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Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50-deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function., Introduction Neurodevelopmental disorders (NDDs) are a heterogeneous group of neurological and related neuropsychiatric conditions including intellectual disability (ID), autism spectrum disorder (ASD), and developmental and epileptic encephalopathies that manifest during [...]

Cell lineage plasticity is one of the major causes for the failure of targeted therapies in various cancers. However, the driver and actionable drug targets in promoting cancer cell lineage plasticity are scarcely identified. Here, we found that a G protein-coupled receptor, ADORA2A, is specifically upregulated during neuroendocrine differentiation, a common form of lineage plasticity in prostate cancer and lung cancer following targeted therapies. Activation of the ADORA2A signaling rewires the proline metabolism via an ERK/MYC/PYCR cascade. Increased proline synthesis promotes deacetylases SIRT6/7-mediated deacetylation of histone H3 at lysine 27 (H3K27), and thereby biases a global transcriptional output toward a neuroendocrine lineage profile. Ablation of Adora2a in genetically engineered mouse models inhibits the development and progression of neuroendocrine prostate and lung cancers, and, intriguingly, prevents the adenocarcinoma-to-neuroendocrine phenotypic transition. Importantly, pharmacological blockade of ADORA2A profoundly represses neuroendocrine prostate and lung cancer growth in vivo. Therefore, we believe that ADORA2A can be used as a promising therapeutic target to govern the epigenetic reprogramming in neuroendocrine malignancies., Introduction Lineage plasticity is often exploited by cancer cells to acquire therapeutic resistance (1). Lineage transition from adenocarcinoma (AD) to aggressive neuroendocrine (NE) derivatives is a common type of cancer [...]

In the present investigation, a QM/MM approach was used to better understand the effect of the second environmental shell of the active site on the catalytic conversion of acetylene to acetaldehyde by acetylene hydratase (AH). In addition, the effect of substituting W-coordinating sulfur atoms with selenium atoms was done to provide insight into the influence of the W-coordinating atoms on the catalytic reaction. From the results, it found that the presence of the second shell environment had a significant effect on the reaction. Specifically, in the absence of the MM second shell environment (i.e., QM-cluster model), the rate-determining step is defined by the first proton transfer step. In contrast, for the QM/MM model, the rate-determining step is defined by the water attacking step. Moreover, with the presence of the MM second shell environment, a key intermediate found in the DFT-cluster investigation does not exist in the QM/MM investigation. Rather, what was a two-step process in the DFT-cluster study was calculated to occur in a single step for the QM/MM study. Regarding the sulfur to selenium substitutions, it was found that Gibbs energy for the acetylene binding phase was significantly affected. Notably, the trans-position selenium made the binding of acetylene 65.6 kJ [mol.sup.-1] less endergonic. Moreover, the overall reaction became 38.2 kJ [mol.sup.-1] less endergonic compared with the wild type (WT) AH model. Thus, the substitution of key W-coordinating sulfur atoms with selenium atoms may offer a means to enhance the catalytic mechanism of AH considerably. Key words: acetylene hydratase, dithiolene, diselenolene, density functional theory, QM/MM. Dans le cadre de la presente etude, nous avons utilise une methode de mecanique quantique et de mecanique moleculaire (QM/MM) afin de mieux comprendre l'effet de la seconde couche dans l'environnement du site actif de l'acetylène hydratase (AH) sur la transformation catalytique de l'acetylène en acetaldehyde. De plus, nous avons substitue les atomes de soufre coordonnant l'atome de W par des atomes de selenium afin d'expliquer l'influence des atomes coordonnant le W sur la reaction catalytique. D'après les resultats, la presence de la deuxième couche de l'environnement a un effet considerable sur la reaction. En effet, en absence de la deuxième couche MM de l'environnement (c.-a-d. le modèle QM de l'agregat), l'etape limitante de la reaction est celle du transfert du premier proton. Par contre, avec le modèle QM/MM, l'etape limitante de la reaction est celle de l'attaque par la molecule d'eau. De plus, en presence de la deuxième couche MM de l'environnement, nous avons trouve dans la modelisation de l'agregat par DFT un intermediaire cle qui n'existe pas dans la modelisation par QM/MM. Ce qui etait un processus en deux etapes dans la modelisation de l'agregat par DFT a plutot ete calcule comme se produisant en une seule etape dans la modelisation par QM/MM. En ce qui concerne la substitution des atomes de soufre par des atomes de selenium, nous avons constate qu'elle avait un effet considerable sur l'energie de Gibbs de la phase de liaison de l'acetylène. Notons par ailleurs que la configuration trans des atomes de selenium rendait la liaison de l'acetylène moins endergonique de 65,6 kJ*[mol.sup.1]. De plus, la reaction globale s'est revelee 38,2 kJ*[mol.sup.1] moins endergonique comparativement au modèle de l'AH de type sauvage. Par consequent, la substitution d'atomes de soufre determinants qui coordonnent l'atome de W par des atomes de selenium pourrait se reveler un moyen d'ameliorer considerablement le mecanisme catalytique de l'AH. [Traduit par la Redaction] Mots-cles : acetylène hydratase, dithiolène, diselenolène, theorie de la fonctionnelle de la densite, QM/MM., Introduction Due to the dithiolene ligand's ability to form stable complexes with various highly oxidized metals and the unique optical, electrical, and magnetic properties of the metal complexes formed, the [...]

