Polymerization dynamics of double-stranded biopolymers: chemical kinetic approach

The polymerization dynamics of double-stranded polymers, such as actin filaments, is investigated theoretically using simple chemical kinetic models that explicitly take into account some microscopic details of the polymer structure and the lateral interactions between the protofilaments. By considering all possible molecular configurations, the exact analytical expressions for the growth velocity and dispersion for two-stranded polymers are obtained in the case of the growing at only one end, and for the growth from both polymer ends. Exact theoretical calculations are compared with the predictions of approximate multilayer models that consider only a finite number of the most relevant polymer configurations. Our theoretical approach is applied to analyze the experimental data on the growth and fluctuations dynamics of individual single actin filaments.     

Electronically activated actin protein polymerization and alignment

Biological systems are the paragon of dynamic self-assembly, using a combination of spatially localized protein complexation, ion concentration, and protein modification to coordinate a diverse set of self-assembling components. Biomimetic materials based upon biologically inspired design principles or biological components have had some success at replicating these traits, but have difficulty capturing the dynamic aspects and diversity of biological self-assembly. Here, we demonstrate that the polymerization of ion-sensitive proteins can be dynamically regulated using electronically enhanced ion mixing and monomer concentration. Initially, the global activity of the cytoskeletal protein actin is inhibited using a low-ionic strength buffer that minimizes ion complexation and protein-protein interactions. Nucleation and growth of actin filaments are then triggered by a low-frequency AC voltage, which causes local enhancement of the actin monomer concentration and mixing with Mg(2+). The location and extent of polymerization are governed by the voltage and frequency, producing highly ordered structures unprecedented in bulk experiments. Polymerization rate and filament orientation could be independently controlled using a combination of low-frequency (approximately 100 Hz) and high frequency (1 MHz) AC voltages, creating a range of macromolecular architectures from network hydrogel microparticles to highly aligned arrays of actin filaments with approximately 750 nm periodicity. Since a wide range of proteins are activated upon complexation with charged species, this approach may be generally applicable to a variety of biopolymers and proteins.     

Kinetic Insights into the Elongation Reaction of Actin Filaments as a Function of Temperature,Pressure, and Macromolecular Crowding

Actin polymerization is an essential process in eukaryotic cells that provides a driving force for motility and mechanical resistance for cell shape. By using preformed gelsolin–actin nuclei and applying stopped‐flow methodology, we quantitatively studied the elongation kinetics of actin filaments as a function of temperature and pressure in the presence of synthetic and protein crowding agents. We show that the association of actin monomers to the pointed end of double‐stranded helical actin filaments (F‐actin) proceeds via a transition state that requires an activation energy of 56 kJ mol^?1 for conformational and hydration rearrangements, but exhibits a negligible activation volume, pointing to a compact transition state that is devoid of packing defects. Macromolecular crowding causes acceleration of the F‐actin elongation rate and counteracts the deteriorating effect of pressure. The results shed new light on the combined effect of these parameters on the polymerization process of actin, and help us understand the temperature and pressure sensitivity of actin polymerization under extreme conditions.     

Temperature-dependent elasticity of microtubules

Central to the biological function of microtubules is their ability to modify their length which occurs by addition and removal of subunits at the ends of the polymer, both in vivo and in vitro. This dynamic behavior is strongly influenced by temperature. Here, we show that the lateral interaction between tubulin subunits forming microtubule is strongly temperature dependent. Microtubules deposited on prefabricated substrates were deformed in an atomic force microscope during imaging, in two different experimental geometries. Microtubules were modeled as anisotropic, with the Young's modulus corresponding to the resistance of protofilaments to stretching and the shear modulus describing the weak interaction between the protofilaments. Measurements involving radial compression of microtubules deposited on flat mica confirm that microtubule elasticity depends on the temperature. Bending measurements performed on microtubules deposited on lithographically fabricated substrates show that this temperature dependence is due to changing shear modulus, implying that the lateral interaction between the protofilaments is strongly determined by the temperature. These measurements are in good agreement with previously reported measurements of the disassembly rate of microtubules, demonstrating that the mechanical and dynamic properties of microtubules are closely related.     

