A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2.

The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein-Barr virus, present a significant burden to global public health. Their envelopes contain at least ten different glycoproteins, which are necessary for host cell tropism, attachment and entry. The best conserved among them, glycoprotein B (gB), is essential as it performs membrane fusion by undergoing extensive rearrangements from a prefusion to postfusion conformation.

Structural Heterogeneity of Proteoform-Ligand Complexes in Adenosine Monophosphate-Activated Protein Kinase Uncovered by Integrated Top-Down Mass Spectrometry.

Adenosine monophosphate-activated protein kinase (AMPK) is a heterotrimeric complex (αβγ) that serves as a master regulator of cellular metabolism, making it a prominent drug target for various diseases. Post-translational modifications (PTMs) and ligand binding significantly affect the activity and function of AMPK. However, the dynamic interplay of PTMs, noncovalent interactions, and higher-order structures of the kinase complex remains poorly understood.

From Science to Fiction - Connecting In Vivo and In Vitro Results in Polyprotein Processing of Coronaviruses.

Polyprotein processing is a common strategy in many positive sense single-stranded RNA ((+)ssRNA) viruses. This highly regulated process is crucial for viral progeny and ensures the release of functional replicase proteins in the correct location and at the right time. Coronaviruses (CoVs) have one of the largest genomes on average among (+)ssRNA viruses requiring a unique replication-transcription complex (RTC) with proofreading function that prevents error catastrophe.

A bottom-up approach to find lead compounds in expansive chemical spaces.

Drug discovery starts with the identification of a "hit" compound that, following a long and expensive optimization process, evolves into a drug candidate. Bigger screening collections increase the odds of finding more and better hits. For this reason, large pharmaceutical companies have invested heavily in high-throughput screening (HTS) collections that can contain several million compounds.

Identification of the human cytomegalovirus gHgLgO trimer as the central player in virion infectivity.

Glycoproteins in the viral envelope of human cytomegalovirus (HCMV) orchestrate virion tethering, receptor recognition and fusion with cellular membranes. The glycoprotein gB acts as fusion protein. The gHgL complexes gHgLgO and gHgLpUL(128,130,131A) define the HCMV cell tropism.

Structure-based discovery of thiamine uptake inhibitors.

Background And Purpose: Thiamine (vitamin B) is an essential coenzyme and catalyses various reactions in central metabolic pathways. Since mammals have lost the ability to synthesise thiamine de novo, this micronutrient has to be imported via the high affinity solute carriers SLC19A2 and A3 across the plasma membrane. Perturbations of these transport systems have severe effects on human health.

Model-free photon analysis of diffusion-based single-molecule FRET experiments.

Photon-by-photon analysis tools for diffusion-based single-molecule Förster resonance energy transfer (smFRET) experiments often describe protein dynamics with Markov models. However, FRET efficiencies are only projections of the conformational space such that the measured dynamics can appear non-Markovian. Model-free methods to quantify FRET efficiency fluctuations would be desirable in this case.

From Membrane Composition to Antimicrobial Strategies: Experimental and Computational Approaches to AMP Design and Selectivity.

The United Nations have committed to end the epidemics of communicable diseases by 2030 (SDG Target 3.3). In contrast with this ambition, the rise of Multi Drug Resistant (MDR) and Pan Drug Resistant (PDR) bacteria poses a threat of a return to the pre-antibiotic era.

Kaposi's sarcoma-associated herpesvirus ORF61 protein sequesters APOBEC3B in filamentous aggregates.

Herpesviruses are large DNA viruses that encode homologs of cellular enzymes. The viral ribonucleotide reductase, which consists of large R1 and small R2 subunits, is required for deoxyribonucleotide synthesis. However, herpesviruses have repurposed the R1 subunit for additional non-canonical functions in virus-host interaction and immune evasion.

Structural stability of chromophore-grafted Ubiquitin mutants in vacuum.

Structural biology is witnessing a transformative era with gas-phase techniques such as native mass spectrometry (MS), ion mobility, and single-particle imaging (SPI) emerging as critical tools for studying biomolecular assemblies like protein capsids in their native states. SPI with X-ray free-electron lasers has the potential to allow for capturing atomic-resolution structures of proteins without crystallization. However, determining particle orientation during exposure remains a major challenge, compounded by the heterogeneity of the protein complexes.

Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation in .

Proteases regulate important biological functions. Here, we present the structural and functional characterization of three previously uncharacterized aspartic proteases in . We show that these proteases have structural hallmarks of retropepsin peptidases and play redundant roles for cell survival under hypoosmotic stress conditions.

Identification and genomic characterisation of known and novel highly divergent sapoviruses in frugivorous and insectivorous bats in Nigeria.

Sapovirus (SaV) infections have been linked with moderate-to-severe acute gastroenteritis (AGE) in animals and humans and represent a significant risk to public health. SaVs from animals including pigs, chimpanzees, and rodents have been reported to be closely related with human SaVs, indicating the possibility of cross-species transmission. Divergent SaVs have been reported in various bat species across various continents including Asia, Europe, Oceania and Africa.

Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15.

Since the emergence of SARS-CoV-2 at the end of 2019, the virus has caused significant global health and economic disruptions. Despite the rapid development of antiviral vaccines and some approved treatments such as remdesivir and paxlovid, effective antiviral pharmacological treatments for COVID-19 patients remain limited. This study explores Nsp15, a 3'-uridylate-specific RNA endonuclease, which has a critical role in immune system evasion and hence in escaping the innate immune sensors.

Salipro technology in membrane protein research.

