Molecular mechanisms of stress-induced reactivation in mumps virus condensates.

Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular stress disrupts the metastable host-virus equilibrium in persistent infection and induces viral replication in a culture model of mumps virus. Using a combination of cell biology, whole-cell proteomics, and cryo-electron tomography, we show that persistent viral replication factories are dynamic condensates and identify the largely disordered viral phosphoprotein as a driver of their assembly. Upon stress, increased phosphorylation of the phosphoprotein at its interaction interface with the viral polymerase coincides with the formation of a stable replication complex. By obtaining atomic models for the authentic mumps virus nucleocapsid, we elucidate a concomitant conformational change that exposes the viral genome to its replication machinery. These events constitute a stress-mediated switch within viral condensates that provide an environment to support upregulation of viral replication.

Systematic discovery of biomolecular condensate-specific protein phosphorylation.

Reversible protein phosphorylation is an important mechanism for regulating (dis)assembly of biomolecular condensates. However, condensate-specific phosphosites remain largely unknown, thereby limiting our understanding of the underlying mechanisms. Here, we combine solubility proteome profiling with phosphoproteomics to quantitatively map several hundred phosphosites enriched in either soluble or condensate-bound protein subpopulations, including a subset of phosphosites modulating protein-RNA interactions. We show that multi-phosphorylation of the C-terminal disordered segment of heteronuclear ribonucleoprotein A1 (HNRNPA1), a key RNA-splicing factor, reduces its ability to locate to nuclear clusters. For nucleophosmin 1 (NPM1), an essential nucleolar protein, we show that phosphorylation of S254 and S260 is crucial for lowering its partitioning to the nucleolus and additional phosphorylation of distal sites enhances its retention in the nucleoplasm. These phosphorylation events decrease RNA and protein interactions of NPM1 to regulate its condensation. Our dataset is a rich resource for systematically uncovering the phosphoregulation of biomolecular condensates.

Aggregation and disaggregation features of the human proteome.

Protein aggregates have negative implications in disease. While reductionist experiments have increased our understanding of aggregation processes, the systemic view in biological context is still limited. To extend this understanding, we used mass spectrometry-based proteomics to characterize aggregation and disaggregation in human cells after non-lethal heat shock. Aggregation-prone proteins were enriched in nuclear proteins, high proportion of intrinsically disordered regions, high molecular mass, high isoelectric point, and hydrophilic amino acids. During recovery, most aggregating proteins disaggregated with a rate proportional to the aggregation propensity: larger loss in solubility was counteracted by faster disaggregation. High amount of intrinsically disordered regions were associated with faster disaggregation. However, other characteristics enriched in aggregating proteins did not correlate with the disaggregation rates. In addition, we analyzed changes in protein thermal stability after heat shock. Soluble remnants of aggregated proteins were more thermally stable compared with control condition. Therefore, our results provide a rich resource of heat stress-related protein solubility data and can foster further studies related to protein aggregation diseases.

Thermal proteome profiling for interrogating protein interactions.

Thermal proteome profiling (TPP) is based on the principle that, when subjected to heat, proteins denature and become insoluble. Proteins can change their thermal stability upon interactions with small molecules (such as drugs or metabolites), nucleic acids or other proteins, or upon post-translational modifications. TPP uses multiplexed quantitative mass spectrometry-based proteomics to monitor the melting profile of thousands of expressed proteins. Importantly, this approach can be performed in vitro, in situ, or in vivo. It has been successfully applied to identify targets and off-targets of drugs, or to study protein-metabolite and protein-protein interactions. Therefore, TPP provides a unique insight into protein state and interactions in their native context and at a proteome-wide level, allowing to study basic biological processes and their underlying mechanisms.

Venom natriuretic peptides guide the design of heart failure therapeutics.