Author(s): Chen Fan [sup.1] , Nattakan Sukomon [sup.1] , Emelie Flood [sup.2] , Jan Rheinberger [sup.1] [sup.4] , Toby W. Allen [sup.2] , Crina M. Nimigean [sup.1] [sup.3] Author Affiliations: [...], Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present.sup.1. In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency.sup.1,2. A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a 'ball-and-chain' mechanism.sup.3-7. Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum--a purely calcium-gated and inactivating channel--in a lipid environment. In the absence of Ca.sup.2+, we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca.sup.2+-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism. Cryo-electron microscopy structures and molecular dynamics simulations of the calcium-activated potassium channel MthK from Methanobacterium thermoautotrophicum are used to show that gating of this channel involves a ball-and-chain inactivation mechanism mediated by a previously unresolved N-terminal peptide.

Background: Castrodia elata Blume (G. elata) is a traditional Chinese herb used for centuries in folk medicine. Due to the claimed anticonvulsant properties of C. elata, it is expected that [...]

Low-barrier molecular rotary motors having rotaxane architecture are constructed by using a cucurbituril host and a polyyne guest serving as stator and rotator. The repulsive interaction between there components is analyzed by using molecular mechanics calculations and is verified by X-ray crystallography with many synthetic host-guest complexes.

The underlying effects of the inhibition of cysteine proteases are examined by using classical molecular dynamic simulations and combined quantum mechanics/molecular modeling (QM/MM) calculations for the E64c-cathepsin B complex. The results provide insight into the hydrogen bonding network between the enzyme and the E64c, which influenced the stereoselectivity of the subsequent ring opening reaction by governing the distance between the attacking thiolate and the attacked C2 atom of the epoxide ring.

The structural data for the wild type hepatitis delta virus (HDV) genomic ribozyme was used to explain combined quantum chemical/molecular mechanical calculations for the C75 general base pathway. The calculations showed that C75 is capable to act as the general base in combination with the hydrated magnesium ion as the general acid.

The broadband dielectric relaxation spectroscopy (DRS) covering a temperature range of more than 200 K was used to study the molecular mobility of amorphous ibuprofen. The results confirmed the strong tendency of ibuprofen to form hydrogen bonded aggregates, such as dimers and trimers either cyclic or linear that are controlled by the molecular mobility of ibuprofen.

The structure and dynamics of a supramolecular polymer formed by a bisurea-type compound in an apolar solvent, n-dodecane ([C.sub.12]), are examined. A structural model based on molecular mechanics and dynamics simulations is described for the supramolecular polymer formed in 2,4-bis(2-ethylhexylureido)d(EHUT)/[C.sub.12].

Probability distribution analysis (PDA) is used for quantitatively analyzing single-molecule (SM) data obtained in Forster resonance energy transfer (FRET) or fluorescent polarization experiments. Tools such as maximum entropy method (MEM) and combined mean donor fluorescence lifetime analysis are developed to distinguish whether extra broadening of PDA histograms is attributed to structural heterogeneities or dye artifacts.

The studies on the molecular mechanism observed in double-network (DN) hydrogels obtained from poly(2-acrlamido-2-methyl-1-propanesulfonic acid) (PAMPS) polyelectrolyte network and poly(acrylamide) (PAAm) linear polymer are reported. The mechanism provides insight into the periodic compositional fluctuations in the micrometer range induced by large strain deformation.

A coarse-grained molecular simulation study is employed to study the molecular mechanisms involved in the interactions of the lipid bilayers with supports. The behavior of the bilayer system is shown to completely change on being supported by the hydrophilic surface.

The Nature Insight 'Frontiers in Biology' aims to cover timely and important developments across biology, ranging from subcellular molecular mechanisms to whole-organism physiology, and biomedicine. The Insight begins with a [...]