Droplet organelles?

Cells contain numerous, molecularly distinct cellular compartments that are not enclosed by lipid bilayers. These compartments are implicated in a wide range of cellular activities, and they have been variously described as bodies, granules, or organelles. Recent evidence suggests that a liquid–liquid phase separation (LLPS) process may drive their formation, possibly justifying the unifying term “droplet organelle”. A veritable deluge of recent publications points to the importance of low‐complexity proteins and RNA in determining the physical properties of phase‐separated structures. Many of the proteins linked to such structures are implicated in human diseases, such as amyotrophic lateral sclerosis (ALS). We provide an overview of the organizational principles that characterize putative “droplet organelles” in healthy and diseased cells, connecting protein biochemistry with cell physiology.     

Building self-avoiding lattice models of proteins using a self-consistent field optimization

We present an algorithm to build self-avoiding lattice models of chain molecules with low RMS deviation from their actual 3D structures. To find the optimal coordinates for the lattice chain model, we minimize a function that consists of three terms: (1) the sum of squared deviations of link coordinates on a lattice from their off-lattice values, (2) the sum of “short-range” terms, penalizing violation of chain connectivity, and (3) the sum of “long-range” repulsive terms, penalizing chain self-intersections. We treat this function as a chain molecule “energy” and minimize it using self-consistent field (SCF) theory to represent the pairwise link repulsions as 3D fields acting on the links. The statistical mechanics of chain molecules enables computation of the chain distribution in this field on the lattice. The field is refined by iteration to become self-consistent with the chain distribution, then dynamic programming is used to find the optimal lattice model as the “lowest-energy” chain pathway in this SCF. We have tested the method on one of the coarsest (and most difficult) lattices used for model building on proteins of all structural types and show that the method is adequate for building self-avoiding models of proteins with low RMS deviations from the actual structures. © 1996 Wiley-Liss, Inc.     

Problems in the estimation of mutation rates and in the detection of induced mutations in man

The contribution of nuclear-directed protein synthesis in the repair of lethal and mitochondrial genetic damage after UV-irradiation of exponential and stiationary phase haploid yeast cells was examined. This was carried out using cycloheximide (CH), a specific inhibitor of nuclear protein synthesis. It appears that nuclear protein synthesis required for the increase in survival seen after the liquid holding of cells at both stages, as well as for the “petite” recovery seen after the liquid holding of exponential phase cells. The characteristic negative liquid holding effect observed for the UV induction of “petites” in stationary phase cells (increase of the frequency of “petites” during storage) remained following all the treatments which inhibited nuclear protein synthesis. However, the application of photoreactivating light following dark holding with cycloheximide indicates that some steps of the repair of both nuclear and mitochondrial damage are performed in the absence of a synthesis of proteins.     

The temperature dependence of water and counter ion order in soap-water mesophases. A deuterium and sodium NMR study

Deuterium magnetic resonance (DMR) spectra of the water and hydrocarbon chains in potassium and sodium palmitates and sodium magnetic resonance spectra of sodium in sodium palmitate demonstrate correlations between water, hydrocarbon chain and counter ion order. In the lamellar phase of potassium palmitate the order parameters inferred from DMR splittings of D₂O and the first few methylene chain segments initially increase and then decrease with increasing temperature. This is explained in terms of a model where the lipid-water structure at low temperatures imposes a direction for which all the order parameters are smaller than for the higher temperature structure for purely geometric reasons. As temperature increases the structuring effect of water decreases and there is an “apparent” increase in order until at even higher temperatures there is an intrinsic decrease in order parameter. In addition, for potassium palmitate the DMR splittings of D₂O and the first few methylene segments indicate a “phase transition” within the liquid crystalline phase.     

Membrane Bending Moduli of Coexisting Liquid Phases Containing Transmembrane Peptide

A number of highly curved membranes in vivo, such as epithelial cell microvilli, have the relatively high sphingolipid content associated with “raft-like” composition. Given the much lower bending energy measured for bilayers with “nonraft” low sphingomyelin and low cholesterol content, observing high curvature for presumably more rigid compositions seems counterintuitive. To understand this behavior, we measured membrane rigidity by fluctuation analysis of giant unilamellar vesicles. We found that including a transmembrane helical GWALP peptide increases the membrane bending modulus of the liquid-disordered (Ld) phase. We observed this increase at both low-cholesterol fraction and higher, more physiological cholesterol fraction. We find that simplified, commonly used Ld and liquid-ordered (Lo) phases are not representative of those that coexist. When Ld and Lo phases coexist, GWALP peptide favors the Ld phase with a partition coefficient of 3–10 depending on mixture composition. In model membranes at high cholesterol fractions, Ld phases with GWALP have greater bending moduli than the Lo phase that would coexist.     

