Structural basis of RNA processing by human mitochondrial RNase P.

Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing.

Extension and improvement of the methanol-d NMR thermometer calibration.

NMR thermometers are a convenient way to determine the temperature inside the sample of an NMR spectrometer. They rely on signals with strongly temperature-dependent chemical shifts, often of OH groups; 99.8% perdeuterated methanol is an established example which is particularly well suited for modern, high-sensitivity spectrometers, but it is so far calibrated only in the range of 282 to 330 K.

Thermodynamic Uncertainty Relation Bounds the Extent of Anomalous Diffusion.

In a finite system driven out of equilibrium by a constant external force the thermodynamic uncertainty relation (TUR) bounds the variance of the conjugate current variable by the thermodynamic cost of maintaining the nonequilibrium stationary state. Here we highlight a new facet of the TUR by showing that it also bounds the timescale on which a finite system can exhibit anomalous kinetics. In particular, we demonstrate that the TUR bounds subdiffusion in a single file confined to a ring as well as a dragged Gaussian polymer chain even when detailed balance is satisfied.

Pore-Bound Water at the Key Residue Histidine 37 in Influenza A M2.

Atomic details of structured water molecules are indispensable to understand the thermodynamics of important biological processes including the proton conduction mechanism of the M2 protein. Despite the expectation of structured water molecules based on crystal structures of Influenza A M2, only two water populations have been observed by NMR in reconstituted lipid bilayer samples. These are the bulk- and lipid-associated water populations typically seen in membrane samples.

NMR hawk-eyed view of AlphaFold2 structures.

The prediction of the three-dimensional (3D) structure of proteins from the amino acid sequence made a stunning breakthrough reaching atomic accuracy. Using the neural network-based method AlphaFold2, 3D structures of almost the entire human proteome have been predicted and made available (https://www.alphafold.

H, C and N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2.

The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7-33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses.

Time-Lagged Independent Component Analysis of Random Walks and Protein Dynamics.

Time-lagged independent component analysis (tICA) is a widely used dimension reduction method for the analysis of molecular dynamics (MD) trajectories and has proven particularly useful for the construction of protein dynamics Markov models. It identifies those "slow" collective degrees of freedom onto which the projections of a given trajectory show maximal autocorrelation for a given lag time. Here we ask how much information on the actual protein dynamics and, in particular, the free energy landscape that governs these dynamics the tICA-projections of MD-trajectories contain, as opposed to noise due to the inherently stochastic nature of each trajectory.

ZC3HC1 Is a Novel Inherent Component of the Nuclear Basket, Resident in a State of Reciprocal Dependence with TPR.

The nuclear basket (NB) scaffold, a fibrillar structure anchored to the nuclear pore complex (NPC), is regarded as constructed of polypeptides of the coiled-coil dominated protein TPR to which other proteins can bind without contributing to the NB's structural integrity. Here we report vertebrate protein ZC3HC1 as a novel inherent constituent of the NB, common at the nuclear envelopes (NE) of proliferating and non-dividing, terminally differentiated cells of different morphogenetic origin. Formerly described as a protein of other functions, we instead present the NB component ZC3HC1 as a protein required for enabling distinct amounts of TPR to occur NB-appended, with such ZC3HC1-dependency applying to about half the total amount of TPR at the NEs of different somatic cell types.

Structure and Absolute Configuration of Phenanthro-perylene Quinone Pigments from the Deep-Sea Crinoid .

Two new water-soluble phenanthroperylene quinones, gymnochrome H () and monosulfated gymnochrome A (), as well as the known compounds gymnochrome A () and monosulfated gymnochrome D () were isolated from the deep-sea crinoid , which had been collected in the deep sea of Japan. The structures of the compounds were elucidated by spectroscopic analysis including HRMS, 1D H and C NMR, and 2D NMR. The absolute configuration was determined by ECD spectroscopy, analysis of -couplings and ROE contacts, and DFT calculations.

Fusion pores with low conductance are cation selective.

Many neurotransmitters are organic ions that carry a net charge, and their release from secretory vesicles is therefore an electrodiffusion process. The selectivity of early exocytotic fusion pores is investigated by combining electrodiffusion theory, measurements of amperometric foot signals from chromaffin cells with anion substitution, and molecular dynamics simulation. The results reveal that very narrow fusion pores are cation selective, but more dilated fusion pores become anion permeable.

The structure of a dimeric form of SARS-CoV-2 polymerase.

The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) to replicate and transcribe its genome. Previous structures of the RdRp revealed a monomeric enzyme composed of the catalytic subunit nsp12, two copies of subunit nsp8, and one copy of subunit nsp7. Here we report an alternative, dimeric form of the enzyme and resolve its structure at 5.

The Barrier for CO Functionalization to Formate on Hydrogenated Pt.

