ATP regulates RNA‐driven cold inducible RNA binding protein phase separation

Intrinsically disordered proteins and proteins containing intrinsically disordered regions are highly abundant in the proteome of eukaryotes and are extensively involved in essential biological functions. More recently, their role in the organization of biomolecular condensates has become evident and along with their misregulation in several neurologic disorders. Currently, most studies involving these proteins are carried out in vitro and using purified proteins. Given that in cells, condensate‐forming proteins are exposed to high, millimolar concentrations of cellular metabolites, we aimed to reveal the interactions of cellular metabolites and a representative condensate‐forming protein. Here, using the arginine–glycine/arginine–glycine–glycine (RG/RGG)‐rich cold inducible RNA binding protein (CIRBP) as paradigm, we studied binding of the cellular metabolome to CIRBP. We found that most of the highly abundant cellular metabolites, except nucleotides, do not directly bind to CIRBP. ATP, ADP, and AMP as well as NAD⁺, NADH, NADP⁺, and NADPH directly interact with CIRBP, involving both the folded RNA‐recognition motif and the disordered RG/RGG region. ATP binding inhibited RNA‐driven phase separation of CIRBP. Thus, it might be beneficial to include cellular metabolites in in vitro liquid–liquid phase separation studies of RG/RGG and other condensate‐forming proteins in order to better mimic the cellular environment in the future.     

Macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of biomolecular condensates

The interfacial tension of phase‐separated biomolecular condensates affects their fusion and multiphase organization, and yet how this important property depends on the composition and interactions of the constituent macromolecules is poorly understood. Here we use molecular dynamics simulations to determine the interfacial tension and phase equilibrium of model condensate‐forming systems. The model systems consist of binary mixtures of Lennard‐Jones particles or chains of such particles. We refer to the two components as drivers and regulators; the former has stronger self‐interactions and hence a higher critical temperature (T _c) for phase separation. In previous work, we have shown that, depending on the relative strengths of driver‐regulator and driver‐driver interactions, regulators can either promote or suppress phase separation (i.e., increase or decrease T _c). Here we find that the effects of regulators on T _c quantitatively match the effects on interfacial tension (γ). This important finding means that, when a condensate‐forming system experiences a change in macromolecular composition or a change in intermolecular interactions (e.g., by mutation or posttranslational modification, or by variation in solvent conditions such as temperature, pH, or salt), the resulting change in T _c can be used to predict the change in γ and vice versa. We also report initial results showing that disparity in intermolecular interactions drives multiphase coexistence. These findings provide much needed guidance for understanding how biomolecular condensates mediate cellular functions.     

Liquid–liquid phase separation of tau: From molecular biophysics to physiology and disease

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.     

Direct Evidence from Nuclear Magnetic Resonance Studies for Bound Sodium in Frog Skeletal Muscle

The recent work of Cope on ²³Na magnetic resonance studies of frog muscle has been repeated with the view of investigating certain objections which can be raised concerning the original studies. The present work leads to the conclusion that Cope's results concerning bound sodium are essentially correct in that a large fraction of the ²³Na present does not contribute normally to a detectable nuclear magnetic resonance (NMR) signal. This “missing” signal can be detected at high radio-frequency intensity however, and a signal-saturation study distinctly reveals its presence.     

Double-quantum-filtered 23Na NMR study of intracellular sodium in the perfused liver.

We acquired double-quantum-filtered 23Na NMR spectra from perfused liver, using a range of tau values from 0.2 to 24 ms, where tau is the separation between the first and second pi/2 pulses in the radio-frequency pulse sequence. For each tau value we compared the amplitude of the double-quantum-filtered 23Na NMR signal acquired from intracellular sodium ions when the liver was perfused with buffer containing the "shift reagent" Dy(PPP)2 to the amplitude of the total double-quantum-filtered 23Na NMR signal acquired when the liver was perfused with buffer containing no Dy(PPP)2. For tau < or = 4 ms, the average ratio of the two amplitudes was 0.98 +/- 0.03 (mean +/- SEM). For tau > or = 8 ms, the average ratio was significantly less than 1. These results demonstrate that double-quantum-filtered 23Na NMR signals acquired from perfused liver using short tau values arise almost exclusively from intracellular sodium ions, but double-quantum-filtered 23Na NMR signals acquired from perfused liver using long tau values contain contributions from both intracellular and extracellular sodium ions. This conclusion suggests that multiple-quantum-filtered 23Na NMR spectroscopy will be useful in studying intracellular sodium levels in the perfused liver, and possibly in the intact liver in vivo.     