Temperature-induced vertical shift of proteins in membranes

Thermotropic changes in the transverse order of microsomal membranes isolated from Tetrahymena are revealed by low-angle X-ray diffraction. These are correlated with the lateral order of the membrane lipids by wide-angle X-ray diffraction. Upon lowering the temperature from 28 °C to 2 °C, the Bragg period of the membrane stack reveals an abrupt increase of ~3.0 nm at ~19 °C, which is reversible upon reheating to 28 °C. This is coupled with an alteration in the electron density profile, revealing a shift of mass from the hydrophobic core towards one of the two hydrophilic surfaces. Between 35 °C and 0 °C, the membrane lipids undergo a broad, thermotropic “two-stage” liquid crystalline ? crystalline phase separation with a “breakpoint” at ~18 °C. This breakpoint signals an abrupt lipid redistribution, presumably due to a change in the composition of the two coexisting liquid crystalline and crystalline lipid phases. We conclude: (1) the temperature-induced mass shift reflects a shift in the transverse partition of proteins in membranes; (2) this is triggered by an abrupt lipid redistribution occurring during a broad liquid crystalline ? crystalline phase separation.     

Structural analysis of the S-Layer of Lampropedia hyalina

The two-dimensional (2D) structure of the regularly structured surface layer (S-layer) of the gram-negative eubacterium Lampropedia hyalina has been determined at the molecular level to a nominal resolution of 2.1 nm by transmission electron microscopy and digital image processing. The inner, or “perforate,” layer consists of dimeric block-shaped units located at two-fold symmetry axes. These morphological dimers associate around three-fold symmetry axes to form a continuous layer with p6 symmetry and a lattice constant of 14.6 ± 0.4 nm. Scanning transmission electron microscopy (STEM) yields a mass-per-area (MPA) value for the perforate layer of 3.5 kDa/nm². The outer, or “punctate,” layer is composed of long, roughly cylindrical units centered on six-fold symmetry axes, which are connected by six fine linking arms joining at the three-fold symmetry axes to create a hexagonal layer with a lattice constant of 25.6 ± 0.5 nm. The MPA of the “composite”-i.e., perforate plus punctate—layer is 10.2 kDa/nm².     

Phase response properties of half-center oscillators

We examine the phase response properties of half-center oscillators (HCOs) that are modeled by a pair of Morris-Lecar-type neurons connected by strong fast inhibitory synapses. We find that the two basic mechanisms for half-center oscillations, “release” and “escape”, give rise to strikingly different phase response curves (PRCs). Release-type HCOs are most sensitive to perturbations delivered to cells at times when they are about to transition from the active to the suppressed state, and PRCs are dominated by a large negative peak (phase delays) at corresponding phases. On the other hand, escape-type HCOs are most sensitive to perturbations delivered to cells at times when they are about to transition from the suppressed to the active state, and PRCs are dominated by a large positive peak (phase advances) at corresponding phases. By analyzing the phase space structure of Morris-Lecar-type HCO models with fast synaptic dynamics, we identify the dynamical mechanisms underlying the shapes of the PRCs. To demonstrate the significance of the different shapes of the PRCs for the release-type and escape-type HCOs, we link the shapes of the PRCs to the different frequency modulation properties of release-type and escape-type HCOs, and we show that the different shapes of the PRCs for the release-type and escape-type HCOs can lead to fundamentally different phase-locking dynamics.     

Separation of liquid phases in giant vesicles of ternary mixtures of phospholipids and cholesterol

We use fluorescence microscopy to directly observe liquid phases in giant unilamellar vesicles. We find that a long list of ternary mixtures of high melting temperature (saturated) lipids, low melting temperature (usually unsaturated) lipids, and cholesterol produce liquid domains. For one model mixture in particular, DPPC/DOPC/Chol, we have mapped phase boundaries for the full ternary system. For this mixture we observe two coexisting liquid phases over a wide range of lipid composition and temperature, with one phase rich in the unsaturated lipid and the other rich in the saturated lipid and cholesterol. We find a simple relationship between chain melting temperature and miscibility transition temperature that holds for both phosphatidylcholine and sphingomyelin lipids. We experimentally cross miscibility boundaries both by changing temperature and by the depletion of cholesterol with beta-cyclodextrin. Liquid domains in vesicles exhibit interesting behavior: they collide and coalesce, can finger into stripes, and can bulge out of the vesicle. To date, we have not observed macroscopic separation of liquid phases in only binary lipid mixtures.     

