Opposite effects of electrostatics and steric exclusion on bundle formation by F-actin and other filamentous polyelectrolytes

The structure and mechanics of the cell cortex depend on the location and adhesion state

Cells exist in different phenotypes and can transition between them. A phenotype may be characterized by many different aspects. Here, we focus on the example of whether the cell is adhered or suspended and choose particular parameters related to the structure and mechanics of the actin cortex. The cortex is essential to cell mechanics, morphology, and function, such as for adhesion, migration, and division of animal cells. To predict and control cellular functions and prevent malfunctioning, it is necessary to understand the actin cortex. The structure of the cortex governs cell mechanics; however, the relationship between the architecture and mechanics of the cortex is not yet well enough understood to be able to predict one from the other. Therefore, we quantitatively measured structural and mechanical cortex parameters, including cortical thickness, cortex mesh size, actin bundling, and cortex stiffness. These measurements required developing a combination of measurement techniques in scanning electron, expansion, confocal, and atomic force microscopy. We found that the structure and mechanics of the cortex of cells in interphase are different depending on whether the cell is suspended or adhered. We deduced general correlations between structural and mechanical properties and show how these findings can be explained within the framework of semiflexible polymer network theory. We tested the model predictions by perturbing the properties of the actin within the cortex using compounds. Our work provides an important step toward predictions of cell mechanics from cortical structures and suggests how cortex remodeling between different phenotypes impacts the mechanical properties of cells.

Both Las17-binding sites on Arp2/3 complex are important for branching nucleation and assembly of functional endocytic actin networks in S. cerevisiae

Arp2/3 complex nucleates branched actin filaments that drive membrane invagination during endocytosis and leading-edge protrusion in lamellipodia. Arp2/3 complex is maximally activated in vitro by binding of a WASP family protein to two sites-one on the Arp3 subunit and one spanning Arp2 and ARPC1-but the importance of each site in the regulation of force-producing actin networks is unclear. Here, we identify mutations in budding yeast Arp2/3 complex that decrease or block engagement of Las17, the budding yeast WASP, at each site. As in the mammalian system, both sites are required for maximal activation in vitro. Dimerization of Las17 partially restores activity of mutations at both CA-binding sites. Arp2/3 complexes defective at either site assemble force-producing actin networks in a bead motility assay, but their reduced activity hinders motility by decreasing actin assembly near the bead surface and by failing to suppress actin filament bundling within the networks. While even the most defective Las17-binding site mutants assembled actin filaments at endocytic sites, they showed significant internalization defects, potentially because they lack the proper architecture to drive plasma membrane remodeling. Together, our data indicate that both Las17-binding sites are important to assemble functional endocytic actin networks in budding yeast, but Arp2/3 complex retains some activity in vitro and in vivo even with a severe defect at either Las17-binding site.

Nonmonotonic electrophoretic mobility of rodlike polyelectrolytes by multivalent coions in added salt

It is well established that when multivalent counterions or salts are added to a solution of highly charged polyelectrolytes (PEs), correlation effects can cause charge inversion of the PE, leading to electrophoretic mobility (EM) reversal. In this work, we use coarse-grained molecular-dynamics simulations to unravel the less understood effect of coion valency on EM reversal for rigid DNA-like PEs. We find that EM reversal induced by multivalent counterions is suppressed with increasing coion valency in the salt added and eventually vanishes. Further, we find that EM is enhanced at fixed low salt concentrations for salts with monovalent counterions when multivalent coions with increasing valency are introduced. However, increasing the salt concentration causes a crossover that leads to EM reversal which is enhanced by increasing coion valency at high salt concentration. Remarkably, this multivalent coion-induced EM reversal persists even for low values of PE linear charge densities where multivalent counterions alone cannot induce EM reversal. These results facilitate tuning PE-PE interactions and self-assembly with both coion and counterion valencies.

Interactions between Rigid Polyelectrolytes Mediated by Ordering and Orientation of Multivalent Nonspherical Ions in Salt Solutions

Multivalent ions in solutions with polyelectrolytes (PEs) induce electrostatic correlations that can drastically change ion distributions around the PEs and their mutual interactions. Using coarse-grained molecular dynamics simulations, we show how in addition to valency, ion shape and concentration can be harnessed as tools to control rigid like-charged PE-PE interactions. We demonstrate a correlation between the orientational ordering of aspherical ions and how they mediate the effective PE-PE attraction induced by multivalency. The interaction type, strength, and range can thus be externally controlled in ionic solutions. Our results can be used as generic guidelines to tune the self-assembly of like-charged polyelectrolytes by variation of the characteristics of the ions.

