bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of capsaicin derivatives as prohibitin ligands to modulate the Aurora kinase A/PHB2 interaction in cancer cells
Authors: Djehal Amel , Caron Claire , Giordano Deborah , Pizza Valentina , Farin Kimberley , Facchiano Angelo , Désaubry Laurent , Bertolin Giulia 
Published: June 2024

AbstractAurora kinase A/AURKA is a serine/threonine kinase overexpressed in a variety of solid and hematological malignancies. In the last decades, clinical trials aiming to counteract the overexpression of AURKA turned out to be largely unsuccessful. Meanwhile, recent discoveries pointed at new functions of AURKA at the subcellular level, including at mitochondria. At this location, AURKA induces organelle clearance by mitophagy by acting in complex with the mitophagy mediator LC3, and its inner mitochondrial membrane receptor PHB2. The natural polyphenol xanthohumol was shown to act as a PHB2 ligand, altering the interaction between AURKA and PHB2 and restoring mitochondrial functions in cancer cells. However, its chemical nature prevents its broader use as an anti-cancer agent.Using Förster’s Resonance Energy Transfer/Fluorescence Lifetime Imaging Microscopy (FRET/FLIM) in live breast cancer cells, we here explore the effects of alternative PHB ligands in altering the proximity between AURKA and PHB2. Among the already-available compounds, we found that the pungent natural product capsaicin partially alters the AURKA/PHB2 protein-protein proximity. We then synthesized 16 novel capsaicin analogues to enhance the effects of capsaicin. We found that replacing the long hydrophobic acyl moiety by a butyryl one increases the AURKA/PHB2 interaction. Among the capsaicin derivatives carrying this modification, we uncover that compound 12 and 13 enhance the AURKA/PHB2 proximity. Molecular docking approaches corroborate FRET/FLIM data, and we visualize compound 12 and 13 in complex with AURKA, PHB2 and LC3. We show that compound 12 and 13 stabilize the AURKA/PHB2 interaction, and that they can bind to the inhibitory pocket of PHB2 and to the AURKA active site.Together, our data indicate that compound 12 and 13 are promising PHB ligands acting on the AURKA/PHB2 interaction. Through their molecular action on either AURKA or PHB2, they may provide the basis for the development of new anticancer drugs targeting the mitochondrial functions of AURKA.HighlightsThe cancer-related kinase Aurora A/AURKA interacts with the mitochondrial protein PHB2 to induce mitophagy in cancer cells.Among the available PHB ligands, capsaicin mildly lowers the AURKA/PHB2 interaction.Screening of 16 newly-synthesized capsaicin derivatives show differential effects on the AURKA/PHB2 interaction.Compound 12 and 13 stabilize the AURKA/PHB2 interaction.Compound 12 and 13 bind to the AURKA active site and to the PHB2 inhibitory pocket.
Specific presynaptic functions require distinct Drosophila Cav2 splice isoforms
Authors: Bell Christopher , Kilo Lukas , Gottschalk Daniel , Arian Jashar , Deneke Lea , Kern Hanna , Rickert Christof , Kobler Oliver , Strauß Julia , Heine Martin , Duch Carsten , Ryglewski Stefanie 
Published: June 2024