Heart failure (HF) affects over 26 million people world-wide. It is a syndrome triggered by loss of normal cardiac function due to many acute (eg myocardial infarction) and/or chronic (eg hypertension) causes and characterized by mixed beneficial and deleterious activation of a complex of multifaceted neurohormonal systems the net effect of which frequently is further adverse disruption of pressure-volume homeostasis. Unlike the situation in chronic heart failure, current strategies for treatment of acute heart failure are empirical and lack a strong evidence base. Management includes any of a combination of vasodilators, diuretics and ionotropic agents depending on the hemodynamic profile of the patient. Despite the improvement in the options available to improve outcomes in patients with chronic HF, for several decades little gain has been made in the treatment of the acute decompensated state. Morbidity and mortality rates remain high necessitating new therapeutic agents. The cardiac natriuretic peptides (NPs) are key hormones in pressure-volume homoeostasis. There are three isoforms of mammalian NPs, namely ANP, BNP and CNP. These peptides bind to membrane-bound NP receptors (NPRs) on the heart, vasculature and kidney to lower blood pressure and circulating volume. Intravenous infusion of NPs in HF patients improves hemodynamic status but is associated with occasional severe hypotension. Apart from mammalian NPs, snake venom NPs are an excellent source of pharmacologically distinct ligands that offer the possibility of engineering NPs for therapeutic purposes. Venom NPs have long half-lives, differential NPR activation profiles and varied NPR specificity. The scaffolds of venom NPs encode the molecular information for designing NPs with longer half-lives and improved and differential vascular and renal functions. This review focuses on the structure-function paradigm of mammalian and venom NPs and the different peptide engineering strategies that have been utilized in the design of clinically relevant new NP-analogues.

Decoding the molecular switches of natriuretic peptides which differentiate its vascular and renal functions.

Heart failure (HF) is associated with high morbidity and mortality. Dysfunction of blood pressure and/or volume homeostatic processes result in lower perfusion and/or congestion. Treatment strategies exerting differential effects on pressure and volume mechanisms are critical in handling patients with HF. Atrial natriuretic peptides (ANPs) are a key hormone in maintaining circulation. It binds to NP receptor-A (NPR-A) on vasculature, kidneys and nervous system to lowers blood pressure and volume. It exerts a concentration-dependent pharmacological activity, and only increased renal excretion of water and sodium at low doses and vasodilation along with renal effects at slightly higher doses. Recently, we showed that K-Ring (conserved ring of krait venom NP) elicited only vasodilatory properties despite its ability to evoke NPR-A. Through systematic analysis of the structure-function relationships of K-Ring, we have delineated the molecular switches that control vasodilatory and diuretic properties of NPs in anesthetized rats. In the process, we have identified residues that - (a) differentiate vascular and renal functions, (b) affect heart rate and pulse pressure, (c) exhibit sustained effect on vasodilatory function and (d) forceful diuresis switches. Furthermore, we have shown these residues to have equivalent effects on ANP scaffold, thereby introducing modularity in designing function-based ANP analogs. By comparing the ability of designed NPs to evoke cGMP levels, we propose a hypothetical mechanism for the observed tissue-specific effects. The present study opens new avenues in the development of suitable therapeutic agents for personalized care for HF patients.

Tail wags the dog: activity of krait natriuretic peptide is determined by its C-terminal tail in a natriuretic peptide receptor-independent manner.

Natriuretic peptides (NPs) are potent vasoactive hormones, which maintain pressure-volume homoeostasis. Snake venom NPs exhibit distinct biological activity compared with mammalian NPs due to subtle changes in their sequences. We recently identified a new NP from krait venom (KNP), with an unusual 38-residue long C-terminal tail, which has a propensity to form an α-helix. KNP mediates vasodilation via NP receptor (NPR) independent mechanisms on pre-contracted aortic strips in contrast with classical NPs. The infusion of KNP in anaesthetized rats resulted in a prolonged and sustained drop in blood pressure (BP) and heart rate (HR) with no renal effects in contrast with mammalian counterparts. Deletion mutant studies have revealed the presence of two functional segments in KNP, namely Ring and Helix. Although the Ring interacts with NPR, its contribution to the activity of KNP is shown to be negligible as both KNP and Helix elicit equipotent endothelium-dependent vasorelaxation. Further, KNP and Helix signalled through endothelial nitric oxide (NO) to mediate NPR-independent vasodilation. Thus, KNP exhibits non-canonical characteristics through its C-terminal tail, despite a functional NP ring. The present study has altered the paradigm of NP biology through the understanding of structure-function relationships and may serve as a lead for the design of novel hypotensive agents.