Actin Bundle Nanomechanics and Organization Are Modulated by Macromolecular Crowding and Electrostatic Interactions

The structural and mechanical properties of actin bundles are essential to eukaryotic cells, aiding in cell motility and mechanical support of the plasma membrane. Bundle formation occurs in crowded intracellular environments composed of various ions and macromolecules. Although the roles of cations and macromolecular crowding in the mechanics and organization of actin bundles have been independently established, how changing both intracellular environmental conditions influence bundle mechanics at the nanoscale has yet to be established. Here we investigate how electrostatics and depletion interactions modulate the relative Young’s modulus and height of actin bundles using atomic force microscopy. Our results demonstrate that cation- and depletion-induced bundles display an overall reduction of relative Young’s modulus depending on either cation or crowding concentrations. Furthermore, we directly measure changes to cation- and depletion-induced bundle height, indicating that bundles experience alterations to filament packing supporting the reduction to relative Young’s modulus. Taken together, our work suggests that electrostatic and depletion interactions may act counteractively, impacting actin bundle nanomechanics and organization.

Quantification of the mesh structure of bundled actin filaments

Biopolymer networks are essential for a wide variety of cellular functions. The biopolymer actin is known to self-assemble into a variety of spatial structures in response to physiological and physical mechanisms. So far, the mechanics of networks of single actin filaments and bundles has previously been described. However, the spatial structure of actin bundles remains poorly understood. Here, we investigate this question by bundling actin filaments with systematically varied concentrations of known physical bundling agents (MgCl2 and PEG) and physiological bundling agents (α-actinin and fascin). We image bundled actin networks with confocal microscopy and perform analysis to describe their mesh size and the nearest-distance distribution, which we call "mesh structure". We find that the mesh size ξ scales universally with actin concentration as ξ ∼ [actin]-1/2. However, the dependence of ξ on the concentration of the bundling agent depends on the agent used. Finally, we find that nearest-distance distributions are best fit by Weibull and Gamma distributions. A complete understanding of the mesh structure of biopolymer networks leads to a more mechanistic understanding of the structure of the cytoskeleton, and can be exploited to design filters with variable porosity for microfluidic devices.

Regulation of Actin Bundle Mechanics and Structure by Intracellular Environmental Factors

The mechanical and structural properties of actin cytoskeleton drive various cellular processes, including structural support of the plasma membrane and cellular motility. Actin monomers assemble into double-stranded helical filaments as well as higher-ordered structures such as bundles and networks. Cells incorporate macromolecular crowding, cation interactions, and actin-crosslinking proteins to regulate the organization of actin bundles. Although the roles of each of these factors in actin bundling have been well-known individually, how combined factors contribute to actin bundle assembly, organization, and mechanics is not fully understood. Here, we describe recent studies that have investigated the mechanisms of how intracellular environmental factors influence actin bundling. This review highlights the effects of macromolecular crowding, cation interactions, and actin-crosslinking proteins on actin bundle organization, structure, and mechanics. Understanding these mechanisms is important in determining in vivo actin biophysics and providing insights into cell physiology.

Polyelectrolyte Gels Formed by Filamentous Biopolymers: Dependence of Crosslinking Efficiency on the Chemical Softness of Divalent Cations

Filamentous anionic polyelectrolytes are common in biological materials. Some examples are the cytoskeletal filaments that assemble into networks and bundled structures to give the cell mechanical resistance and that act as surfaces on which enzymes and other molecules can dock. Some viruses, especially bacteriophages are also long thin polyelectrolytes, and their bending stiffness is similar to those of the intermediate filament class of cytoskeletal polymers. These relatively stiff, thin, and long polyelectrolytes have charge densities similar to those of more flexible polyelectrolytes such as DNA, hyaluronic acid, and polyacrylates, and they can form interpenetrating networks and viscoelastic gels at volume fractions far below those at which more flexible polymers form hydrogels. In this report, we examine how different types of divalent and multivalent counterions interact with two biochemically different but physically similar filamentous polyelectrolytes: Pf1 virus and vimentin intermediate filaments (VIF). Different divalent cations aggregate both polyelectrolytes similarly, but transition metal ions are more efficient than alkaline earth ions and their efficiency increases with increasing atomic weight. Comparison of these two different types of polyelectrolyte filaments enables identification of general effects of counterions with polyelectrolytes and can identify cases where the interaction of the counterions and the filaments exhibits stronger and more specific interactions than those of counterion condensation.

The vimentin cytoskeleton: when polymer physics meets cell biology

The proper functions of tissues depend on the ability of cells to withstand stress and maintain shape. Central to this process is the cytoskeleton, comprised of three polymeric networks: F-actin, microtubules, and intermediate filaments (IFs). IF proteins are among the most abundant cytoskeletal proteins in cells; yet they remain some of the least understood. Their structure and function deviate from those of their cytoskeletal partners, F-actin and microtubules. IF networks show a unique combination of extensibility, flexibility and toughness that confers mechanical resilience to the cell. Vimentin is an IF protein expressed in mesenchymal cells. This review highlights exciting new results on the physical biology of vimentin intermediate filaments and their role in allowing whole cells and tissues to cope with stress.