Structural dynamics of the complex of calmodulin with a minimal functional construct of eukaryotic elongation factor 2 kinase and the role of Thr348 autophosphorylation

The calmodulin (CaM) activated α‐kinase, eukaryotic elongation factor 2 kinase (eEF‐2K), plays a central role in regulating translational elongation by phosphorylating eukaryotic elongation factor 2 (eEF‐2), thereby reducing its ability to associate with the ribosome and suppressing global protein synthesis. Using TR (for truncated), a minimal functional construct of eEF‐2K, and utilizing hydrogen/deuterium exchange mass spectrometry (HXMS), solution‐state nuclear magnetic resonance (NMR) and biochemical approaches, we investigate the conformational changes accompanying complex formation between Ca²⁺‐CaM and TR and the effects of autophosphorylation of the latter at Thr348, its primary regulatory site. Our results suggest that a CaM C‐lobe surface, complementary to the one involved in recognizing the calmodulin‐binding domain (CBD) of TR, provides a secondary TR‐interaction platform. CaM helix F, which is part of this secondary surface, responds to both Thr348 phosphorylation and pH changes, indicating its integration into an allosteric network that encompasses both components of the Ca²⁺‐CaM•TR complex. Solution NMR data suggest that CaM_H107K, which carries a helix F mutation, is compromised in its ability to drive the conformational changes in TR necessary to enable efficient Thr348 phosphorylation. Biochemical studies confirm the diminished capacity of CaM_H107K to induce TR autophosphorylation compared to wild‐type CaM.     

A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates

Membraneless organelles are cellular compartments that form by liquid–liquid phase separation of one or more components. Other molecules, such as proteins and nucleic acids, will distribute between the cytoplasm and the liquid compartment in accordance with the thermodynamic drive to lower the free energy of the system. The resulting distribution colocalizes molecular species to carry out a diversity of functions. Two factors could drive this partitioning: the difference in solvation between the dilute versus dense phase and intermolecular interactions between the client and scaffold proteins. Here, we develop a set of knowledge‐based potentials that allow for the direct comparison between stickiness, which is dominated by desolvation energy, and pairwise residue contact propensity terms. We use these scales to examine experimental data from two systems: protein cargo dissolving within phase‐separated droplets made from FG repeat proteins of the nuclear pore complex and client proteins dissolving within phase‐separated FUS droplets. These analyses reveal a close agreement between the stickiness of the client proteins and the experimentally determined values of the partition coefficients (R > 0.9), while pairwise residue contact propensities between client and scaffold show weaker correlations. Hence, the stickiness of client proteins is sufficient to explain their differential partitioning within these two phase‐separated systems without taking into account the composition of the condensate. This result implies that selective trafficking of client proteins to distinct membraneless organelles requires recognition elements beyond the client sequence composition.StatementEmpirical potentials for amino acid stickiness and pairwise residue contact propensities are derived. These scales are unique in that they enable direct comparison of desolvation versus contact terms. We find that partitioning of a client protein to a condensate is best explained by amino acid stickiness.     

N‐terminal acetylation modestly enhances phase separation and reduces aggregation of the low‐complexity domain of RNA‐binding protein fused in sarcoma

The RNA‐binding protein fused in sarcoma (FUS) assembles via liquid–liquid phase separation (LLPS) into functional RNA granules and aggregates in amyotrophic lateral sclerosis associated neuronal inclusions. Several studies have demonstrated that posttranslational modification (PTM) can significantly alter FUS phase separation and aggregation, particularly charge‐altering phosphorylation of the nearly uncharged N‐terminal low complexity domain of FUS (FUS LC). However, the occurrence and impact of N‐terminal acetylation on FUS phase separation remains unexplored, even though N‐terminal acetylation is the most common PTM in mammals and changes the charge at the N‐terminus. First, we find that FUS is predominantly acetylated in two human cell types and stress conditions. Next, we show that recombinant FUS LC can be acetylated when co‐expressed with the NatA complex in Escherichia coli. Using NMR spectroscopy, we find that N‐terminal acetylated FUS LC (FUS LC Nt‐Ac) does not notably alter monomeric FUS LC structure or motions. Despite no difference in structure, Nt‐Ac‐FUS LC phase separates more avidly than unmodified FUS LC. More importantly, N‐terminal acetylation of FUS LC reduces aggregation. Our findings highlight the importance of N‐terminal acetylation of proteins that undergo physiological LLPS and pathological aggregation.     