Understanding heterogeneous catalysis is based on knowing the energetic stability of adsorbed reactants, intermediates, and products as well as the energetic barriers separating them. We report an experimental determination of the barrier to CO functionalization to form bidentate formate on a hydrogenated Pt surface and the corresponding reaction energy. This determination was possible using velocity resolved kinetics, which simultaneously provides information about both the dynamics and rates of surface chemical reactions.

Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

Group-aggregated responses to tuberculosis (TB) have been well characterized on a molecular level. However, human beings differ and individual responses to infection vary. We have combined a novel approach to individual gene set analysis (GSA) with the clustering of transcriptomic profiles of TB patients from seven datasets in order to identify individual molecular endotypes of transcriptomic responses to TB.

Antidepressant-Like Effects of Chronic Guanosine in the Olfactory Bulbectomy Mouse Model.

Major depressive disorder (MDD) leads to pervasive changes in the health of afflicted patients. Despite advances in the understanding of MDD and its treatment, profound innovation is needed to develop fast-onset antidepressants with higher effectiveness. When acutely administered, the endogenous nucleoside guanosine (GUO) shows fast-onset antidepressant-like effects in several mouse models, including the olfactory bulbectomy (OBX) rodent model.

Inside a Shell-Organometallic Catalysis Inside Encapsulin Nanoreactors.

Compartmentalization of chemical reactions inside cells are a fundamental requirement for life. Encapsulins are self-assembling protein-based nanocompartments from the prokaryotic repertoire that present a highly attractive platform for intracellular compartmentalization of chemical reactions by design. Using single-molecule Förster resonance energy transfer and 3D-MINFLUX analysis, we analyze fluorescently labeled encapsulins on a single-molecule basis.

En route to dynamic life processes by SNARE-mediated fusion of polymer and hybrid membranes.

A variety of artificial cells springs from the functionalization of liposomes with proteins. However, these models suffer from low durability without repair and replenishment mechanisms, which can be partly addressed by replacing the lipids with polymers. Yet natural membranes are also dynamically remodeled in multiple cellular processes.

Pre-mRNA Processing Factors and Retinitis Pigmentosa: RNA Splicing and Beyond.

Retinitis pigmentosa (RP) is the most common inherited retinal disease characterized by progressive degeneration of photoreceptors and/or retinal pigment epithelium that eventually results in blindness. Mutations in pre-mRNA processing factors () have been linked to 15-20% of autosomal dominant RP (adRP) cases. Current evidence indicates that mutations cause retinal specific global spliceosome dysregulation, leading to mis-splicing of numerous genes that are involved in a variety of retina-specific functions and/or general biological processes, including phototransduction, retinol metabolism, photoreceptor disk morphogenesis, retinal cell polarity, ciliogenesis, cytoskeleton and tight junction organization, waste disposal, inflammation, and apoptosis.

Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis.

Molnupiravir is an orally available antiviral drug candidate currently in phase III trials for the treatment of patients with COVID-19. Molnupiravir increases the frequency of viral RNA mutations and impairs SARS-CoV-2 replication in animal models and in humans. Here, we establish the molecular mechanisms underlying molnupiravir-induced RNA mutagenesis by the viral RNA-dependent RNA polymerase (RdRp).

Early Divergence in Misfolding Pathways of Amyloid-Beta Peptides.

The amyloid cascade hypothesis proposes that amyloid-beta (Aβ) aggregation is the initial triggering event in Alzheimer's disease. Here, we utilize NMR spectroscopy and monitor the structural dynamics of two variants of Aβ, Aβ40 and Aβ42, as a function of temperature. Despite having identical amino acid sequence except for the two additional C-terminal residues, Aβ42 has higher aggregation propensity than Aβ40.

RIM-Binding Protein 2 Organizes Ca Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.

Rab-interacting molecule (RIM)-binding protein 2 (BP2) is a multidomain protein of the presynaptic active zone (AZ). By binding to RIM, bassoon (Bsn), and voltage-gated Ca channels (Ca), it is considered to be a central organizer of the topography of Ca and release sites of synaptic vesicles (SVs) at the AZ. Here, we used RIM-BP2 knock-out (KO) mice and their wild-type (WT) littermates of either sex to investigate the role of RIM-BP2 at the endbulb of Held synapse of auditory nerve fibers (ANFs) with bushy cells (BCs) of the cochlear nucleus, a fast relay of the auditory pathway with high release probability.

Non-structural protein 5 (NS5) as a target for antiviral development against established and emergent flaviviruses.

Flaviviruses are among the most critical pathogens in tropical regions and cause a growing number of severe diseases in developing countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Among the ten proteins encoded in the flavivirus RNA, non-structural protein 5, NS5, is a promising drug target.

Microbial production and recovery of hybrid biopolymers from wastes for industrial applications- a review.

Agro-industrial wastes to be a global concern since agriculture and industrial processes are growing exponentially with the fast increase of the world population. Biopolymers are complex molecules produced by living organisms, but also found in many wastes or derived from wastes. The main drawbacks for the use of polymers are the high costs of the polymer purification processes from waste and the scale-up in the case of biopolymer production by microorganisms.