Conformational behavior of a semiflexible dipolar chain with a variable relative size of charged groups via molecular dynamics simulations

The conformational behavior of an isolated semiflexible dipolar chain has been studied by molecular dynamics simulations. The dipolar chain was modeled as a backbone chain of charged beads, each containing an oppositely charged unit connected to it by a rigid spring. The main focus was on the effect of the backbone chain rigidity and the size of the charged groups on the morphology of the collapsed states of the chain formed in low-polar media where the electrostatic interactions are essential. It has been found that the stable globular conformations of the long chain of N = 256 backbone beads are a toroid and an elliptical globule. The macroscopic parameters (such as the radius of gyration and shape factors) as well as the local characteristics of these conformations (radial density distributions of ions, orientational correlations of chain segments, dipoles etc.) are studied depending on the chain stiffness. The regions of stability of a torus and an elliptical globule are found for the dipolar chains with variable dipole length and stiffness, which depend on the strength of electrostatic interactions. It has been shown that a size asymmetry of oppositely charged beads destabilizes globular states favoring elongated chain conformations. A coexistence of various metastable states was demonstrated for shorter chains of N = 128, 64, and 32.

Ion-Induced Formation of Nanocrystalline Cellulose Colloidal Glasses Containing Nematic Domains

Controlling the assembly of colloids in dispersion is a fundamental approach toward the production of functional materials. Nanocrystalline cellulose (NCC) is a charged nanoparticle whose colloidal interactions can be modulated from repulsive to attractive by increasing ionic strength. Here, we combine polarized optical microscopy, rheology, and small-angle scattering techniques to investigate (i) the concentration-driven transition from isotropic dispersion to cholesteric liquid crystals and (ii) salt-induced NCC phase transitions. In particular, we report on the formation of NCC attractive glasses containing nematic domains. At increasing NCC concentration, a structure peak was observed in small-angle X-ray scattering (SAXS) patterns. The evolution of the structure peak demonstrates the decrease in NCC interparticle distance, favoring orientational order during the isotropic-cholesteric phase transition. Small amounts of salt reduce the cholesteric volume fraction and pitch by a decrease in excluded volume. Beyond a critical salt concentration, NCC forms attractive glasses due to particle caging and reduced motility. This results in a sharp increase in viscosity and formation of viscoelastic glasses. The presence of nematic domains is suggested by the appearance of interference colors and the Cox-Merz rule failure and was confirmed by an anisotropic SAXS scattering pattern at q ranges associated with the presence of nematic domains. Thus, salt addition allows the formation of NCC attractive glasses with mechanical properties similar to those of gels while remaining optically active owed to entrapped nematic domains.

Role of metallic core for the stability of virus-like particles in strongly coupled electrostatics

Electrostatic interactions play important roles in the formation and stability of viruses and virus-like particles (VLPs) through processes that often involve added, or naturally occurring, multivalent ions. Here, we investigate the electrostatic or osmotic pressure acting on the proteinaceous shell of a generic model of VLPs, comprising a charged outer shell and a metallic nanoparticle core, coated by a charged layer and bathed in an aqueous electrolyte solution. Motivated by the recent studies accentuating the role of multivalent ions for the stability of VLPs, we focus on the effects of multivalent cations and anions in an otherwise monovalent ionic solution. We perform extensive Monte-Carlo simulations based on appropriate Coulombic interactions that consistently take into account the effects of salt screening, the dielectric polarization of the metallic core, and the strong-coupling electrostatics due to multivalent ions. We specifically study the intricate roles these factors play in the electrostatic stability of the model VLPs. It is shown that while the insertion of a metallic nanoparticle by itself can produce negative, inward-directed, pressure on the outer shell, addition of only a small amount of multivalent counterions can robustly engender negative pressures, enhancing the VLP stability across a wide range of values for the system parameters.

Histones bundle F-actin filaments and affect actin structure

Histones are small polycationic proteins complexed with DNA located in the cell nucleus. Upon apoptosis they are secreted from the cells and react with extracellular polyanionic compounds. Actin which is a polyanionic protein, is also secreted from necrotic cells and interacts with histones. We showed that both histone mixture (histone type III) and the recombinant H2A histone bundles F-actin, increases the viscosity of the F-actin containing solution and polymerizes G-actin. The histone-actin bundles are relatively insensitive to increase of ionic strength, unlike other polycation, histatin, lysozyme, spermine and LL-37 induced F-actin bundles. The histone-actin bundles dissociate completely only in the presence of 300–400 mM NaCl. DNA, which competes with F-actin for histones, disassembles histone induced actin bundles. DNase1, which depolymerizes F- to G-actin, actively unbundles the H2A histone induced but slightly affects the histone mixture induced actin bundles. Cofilin decreases the amount of F-actin sedimented by low speed centrifugation, increases light scattering and viscosity of F-actin-histone mixture containing solutions and forms star like superstructures by copolymerizing G-actin with H2A histone. The results indicate that histones are tightly attached to F-actin by strong electrostatic and hydrophobic forces. Since both histones and F-actin are present in the sputum of patients with cystic fibrosis, therefore, the formation of the stable histone-actin bundles can contribute to the pathology of this disease by increasing the viscosity of the sputum. The actin-histone interaction in the nucleus might affect gene expression.