Direct measurement of increased myocardial cellular23Na NMR signals in perfused guinea-pig heart induced by dihydroouabain and grayanotoxin-I

The effects of the cardiac glycoside dihydroouabain (DHO), and the ericaceous toxin grayanotoxin-I (GTX-I) on myocardial cellular sodium (Na_i) concentrations were investigated using sodium-23 nuclear magnetic resonance (²³Na NMR) spectroscopy at 30°C in isolated perfused guinea-pig hearts. The Na_i NMR signals from perfused Langendorff heart preparations were obtained by the modified inversion recovery (IR) method based on the previous observation that the spin-lattice relaxation time (T₁) of the Na_i (25 or 34 msec at 8.46 Tesla (T)) is much faster than that of extracellular sodium (64 msec at 9.4 T). Na_i was estimated from the calibration curve of the frequency area of the²³Na NMR FT spectra plotted against the standard Na concentration. The Na_i concentration of the heart increased concomitantly with the positive inotropic effects (PIE) of DHO, GTX-I and monensin (MON). The cumulative sequential addition of DHO (5×10^–6 M), GTX-I (7×10^–8 M) and MON (5×10^–6 M), each of which alone induced no appreciable PIE, produced a 22% elevation in Na_i concentration relative to that of the control (100%) accompanying a PIE of 44%. The mechanism of this Na_i elevation induced by combinational addition of DHO, GTX-I and MON may be mediated as follows: GTX-I increases the net Na-influxvia Na⁺ channels; DHO inhibits the pumping out of Na⁺ from the cell; and MON transports external Na⁺ into the cell, acting as a sodium ionophore. Consequently, these drugs act synergistically to increase the Na_i, thereby increasing the intracellular Ca²⁺ concentrationvia Na⁺–Ca²⁺ exchange.     

A Na NMR study of the effect of (+) and (−) arabitol on NaDNA in aqueous solution

The ²³Na NMR quadrupolar relaxation in NaDNA aqueous solutions has been investigated in the presence of (+) and (−) arabitol. Quite different results were produced by the enantiomers, i.e. the addition of (+) arabitol produced a small increase of the ²³Na NMR relaxation rates, while in the presence of (−) arabitol a significant decrease was observed. These findings were analysed and discussed in terms of an effective interaction of (−) arabitol with DNA.     

Na-NMR Studies of the Intracellular Sodium Ion Concentration in the Halotolerant Alga Dunaliella salina

The Intracellular Na⁺ concentration in the halotolerant alga Dunaliella salina was measured in intact cells by ²³Na-NMR spectroscopy, utilizing the dysprosium tripolyphosphate complex as a sodium shift reagent, and was found to be 88 ± 28 millimolar. Intracellular sodium ion content and intracellular volume were the same, within the experimental error, in cells adapted to grow in media containing between 0.1 and 4.0 molar NaCl. These values assume extracellular and intracellular NMR visibilities of the ²³Na nuclei of 100 and 40%, respectively. The relaxation rate of intracellular sodium was enhanced with increasing salinity of the growth medium, in parallel to the intracellular osmosity due to the presence of glycerol, indicating that Na⁺ ions and glycerol are codistribbuted within the cell volume.     

Nuclear magnetic resonance of tissue Na correlation time

Shporer and Civan (Biochim. Biophys. Acta (1974) 354, 291–304) reported the effect of magnetic-field strength on the NMR relaxation times of ²³Na in frog skeletal muscle. From these data, they estimated the correlation time τ_c for bound ²³Na whose tumbling is severely restricted, and they suggested that the fraction of bound ²³Na does not exceed some few percent of the total ²³Na population. However, a step in their theoretical approach seems oversimplified. With an improved approach, we obtained an effective τ_c of 4–9 ns for bound ²³Na. This value is some 10 times shorter than the corresponding value estimated by them from the same data. On the other hand, their conclusion concerning the amount of bound ²³Na seems to remain valid. The origin of the observed difference between the two transverse relaxation times of tissue ²³Na is also discussed.     