Reconstitution and direct extraction of membrane proteins using saposins is an emerging technique for solubilizing and stabilizing membrane proteins. The Salipro technology offers several advantages over traditional detergent solubilization, including a more native lipid environment, increased protein stability, and maintenance of functionality. This review covers recent studies that have used Salipros to characterize membrane proteins, as well as advances in direct extraction methods that have enabled the structural and functional characterization of a variety of targets.

Sla2 is a core interaction hub for clathrin light chain and the Pan1/End3/Sla1 complex.

The interaction network of Sla2, a vital endocytic mid-coat adaptor protein, undergoes constant rearrangement. Sla2 serves as a scaffold linking the membrane to the actin cytoskeleton, with its role modulated by the clathrin light chain (CLC), which inhibits Sla2's function under certain conditions. We show that Sla2 has two independent binding sites for CLC: one previously described in homologs of fungi (Sla2) and metazoa (Hip1R), and a second found only in Fungi.

Advancing time-resolved structural biology: latest strategies in cryo-EM and X-ray crystallography.

Structural biology offers a window into the functionality of molecular machines in health and disease. A fundamental challenge lies in capturing both the high-resolution structural details and dynamic changes that are essential for function. The high-resolution methods of X-ray crystallography and electron cryo-microscopy (cryo-EM) are mainly used to study ensembles of static conformations but can also capture crucial dynamic transition states.

Inhibitory effect of plant flavonoid cyanidin on oral microbial biofilm.

Unlabelled: As primary colonizers of the tooth surface, oral streptococci play a crucial role in dental caries development. Numerous natural compounds, including flavonoids, are emerging as promising agents for inhibiting dental biofilm formation without compromising bacterial viability, underscoring their potential in non-bactericidal antibiofilm strategies. This study investigated the effects and mechanism of action of the unmodified plant flavonoid cyanidin on the growth and sucrose-dependent biofilm formation of oral streptococci, with a particular focus on the cariogenic pathogen .

X-ray spectroscopy meets native mass spectrometry: probing gas-phase protein complexes.

Gas-phase activation and dissociation studies of biomolecules, proteins and their non-covalent complexes using X-rays hold great promise for revealing new insights into the structure and function of biological samples. This is due to the unique properties of X-ray molecular interactions, such as site-specific and rapid ionization. In this perspective, we report and discuss the promise of first proof-of-principle studies of X-ray-induced dissociation of native (structurally preserved) biological samples ranging from small 17 kDa monomeric proteins up to large 808 kDa non-covalent protein assemblies conducted at a synchrotron (PETRA III) and a free-electron laser (FLASH2).

Surface Modification of Mesoporous Silica Nanoparticles as a Means to Introduce Inherent Cancer-Targeting Ability in a 3D Tumor Microenvironment.

Mesoporous silica nanoparticles (MSNs) have emerged as promising drug carriers that can facilitate targeted anticancer drug delivery, but efficiency studies relying on active targeting mechanisms remain elusive. This study implements in vitro 3D cocultures, so-called microtissues, to model a physiologically relevant tumor microenvironment (TME) to examine the impact of surface-modified MSNs without targeting ligands on the internalization, cargo delivery, and cargo release in tumor cells and cancer-associated fibroblasts. Among these, acetylated MSNs most effectively localized in tumor cells in a 3D setting containing collagen, while other MSNs did so to a lesser degree, most likely due to remaining trapped in the extracellular matrix of the TME.

Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation in .

Proteases regulate important biological functions. Here we present the structural and functional characterization of three previously uncharacterized aspartic proteases in . We show that these proteases have structural hallmarks of retropepsin peptidases and play redundant roles for cell survival under hypoosmotic stress conditions.

Stepwise recruitment of chaperone Hsc70 by DNAJB1 produces ordered arrays primed for bursts of amyloid fibril disassembly.

The Hsp70 chaperone system is capable of disassembling pathological aggregates such as amyloid fibres associated with serious degenerative diseases. Here we examine the role of the J-domain protein co-factor in amyloid disaggregation by the Hsc70 system. We used cryo-EM and tomography to compare the assemblies with wild-type DNAJB1 or inactive mutants.

AlphaPulldown2-a general pipeline for high-throughput structural modeling.

Summary: AlphaPulldown2 streamlines protein structural modeling by automating workflows, improving code adaptability, and optimizing data management for large-scale applications. It introduces an automated Snakemake pipeline, compressed data storage, support for additional modeling backends like UniFold and AlphaLink2, and a range of other improvements. These upgrades make AlphaPulldown2 a versatile platform for predicting both binary interactions and complex multi-unit assemblies.

Broadly neutralizing antibodies isolated from HEV convalescents confer protective effects in human liver-chimeric mice.

Hepatitis E virus (HEV) causes 3.3 million symptomatic cases and 44,000 deaths per year. Chronic infections can arise in immunocompromised individuals, and pregnant women may suffer from fulminant disease as a consequence of HEV infection.

Mechanism of Centrosomal Protein 55 (CEP55) Loading Into Exosomes.

Up-regulation of Centrosomal Protein 55 (CEP55) in cancer cells increases malignancy, and the protein can be transferred via exosomes. However, the mechanism of how CEP55 is delivered to exosomes is unknown. In this study, we addressed this issue and analysed trafficking of EGFP-CEP55 from early to late endosomes by using high-resolution microscopy.

Structural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria.

Dinucleases of the DEDD superfamily, such as oligoribonuclease, Rexo2 and nanoRNase C, catalyze the essential final step of RNA degradation, the conversion of di- to mononucleotides. The active sites of these enzymes are optimized for substrates that are two nucleotides long, and do not discriminate between RNA and DNA. Here, we identified a novel DEDD subfamily, members of which function as dedicated deoxydinucleases (diDNases) that specifically hydrolyze single-stranded DNA dinucleotides in a sequence-independent manner.