Charged Molecules Modulate the Volume Exclusion Effects Exerted by Crowders on FtsZ Polymerization

We have studied the influence of protein crowders, either combined or individually, on the GTP-induced FtsZ cooperative assembly, crucial for the formation of the dynamic septal ring and, hence, for bacterial division. It was earlier demonstrated that high concentrations of inert polymers like Ficoll 70, used to mimic the crowded cellular interior, favor the assembly of FtsZ into bundles with slow depolymerization. We have found, by fluorescence anisotropy together with light scattering measurements, that the presence of protein crowders increases the tendency of FtsZ to polymerize at micromolar magnesium concentration, being the effect larger with ovomucoid, a negatively charged protein. Neutral polymers and a positively charged protein also diminished the critical concentration of assembly, the extent of the effect being compatible with that expected according to pure volume exclusion models. FtsZ polymerization was also observed to be strongly promoted by a negatively charged polymer, DNA, and by some unrelated polymers like PEGs at concentrations below the crowding regime. The influence of mixed crowders mimicking the heterogeneity of the intracellular environment on the tendency of FtsZ to assemble was also studied and nonadditive effects were found to prevail. Far from exactly reproducing the bacterial cytoplasm environment, this approach serves as a simplified model illustrating how its intrinsically crowded and heterogeneous nature may modulate FtsZ assembly into a functional Z-ring.

Dynamics of counterion-induced attraction between vimentin filaments followed in microfluidic drops

Intermediate filaments (IFs) are fiber-forming proteins and part of the cytoskeleton of eukaryotes. In vitro the network formation of purified IF systems is mediated, for example, by the interaction with multivalent ions. The understanding of these interaction mechanisms increases the knowledge of the cytoskeleton on a fundamental level. Here, we employ time-lapse fluorescence microscopy to directly image the evolution of network formation of vimentin IFs upon addition of divalent ions. We are thus able to follow the process starting a few seconds after the first encounter of free filaments and ions up to several minutes when the networks are in equilibrium. The local protein density in the compacted networks can reach a factor of 45 higher than the original solution concentration. The competition between mono- and divalent ion condensation onto the protein explains our observations and reveals the polyelectrolyte nature of vimentin as a reason for the protein attraction in the presence of small cations. The method for time-lapse studies in microfluidic drops presented here can be generalized to other dynamic systems.

Polyelectrolyte properties of filamentous biopolymers and their consequences in biological fluids

Anionic polyelectrolyte filaments are common in biological cells. DNA, RNA, the cytoskeletal filaments F-actin, microtubules, and intermediate filaments, and polysaccharides such as hyaluronan that form the pericellular matrix all have large net negative charge densities distributed over their surfaces. Several filamentous viruses with diameters and stiffnesses similar to those of cytoskeletal polymers also have similar negative charge densities. Extracellular protein filaments such collagen, fibrin and elastin, in contrast, have notably smaller charge densities and do not behave as highly charged polyelectrolytes in solution. This review summarizes data that demonstrate generic counterion-mediated effects on four structurally unrelated biopolymers of similar charge density: F-actin, vimentin, Pf1 virus, and DNA, and explores the possible biological and pathophysiological consequences of the polyelectrolyte properties of biological filaments.

Structure and function of palladin's actin binding domain

Here, we report the NMR structure of the actin-binding domain contained in the cell adhesion protein palladin. Previously, we demonstrated that one of the immunoglobulin domains of palladin (Ig3) is both necessary and sufficient for direct filamentous actin binding in vitro. In this study, we identify two basic patches on opposite faces of Ig3 that are critical for actin binding and cross-linking. Sedimentation equilibrium assays indicate that the Ig3 domain of palladin does not self-associate. These combined data are consistent with an actin cross-linking mechanism that involves concurrent attachment of two actin filaments by a single palladin molecule by an electrostatic mechanism. Palladin mutations that disrupt actin binding show altered cellular distributions and morphology of actin in cells, revealing a functional requirement for the interaction between palladin and actin in vivo.

LL-37 induces polymerization and bundling of actin and affects actin structure

Actin exists as a monomer (G-actin) which can be polymerized to filaments) F-actin) that under the influence of actin-binding proteins and polycations bundle and contribute to the formation of the cytoskeleton. Bundled actin from lysed cells increases the viscosity of sputum in lungs of cystic fibrosis patients. The human host defense peptide LL-37 was previously shown to induce actin bundling and was thus hypothesized to contribute to the pathogenicity of this disease. In this work, interactions between actin and the cationic LL-37 were studied by optical, proteolytic and surface plasmon resonance methods and compared to those obtained with scrambled LL-37 and with the cationic protein lysozyme. We show that LL-37 binds strongly to CaATP-G-actin while scrambled LL-37 does not. While LL-37, at superstoichiometric LL-37/actin concentrations polymerizes MgATP-G-actin, at lower non-polymerizing concentrations LL-37 inhibits actin polymerization by MgCl₂ or NaCl. LL-37 bundles Mg-F-actin filaments both at low and physiological ionic strength when in equimolar or higher concentrations than those of actin. The LL-37 induced bundles are significantly less sensitive to increase in ionic strength than those induced by scrambled LL-37 and lysozyme. LL-37 in concentrations lower than those needed for actin polymerization or bundling, accelerates cleavage of both monomer and polymer actin by subtilisin. Our results indicate that the LL-37-actin interaction is partially electrostatic and partially hydrophobic and that a specific actin binding sequence in the peptide is responsible for the hydrophobic interaction. LL-37-induced bundles, which may contribute to the accumulation of sputum in cystic fibrosis, are dissociated very efficiently by DNase-1 and also by cofilin.