AbstractThe multiplicity of neural circuits that accommodate the sheer infinite number of computations conducted by brains requires diverse synapse and neuron types. At many vertebrate synapses release probability and other aspects of presynaptic function are tuned by different combinations of Cav2.1, Cav2.2, and Cav2.3 channels. By contrast, most invertebrate genomes contain only oneCav2gene. The one Drosophila Cav2 homolog, cacophony (cac), localizes to presynaptic active zones (AZs) to induce synaptic vesicle release. We hypothesize that Drosophila cac functional diversity is enhanced by two specific exon pairs that are mutually exclusively spliced and not conserved in vertebrates, one in the voltage sensor and one in the intracellular loop containing the binding site(s) for Caβand G-protein βγ subunits. We test our hypothesis by combining opto– and electrophysiological with neuroanatomical approaches at a fast glutamatergic model synapse, the Drosophila larval neuromuscular junction. We find that alternative splicing in the voltage sensor affects channel activation voltage and is imperative for normal synapse function. Only the isoform with the higher activation voltage localizes to the presynaptic AZ and mediates evoked release. Removal of these cac splice isoforms renders fast glutamatergic synapses non-functional. By contrast, alternative splicing at the other alternative exon that encodes the intracellular loop between the first and the second homologous repeats does not affect cac presynaptic AZ localization, but it tunes multiple aspects of presynaptic function. While expression of one exon yields normal transmission, expression of the other exon reduces channel number in the AZ and thus release probability. This also abolishes presynaptic homeostatic plasticity. Moreover, reduced channel number upon selective exon excision increases paired pulse ratios and the variability of synaptic depression during low frequency stimulation trains (1 and 10 Hz), and thus affects short term plasticity. Effects on short term plasticity can be rescued by increasing the external calcium concentration to match release probability to control. In sum, in Drosophila alternative splicing provides a mechanism to regulate different aspects of presynaptic functions with only oneCav2gene.
Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy
Authors: Ardiansyah Edwin , Riza Anca-Lelia , Dian Sofiati , Ganiem Ahmad Rizal , Alisjahbana Bachti , Setiabudiawan Todia P , Laarhoven Arjan van , Crevel Reinout van , Kumar Vinod 
Published: June 2024

SummaryExisting genotype imputation reference panels are mainly derived from European populations, limiting their accuracy in non-European populations. To improve imputation accuracy for Indonesians, the world’s fourth most populous country, we combined Whole Genome Sequencing (WGS) data from 227 West Javanese individuals with East Asian data from the 1000 Genomes Project. This created three reference panels: EAS 1KGP3 (EASp), Indonesian (INDp), and a combined panel (EASp+INDp). We also used ten West-Javanese samples with WGS and SNP-typing data for benchmarking. We identified 1.8 million novel single nucleotide variants (SNVs) in the West Javanese population, which, while similar to the East Asians, are distinct from the Central Indonesian Flores population. Adding INDp to the EASp reference panel improved imputation accuracy (R2) from 0.85 to 0.90, and concordance from 87.88% to 91.13%. These findings underscore the importance of including Indonesian genetic data in reference panels, advocating for broader WGS of diverse Indonesian populations to enhance genomic studies.
Temporal Structure of Music Improves the Cortical Encoding of Speech
Authors: Fernández-Merino Laura , Lizarazu Mikel , Molinaro Nicola , Kalashnikova Marina 
Published: June 2024

AbstractLong and short-term musical training has been proposed to improve efficiency of cortical tracking of speech, the mechanism through which brain oscillations synchronize to the acoustic temporal structure of external stimuli. Here, we study how different rhythm structures of the musical signal can guide the temporal dynamics of auditory oscillations phase-aligned to the speech envelope. For this purpose, we investigated the effects of prior exposure to rhythmically structured musical sequences on cortical tracking of speech in Basque-Spanish bilingual adults. We conducted two EEG experiments where participants were presented with sentences in Basque and Spanish preceded by musical sequences that differed in their beat structure. The beat structure of the musical sequences was created to 1) reflect and match the syllabic structure of the sentences, 2) reflect a regular rhythm but not match the syllabic structure of the sentences, and 3) follow an irregular rhythm. First, we showed that the regularity found in the rhythmic structure of music acts as a temporal guide for brain oscillations. Second, our findings suggest that not only the regularity in music is crucial but so is adjusting this regularity to optimally reflect the rhythmic characteristics of the language. Third, despite finding some differences across frequencies for each language, we still found a strong effect of rhythm regularity on cortical tracking of speech. We showed that rhythm, inherent in musical signals, guides the adaptation of brain oscillations, by adapting the temporal dynamics of the oscillatory activity to the rhythmic scaffolding of the musical signal.
AIVE: accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis
Authors: Park Jongkeun , Choi Won Jong , Seong Do Young , Jeong Seung Pil , Lee Ju Young , Park Hyo Jeong , Chung Dae Sun , Yi Ki Jong , Kim Uijin , Yoon Ga-Yeon , Kim Hyeran , Kim Taehoon , Go Sooyeon , Min Eun Jeong , Cho Hyun-Soo , Cho Nam-Hyuk , Hong Dongwan 
Published: June 2024

