Biochemical Timekeeping Via Reentrant Phase Transitions

Appreciation for the role of liquid–liquid phase separation in the functional organization of cellular matter has exploded in recent years. More recently there has been a growing effort to understand the principles of heterotypic phase separation, the demixing of multiple proteins and nucleic acids into a single functional condensate. A phase transition is termed reentrant if it involves the transformation of a system from one state into a macroscopically similar or identical state via at least two phase transitions elicited by variation of a single parameter. Reentrant liquid–liquid phase separation can occur when the condensation of one species is tuned by another. Reentrant phase transitions have been modeled in vitro using protein and RNA mixtures. These biochemical studies reveal two features of reentrant phase separation that are likely important to functional cellular condensates: (1) the ability to generate condensates with layered functional topologies, and (2) the ability to generate condensates whose composition and duration are self-limiting to enable a form of biochemical timekeeping. We relate these biochemical studies to potential cellular examples and discuss how layered topologies and self-regulation may impact key biological processes.     

Assembling the right type of switch: Protein condensation to signal cell death

Protein phase transitions are particularly amenable for cell signalling as these highly cooperative processes allow cells to make binary decisions in response to relatively small intracellular changes. The different processes of condensate formation and the distinct material properties of the resulting condensates provide a dictionary to modulate a range of decisions on cell fate. We argue that, on the one hand, the reversibility of liquid demixing offers a chance to arrest cell growth under specific circumstances. On the other hand, the transition to amyloids is better suited for terminal decisions such as those leading to apoptosis and necrosis. Here, we review recent examples of both scenarios, highlighting how mutations in signalling proteins affect the formation of biomolecular condensates with drastic effects on cell survival.     

Phase separation of chromatin and small RNA pathways in plants

Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the fundamental driving force and biological relevance of such spatial differentiation is largely unknown. Liquid–liquid phase separation (LLPS) is a natural propensity of demixing liquid phases and has been recently suggested to mediate the formation of biomolecular condensates that are relevant to diverse cellular processes. LLPS provides a mechanistic explanation for the self-assembly of subcellular structures by which the efficiency and specificity of certain cellular reactions are achieved. In plants, LLPS has been observed for several key factors in the chromatin and small RNA pathways. For example, the formation of facultative and obligate heterochromatin involves the LLPS of multiple relevant factors. In addition, phase separation is observed in a set of proteins acting in microRNA biogenesis and the small interfering RNA pathway. In this Focused Review, we highlight and discuss the recent findings regarding phase separation in the epigenetic mechanisms of plants.     

Phase changes and mosaic formation in single and mixed phospholipid monolayers at the oil-water interface

Insoluble monolayers of phosphatidylcholines and ethanolamines show first-order phase transitions at hydrocarbon-water interfaces, depending on the temperature and chain length. In mixed monolayers of two phosphatidylcholines of different chain lengths, or of phosphatidylcholines and ethanolamines of the same chain length, demixing occurs at the phase transition.     

Time-Resolved study of network self-organization from a biopolymeric solution

Time-resolved studies of network self-organization from homogeneous solutions of the representative biostructural polymer agarose are presented. Solutions are temperature quenched and observed by several techniques. Consistent with previous suggestions by the authors, experiments at concentrations up to about 1.75% w/v provide direct kinetic evidence for the occurrence of at least two distinct processes, leading, in sequence, to self-assembly. These are as follows: (a) a liquid–liquid phase separation of the solution occurring via spinodal demixing and resulting in two sets of regions that have, respectively, higher and lower than average concentrations of random-coiled polymers; and (b) the subsequent 2 coils → double helix transition and accompanying cross-linking and gelation (due to branching of double helices), occurring in the high-concentration regions. The size of the high-concentration regions depends upon agarose concentration and quenching temperature, and is in the range from a fraction of micrometers to a few micrometers, in agreement with earlier experiments. Bundling of the double-helical segments is known to follow self-assembly and can be considered as a third step (gel curing). This follows from the thermo-dynamic instability of the helical segments in the solvent, behaving as a system of rod-like particles connected by more or less flexible joints. The two processes leading in succession to self-assembly are discussed in terms of a phase diagram consistent with available data. Their time scales differ remarkably. At the end of the first process, all polymers remain random coiled and freely drifting. Much later coil–helix transition is observed, always in coincidence with polymer cross-linking and gelation. The enhancement of concentration of random-coiled polymers in specific regions of the sol caused by spinodal demixing is thus a prerequisite for self-assembly of these biostructural gels in the concentration interval studied. Conceptually, concentration enhancements of this type can provide a new pathway for promotion of functional biomolecular interactions even at very low average concentrations. The mechanism will work identically if the region of instability is reached by varying the polymer concentration (e.g., by biosynthesis), rather than by temperature quenching.     