Actin filament attachments for sustained motility in vitro are maintained by filament bundling

We reconstructed cellular motility in vitro from individual proteins to investigate how actin filaments are organized at the leading edge. Using total internal reflection fluorescence microscopy of actin filaments, we tested how profilin, Arp2/3, and capping protein (CP) function together to propel thin glass nanofibers or beads coated with N-WASP WCA domains. Thin nanofibers produced wide comet tails that showed more structural variation in actin filament organization than did bead substrates. During sustained motility, physiological concentrations of Mg(2+) generated actin filament bundles that processively attached to the nanofiber. Reduction of total Mg(2+) abolished particle motility and actin attachment to the particle surface without affecting actin polymerization, Arp2/3 nucleation, or filament capping. Analysis of similar motility of microspheres showed that loss of filament bundling did not affect actin shell formation or symmetry breaking but eliminated sustained attachments between the comet tail and the particle surface. Addition of Mg(2+), Lys-Lys(2+), or fascin restored both comet tail attachment and sustained particle motility in low Mg(2+) buffers. TIRF microscopic analysis of filaments captured by WCA-coated beads in the absence of Arp2/3, profilin, and CP showed that filament bundling by polycation or fascin addition increased barbed end capture by WCA domains. We propose a model in which CP directs barbed ends toward the leading edge and polycation-induced filament bundling sustains processive barbed end attachment to the leading edge.

Supramolecular cellular filament systems: how and why do they form?

All cells, from simple bacteria to complex human tissues, rely on extensive networks of protein fibers to help maintain their proper form and function. These filament systems usually do not operate as single filaments, but form complex suprastructures, which are essential for specific cellular functions. Here, we describe the progress in determining the architectures of molecular filamentous suprastructures, the principles leading to their formation, and the mechanisms by which they may facilitate function. The complex eukaryotic cytoskeleton is tightly regulated by a large number of actin- or microtubule-associated proteins. In contrast, recently discovered bacterial actins and tubulins have few associated regulatory proteins. Hence, the quest to find basic principles that govern the formation of filamentous suprastructures is simplified in bacteria. Three common principles, which have been probed extensively during evolution, can be identified that lead to suprastructures formation: cationic counterion fluctuations; self-association into liquid crystals; and molecular crowding. The underlying physics of these processes will be discussed with respect to physiological circumstance.

Macromolecular crowding regulates assembly of mRNA stress granules after osmotic stress: new role for compatible osmolytes

The massive uptake of compatible osmolytes such as betaine, taurine, and myo-inositol is a protective response shared by all eukaryotes exposed to hypertonic stress. Their accumulation results mostly from the expression of specific transporters triggered by the transcriptional factor NFAT5/TonEBP. This allows the recovery of the cell volume without increasing intracellular ionic strength. In this study we consider the assembly and dissociation of mRNA stress granules (SGs) in hypertonic-stressed cells and the role of compatible osmolytes. In agreement with in vitro results obtained on isolated mRNAs, both macromolecular crowding and a high ionic strength favor the assembly of SGs in normal rat kidney epithelial cells. However, after hours of constant hypertonicity, the slow accumulation in the cytoplasm of compatible osmolytes via specific transporters both reduces macromolecular crowding and ionic strength, thus leading to the progressive dissociation of SGs. In line with this, when cells are exposed to hypertonicity to accumulate a large amount of compatible osmolytes, the formation of SGs is severely impaired, and cells increase their chances of survival to another hypertonic episode. Altogether, these results indicate that the impact of compatible osmolytes on the mRNA-associated machineries and especially that associated with SGs may play an important role in cell resistance and adaption to hyperosmolarity in many tissues like kidney and liver.

Surface contact stimulates the just-in-time deployment of bacterial adhesins

The attachment of bacteria to surfaces provides advantages such as increasing nutrient access and resistance to environmental stress. Attachment begins with a reversible phase, often mediated by surface structures such as flagella and pili, followed by a transition to irreversible attachment, typically mediated by polysaccharides. Here we show that the interplay between pili and flagellum rotation stimulates the rapid transition between reversible and polysaccharide-mediated irreversible attachment. We found that reversible attachment of Caulobacter crescentus cells is mediated by motile cells bearing pili and that their contact with a surface results in the rapid pili-dependent arrest of flagellum rotation and concurrent stimulation of polar holdfast adhesive polysaccharide. Similar stimulation of polar adhesin production by surface contact occurs in Asticcacaulis biprosthecum and Agrobacterium tumefaciens. Therefore, single bacterial cells respond to their initial contact with surfaces by triggering just-in-time adhesin production. This mechanism restricts stable attachment to intimate surface interactions, thereby maximizing surface attachment, discouraging non-productive self-adherence, and preventing curing of the adhesive.