AbstractAn unprecedented amount of SARS-CoV-2 data has been accumulated compared with previous infectious diseases, enabling insights into its evolutionary process and more thorough analyses. This study investigates SARS-CoV-2 features as it evolved to evaluate its infectivity. We examined viral sequences and identified the polarity of amino acids in the Receptor Binding Motif (RBM) region. We detected an increased frequency of amino acid substitutions to lysine (K) and arginine (R) in Variants of Concern (VOCs). As the virus evolved to Omicron, commonly occurring mutations became fixed components of the new viral sequence. Furthermore, at specific positions of VOCs, only one type of amino acid substitution and a notable absence of mutations at D467 was detected. We found that the binding affinity of SARS-CoV-2 lineages to the ACE2 receptor was impacted by amino acid substitutions. Based on our discoveries, we developed APESS, an evaluation model evaluating infectivity from biochemical and mutational properties. In silico evaluation using real-world sequences and in vitro viral entry assays validated the accuracy of APESS and our discoveries. Using Machine Learning, we predicted mutations that had the potential to become more prominent. We created AIVE, a web-based system, accessible athttps://ai-ve.orgto provide infectivity measurements of mutations entered by users. Ultimately, we established a clear link between specific viral properties and increased infectivity, enhancing our understanding of SARS-CoV-2 and enabling more accurate predictions of the virus.
Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome
Authors: Klein Marius , Wild Klemens , Sinning Irmgard 
Published: June 2024

AbstractMost nascent chains undergo rapid co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine excision (NME) by Methionine Aminopeptidases (MAP1 and MAP2), and N-terminal acetylation (NTA) by N-Acetyl-Transferase A (NatA), is the most common set of subsequent modifications carried out on the ribosome. How these two enzymatic processes are coordinated in quick succession in the context of a rapidly translating ribosome has remained elusive.Here, we report that human NatA occupies a non-intrusive ‘distal’ binding site on the ribosome which does not interfere with most other ribosome associated factors (RAFs). In this position, NatA can partake in a coordinated and dynamic assembly with MAP1 through a complex scaffolding function of the abundant Nascent Polypeptide Associated Complex (NAC). Alternatively, MAP2 can co-occupy the PTE with NatA in preparation for successive NME and NTA. In contrast to MAP1, MAP2 completely covers the PTE and is thus incompatible with NAC and MAP1 recruitment. Both assemblies can compile on the human ribosome independent of nascent chain substrates. Together, our structures provide the structural framework for the rapid coordinated orchestration of NME and NTA in protein biogenesis.
Structural studies of KCTD1 and its disease-causing mutant P20S provide insights into the protein function and misfunction
Authors: Balasco Nicole , Ruggiero Alessia , Smaldone Giovanni , Pecoraro Giovanni , Coppola Luigi , Pirone Luciano , Pedone Emilia M. , Esposito Luciana , Berisio Rita , Vitagliano Luigi 
Published: June 2024

AbstractMembers of the KCTD protein family play key roles in fundamental physio-pathological processes. A plethora of literature studies have demonstrated their involvement in cancer, neurodevelopmental disorders, and genetic diseases. Despite two decades of intense investigations, the definition of structure-(mis)function relationships for these proteins is still rather limited. Here, we derived atomic-level structural data on KCTD1, by determining the crystal structure of its P20S mutant, which causes the scalp-ear-nipple syndrome, and performing molecular dynamics simulations. In addition to the expected folded domains (BTB and CTD) the crystal structure unravels that also the N-terminal region that precedes the BTB domain (preBTB) adopts a folded polyproline II (PPII) state. The global structure of the KCTD1 pentamer is characterized by an intricate architecture in which the different subunits mutually exchange domains to generate a closed domain swapping motif. In this framework, the BTB domain of each chain makes peculiar contact with the preBTB and the CTD regions of an adjacent chain. Indeed, the BTB-preBTB interaction is made of a PPII-PPII recognition motif whereas the BTB-CTD contacts are mediated by an unusual (+/-) helix discontinuous association. The inspection of the protein structure, along with the data that emerged from the MD data, provides a clear explanation of the pathogenicity of the SENS mutation P20S and unravels the role of the BTB-preBTB interaction in the insurgence of the disease. Finally, the presence of potassium bound to the central cavity of the CTD pentameric assembly provides insights into the role of the protein in metal homeostasis.
Lineage tracing ofShh+floor plate cells and dynamics of dorsal-ventral gene expression in the regenerating axolotl spinal cord
Authors: Arbanas Laura I. , Costa Emanuel Cura , Chara Osvaldo , Otsuki Leo , Tanaka Elly M. 
Published: June 2024