Comparison of Poisson-Boltzmann and condensation model expression for the colligative properties of cylindrical polyions

Closed-form expression have been derived for the polyelectrolyte contribution to the colligative properties of solutions containing rodlike polyions in the presence of excess added salt. The derivations are based on: the conventional Poisson-Boltzmann equation for cylindrical symmetry; the thermodynamics of the cell model developed by Marcus [J. Chem. Phys. 23 , 1057–1068 (1955)]; and an equation derived from the cylindrical Poisson-Boltzmann cell model by Anderson and Record [Biophys. Chem. 11 , 353–360 (1980)]. Subject to the inherent limitations of the Poisson-Boltzmann approximation [Fixman (1979) J. Chem. Phys. 70 , 4995–5005], the resulting expressions are nevertheless applicable outside the “limit of infinite dilution.” They conform over a range of salt concentrations to the limiting laws deduced by Manning from the hypothesis of counterion condensation [J. Chem. Phys. 51 , 924–933 (1969)]. This hypothesis is found to be compatible with the Poisson-Boltzmann cell model but is not required in the derivation of the thermodynamic coefficients presented here. It is demonstrated that the magnitude of the polyion axial charge density plays a critical role in determining the low-salt limiting forms of the colligative properties obtained from the Poisson-Boltzmann equation, in close analogy with Manning's model.     

SYMMETRY,LOCOMOTION, AND THE EVOLUTION OF AN ANTERIOR END: A LESSON FROM SEA URCHINS

Bilaterally symmetrical, “regular” sea urchins in the Family Echinometridae (Class Echinoidea; Phylum Echinodermata) were found to lack a locomotor anterior. Heterocentrotus mammillatus and Echinometra mathaei were observed while locomoting. Members of both ellipsoidal species were found to proceed with their short or long axis foremost with statistically equivalent frequencies. This finding demonstrates that the evolution of bilateral symmetry is not always accompanied by the evolution of a locomotor “anterior” end. The elliptical echinometrid sea urchins provide a particularly appropriate study group for investigating the relationship between the evolution of body form and locomotor behavior. Although the radially symmetrical regular sea urchins, from which the echinometrids sprang, lack a locomotor anterior, all “irregular” echinoids, which are also derived from a regular ancestor but are bilaterally symmetrical, possess an “obligate” locomotor anterior. The symmetry and behavior exhibited by the elliptical echinometrid sea urchins therefore demonstrates that the first irregular echinoids (which exhibit bilateral symmetry by definition) need not have possessed a locomotor anterior as they do today.     

Preparative high-performance liquid partition chromatography of proteins.

Methods for preparative high-performance liquid chromatography (hplc) of proteins are described. Both normal and reverse-phase chromatography were studied and adapted to the fractionation of proteins in quantities of up to 50 mg. Lichrosorb Diol was used as a “normal phase” for chromatography of hydrophobic proteins. Lichrosorb RP-8 was used for reversephase chromatography of proteins.     

The accommodation index measures the perturbation associated with insertions and deletions in coiled‐coils: Application to understand signaling in histidine kinases

Coiled‐coils are essential components of many protein complexes. First discovered in structural proteins such as keratins, they have since been found to figure largely in the assembly and dynamics required for diverse functions, including membrane fusion, signal transduction and motors. Coiled‐coils have a characteristic repeating seven‐residue geometric and sequence motif, which is sometimes interrupted by the insertion of one or more residues. Such insertions are often highly conserved and critical to interdomain communication in signaling proteins such as bacterial histidine kinases. Here we develop the “accommodation index” as a parameter that allows automatic detection and classification of insertions based on the three dimensional structure of a protein. This method allows precise identification of the type of insertion and the “accommodation length” over which the insertion is structurally accommodated. A simple theory is presented that predicts the structural perturbations of 1, 3, 4 residue insertions as a function of the length over which the insertion is accommodated. Analysis of experimental structures is in good agreement with theory, and shows that short accommodation lengths give rise to greater perturbation of helix packing angles, changes in local helical phase, and increased structural asymmetry relative to long accommodation lengths. Cytoplasmic domains of histidine kinases in different signaling states display large changes in their accommodation lengths, which can now be seen to underlie diverse structural transitions including symmetry/asymmetry and local variations in helical phase that accompany signal transduction.     