Studies of thermotropic phospholipid phase transitions using scanning densitometry

The thermotropic phase transitions were determined for a variety of phospholipids including dimyristoyl (DMPC) and distearoyl phosphatidylcholine (DSPC); dimyristoyl (DMPE), dioleoyl (DOPE) and egg phospatidylethanolamine (PE); egg and bovine brain sphingomyelin (SM) and bovine brain phosphatidylserine (PS) in the presence and absence of calcium or magnesium. The gel to liquid crystal phase transition is accompanied by a 2–4% increase in volume for a variety of phospholipids. This transition can be readily detected by scanning densitometry with multilamellar suspensions of phospholipids. In contrast, the liquid crystal to hexagonal phase transition does not involve any detectable change in volume. In addition, the volume coefficient of expansion for the hexagonal phase is similar to that found for several other bilayer systems. PS in the presence of Ca²⁺, SMs and DMPC at 50°C all have lower values of the volume coefficient of expansion. This property may be correlated with the resistance of these systems to the formation of additional gauche isomers in the hydrocarbon chains with increasing temperatures resulting in lowered permeability.     

Karyopherins and condensates

Several aggregation-prone RNA-binding proteins, including FUS, EWS, TAF15, hnRNP A1, hnRNP A2, and TDP-43, are mutated in neurodegenerative diseases. The nuclear–cytoplasmic distribution of these proteins is controlled by proteins in the karyopherin family of nuclear transport factors (Kaps). Recent studies have shown that Kaps not only transport these proteins but also inhibit their self-association/aggregation, acting as molecular chaperones. This chaperone activity is impaired for disease-causing mutants of the RNA-binding proteins. Here, we review physical data on the mechanisms of self-association of several disease-associated RNA-binding proteins, through liquid–liquid phase separation and amyloid fiber formation. In each case, we relate these data to biophysical, biochemical, and cell biological data on the inhibition of self-association by Kaps. Our analyses suggest that Kaps may be effective chaperones because they contain large surfaces with diverse physical properties that enable them to engage multiple different regions of their cargo proteins, blocking self-association.     

Nucleic acid actions on abnormal protein aggregation,phase transitions and phase separation

Liquid–liquid phase separation (LLPS) and phase transitions (PT) of proteins, which include the formation of gel- and solid-like species, have been characterized as physical processes related to the pathology of conformational diseases. Nucleic acid (NA)-binding proteins related to neurodegenerative disorders and cancer were shown by us and others to experience PT modulated by different NAs. Herein, we discuss recent work on phase separation and phase transitions of two amyloidogenic proteins, i.e. the prion protein (PrP) and p53, which undergo conformational changes and aggregate upon NA interaction. The role of different NAs in these processes is discussed to shed light on the relevance of PSs and PTs for both the functional and pathological roles of these mammalian proteins.     

Polymorphic phase behavior of platelet-activating factor.

Vibrational Raman and 31P NMR spectroscopic experiments have been performed as a function of temperature on aqueous dispersions of 1-0-octadecyl-2-acetoyl-sn-glycero-3-phosphocholine, a chemically synthesized platelet-activating factor. In the temperature range of -7 to 30 degrees C, the C(18)/PAF-H2O system is shown, upon heating, to undergo two thermal phase transitions centered at 9.2 degrees and 18.4 degrees C. The low temperature transition, attributed to the interdigitated lamellar gel (II)----gel (I) phase transition, is characterized by the breakdown of large lamellar organizations into small, but aggregated, bilayer vesicles. The high-temperature transition corresponds to the interdigitated lamellar gel (I)----micellar transition. The molecular ordering and packing structure of C(18)/PAF in the two lamellar phases and phase transition regions are described. It appears that the interdigitated lamellar gel (I) phase is unique for C(18)/PAF dispersions when compared with the behavior of other chemically closely related phospholipids in excess water.     

Kinetics of the lamellar and hexagonal phase transitions in phosphatidylethanolamine. Time-resolved x-ray diffraction study using a microwave-induced temperature jump.