Treadmilling of actin filaments via Brownian dynamics simulations

Actin polymerization is coupled to the hydrolysis of adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and inorganic phosphate (P(i)). Therefore, each protomer within an actin filament can attain three different nucleotide states corresponding to bound ATP, ADP/P(i), and ADP. These protomer states form spatial patterns on the growing (or shrinking) filaments. Using Brownian dynamics simulations, the growth behavior of long filaments is studied, together with the associated protomer patterns, as a function of ATP-actin monomer concentration, C(T), within the surrounding solution. For concentrations close to the critical concentration C(T)=C(T,cr), the filaments undergo treadmilling, i.e., they grow at the barbed and shrink at the pointed end, which leads to directed translational motion of the whole filament. The corresponding nonequilibrium states are characterized by several global fluxes and by spatial density and flux profiles along the filaments. We focus on a certain set of transition rates as deduced from in vitro experiments and find that the associated treadmilling (or turnover) rate is about 0.08 monomers per second.     

Vinblastine perturbation of tubulin protofilament structure: a computational insight

Tubulin is a heterodimeric protein whose self assembly leads to the formation of protofilaments and of more complex structures called microtubules, key components of the cytoskeleton which have a fundamental role in the cell division process. Due to its biological function, tubulin is the target of many antitumoral molecules that exert their action on proliferating tumoral cells. Among these drugs, vinblastine has been widely used in therapy for a long time, albeit its mechanism of interaction with tubulin has remained elusive until recently. Vinblastine acts as a microtubule destabilizing agent and induces the formation of curved or ring-shaped tubulin polymers instead of linear protofilaments in vitro. In this paper we compare, using molecular dynamics simulations and free energy calculations, the network of interactions that allow the assembly of model linear protofilaments with those present in curved tubulin polymers complexed with vinblastine. It is shown that vinblastine, wedging between tubulin heterodimers, actually mediates part of the interactions between them and acts by crosslinking the two proteins, leading to the observed curved polymers rather than to their disassembly.     

Effects of novel taxanes SB-T-1213 and IDN5109 on tubulin polymerization and mitosis

SB-T-1213 and IDN5109 are semisynthetic, orally available taxanes that are up to 400-fold more active than paclitaxel against drug-resistant cells. IDN5109 is in clinical trials. We investigated the primary target for SB-T-1213 and IDN5109 and whether the compounds interact with microtubules differently than paclitaxel. Unlike paclitaxel, at 1-10 microM both novel taxanes initiate microtubule polymerization in vitro with no lag. They enhance polymerization equally or more potently than paclitaxel. SB-T-1213 induces unusual microtubules with attached extra protofilaments or open sheets, and IDN5109 induces large protofilamentous sheets. Both inhibit HeLa cell proliferation, block mitosis at the metaphase/anaphase transition, bundle microtubules at high drug concentrations, and induce abnormal metaphase spindles and apoptosis. They target microtubules but alter their polymerization and structure differently than paclitaxel. These differences may play a role in their enhanced cytotoxicity and efficacy.     

Polymerization of actin filaments coupled with adenosine triphosphate hydrolysis: Brownian dynamics and theoretical analysis

Polymerization dynamics of single actin filaments coupled with adenosine triphosphate (ATP) hydrolysis is investigated via both theoretical analysis and Brownian dynamics simulations. Brownian dynamics simulations have been applied recently to study the growth behaviors of long filaments as a function of the free actin monomer concentrations, C(T), which is found to be in agreement with the associated experiments. In the present study, both ATP cap length and length diffusivity are studied as a function of the free ATP-actin monomer concentrations, C(T). The exact analytical expressions are found to be in perfect consistency with Brownian dynamics simulations. Likewise, we find that the length diffusion coefficient is peaked near the critical concentration, C(T,cr). It is, therefore, expected that the dependence of length diffusivity on ATP-actin monomer concentrations is utilized to analyze the surprising experiments on the length fluctuations of individual actin filaments.     