A defined α-helix in the bifunctional O-glycosylated natriuretic peptide TcNPa from the venom of Tropidechis carinatus.

Natriuretic peptides (NP) play important roles in human cardiac physiology through their guanylyl cyclase receptors NPR-A and NPR-B. Described herein is a bifunctional O-glycosylated natriuretic peptide, TcNPa, from Tropidechis carinatus venom and it unusually targets both NPR-A and NPR-B. Characterization using specific glycosidases and ETD-MS identified the glycan as galactosyl-ß(1-3)-N-acetylgalactosamine (Gal-GalNAc) and was α-linked to the C-terminal threonine residue. TcNPa contains the characteristic NP 17-membered disulfide ring with conserved phenylalanine and arginine residues. Both glycosylated and nonglycosylated forms were synthesized by Fmoc solid-phase peptide synthesis and NMR analysis identified an α-helix within the disulfide ring containing the putative pharmacophore for NPR-A. Surprisingly, both forms activated NPR-A and NPR-B and were relatively resistant towards proteolytic degradation in plasma. This work will underpin the future development of bifunctional NP peptide mimetics.

Defining basic rules for hardening influenza A virus liquid condensates.

In biological systems, liquid and solid-like biomolecular condensates may contain the same molecules but their behaviour, including movement, elasticity, and viscosity, is different on account of distinct physicochemical properties. As such, it is known that phase transitions affect the function of biological condensates and that material properties can be tuned by several factors including temperature, concentration, and valency. It is, however, unclear if some factors are more efficient than others at regulating their behaviour. Viral infections are good systems to address this question as they form condensates de novo as part of their replication programmes. Here, we used influenza A virus (IAV) liquid cytosolic condensates, AKA viral inclusions, to provide a proof of concept that liquid condensate hardening via changes in the valency of its components is more efficient than altering their concentration or the temperature of the cell. Liquid IAV inclusions may be hardened by targeting vRNP (viral ribonucleoprotein) interactions via the known NP (nucleoprotein) oligomerising molecule, nucleozin, both in vitro and in vivo without affecting host proteome abundance nor solubility. This study is a starting point for understanding how to pharmacologically modulate the material properties of IAV inclusions and may offer opportunities for alternative antiviral strategies.

Cells are organized into compartments that carry out specific functions. Envelope-like membranes enclose some of those compartments, while others remain unenclosed. The latter are called biomolecular condensates, and they can shift their physical states from a more liquid to a more solid form, which may affect how well they function. Temperature, molecular concentration and molecular interactions affect the physical state of condensates. Understanding what causes physical shifts in biomolecular condensates could have important implications for human health. For example, many viruses, including influenza, HIV, rabies, measles and the virus that causes COVID-19, SARS-CoV-2, use biomolecular condensates to multiply in cells. Changing the physical state of biomolecular condensates to one that hampers viruses' ability to multiply could be an innovative approach to treating viruses. Etibor et al. show that it is possible to harden condensates produced by influenza A virus. In the experiments, the researchers manipulated the temperature, molecular concentration and strength of connections between molecules in condensates created by influenza A-infected cells. Then, they measured their effects on the condensate's physical state. The experiments showed that using drugs that strengthen the bonds between molecules in condensates was the most effective strategy for hardening. Studies in both human cells and mice showed that using drugs to harden condensate in infected cells did not harm the cells or the animal and disabled the virus. The experiments provide preliminary evidence that using drugs to harden biomolecular condensates may be a potential treatment strategy for influenza A. More studies are necessary to test this approach to treating influenza A or other viruses that use condensates. If they are successful, the drug could add a new tool to the antiviral treatment toolbox.