Comments

Abstract

Animal Models

Upon reading the forum papers we note that “stealth” properties of liposomes apparently still have not been examined extensively in any animal model other than relatively young rodents (mainly mice). The “stealth” concept would be enhanced by studies in species other than mice. If opsonic properties of blood proteins, particularly the presence of naturally-occurring antibodies to phospholipids and cholesterol and resultant complement activation, have any relevance to the removal of liposomes from mouse blood, then it is possible that different liposomes will exhibit “stealth” properties under other circumstances (such as in older mice that often have high titers of antibodies to lipids) or in other animal species. In view of the presumed interest in the commercial exploitation of “stealth” technology it would seem useful to have validating experiments performed in other species, such as dogs, pigs, sheep, and especially in primates.     

Calculation of intermolecular interaction strengths in the P beta' phase in lipid bilayers. Implications for theoretical models.

The existence of the P beta' phase in certain lipid bilayers is evidence that molecular interactions between lipids are capable of producing unusual large-scale structures at or near biological conditions. The problem of identifying the specific intermolecular interactions responsible for the structures requires construction of theoretical models capable of clear predictions of the observable consequences of postulated intermolecular interactions. To this end we have carried out a twofold modeling effort aimed at understanding the ripple phase. First, we have performed detailed numerical calculations of potential energies of interaction between pairs and triplets of lipid molecules having different chain tilt angles and relative vertical alignments. The calculations support the notion that chain tilting in the gel phase is a result of successive 3-5-A displacements of neighboring molecules perpendicular to the bilayer plane rather than long-range cooperative chain tilting. Secondly, we have used these results as a guide to formulate a new lattice model for lipid bilayer condensed phases. The new model is less complex than our earlier model and it includes interactions which are, based on the energy calculations, more likely to be responsible for the ripple phase. In a certain limit the model maps onto the chiral clock model, a model of much interest in condensed matter theory. In this limit the model exhibits a chain-tilted ordered phase followed by (as temperature increases) a modulated phase followed by a disordered phase. Within this limit we discuss the properties of the model and compare structures of the modulated phase exhibited by the model with experimental data for the P beta' phase in lipid bilayers.     

Two enzyme active transport in vitro with ph induced asymmetrical functional structures: I. The model and its analytical treatment

A class of systems is characterized by the asymmetrical distribution of a sink and a source reaction, the asymmetry of the global chemical equation (energy liberation) and by an asymmetrical one-wave space profile. These systems belong to the family of primary chemical cells and can deplete and enrich the media they separate. A “ one way ” transport-reaction chain is needed for specific “ real ” active transport. A two enzyme model of this class is described in which the spatial asymmetry is due to a (diffusive) pH gradient; this distribution of “ potential ” enzyme activities is called the “ functional structure ”. Equal potential enzyme activities and absence of reactive back action on local pH are assumed in the “ square model ” version of the pump. Analytical expressions of the enzymatic diffusion reactions are derived for zero and first order kinetics, i.e. in function of substrate concentrations. Tables of equations are presented. The intrinsic properties of the pump are characterized by (dimensionless) transport reaction parameters, (membrane composition); the “ potential ” activity is controlled by the pH gradient; the “ effective ” pumping is also a function of the substrate concentrations on the boundaries.     

Assembly of Mitotic Structures through Phase Separation

Cells compartmentalize biochemical reactions using organelles, which can be membrane enclosed or built entirely of proteins and ribonucleic acids. Recent studies indicate that many organelles that lack membranes have liquid-like properties, including the ability to flow, fuse, and undergo rapid internal rearrangement. The assembly of these “biomolecular condensates” has been described as liquid–liquid phase separation, whereby their constituent components demix from the cytoplasm, similar to water separating from oil. Other studies suggest that protein phase separation followed by maturation, where intramolecular connections strengthen over time, can lead to gel- or glass-like states. This review discusses how the principles of phase separation might help to understand the assembly and behavior of organelles that operate in mitosis, when the cell assembles the mitotic spindle to segregate chromosomes. Special attention is given to the mitotic pericentriolar material of centrosomes and the spindle matrix.     

The self-assembly and liquid crystal formation of d(GpGpApGpG)

d(GpGpApGpG) dissolved in water forms liquid crystalline phases of the cholesteric and hexagonal type. The building blocks of the phases are columnar four-stranded aggregates composed of G quartets. The diameter of the columnar aggregates is larger and the melting temperature is lower than for homoguanylic derivatives, indicating a distorsion and loss of stability due to the presence of adenines, which do not form a hydrogen-bonded quartet. The present study shows that, as often observed for single crystals, it is possible also in the liquid crystalline phase to construct long columnar aggregates composed of shorter segments of the blunt-end type in a “closed architecture.” © 1997 John Wiley & Sons, Inc. Biopoly 42: 561–574, 1997