Suberic Acid Acts as a Dissolving Agent as Well as a Crosslinker for Natural Polymers (Carbohydrate and Protein): A Detailed Discussion on the Chemistry Behind the Interaction

The natural polysaccharide chitosan and the natural protein collagen are widely used for the preparation of biopolymer materials in the presence of suitable crosslinkers. In this study, crosslinking feasibility of a dicarboxylic acid, namely suberic acid was tested using chitosan and collagen and in addition, thermal and mechanical properties were also tested for the resulting biopolymers. A 3D scaffold biopolymer material was prepared using chitosan at 1.0% (w/v) in the presence of suberic acid at 0.2% (w/v), similarly collagen 0.5% (w/v) in the presence of suberic acid 0.2% (w/v). Upon interaction, both the biopolymers displayed appreciable mechanical and thermal properties which add value to the biopolymers for biomedical applications. Molecular docking studies suggests the non-covalent interactions between the natural polymers and suberic acid is the reason behind the improved properties.     

Structural Basis of Microtubule Stabilization by Laulimalide and Peloruside A

Laulimalide and peloruside A are microtubule‐stabilizing agents (MSAs), the mechanism of action on microtubules of which is poorly defined. Here, using X‐ray crystallography it is shown that laulimalide and peloruside A bind to a unique non‐taxane site on β‐tubulin and use their respective macrolide core structures to interact with a second tubulin dimer across protofilaments. At the same time, they allosterically stabilize the taxane‐site M‐loop that establishes lateral tubulin contacts in microtubules. Structures of ternary complexes of tubulin with laulimalide/peloruside A and epothilone A are also solved, and a crosstalk between the laulimalide/peloruside and taxane sites via the M‐loop of β‐tubulin is found. Together, the data define the mechanism of action of laulimalide and peloruside A on tubulin and microtubules. The data further provide a structural framework for understanding the synergy observed between two classes of MSAs in tubulin assembly and the inhibition of cancer cell growth.     

Microtubules and actin filaments in teleost visual cone elongation and contraction.

Teleost retinal cones contract in light and elongate in darkness. This paper describes the disposition of microtubules and cytoplasmic filaments in cone cells of 2 species of fish (Haemulon sciurus and Lutjanus griseus). In Haemulon, the neck-like "myoid" region of the cone changes in length from 5 mu to 75 mu. Maximal observed rates of elongation and contraction are comparable to that of chromosome movement in mitosis (2-3 mu/min). Microtubules presumably participate in cone elongation, since numerous longitudinal microtubules are present in the myoid region, and colchicine blocks dark-induced elongation. Myoid shortening, on the other hand, appears to be an active contractile process. Disruption of microtubules in dark-adapted cones does not produce myoid shortening in the absence of light, and light-induced myoid shortening is blocked by cytochalasin-B. Cone cells possess longitudinally-oriented thin filaments which bind myosin subfragment-1 to form arrowhead complexes typical of muscle actin. Myoid thin filaments are clearly observed in negatively stained preparations of isolated cones which have been disrupted with detergent after attachment to grids. These myoid filaments are not, however, generally preserved by conventional fixation, though bundles of thin filaments are preserved in other regions of the cell. Thus, actin filaments are poorly retained by fixation in precisely the region of the cone cell where contraction occurs. Cone cells also possess longitudinally-oriented thick filaments 130-160 A in diameter. That these thick filaments may be myosin is suggested by the presence of side-arms with approximately 150 A periodicity. The linear organization of the contractile apparatus of the retinal cone cell makes this cell a promising model for morphological characterization of the disposition of actin and myosin filaments during contraction in a nonmuscle cell.     

Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements

DNA nanotubes provide a programmable architecture for molecular self-assembly and can serve as model systems for one-dimensional biomolecular assemblies. While a variety of DNA nanotubes have been synthesized and employed as models for natural biopolymers, an extensive investigation of DNA nanotube kinetics and thermodynamics has been lacking. Using total internal reflection microscopy, DNA nanotube polymerization was monitored in real time at the single filament level over a wide range of free monomer concentrations and temperatures. The measured polymerization rates were subjected to a global nonlinear fit based on polymerization theory in order to simultaneously extract kinetic and thermodynamic parameters. For the DNA nanotubes used in this study, the association rate constant is (5.99 ± 0.15) × 10⁵ M^–1 s^–1, the enthalpy is 87.9 ± 2.0 kcal mol^–1, and the entropy is 0.252 ± 0.006 kcal mol^–1 K^–1. The qualitative and quantitative similarities between the kinetics of DNA nanotubes, actin filaments, and microtubules polymerization highlight the prospect of building complex dynamic systems from DNA molecules inspired by biological architecture.     

