Orientational restraints such as residual dipolar couplings promise to overcome many of the problems that traditionally limited liquid-state nuclear magnetic resonance spectroscopy. Recently, we ...developed methods to predict a molecular alignment tensor and thus residual dipolar couplings for a given molecular structure. This provides many new opportunities for the study of the structure and dynamics of proteins, nucleic acids, oligosaccharides and small molecules. This protocol details the use of the software PALES (Prediction of AlignmEnt from Structure) for prediction of an alignment tensor from a known three-dimensional (3D) coordinate file of a solute. The method is applicable to alignment of molecules in many neutral and charged orienting media and takes into account the molecular shape and 3D charge distribution of the molecule.
The etiologic agent of the Covid-19 pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral membrane of SARS-CoV-2 surrounds a helical nucleocapsid in which the viral ...genome is encapsulated by the nucleocapsid protein. The nucleocapsid protein of SARS-CoV-2 is produced at high levels within infected cells, enhances the efficiency of viral RNA transcription, and is essential for viral replication. Here, we show that RNA induces cooperative liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid protein. In agreement with its ability to phase separate in vitro, we show that the protein associates in cells with stress granules, cytoplasmic RNA/protein granules that form through liquid-liquid phase separation and are modulated by viruses to maximize replication efficiency. Liquid-liquid phase separation generates high-density protein/RNA condensates that recruit the RNA-dependent RNA polymerase complex of SARS-CoV-2 providing a mechanism for efficient transcription of viral RNA. Inhibition of RNA-induced phase separation of the nucleocapsid protein by small molecules or biologics thus can interfere with a key step in the SARS-CoV-2 replication cycle.
The protein Tau aggregates into tangles in the brain of patients with Alzheimer's disease. In solution, however, Tau is intrinsically disordered, highly soluble, and binds to microtubules. It is ...still unclear what initiates the conversion from an innocuous phase of high solubility and functionality to solid-like neurotoxic deposits. Here, we show that the microtubule-binding repeats of Tau, which are lysine-rich, undergo liquid-liquid phase separation in solution. Liquid-liquid demixing causes molecular crowding of amyloid-promoting elements of Tau and drives electrostatic coacervation. Furthermore, we demonstrate that three-repeat and four-repeat isoforms of Tau differ in their ability for demixing. Alternative splicing of Tau can thus regulate the formation of Tau-containing membrane-less compartments. In addition, phosphorylation of Tau repeats promotes liquid-liquid phase separation at cellular protein conditions. The combined data propose a mechanism in which liquid droplets formed by the positively charged microtubule-binding domain of Tau undergo coacervation with negatively charged molecules to promote amyloid formation.Tau forms aggregates in the brains of Alzheimer patients. Here, the authors identify conditions, where the microtubule-binding repeats of Tau undergo a phosphorylation-dependent liquid-liquid phase separation, leading to molecular crowding in the formed Tau liquid droplets and characterize them by NMR and other biophysical methods.
Motions in biomolecules are critical for biochemical reactions. In cells, many biochemical reactions are executed inside of biomolecular condensates formed by ultradynamic intrinsically disordered ...proteins. A deep understanding of the conformational dynamics of intrinsically disordered proteins in biomolecular condensates is therefore of utmost importance but is complicated by diverse obstacles. Here we review emerging data on the motions of intrinsically disordered proteins inside of liquidlike condensates. We discuss how liquid–liquid phase separation modulates internal motions across a wide range of time and length scales. We further highlight the importance of intermolecular interactions that not only drive liquid–liquid phase separation but appear as key determinants for changes in biomolecular motions and the aging of condensates in human diseases. The review provides a framework for future studies to reveal the conformational dynamics of intrinsically disordered proteins in the regulation of biomolecular condensate chemistry.
Significance Tau is an important microtubule-associated protein. Although the structureâfunction relationship of Tau has been intensively studied for many years primarily by molecular biology and ...biochemical approaches, little is still known about the molecular mechanisms by which Tau interacts with microtubules and promotes microtubule assembly. Here, we provide detailed insight into the Tauâmicrotubule association by using NMR spectroscopy and mass spectrometry. We show that Tau binds to microtubules by using small groups of residues, which are important for pathological aggregation of Tau. We further show that Tau stabilizes a straight protofilament conformation by binding to a hydrophobic pocket in between tubulin heterodimers. Our work is thus relevant to normal Tau action development and in Tau-related neurodegenerative diseases.