The kinetics of the thermotropic lamellar gel (L beta')/lamellar liquid crystal (L alpha) and L alpha/inverted hexagonal (HII) phase transitions in fully hydrated dihexadecylphosphatidylethanolamine (DHPE) have been studied. Measurements were made by using time-resolved x-ray diffraction (TRXRD) to monitor progress of the transitions. In these studies microwave energy at 2.5 GHz was used to increase the sample temperature rapidly and uniformly through the phase transition regions. The L beta'/L alpha and L alpha/HII transitions of DHPE were examined under active microwave heating and passive cooling. The transitions were found to be repeatable and reversible, and to have an upper bound on the time required to complete the transition of less than 3 s. Regardless of the direction of the transition, both phase transitions appeared to be two-state with no accumulation of intermediates to within the sensitivity limits of the TRXRD method. The rate and amplitude of the temperature jump can be controlled by regulating microwave radiation input power. A temperature jump rate of 29 degrees C/s was obtained at a final microwave power setting of 120 W. Comparisons between previously reported fluid flow (Caffrey, M. 1985. Biochemistry. 24:4826-4844) and microwave heating studies suggest that the determination of limiting transit times will require faster heating.     

A temperature–concentration (T–X) phase diagram calculated using the mean field theory for liquid crystals

Phase-line equations for smectic–hexatic phase transitions in liquid crystals were derived using the Landau phenomenological theory. In particular, second-order transitions for the smectic-A–smectic-C (SmA–SmC) and hexatic-B–hexatic-F (or HexI) transitions were studied and the tricritical points for these transitions were located. The calculated phase-line equations were fitted (using experimental data for various liquid crystals) to construct a generalized T–X phase diagram. It was shown that the T–X phase diagram calculated from the free energy adequately describes the observed behavior of liquid crystals during smectic–hexatic transitions.     

Calcium-binding and temperature induced transitions in equine lysozyme: new insights from the pCa-temperature "phase diagrams"

The most universal approach to the studies of metal binding properties of single-site metal binding proteins, i.e., construction of a "phase diagram" in coordinates of free metal ion concentration-temperature, has been applied to equine lysozyme (EQL). EQL has one relatively strong calcium binding site and shows two thermal transitions, but only one of them is Ca(2+)-dependent. It has been found that the Ca(2+)-dependent behavior of the low temperature thermal transition (I) of EQL can be adequately described based upon the simplest four-states scheme of metal- and temperature-induced structural changes in a protein. All thermodynamic parameters of this scheme were determined experimentally and used for construction of the EQL phase diagram in the pCa-temperature space. Comparison of the phase diagram with that for alpha-lactalbumin (alpha-LA), a close homologue of lysozyme, allows visualization of the differences in thermodynamic behavior of the two proteins. The thermal stability of apo-EQL (transition I) closely resembles that for apo-alpha-LA (mid-temperature 25 degrees C), while the thermal stabilities of their Ca(2+)-bound forms are almost indistinguishable. The native state of EQL has three orders of magnitude lower affinity for Ca(2+) in comparison with alpha-LA while its thermally unfolded state (after the I transition) has about one order lower (K = 15M(-1)) affinity for calcium. Circular dichroism studies of the apo-lysozyme state after the first thermal transition show that it shares common features with the molten globule state of alpha-LA.     

Thermal response of Langmuir-Blodgett films of dipalmitoylphosphatidylcholine studied by atomic force microscopy and force spectroscopy

The topographic evolution of supported dipalmitoylphosphatidylcholine (DPPC) monolayers with temperature has been followed by atomic force microscopy in liquid environment, revealing the presence of only one phase transition event at approximately 46 degrees C. This finding is a direct experimental proof that the two phase transitions observed in the corresponding bilayers correspond to the individual phase transition of the two leaflets composing the bilayer. The transition temperature and its dependency on the measuring medium (liquid saline solution or air) is discussed in terms of changes in van der Waals, hydration, and hydrophobic/hydrophilic interactions, and it is directly compared with the transition temperatures observed in the related bilayers under the same experimental conditions. Force spectroscopy allows us to probe the nanomechanical properties of such monolayers as a function of temperature. These measurements show that the force needed to puncture the monolayers is highly dependent on the temperature and on the phospholipid phase, ranging from 120+/-4 pN at room temperature (liquid condensed phase) to 49+/-2 pN at 65 degrees C (liquid expanded phase), which represents a two orders-of-magnitude decrease respective to the forces needed to puncture DPPC bilayers. The topographic study of the monolayers in air around the transition temperature revealed the presence of boundary domains in the monolayer surface forming 120 degrees angles between them, thus suggesting that the cooling process from the liquid-expanded to the liquid-condensed phase follows a nucleation and growth mechanism.     