Towards high throughput production of artificial egg oocytes using microfluidics

The production of micron-size droplets using microfluidic tools offers new opportunities to carry out biological assays in a controlled environment. We apply these strategies by using a flow-focusing microfluidic device to encapsulate Xenopus egg extracts, a biological system recapitulating key events of eukaryotic cell functions in vitro. We present a method to generate monodisperse egg extract-in-oil droplets and use high-speed imaging to characterize the droplet pinch-off dynamics leading to the production of trains of droplets. We use fluorescence microscopy to show that our method does not affect the biological activity of the encapsulated egg extract by observing the self-organization of microtubules and actin filaments, two main biopolymers of the cell cytoskeleton, encapsulated in the produced droplets. We anticipate that this assay might be useful for quantitative studies of biological systems in a confined environment as well as high throughput screenings for drug discovery.     

p41-Arc, a regulatory subunit of Arp2/3 complex, can induce premature senescence in the absence of p53 and Rb

Cellular senescence is a tumor-suppressive process instigated by proliferation in the absence of telomere replication, by cellular stresses such as oncogene activation, or by activation of the tumor suppressor proteins, such as Rb or p53. This process is characterized by an irreversible cell cycle exit, a unique morphology, and expression of senescence-associated-β-galactosidase (SA-β-gal). Despite the potential biological importance of cellular senescence, little is known of the mechanisms leading to the senescent phenotype. p41-Arc has been known to be a putative regulatory component of the mammalian Arp2/3 complex, which is required for the formation of branched networks of actin filaments at the cell cortex. In this study, we demonstrate that p41-Arc can induce senescent phenotypes when it is overexpressed in human tumor cell line, SaOs-2, which is deficient in p53 and Rb tumor suppressor genes, implying that p41 can induce senescence in a p53-independent way. p41-Arc overexpression causes a change in actin filaments, accumulating actin filaments in nuclei. Therefore, these results imply that a change in actin filament can trigger an intrinsic senescence program in the absence of p53 and Rb tumor suppressor genes.     

Mechanism of actin polymerization by myosin subfragment-1 probed by dynamic light scattering

Monomeric actin (G-actin) polymerizes spontaneously into helical filaments in the presence of inorganic salts. The slowest, rate-limiting step of the polymerization process is formation of actin trimers, the smallest oligomers that serve as nuclei for fast filament growth (filament elongation) by monomer addition at the filament ends. In low ionic-strength solutions, actin can be polymerized by myosin subfragment-1 (S1). In early works it has been suggested that G-actin-S1 1:1 complexes (GS) assemble into filaments according to the nucleation-filament elongation scheme. Subsequent studies indicated that one S1 molecule can bind two actin monomers, and that oligomerization of the initial complexes is a fast reaction. This has led to suggest an alternative mechanism, with a ternary G(2)S complex and its oligomers being predominant intermediates of S1-induced assembly of G-actin into filaments. We used dynamic light scattering to analyze the initial steps of S1-induced polymerization of actin. Our results suggest formation of GS complexes and their oligomers in the presence of S1 equimolar to or in excess over actin. We confirm formation of G(2)S complexes as intermediates of S1-induced polymerization in the presence of actin in excess over S1.     

Guidance of actin filament elongation on filament-binding tracks

Biomolecular motors, which convert chemical energy into mechanical work in intracellular processes, have high potential in bionanotechnology in vitro as molecular shuttles or nanoscale actuators. In this context, guided elongation of actin filaments in vitro could be used to lay tracks for myosin motor-based shuttles or to direct nanoscale actuators based on actin filament end-tracking motors. To guide the direction of filament polymerization on surfaces, microcontact printing was used to create tracks of chemically modified myosin, which binds to, but cannot exert force on, filaments. These filament-binding tracks captured nascent filaments from solution and guided the direction of their subsequent elongation. The effect of track width and protein surface density on filament alignment and elongation rate was quantified. These results indicate that microcontact printing is a useful method for guiding actin filament polymerization in vitro for biomolecular motor-based applications.     