Thermal proteome profiling: Insights into protein modifications, associations, and functions.

Tracking proteins' biophysical characteristics on a proteome-wide scale can provide valuable information on their functions and interactions. Thermal proteome profiling (TPP) is a multiplexed quantitative proteomics approach that measures changes in protein thermal stability-a key biophysical property-across different cellular states. Developed in 2014, as a target-deconvolution assay for drugs and other small molecules, TPP has since evolved to a system-level biochemical omics technique providing insights into context-dependent changes in protein states. In this review, we summarise key advances in the experimental and data analysis pipeline that have aided this transformation and discuss the recent developments and applications of TPP.

A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles.

Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. However, current data analysis strategies use preset thresholds that can lead to suboptimal sensitivity/specificity tradeoffs and limited comparability across datasets. Here, we present a method based on statistical hypothesis testing on curves, which provides control of the false discovery rate. We apply it to several datasets probing epigenetic drugs and a metabolite. This leads us to detect off-target drug engagement, including the finding that the HDAC8 inhibitor PCI-34051 and its analog BRD-3811 bind to and inhibit leucine aminopeptidase 3. An implementation is available as an R package from Bioconductor ( https://bioconductor.org/packages/TPP2D ). We hope that our method will facilitate prioritizing targets from thermal profiling experiments.

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP.

Adenosine triphosphate (ATP) plays fundamental roles in cellular biochemistry and was recently discovered to function as a biological hydrotrope. Here, we use mass spectrometry to interrogate ATP-mediated regulation of protein thermal stability and protein solubility on a proteome-wide scale. Thermal proteome profiling reveals high affinity interactions of ATP as a substrate and as an allosteric modulator that has widespread influence on protein complexes and their stability. Further, we develop a strategy for proteome-wide solubility profiling, and discover ATP-dependent solubilization of at least 25% of the insoluble proteome. ATP increases the solubility of positively charged, intrinsically disordered proteins, and their susceptibility for solubilization varies depending on their localization to different membrane-less organelles. Moreover, a few proteins, exhibit an ATP-dependent decrease in solubility, likely reflecting polymer formation. Our data provides a proteome-wide, quantitative insight into how ATP influences protein structure and solubility across the spectrum of physiologically relevant concentrations.

Proteomic comparisons of venoms of long-term captive and recently wild-caught Eastern brown snakes (Pseudonaja textilis) indicate venom does not change due to captivity.

UNLABELLED: Snake venom is a highly variable phenotypic character, and its variation and rapid evolution are important because of human health implications. Because much snake antivenom is produced from captive animals, understanding the effects of captivity on venom composition is important. Here, we have evaluated toxin profiles from six long-term (LT) captive and six recently wild-caught (RC) eastern brown snakes, Pseudonaja textilis, utilizing gel electrophoresis, HPLC-MS, and shotgun proteomics. We identified proteins belonging to the three-finger toxins, group C prothrombin activators, Kunitz-type serine protease inhibitors, and phospholipases A2, among others. Although crude venom HPLC analysis showed LT snakes to be higher in some small molecular weight toxins, presence/absence patterns showed no correlation with time in captivity. Shotgun proteomics indicated the presence of similar toxin families among individuals but with variation in protein species. Although no venom sample contained all the phospholipase A2 subunits that form the textilotoxin, all did contain both prothrombin activator subunits. This study indicates that captivity has limited effects on venom composition, that venom variation is high, and that venom composition may be correlated to geographic distribution. BIOLOGICAL SIGNIFICANCE: Through proteomic comparisons, we show that protein variation within LT and RC groups of snakes (Pseudonaja textilis) is high, thereby resulting in no discernible differences in venom composition between groups. We utilize complementary techniques to characterize the venom proteomes of 12 individual snakes from our study area, and indicate that individuals captured close to one another have more similar venom gel electrophoresis patterns than those captured at more distant locations. These data are important for understanding natural variation in and potential effects of captivity on venom composition.