Nmr studies of mixtures of poly-L-lysine hydrobromide with water

¹H, ²H, ¹³C, and ⁸¹Br nmr measurements of mixtures of poly-L -lysine hydrobromide with water have been carried out over a range of temperatures and water contents. When n (number of molecules of water per residue) ～13 at room temperature, a transition occurs from a gel to a liquid phase. The liquid phase contains polymer molecules that are flexible, but contain more intramolecular structure than the same molecules in trifluoracetic acid solution. The gel phase contains junction zones of hexagonally packed α-helices, linked by flexible regions of polypeptide chain. The α-helical residues impart to their associated water molecules a slight anisotropy of motion, which is dectable by ²H nmr. These residues bind up to about seven molecules of water each; the other six required to complete the gel–liquid transition space out the polymer molecules, allowing increased segmental motion of the residues in the flexible regions. This increased motion reduces the energy of the flexible regions and thus increases the proportion of residues in them (increasing the temperature has the same effect); the transition occurs when insufficient residues remain in the α-helical junction zones.     

The phase behaviour of 1,2-diacyl-3-monogalactosyl-sn-glycerol derivatives

Monogalactosyldiacylglycerol was isolated from the blue-green alga Anacystis nidulans. Part of this lipid, which is rich in the 1–16:1/2–16:0 derivative, was hydrogenated to yield a lipid fraction rich in the 1–16:0/2–16:0 derivative. The phase behaviour of the two fractions were studied using differential scanning calorimetry, wide-angle X-ray diffraction and freeze-fracture electron microscopy. Both fractions exhibited complex polymorphic behaviour. Two distinct gel phases were identified; a stable form (MGDG₁) and a metastable form (MGDG_II). The transition temperatures for the two forms were 345 K and 325 K for the 1–16:0/2–16:0 fraction and 311 K and 279 K for the 1–16:1/2–16:0 fraction, respectively. The corresponding enthalpy values were 59.3 and 24.5 kJ · mol⁻¹ and 51.4 and 11.5 kJ · mol⁻¹. Inverted hexagonal (H₁₁) phases were seen at higher temperatures. The transition to the H₁₁ phase appears to occur directly from MGDG₁ gel phase, but may involve the formation of a lamellar liquid -crystalline phase existing between the melting points of the two gel phases in the case of the transitions from the MGDG₁₁ gel phase.     

GPU-accelerated replica exchange molecular simulation on solid–liquid phase transition study of Lennard-Jones fluids

Determining the solid–liquid phase transition point by conventional molecular dynamics (MD) simulations is difficult because of the tendency of the system to get trapped in local minimum energy states at low temperatures and hysteresis during cooling and heating cycles. The replica exchange method, used in performing many MD simulations of the system at different temperature conditions simultaneously and performs exchanges of these temperatures at certain intervals, has been introduced as a tool to overcome this local-minimum problem. However, around the phase transition temperature, a greater number of different temperatures are required to adequately find the phase transition point. In addition, the number of different temperature values increases when treating larger systems resulting in huge computation times. We propose a computational acceleration of the replica exchange MD simulation on graphics processing units (GPUs) in studying first-order solid–liquid phase transitions of Lennard-Jones (LJ) fluids. The phase transition temperature for a 108-atom LJ fluid has been calculated to validate our new code. The result corresponds with that of a previous study using multicanonical ensemble. The computational speed is measured for various GPU-cluster sizes. A peak performance of 196.3 GFlops with one GPU and 8.13 TFlops with 64 GPUs is achieved.     

Phasing in on the cell cycle

Just like all matter, proteins can also switch between gas, liquid and solid phases. Protein phase transition has claimed the spotlight in recent years as a novel way of how cells compartmentalize and regulate biochemical reactions. Moreover, this discovery has provided a new framework for the study of membrane-less organelle biogenesis and protein aggregation in neurodegenerative disorders. We now argue that this framework could be useful in the study of cell cycle regulation and cancer. Based on our work on phase transitions of arginine-rich proteins in neurodegeneration, via combining mass spectroscopy with bioinformatics analyses, we found that also numerous proteins involved in the regulation of the cell cycle can undergo protein phase separation. Indeed, several proteins whose function affects the cell cycle or are associated with cancer, have been recently found to phase separate from the test tube to cells. Investigating the role of this process for cell cycle proteins and understanding its molecular underpinnings will provide pivotal insights into the biology of cell cycle progression and cancer.     