Controlling the morphology of cross beta-sheet assemblies by rational design

Low molecular weight peptidomimetics with simple amphiphilic sequences can help to elucidate the structures of cross beta-sheet assemblies, such as amyloid fibrils. The peptidomimetics described herein comprise a dibenzofuran template, two peptide strands made up of alternating hydrophilic and hydrophobic residues, and carboxyl termini, each of which can be varied to probe the structural requirements for beta-sheet self-assembly processes. The dibenzofuran template positions the strands approximately 10 A apart, allowing corresponding hydrophobic side chains in the strands to pack into a collapsed U-shaped structure. This conformation is stabilized by hydrophobic interactions, not intramolecular hydrogen bonds. Intermolecular stacking of the collapsed peptidomimetics, enabled by intermolecular hydrogen bonding and hydrophobic interactions, affords 25-27 A wide protofilaments having a cross beta-sheet structure. Association of protofilaments, mediated by the dibenzofuran substructures and driven by the hydrophobic effect, affords 50-60 A wide filaments. These widths can be controlled by changing the length of the peptide strands. Further assembly of the filaments into fibrils or ribbons can be controlled by modification of the template, C-terminus, and buffer ion composition.     

Theory of crosslinked bundles of helical filaments: intrinsic torques in self-limiting biopolymer assemblies

Inspired by the complex influence of the globular crosslinking proteins on the formation of biofilament bundles in living organisms, we study and analyze a theoretical model for the structure and thermodynamics of bundles of helical filaments assembled in the presence of crosslinking molecules. The helical structure of filaments, a universal feature of biopolymers such as filamentous actin, is shown to generically frustrate the geometry of crosslinking between the "grooves" of two neighboring filaments. We develop a coarse-grained model to investigate the interplay between the geometry of binding and mechanics of both linker and filament distortion, and we show that crosslinking in parallel bundles of helical filaments generates intrinsic torques, of the type that tend to wind the bundle superhelically about its central axis. Crosslinking mediates a non-linear competition between the preference for bundle twist and the size-dependent mechanical cost of filament bending, which in turn gives rise to feedback between the global twist of self-assembled bundles and their lateral size. Finally, we demonstrate that above a critical density of bound crosslinkers, twisted bundles form with a thermodynamically preferred radius that, in turn, increases with a further increase in crosslinking bonds. We identify the stiffness of crosslinking bonds as a key parameter governing the sensitivity of bundle structure and assembly to the availability and affinity of crosslinkers.     

Specific interaction of cytochalasins with muscle and platelet actin filaments in vitro

The cytochalasins (CE, CD, CB and H2CB) inhibit numerous cellular processes which require the interaction of actin with other structural and contractile proteins. In this report we describe the effects of the cytochalasins on the viscosity and morphology of muscle and platelet actin. The cytochalasins decreased the viscosity of F-actin solutions. The effect of H2CB, CB and CD ON F-actin viscosity was maximal at concentrations of 20-50 micro M and did not increase with time. In contrast, CE caused a progressive decrease in the viscosity of F-actin solutions which was dependent upon the concentration of CE and the duration of incubation of the CE-actin mixture. After two hours of incubation of drug-actin mixtures, the relative effectiveness of the cytochalasins in reducing the viscosity of F-actin was CE greater than CD greater than CB=H2CB. The effects of CD and CE were paralleled by morphologic changes in negatively stained actin filaments. The effects of the cytochalasins on the viscosity and morphology of muscle and platelet actin were the same whether the drugs were added before or after the polymerization of the protein. These studies show that the interaction of the cytochalasins with actin is highly specific. Because the relative potencies of these drugs for affecting motile processes and the relative affinities of the drugs for binding sites within a variety of cells are CE greater than CD greater than CB=H2CB, the effects of cytochalasins on actin described here may contribute to some of the biological effects of the drugs on motile processes.