The structure, dynamic behavior, and spatial organization of microtubules are regulated by microtubule-associated proteins. An important microtubule-associated protein is the protein Tau, because its microtubule interaction is impaired in the course of Alzheimerâs disease and several other neurodegenerative diseases. Here, we show that Tau binds to microtubules by using small groups of evolutionary conserved residues. The binding sites are formed by residues that are essential for the pathological aggregation of Tau, suggesting competition between physiological interaction and pathogenic misfolding. Tau residues in between the microtubule-binding sites remain flexible when Tau is bound to microtubules in agreement with a highly dynamic nature of the Tauâmicrotubule interaction. By binding at the interface between tubulin heterodimers, Tau uses a conserved mechanism of microtubule polymerization and, thus, regulation of axonal stability and cell morphology.
Biomolecular condensation via liquid–liquid phase separation (LLPS) of intrinsically disordered proteins/regions (IDPs/IDRs), with and without nucleic acids, has drawn widespread interest due to the ...rapidly unfolding role of phase‐separated condensates in a diverse range of cellular functions and human diseases. Biomolecular condensates form via transient and multivalent intermolecular forces that sequester proteins and nucleic acids into liquid‐like membrane‐less compartments. However, aberrant phase transitions into gel‐like or solid‐like aggregates might play an important role in neurodegenerative and other diseases. Tau, a microtubule‐associated neuronal IDP, is involved in microtubule stabilization, regulates axonal outgrowth and transport in neurons. A growing body of evidence indicates that tau can accomplish some of its cellular activities via LLPS. However, liquid‐to‐solid transition resulting in the abnormal aggregation of tau is associated with neurodegenerative diseases. The physical chemistry of tau is crucial for governing its propensity for biomolecular condensation which is governed by various intermolecular and intramolecular interactions leading to simple one‐component and complex multi‐component condensates. In this review, we aim at capturing the current scientific state in unveiling the intriguing molecular mechanism of phase separation of tau. We particularly focus on the amalgamation of existing and emerging biophysical tools that offer unique spatiotemporal resolutions on a wide range of length‐ and time‐scales. We also discuss the link between quantitative biophysical measurements and novel biological insights into biomolecular condensation of tau. We believe that this account will provide a broad and multidisciplinary view of phase separation of tau and its association with physiology and disease.
Pathological aggregation of the protein tau into insoluble aggregates is a hallmark of neurodegenerative diseases. The emergence of disease-specific tau aggregate structures termed tau strains, ...however, remains elusive. Here we show that full-length tau protein can be aggregated in the absence of co-factors into seeding-competent amyloid fibrils that sequester RNA. Using a combination of solid-state NMR spectroscopy and biochemical experiments we demonstrate that the co-factor-free amyloid fibrils of tau have a rigid core that is similar in size and location to the rigid core of tau fibrils purified from the brain of patients with corticobasal degeneration. In addition, we demonstrate that the N-terminal 30 residues of tau are immobilized during fibril formation, in agreement with the presence of an N-terminal epitope that is specifically detected by antibodies in pathological tau. Experiments in vitro and in biosensor cells further established that co-factor-free tau fibrils efficiently seed tau aggregation, while binding studies with different RNAs show that the co-factor-free tau fibrils strongly sequester RNA. Taken together the study provides a critical advance to reveal the molecular factors that guide aggregation towards disease-specific tau strains.
Introduction: Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) have gained wide recognition over the past decade due to their versatile roles in cell ...physiology and pathology. A large repertoire of IDPs/IDPRs has been implicated in numerous diseases, making them potential targets for therapeutic intervention. Recent advances in experimental methods and computational approaches have enabled detection and characterization of these highly dynamic proteins at atomistic detail, thus facilitating disorder/dynamic-based drug discovery.
Areas covered: This article presents an overview of the functional relevance and pathological implications of IDPs/IDPRs in cells. The authors outline the currently available experimental methods employed for structural characterization of these proteins. They also exemplify the practical limitations encountered during such characterization and ways to overcome them. Taken together, the article discusses the plausibility of exploiting protein disorder for drug targeting.
Expert opinion: Disorder-based drug targeting is gearing up in the realm of novel drug discovery approaches. Tools for probing the molecular features of IDPs and IDPRs are rapidly improving and start to provide accurate descriptions of the complex ensembles populated by IDPs/IDPRs. They thus pave the way for the development of drug molecules, which specifically target disease-associated disorder.
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