Resilience and Thresholds in Savannas: Nitrogen and Fire as Drivers and Responders of Vegetation Transition

Resilience theory suggests that ecosystems can persist for long periods, before changing rapidly to a new vegetation phase. Transition between phases occurs when ecological thresholds have been crossed, and is followed by a reorganization of biotic and environmental interactions, leading to the emergence of a new vegetation phase or quasi-stable state. Savannas are dynamic, complex systems in which fire, herbivory, water and nutrient availability interact to determine tree abundance. Phase and transition has been observed in savannas, but the role of these different possible drivers is not always clear. In this study, our objectives were to identify phase and transition in the fossil pollen record, and then to explore the role of nitrogen and fire in these transitions using δ¹⁵N isotopes and charcoal abundance. We present palaeoenvironmental data from the Kruger National Park, South Africa, which show transition between grassland and savanna phases. Our results show transition at the end of the ninth century A.D. from a nutrient- and herbivore-limited grazing lawn, in which fire was absent and C₄ grasses were the dominant and competitively superior plant form, to a water-, fire- and herbivory-limited semi-arid savanna, in which C₄ grasses and C₃ trees and shrubs co-existed. The data accord with theoretical frameworks that predict that variability in ecosystems clusters in regions of higher probability space, interspersed by rapid transitions between these phases. The data are also consistent with the idea that phase transitions involve switching between different dominant driving processes or limiting factors.     

Peptide induced demixing in PG/PE lipid mixtures: A mechanism for the specificity of antimicrobial peptides towards bacterial membranes?

Antimicrobial peptides attract a lot of interest as potential candidates to overcome bacterial resistance. So far, nearly all the proposed scenarios for their mechanism of action are associated with perforating and breaking down bacterial membranes after a binding process. In this study we obtained additional information on peptide induced demixing of bacterial membranes as a possible mechanism of specificity of antimicrobial peptides. We used DSC and FT-IR to study the influence of a linear and cyclic arginine- and tryptophan-rich antimicrobial peptide having the same sequence (RRWWRF) on the thermotropic phase transitions of lipid membranes. The cyclization of the peptide was found to enhance its antimicrobial activity and selectivity ( Dathe, M. Nikolenko, H. Klose, J. Bienert, M. Biochemistry 43 (2004) 9140-9150). A particular preference of the binding of the peptides to DPPG headgroups compared to other headgroups of negatively charged phospholipids, namely DMPA, DPPS and cardiolipin was observed. The main transition temperature of DPPG bilayers was considerably decreased by the bound peptides. The peptides caused a substantial down-shift of the transition of DPPG/DMPC. In contrast, they induced a demixing in DPPG/DPPE bilayers and led to the appearance of two peaks in the DSC curves indicating a DPPG-peptide-enriched domain and a DPPE-enriched domain. These results could be confirmed by FT-IR-spectroscopic measurements. We therefore propose that the observed peptide-induced lipid demixing in PG/PE-membranes could be a further specific effect of the antimicrobial peptides operating only on bacterial membranes, which contain appreciable amounts of PE and PG, and which could in principle also occur in liquid-crystalline membranes.     

The effect of increasing membrane curvature on the phase transition and mixing behavior of a dimyristoyl-sn-glycero-3-phosphatidylcholine/ distearoyl-sn-glycero-3-phosphatidylcholine lipid mixture as studied by Fourier transform infrared spectroscopy and differential scanning calorimetry.

The phase transition behavior of a lipid bilayer of dimyristoyl-sn-glycero-3-phosphatidylcholine/distearoyl-sn-glycero-3- phosphatidylcholine (DMPC-d54/DSPC) (1:1) on a solid support with varying curvatures was investigated with differential scanning calorimetry, infrared spectroscopy, and model calculations. With increasing curvature the temperatures of the liquidus and solidus points are shifted to lower values by up to 7 degrees C and 15 degrees C, and the mixing of the two lipid species in the two phase region is altered. With increasing curvature the DSPC dominates the gel phase, whereas the DMPC-d54 is expelled to the fluid phase. Whereas the planar system shows a nearly simultaneous phase transition of DSPC and DMPC-d54, the spherical system with the highest curvature exhibits an almost complete separation of the phase transitions of the two lipids. Model calculations suggest that the shift of the liquidus point can be understood as a reduction of the lateral pressure in the bilayer with increasing curvature. The shift of the solidus line is interpreted as a result of the increased demixing of the two components in the two-phase region with increasing curvature due to lowering of the lateral pressure.