SYNERGY OF DNA-BENDING NUCLEOID PROTEINS AND MACROMOLECULAR CROWDING IN CONDENSING DNA

Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that this synergy is a simple consequence of the larger diameter and lower net charge density of the protein-DNA filaments as compared to naked DNA, and hence, should be quite general. To illustrate this generality, we use light-scattering to show that the 7kDa basic archaeal nucleoid protein Sso7d from Sulfolobus solfataricus (known to sharply bend DNA) likewise does not significantly condense DNA by itself. However, the resulting protein-DNA fibers are again highly susceptible to crowding-induced condensation. Clearly, if DNA-bending nucleoid proteins fail to condense DNA in dilute solution, this does not mean that they do not contribute to DNA condensation in the context of the crowded living cell.

Actin bundling and polymerisation properties of eukaryotic elongation factor 1 alpha (eEF1A), histone H2A-H2B and lysozyme in vitro

Elongation factor 1 alpha (eEF1A) is a positively charged protein which has been shown to interact with the actin cytoskeleton. However, to date, a specific actin binding site within the eEF1A sequence has not been identified and the mechanism by which eEF1A interacts with actin remains unresolved. Many protein-protein interactions occur as a consequence of their physicochemical properties and actin bundle formation has been shown to result from non-specific electrostatic interaction with basic proteins. This study investigated interactions between actin, eEF1A and two other positively charged proteins which are not regarded as classic actin binding proteins (namely lysozyme and H2A-H2B) in order to compare their actin organising effects in vitro. For the first time using atomic force microscopy (AFM) we have been able to image the interaction of eEF1A with actin and the subsequent bundling of actin in vitro. Interestingly, we found that eEF1A dramatically increases the rate of polymerisation (45-fold above control levels). We also show for the first time that H2A-H2B has remarkably similar effects upon actin bundling (relative bundle size/number) and polymerisation (35-fold increase above control levels) as eEF1a. The presence of lysozyme resulted in bundles which were distinct from those formed due to eEF1A and H2A-H2B. Lysozyme also increased the rate of actin polymerisation above the control level (by 10-fold). Given the striking similarities between the actin bundling and polymerisation properties of eEF1A and H2A-H2B, our results hint that dimerisation and electrostatic binding may provide clues to the mechanism through which eEF1A-actin bundling occurs.

Divalent cation induced actin ring formation

In this paper we explored the effect of copper sulphate on the morphology of actin filaments. Actin filaments attain different shapes and structure when exposed to 2mM concentration of copper sulphate. Lateral branches were observed after 4 h of incubation while shapes like Y- and V- were formed after 8h of incubation. Rings and loops of actin filaments were formed when the concentration of copper sulphate was increased from 2 to 5 mM. Additionally, ring formation was also observed when bead tailed actin filaments were incubated with copper sulphate (5 mM). Electrostatic adhesion energy between ends of actin filaments attracted due to counterion was estimated to be 7.34 kT/μm. Divalent cation induced actin ring formation are similar to toroids of DNA but actin filaments have great bending stiffness due to large diameter of the ring formed. From these results we proposed that polyelectrolyte nature of actin filaments leads to the change in their morphology on exposure to high concentration divalent cations.

Polycation induced actin bundles

Three polycations, polylysine, the polyamine spermine and the polycationic protein lysozyme were used to study the formation, structure, ionic strength sensitivity and dissociation of polycation-induced actin bundles. Bundles form fast, simultaneously with the polymerization of MgATP-G-actins, upon the addition of polycations to solutions of actins at low ionic strength conditions. This indicates that nuclei and/or nascent filaments bundle due to attractive, electrostatic effect of polycations and the neutralization of repulsive interactions of negative charges on actin. The attractive forces between the filaments are strong, as shown by the low (in nanomolar range) critical concentration of their bundling at low ionic strength. These bundles are sensitive to ionic strength and disassemble partially in 100 mM NaCl, but both the dissociation and ionic strength sensitivity can be countered by higher polycation concentrations. Cys374 residues of actin monomers residing on neighboring filaments in the bundles can be cross-linked by the short span (5.4Å) MTS-1 (1,1-methanedyl bismethanethiosulfonate) cross-linker, which indicates a tight packing of filaments in the bundles. The interfilament cross-links, which connect monomers located on oppositely oriented filaments, prevent disassembly of bundles at high ionic strength. Cofilin and the polysaccharide polyanion heparin disassemble lysozyme induced actin bundles more effectively than the polylysine-induced bundles. The actin-lysozyme bundles are pathologically significant as both proteins are found in the pulmonary airways of cystic fibrosis patients. Their bundles contribute to the formation of viscous mucus, which is the main cause of breathing difficulties and eventual death in this disorder.

