability for differentiation and authentication. The HPTLC analysis also includes, for the first time, S. hyssopifolia and other less used Sideritis species. The results might enable the development of a validated phytochemical fingerprint authentication procedure for quality assurance of Sideritis herba.

Different impact of task switching and response-category conflict on subsequent memory.

The impact of cognitive control demands on long-term memory is mixed, with some conflicts leading to better, others leading to worse subsequent memory. The current study was designed to investigate how different types of cognitive control demands modulate the effects on memory. At study, participants had to switch between two classification tasks and later, free recall performance was assessed. The stimuli consisted of two interleaved words, one word had to be categorized and the other word had to be ignored. In four experiments, the congruency between target and ignored words was manipulated by changing the distractor category. This allowed us to investigate the impact of different types of conflict (i.e., task switching, perceptual load, response-category conflict, stimulus-category conflict). The results revealed that task switching impaired memory in all experiments. In Experiment 1, higher perceptual load also impaired memory. Experiments 2-4 showed that the co-activation of two words which required different responses (i.e., response-category conflict) enhanced memory performance but only when the conflict stimuli were presented in pure blocks. Overall, memory performance seems to depend on attentional policies. Withdrawing attention from target encoding results in lower memory performance. In contrast, focusing attention on the target results in enhanced memory performance.

Collective memory for political leaders in a collaborative government system: Evidence for generation-specific reminiscence effects.

Collective memory is shared by a group and is part of that group's identity. Memory for political leaders is a prototypical case of collective memory. The present study investigated collective memory for Swiss federal councilors in order to test the trajectory of collective memory across four different generations (i.e., Millennials, Generation X, Baby-Boomers, and Silents) in a collaborative government system. In contrast to a presidential system, Switzerland is governed by seven equal councilors who share power and responsibilities. Thus, the individual member of the government is less important, and the number of councilors is larger compared to a presidential system, which may influence collective memory. The results revealed a recency effect as well as a generation-specific reminiscence effect, but no primacy effect as reported for presidential systems. These results indicate that the contribution of semantic memory and autobiographic memory to the trajectory of collective memory vary across government systems. Specifically, for a collaborative government system, autobiographic memory has a stronger contribution to the trajectory of collective memory.

Dimer Organization of Membrane-Associated NS5A of Hepatitis†C Virus as Determined by Highly Sensitive 1 H-Detected Solid-State NMR.

The Hepatitis C virus nonstructural protein 5A (NS5A) is a membrane-associated protein involved in multiple steps of the viral life cycle. Direct-acting antivirals (DAAs) targeting NS5A are a cornerstone of antiviral therapy, but the mode-of-action of these drugs is poorly understood. This is due to the lack of information on the membrane-bound NS5A structure. Herein, we present the structural model of an NS5A AH-linker-D1 protein reconstituted as proteoliposomes. We use highly sensitive proton-detected solid-state NMR methods suitable to study samples generated through synthetic biology approaches. Spectra analyses disclose that both the AH membrane anchor and the linker are highly flexible. Paramagnetic relaxation enhancements (PRE) reveal that the dimer organization in lipids requires a new type of NS5A self-interaction not reflected in previous crystal structures. In conclusion, we provide the first characterization of NS5A AH-linker-D1 in a lipidic environment shedding light onto the mode-of-action of clinically used NS5A inhibitors.