AbstractBoth development and regeneration depend on signalling centres, which are sources of locally secreted tissue-patterning molecules. As many signalling centres are decommissioned before the end of embryogenesis, a fundamental question is how signalling centres can be re-induced later in life to promote regeneration after injury. Here, we use the axolotl salamander model (Ambystoma mexicanum) to address how the floor plate is assembled for spinal cord regeneration. The floor plate is an archetypal vertebrate signalling centre that secretesShhligand and patterns neural progenitor cells during embryogenesis. Unlike mammals, axolotls continue to express floor plate genes (includingShh) and downstream dorsal-ventral patterning genes in their spinal cord throughout life, including at steady state. The parsimonious hypothesis thatShh+ cells give rise to functional floor plate cells for regeneration had not been tested. Using HCRin situhybridisation and mathematical modelling, we first quantitated the behaviours of dorsal-ventral spinal cord domains, identifying significant increases in gene expression level and floor plate size during regeneration. Next, we established a transgenic axolotl to specifically label and fate mapShh+ cellsin vivo. We found that labelledShh+cells gave rise to regeneration floor plate, and not to other neural progenitor domains, after tail amputation. Thus, despite changes in domain size and downstream patterning gene expression,Shh+ cells retain their floor plate identity during regeneration, acting as a stable cellular source for this regeneration signalling centre in the axolotl spinal cord.
Interactions with multiple inner kinetochore proteins determine mitotic localization of FACT
Authors: Schweighofer Julia , Mulay Bhagyashree , Hoffmann Ingrid , Vogt Doro , Pesenti Marion E. , Musacchio Andrea 
Published: June 2024

AbstractThe FAcilitates Chromatin Transcription (FACT) complex is a dimeric histone chaperone that operates on chromatin during transcription and replication. FACT also interacts with a specialized centromeric nucleosome containing the histone H3 variant CENP-A and with CENP-TW, two subunits of CCAN, a 16-protein complex associated with CENP-A. The significance of these interactions remains elusive. Here, we show that FACT has multiple additional binding sites on CCAN. The interaction with CCAN is strongly stimulated by casein kinase II (CK2) phosphorylation of FACT. Mitotic localization of FACT to kinetochores is strictly dependent on specific CCAN subcomplexes. Unexpectedly, we also find that DNA readily displaces FACT from CCAN, suggesting that FACT becomes recruited through a pool of CCAN that is not stably integrated into chromatin. Collectively, our results point to a potential role of FACT in chaperoning CCAN during transcription or in the stabilization of CCAN at the centromere during the cell cycle.TeaserDNA-sensitive, direct interactions with multiple inner kinetochore subunits deliver FACT to the kinetochore.
Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding
Authors: Esfahani Behrouz Ghazi , Walia Nidhi , Neselu Kasahun , Garg Yashika , Aragon Mahira , Askenasy Isabel , Wei Hui Alex , Mendez Joshua H. , Stroupe M. Elizabeth 
Published: June 2024