Conformations of semiflexible charged chains: an extended bundle versus repulsive coils

We consider two interacting semiflexible charged chains of length L(c) under shape fluctuations, where the interplay of electric and mechanical properties is found to yield rigidity-sensitive charge modulation and interdistance-dependent persistence length ℓ(p). The resulting conformation is characterized by equilibrium force between the chains and their fractal dimensions. It turns out that ℓ(p) and L(c) emerge as critical factors to determine the force nature as well as chain shapes. We show that conformational fluctuations cause the repulsion of nonsteric origin, and its competition with charge fluctuation effects yields the interchain force modulated by the length scales and counterion valence. As a result, it is predicted that flexible short chains can be more strongly repulsive than rigid long chains, although they carry smaller amount of net charges.

Antiparallel dimer and actin assembly

The antiparallel dimer (APD) is a unique actin species, which can be detected in the early stages of actin polymerization. In this work, we introduce novel tools for examination of the effects of the APD on actin polymerization. We document that bifunctional methanothiosulfonate (MTS) reagents are an attractive alternative to the routinely used p-phenylene maleimide (pPDM) for APD detection, allowing for fast and efficient cross-linking under conditions of actin polymerization at neutral pH. We report also that pyrene-labeled yeast actin mutant A167C/C374A (C167PM) forms significant amounts of stable APD in solution, without chemical cross-linking or polymerization-affecting compounds, and that the kinetics of APD transformation and decay upon actin polymerization can be easily monitored. The dimerization of C167PM has been characterized in sedimentation equilibrium experiments (K(d) approximately 0.3 microM). This new system offers the advantage of assessing the effects of the APD under physiological conditions (pH, ionic strength, and Mg(2+) concentration) and testing for conformational transitions in the APD during nucleation-polymerization reactions or/and in the presence of actin-interacting factors. The results obtained using two different systems (C167PM actin and polylysine-induced polymerization of alpha-actin) show that the APD decays at a rate slower than that at which the filaments elongate, revealing its transient incorporation into filaments, and confirm that it inhibits the nucleation and elongation of actin filaments.

Entropy driven self-assembly of nonamphiphilic colloidal membranes

We demonstrate that homogeneous monodisperse rods in the presence of attractive interactions assemble into equilibrium 2D fluid-like membranes composed of a one-rod length thick monolayer of aligned rods. Unique features of our system allow us to simultaneously investigate properties of these membranes at both continuum and molecular lengthscales. Analysis of thermal fluctuations at continuum lengthscales yields the membranes' lateral compressibility and bending rigidity and demonstrates that the properties of colloidal membranes are comparable to those of traditional lipid bilayers. Fluctuations at molecular lengthscales, in which single rods protrude from the membrane surface, are directly measured by comparing the positions of individual fluorescently labeled rods within a membrane to that of the membrane's continuum conformation. As two membranes approach each other in suspension, protrusion fluctuations are suppressed leading to effective repulsive interactions. Motivated by these observations, we propose an entropic mechanism that explains the stability of colloidal membranes and offers a general design principle for the self-assembly of 2D nanostructured materials from rod-like molecules.

Fluctuations and interactions of semi-flexible polyelectrolytes in columnar assemblies

We have developed a statistical theory for columnar aggregates of semi-flexible polyelectrolytes. The applicability of previous, simplified theories was limited to polyelectrolytes with unrealistically high effective charge and, hence, with strongly suppressed thermal undulations. To avoid this problem, we utilized more consistent approximations for short-range image-charge forces and steric confinement, resulting in new predictions for polyelectrolytes with more practically important, lower effective linear charge densities. In the present paper, we focus on aggregates of wormlike chains with uniform surface charge density, although the same basic ideas may also be applied to structured polyelectrolytes. We find that undulations effectively extend the range of electrostatic interactions between polyelectrolytes upon decreasing aggregate density, in qualitative agreement with previous theories. However, in contrast to previous theories, we demonstrate that steric confinement provides the dominant rather than a negligible contribution at higher aggregate densities and significant quantitative corrections at lower densities, resulting in osmotic pressure isotherms that drastically differ from previous predictions.