Biophysical studies of phase separation integrating experimental and computational methods

Biomolecular phase separation that contributes to the formation of membraneless organelles and biomolecular condensates has recently gained tremendous attention because of the importance of these assemblies in physiology, disease, and engineering applications. Understanding and directing biomolecular phase separation requires a multiscale view of the biophysical properties of these phases. Yet, many classic tools to characterize biomolecular properties do not apply in these condensed phases. Here, we discuss insights obtained from spectroscopic methods, in particular nuclear magnetic resonance and optical spectroscopy, in understanding the molecular and atomic interactions that underlie the formation of protein-rich condensates. We also review approaches closely coupling nuclear magnetic resonance data with computational methods especially coarse-grained and all-atom molecular simulations, which provide insight into molecular features of phase separation. Finally, we point to future methodolical developments, particularly visualizing biophysical properties of condensates in cells.     

Sodium-23 NMR studies of cation-DNA interactions

Sodium-23 NMR has been used to study the extent to which monovalent cations associate with double stranded DNA in aqueous solution (28°C, pH = 7.5). On the basis of the two site model for rapid exchange the ²³Na linewidth can be related to the fraction of sodium ions associated with DNA. To test the applicability to this system of the condensation model for the association of small counterions with polyelectrolytes, the concentration dependence of the sodium linewidth has been determined by making additions of NaCl to solutions of tetraethyl or tetrabutylammonium DNA. ([P], the DNA phosphate concentration was about 0.02M). The resulting titration curves extend over a wide range of the ratio [Na]/[P] (0.3–30). When [Na]/[P] ? 3 only sodium is associated, and the extent to which it compensates the charges on DNA does not vary with the addition of salt, at least until [Na]/[P] ≈ 30, the highest concentration examined. When [Na]/[P] ? 3 the tetraalkylammonium species is also associated with DNA; an equation has been derived to account for the effect on the ²³Na linewidth of the competition between sodium and another monovalent cation. Based on the assumption that the fraction of uncompensated charge remaining on DNA after the condensation of both species is constant, this equation fits all the linewidth data if the charge fraction is in the range 0.25 ± 0.10. The value required by the condensation model for DNA in the presence of monovalent counterions is ξ^?1 = 0.24. The reasonable agreement between experimental and theoretical values of the charge fraction and its invariance with respect to large variations in the concentration of added salt indicate that even in moderately concentrated solutions of DNA, the association of sodium can usefully be described in terms of the condensation model. If the theoretical value of the charge fraction is assumed, it follows from fitting the titration curves that the approximate relative affinities for DNA of Na⁺, Et₄N⁺, and Bu₄N⁺ are in the ratio 20:5:1, and the transverse relaxation rate of condensed sodium is 180 ± 10 s^?1.     

Nuclear Magnetic Resonance of Sodium-23 Linoleate-Water: Basis for an Alternative Interpretation of Sodium-23 Spectra within Cells

The ²³Na spectrum from liquid crystals of sodium linoleate in water has been studied by nuclear magnetic resonance (NMR) techniques. The integrated intensity of the visible central spectral line was 34-39% of the intensity of a reference sample containing an equal quantity and concentration of ²³Na nuclei. Since satellite signals were clearly demonstrable, the effect reflected a nuclear quadrupolar interaction rather than a splitting of the ²³Na into two populations of bound and free nuclei. It is proposed that a similar quadrupolar effect may be the basis for the apparent binding of the ²³Na observed in biological systems.     

