Entropically Driven Order in Crowded Solutions: From Liquid Crystals to Cell Biology

Liquid crystalline and rheological properties of chitin whiskers with different chemical structures and chargeability

The liquid crystalline and rheological properties of chitin whiskers (CHWs) are significant for their application in fabrication of highly ordered composite materials and optical components. The aim of this work was to elucidate the influence of chemical structure and chargeability (zeta potential, electropositivity, electronegativity or zwitterionic character) on the liquid crystalline and rheological properties of CHWs. Firstly, CHWs with different chemical structure, including positively charged whiskers (CHWs and CHWs-D/60 min) and negatively charged whiskers (mCHWs), were designed via acid hydrolysis, deacetylation, and maleation, respectively. Subsequently, the chargeability of the above whiskers was further regulated by protonation or deprotonation. The whisker aqueous suspensions with high zeta potential behaved as nematic liquid crystals or chiral nematic liquid crystals, whereas those with low zeta potential had no liquid crystal characteristics. The viscosity, G', and G" values of the CHWs and CHWs-D/60 min aqueous suspensions treated with protonation were lower than those of the corresponding whiskers treated with deprotonation. However, the mCHWs exhibited different changes in their rheological properties under protonation or deprotonation due to the electronegativity and zwitterionic characteristics. In addition, the effects of ionic strength and pH on the liquid crystalline and rheological properties of CHWs, CHWs-D/60 min, and mCHWs aqueous suspensions varied since the chemical structure and chargeability of whiskers differ.

Nematic liquid crystals of bifunctional patchy spheres

Anisotropic interactions can bring about the formation, through self-assembly, of semi-flexible chains, which in turn can give rise to nematic phases for suitable temperatures and concentrations. A minimalist model constituted of hard cylinders decorated with attractive sites has been already extensively studied numerically. Simulation data shows that a theoretical approach recently proposed is able to properly capture the physical properties of these self-assembly-driven liquid crystals. Here, we investigated a simpler model constituted of bifunctional Kern-Frenkel hard spheres which does not possess steric anisotropy but which can undergo a istropic-nematic transition as a result of their self-assembly into semi-flexible chains. For this model we compare an accurate numerical estimate of isotropic-nematic phase boundaries with theoretical predictions. The theoretical treatment, originally proposed for cylinder-like particles, has been greatly simplified and its predictions are in good agreement with numerical results. Finally, we also assess a crucial, and not obvious, hypothesis used in the theory, i.e. the ability of the Onsager trial function to properly model particle orientation in the presence of aggregation, that has not been properly checked yet.

Selective Precipitation of Proteins

Selective precipitation of proteins can be used as a bulk method to recover the majority of proteins from a crude lysate, as a selective method to fractionate a subset of proteins from a protein solution, or as a very specific method to recover a single protein of interest from a purification step. This unit describes a number of methods suitable for selective precipitation. In each of the protocols that are outlined, the physical or chemical basis of the precipitation process, the parameters that can be varied for optimization, and the basic steps for developing an optimized precipitation are described.

Self-assembly-driven nematization

The anisotropy of attractive interactions between particles can favor, through a self-assembly process, the formation of linear semi-flexible chains. In the appropriate temperatures and concentration ranges, the growing aspect ratio of the aggregates can induce formation of a nematic phase, as recently experimentally observed in several biologically relevant systems. We present here a numerical study of the isotropic-nematic phase boundary for a model of bifunctional polymerizing hard cylinders, to provide an accurate benchmark for recent theoretical approaches and to assess their ability to capture the coupling between self-assembly and orientational ordering. The comparison indicates the importance of properly modeling excluded volume and orientational entropy and provides a quantitative confirmation of some theoretical predictions.

Hierarchical ordering of amyloid fibrils on the mica surface

The aggregation of amyloid peptides into ordered fibrils is closely associated with many neurodegenerative diseases. The surfaces of cell membranes and biomolecules are believed to play important roles in modulation of peptide aggregation under physiological conditions. Experimental studies of fibrillogenesis at the molecular level in vivo, however, are inherently challenging, and the molecular mechanisms of how surface affects the structure and ordering of amyloid fibrils still remain elusive. Herein we have investigated the aggregation behavior of insulin peptides within water films adsorbed on the mica surface. AFM measurements revealed that the structure and orientation of fibrils were significantly affected by the mica lattice and the peptide concentration. At low peptide concentration (~0.05 mg mL(-1)), there appeared a single layer of short and well oriented fibrils with a mean height of 1.6 nm. With an increase of concentration to a range of 0.2-2.0 mg mL(-1), a different type of fibrils with a mean height of 3.8 nm was present. Interestingly, when the concentration was above 2.0 mg mL(-1), the thicker fibrils exhibited two-dimensional liquid-crystal-like ordering probably caused by the combination of entropic and electrostatic forces. These results could help us gain better insight into the effects of the substrate on amyloid fibrillation.

Depletion induced clustering in mixtures of colloidal spheres and fd-virus

We determined the phase boundary of an ideal rod-sphere mixture consisting of fd-virus, which is an established model system for mono-disperse colloidal rods, and density matched mono-disperse polystyrene beads employing diffuse wave spectroscopy. The low volume fraction of fd needed to induce a phase separation at relatively low ionic strength exemplifies the fact that slender rods are very effective depletion agents. Confocal microscopy showed that stable clusters are formed during phase separation. Relaxation after shear deformation of these clusters showed that the phase separation is gas-liquid-like and that the interfacial tension involved is very low as in colloid-polymer mixtures.