Molecular mechanism of bundle formation by the bacterial actin ParM

The actin homolog ParM plays a microtubule-like role in segregating DNA prior to bacterial cell division. Fluorescence and cryo-electron microscopy have shown that ParM forms filament bundles between separating DNA plasmids in vivo. Given the lack of ParM bundling proteins it remains unknown how ParM bundles form at the molecular level. Here we show using time-lapse TIRF microscopy, under in vitro molecular crowding conditions, that ParM-bundle formation consists of two distinct phases. At the onset of polymerization bundle thickness and shape are determined in the form of nuclei of short helically disordered filaments arranged in a liquid-like lattice. These nuclei then undergo an elongation phase whereby they rapidly increase in length. At steady state, ParM bundles fuse into one single large aggregate. This behavior had been predicted by theory but has not been observed for any other cytomotive biopolymer, including F-actin. We employed electron micrographs of ParM rafts, which are 2-D analogs of 3-D bundles, to identify the main molecular interfilament contacts within these suprastructures. The interface between filaments is similar for both parallel and anti-parallel orientations and the distribution of filament polarity is random within a bundle. We suggest that the interfilament interactions are not due to the interactions of specific residues but rather to long-range, counter ion mediated, electrostatic attractive forces. A randomly oriented bundle ensures that the assembly is rigid and that DNA may be captured with equal efficiency at both ends of the bundle via the ParR binding protein.

Direct interaction between anthrax toxin receptor 1 and the actin cytoskeleton

The protective antigen component of anthrax toxin binds the I domain of the anthrax toxin receptors, ANTXR1 and ANTXR2, in a manner akin to how integrins bind their ligands. The I domains of integrins and ANTXR1 both have high- and low-affinity conformations, and the cytosolic tails of these receptors associate with the actin cytoskeleton. The association of ANTXR1 with the cytoskeleton correlates with weakened binding to PA, although a mechanistic explanation for this observation is lacking. Here, we identified a segment in the cytoplasmic tail of ANTXR1 required for its association with the cytoskeleton. We synthesized a 60-mer peptide based on this segment and demonstrated a direct interaction between the peptide and beta-actin, indicating that in contrast to integrins, ANTXR1 does not use an adaptor to bind the cytoskeleton. This peptide orders actin filaments into arrays, demonstrating an actin bundling activity that is novel for a membrane protein.

Salt-induced aggregation of stiff polyelectrolytes

Molecular dynamics simulation techniques are used to study the process of aggregation of highly charged stiff polyelectrolytes due to the presence of multivalent salt. The dominant kinetic mode of aggregation is found to be the case of one end of one polyelectrolyte meeting others at right angles, and the kinetic pathway to bundle formation is found to be similar to that of flocculation dynamics of colloids as described by Smoluchowski. The aggregation process is found to favor the formation of finite bundles of 10-11 filaments at long times. Comparing the distribution of the cluster sizes with the Smoluchowski formula suggests that the energy barrier for the aggregation process is negligible. Also, the formation of long-lived metastable structures with similarities to the raft-like structures of actin filaments is observed within a range of salt concentration.

Buckling-induced zebra stripe patterns in nematic F-actin

Rather than forming a simple and uniform nematic liquid crystal, concentrated solutions of semiflexible polymers, such as F-actin, have been observed to display a spatially periodic switching of the nematic director. When observed with polarization microscopy, these patterns appear as alternating light and dark bands, often referred to as zebra stripe patterns. Zebra stripe patterns, although not fully characterized, are due to periodic orientation distortions in the nematic order. We characterize such patterns by using a combination of two techniques. Using polarization microscopy, we quantify the periodic orientation distortions and show that the magnitude of the order parameter also varies periodically in the striped domains. When using fluorescently labeled filaments as markers, filaments spanning the striped domains are seen to undergo large angle bends. With fluorescence, clear density differences between adjacent stripes are also observed with domains of lesser density corresponding to strongly bent filaments. By directly comparing patterned areas with both polarization and fluorescence techniques, we show that periodic variation in the orientation, order parameter, filament bending, and density are correlated. We propose that these effects originate from the coupling of orientation and density that occurs for highly concentrated solutions of long semiflexible polymers subject to shear flows, as previously proposed [P. de Gennes, Mol. Cryst. Liq. Cryst. (Phila. Pa.) 34, 177 (1977)]. After cessation of shearing, strong interfilament interactions and high compressibility can lead to periodic buckling from the relaxation of filaments stretched during flows. The characterization of zebra stripe patterns presented here provides evidence that buckling in confined F-actin nematics produces strong periodic bending that is responsible for the observed features.

MAP2-mediated in vitro interactions of brain microtubules and their modulation by cAMP

Microtubule-associated proteins (MAPs) are involved in microtubule (MT) bundling and in crossbridges between MTs and other organelles. Previous studies have assigned the MT bundling function of MAPs to their MT-binding domain and its modulation by the projection domain. In the present work, we analyse the viscoelastic properties of MT suspensions in the presence or the absence of cAMP. The experimental data reveal the occurrence of interactions between MT polymers involving MAP2 and modulated by cAMP. Two distinct mechanisms of action of cAMP are identified, which involve on one hand the phosphorylation of MT proteins by the cAMP-dependent protein kinase A (PKA) bound to the end of the N-terminal projection of MAP2, and on the other hand the binding of cAMP to the RII subunit of the PKA affecting interactions between MTs in a phosphorylation-independent manner. These findings imply a role for the complex of PKA with the projection domain of MAP2 in MT-MT interactions and suggest that cAMP may influence directly the density and bundling of MT arrays in dendrites of neurons.