High‐yield recombinant bacterial expression of 13C‐, 15N‐labeled,serine‐16 phosphorylated,murine amelogenin using a modified third generation genetic code expansion protocol

Amelogenin constitutes ~90% of the enamel matrix in the secretory stage of amelogenesis, a still poorly understood process that results in the formation of the hardest and most mineralized tissue in vertebrates—enamel. Most biophysical research with amelogenin uses recombinant protein expressed in Escherichia coli. In addition to providing copious amounts of protein, recombinant expression allows ¹³C‐ and ¹⁵N‐labeling for detailed structural studies using NMR spectroscopy. However, native amelogenin is phosphorylated at one position, Ser‐16 in murine amelogenin, and there is mounting evidence that Ser‐16 phosphorylation is important. Using a modified genetic code expansion protocol we have expressed and purified uniformly ¹³C‐, ¹⁵N‐labeled murine amelogenin (pS16M179) with ~95% of the protein being correctly phosphorylated. Homogeneous phosphorylation was achieved using commercially available, enriched, ¹³C‐, ¹⁵N‐labeled media, and protein expression was induced with isopropyl β‐D‐1‐thiogalactopyranoside at 310 K. Phosphoserine incorporation was verified from one‐dimensional ³¹P NMR spectra, comparison of ¹H‐¹⁵N HSQC spectra, Phos‐tag SDS PAGE, and mass spectrometry. Phosphorus‐31 NMR spectra for pS16M179 under conditions known to trigger amelogenin self‐assembly into nanospheres confirm nanosphere models with buried N‐termini. Lambda phosphatase treatment of these nanospheres results in the dephosphorylation of pS16M179, confirming that smaller oligomers and monomers with exposed N‐termini are in equilibrium with nanospheres. Such ¹³C‐, ¹⁵N‐labeling of amelogenin with accurately encoded phosphoserine incorporation will accelerate biomineralization research to understand amelogenesis and stimulate the expanded use of genetic code expansion protocols to introduce phosphorylated amino acids into proteins.     

Structural mechanism for modulation of functional amyloid and biofilm formation by Staphylococcal Bap protein switch

The Staphylococcal Bap proteins sense environmental signals (such as pH, [Ca²⁺]) to build amyloid scaffold biofilm matrices via unknown mechanisms. We here report the crystal structure of the aggregation‐prone region of Staphylococcus aureus Bap which adopts a dumbbell‐shaped fold. The middle module (MM) connecting the N‐terminal and C‐terminal lobes consists of a tandem of novel double‐Ca²⁺‐binding motifs involved in cooperative interaction networks, which undergoes Ca²⁺‐dependent order–disorder conformational switches. The N‐terminal lobe is sufficient to mediate amyloid aggregation through liquid–liquid phase separation and maturation, and subsequent biofilm formation under acidic conditions. Such processes are promoted by disordered MM at low [Ca²⁺] but inhibited by ordered MM stabilized by Ca²⁺ binding, with inhibition efficiency depending on structural integrity of the interaction networks. These studies illustrate a novel protein switch in pathogenic bacteria and provide insights into the mechanistic understanding of Bap proteins in modulation of functional amyloid and biofilm formation, which could be implemented in the anti‐biofilm drug design.     

Disease‐linked TDP‐43 hyperphosphorylation suppresses TDP‐43 condensation and aggregation

Post‐translational modifications (PTMs) have emerged as key modulators of protein phase separation and have been linked to protein aggregation in neurodegenerative disorders. The major aggregating protein in amyotrophic lateral sclerosis and frontotemporal dementia, the RNA‐binding protein TAR DNA‐binding protein (TDP‐43), is hyperphosphorylated in disease on several C‐terminal serine residues, a process generally believed to promote TDP‐43 aggregation. Here, we however find that Casein kinase 1δ‐mediated TDP‐43 hyperphosphorylation or C‐terminal phosphomimetic mutations reduce TDP‐43 phase separation and aggregation, and instead render TDP‐43 condensates more liquid‐like and dynamic. Multi‐scale molecular dynamics simulations reveal reduced homotypic interactions of TDP‐43 low‐complexity domains through enhanced solvation of phosphomimetic residues. Cellular experiments show that phosphomimetic substitutions do not affect nuclear import or RNA regulatory functions of TDP‐43, but suppress accumulation of TDP‐43 in membrane‐less organelles and promote its solubility in neurons. We speculate that TDP‐43 hyperphosphorylation may be a protective cellular response to counteract TDP‐43 aggregation.     

Molecular basis of ion permeability in a voltage‐gated sodium channel

Voltage‐gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na⁺ ≈ Li⁺ ≫ K⁺, Ca²⁺, Mg²⁺) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.