AbstractEscherichia coliNADPH-dependent assimilatory sulfite reductase (SiR) reduces sulfite by six electrons to make sulfide for incorporation into sulfur-containing biomolecules. SiR has two subunits: an NADPH, FMN, and FAD-binding diflavin flavoprotein and a siroheme/Fe4S4cluster-containing hemoprotein. The molecular interactions that govern subunit binding have been unknown since the discovery of SiR over 50 years ago because SiR is flexible, thus has been intransigent for traditional high-resolution structural analysis. We used a combination of the chameleon® plunging system with a fluorinated lipid to overcome the challenges of preserving a flexible molecule to determine a 2.78 Å-resolution cryo-EM structure of a minimal heterodimer complex. chameleon®, combined with the fluorinated lipid, overcame persistent denaturation at the air-water interface. Using a previously characterized minimal heterodimer reduced the heterogeneity of a structurally heterogeneous complex to a level that could be analyzed using multi-conformer cryo-EM image analysis algorithms. Here, we report the first near-atomic resolution structure of the flavoprotein/hemoprotein complex, revealing how they interact in a minimal interface. Further, we determined the structural elements that discriminate between pairing a hemoprotein with a diflavin reductase, as in theE. colihomolog, or a ferredoxin partner, as in maize (Zea mays).Significance StatementSulfur is one of the essential building blocks of life. Sulfur exists in numerous redox states but only one can be incorporated into biomass – S2-(sulfide). InEscherichia coli, a protein enzyme called sulfite reductase reduces sulfite by six electrons to make sulfide. Typical electron transfer reactions move one or two electrons at a time. The sequential transfer of two electrons three times to complete the conversion of sulfite to sulfide (or nitrite to ammonia) is unique to sulfite or nitrite reductases.E. coliSiR is a two-protein complex composed of a diflavin reductase flavoprotein and an iron metalloenzyme hemoprotein. Until now, the molecular interactions that govern subunit interactions remained a mystery because the extreme flexibility of the flavoprotein subunit, which has challenged X-ray or cryo-EM analysis for over 30 years. In overcoming these challenges, we used a combination of rapid plunging with a high critical-micelle-concentration lipid alongside a biochemically minimized complex to determine the 2.78 Å-resolution cryo-EM structure of a dimer between the flavoprotein and hemoprotein subunits.
δ-containing GABAAreceptors on parvalbumin interneurons modulate neuronal excitability and network dynamics in the mouse medial prefrontal cortex
Authors: Lu Xinguo , Shu Hong-Jin , Lambert Peter M. , Benz Ann , Zorumski Charles F. , Mennerick Steven 
Published: June 2024

AbstractIn medial prefrontal cortex (mPFC), fast-spiking parvalbumin (PV) interneurons regulate excitability and microcircuit oscillatory activity important for cognition. Although PV interneurons inhibit pyramidal neurons, they themselves express δ subunits of GABAA receptors important for slow inhibition. However, the specific contribution of δ-containing GABAA receptors to the function of PV interneurons in mPFC is unclear. We explored cellular, synaptic, and local-circuit activity in PV interneurons and pyramidal neurons in mouse mPFC after selectively deleting δ subunits in PV interneurons (cKO mice). In current-clamp recordings, cKO PV interneurons exhibited a higher frequency of action potentials and higher input resistance than wild type (WT) PV interneurons. Picrotoxin increased firing and GABA decreased firing in WT PV interneurons but not in cKO PV interneurons. The δ-preferring agonist THIP reduced spontaneous inhibitory postsynaptic currents in WT pyramidal neurons but not in cKO pyramidal neurons. In WT slices, depolarizing the network with 400 nM kainate increased firing of pyramidal neurons but had little effect on PV interneuron firing. By contrast, in cKO slices kainate recruited PV interneurons at the expense of pyramidal neurons. At the population level, kainate induced broadband increases in local field potentials in WT but not cKO slices. These results on cells and the network can be understood through increased excitability of cKO PV interneurons. In summary, our study demonstrates that δ-containing GABAA receptors in mPFC PV interneurons play a crucial role in regulating their excitability and the phasic inhibition of pyramidal neurons, elucidating intricate mechanisms governing cortical circuitry.Significance statementBy selectively deleting δ-containing GABAA receptors in PV interneurons, we demonstrate the importance of these receptors on PV interneuron excitability, synaptic inhibition of pyramidal neurons, and circuit function.