Counterion condensation theory of attraction between like charges in the absence of multivalent counterions

There is abundant experimental evidence suggesting the existence of attractive interactions among identically charged polyelectrolytes in ordinary salt solutions. The presence of multivalent counterions is not required. We review the relevant literature in detail and conclude that it merits more attention than it has received. We discuss also some recent observations of a low ionic strength attraction of negatively charged DNA to the region of a negatively charged glass nanoslit where the floor of the nanoslit meets the walls, again in the absence of multivalent ions. On the theoretical side, it has become clear that purely electrostatic interactions require the presence of multivalent counterions if they are to generate like-charge attraction. Any theory of like-charge attraction in the absence of multivalent counterions must therefore contain a non-electrostatic component. We point out that counterion condensation theory, which has predicted like-charge polyelectrolyte attraction in an intermediate range of distances in ordinary 1:1 salt conditions, contains both electrostatic and non-electrostatic elements. The non-electrostatic component of the theory is the modeling constraint that the counterions fall into two explicit populations, condensed and uncondensed. As reviewed in the paper, this physically motivated constraint is supported by strong experimental evidence. We proceed to offer an explanation of the nanoslit observations by showing in an idealized model that the line of intersection of two intersecting planes is a virtual polyelectrolyte. Since we have previously developed a counterion condensation theory of attraction of two like-charged polyelectrolytes, our suggestion is that the DNA is attracted to the virtual polyelectrolytes that may be located in the nanoslit where floor meets walls. We present the detailed calculations needed to document this suggestion: an extension of previous theory to the case of polyelectrolytes with like but not identical charges; the demonstration of counterion condensation on a plane with bare charge density greater than an explicitly exhibited critical value; a calculation of the free energy of the plane; a calculation of the interaction of a line charge polyelectrolyte with a like-charged plane; and the detailed demonstration that the line of intersection of two planes is a virtual polyelectrolyte.

Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs

The free energy of an RNA fold is a combination of favorable base pairing and stacking interactions competing with entropic costs of forming loops. Here we show how loop entropy, surprisingly, can promote tertiary order. A general formula for the free energy of forming multibranch and other RNA loops is derived with a polymer-physics based theory. We also derive a formula for the free energy of coaxial stacking in the context of a loop. Simulations support the analytic formulas. The effects of stacking of unpaired bases are also studied with simulations.

Nanostructural self-assembly of iridescent feather barbules through depletion attraction of melanosomes during keratinization

Avian plumage colours are model traits in understanding the evolution of sexually selected ornamental traits. Paradoxically, iridescent structural colours, probably the most dazzling of these traits, remain the most poorly understood. Though some data suggest that expression of bright iridescent plumage colours produced by highly ordered arrays of melanosomes and keratin is condition-dependent, almost nothing is known of their ontogeny and thus of any developmental mechanisms that may be susceptible to perturbation. Here, we use light and electron microscopy to compare the ontogeny of iridescent male and non-iridescent female feathers in blue-black grassquits. Feather barbules of males contain a single layer of melanosomes bounded by a thin layer of keratin-producing blue iridescent colour, while those of females contain disorganized melanosomes and no outer layer. We found that nanostructural organization of male barbules occurs late in development, following death of the barbule cell, and is thus unlikely to be under direct cellular control, contrary to previous suggestions. Rather, organization appears to be caused by entropically driven self-assembly through depletion attraction forces that pin melanosomes to the edge of barbule cells and to one another. These forces are probably stronger in developing barbules of males than of females because their melanosomes are (i) larger, (ii) more densely packed, and (iii) more homogeneously distributed owing to the more consistent shape of barbules during keratinization. These data provide the first proposed developmental pathway for iridescent plumage colours, and suggest that any condition dependence of iridescent barbules is likely driven by factors other than direct metabolic cost.

Transverse polarizability of an aligned assembly of charged rods

The low-field transverse polarizability of the counterions condensed on an isolated charged rod is small. We show that it can be much larger if the rod is a member of an assembly of aligned rods. The polarization free energy of the assembly of rods in a transverse field is then similar to its polarization free energy in a field parallel to the rods. The polarization free energy of the assembly in a transverse field becomes lower than in a parallel field if the extent of the assembly (as measured, for example, by the diameter of a cylindrical assembly) is larger than the length of the individual rods. We suggest that this model may provide a reasonable explanation for the occurrence of "anomalous" birefringence in systems of interacting charged rodlike particles.

Dynamic flexibility in the structure and function of photosystem II in higher plant thylakoid membranes: the grana enigma

Grana are not essential for photosynthesis, yet they are ubiquitous in higher plants and in the recently evolved Charaphyta algae; hence grana role and its need is still an intriguing enigma. This article discusses how the grana provide integrated and multifaceted functional advantages, by facilitating mechanisms that fine-tune the dynamics of the photosynthetic apparatus, with particular implications for photosystem II (PSII). This dynamic flexibility of photosynthetic membranes is advantageous in plants responding to ever-changing environmental conditions, from darkness or limiting light to saturating light and sustained or intermittent high light. The thylakoid dynamics are brought about by structural and organizational changes at the level of the overall height and number of granal stacks per chloroplast, molecular dynamics within the membrane itself, the partition gap between appressed membranes within stacks, the aqueous lumen encased by the continuous thylakoid membrane network, and even the stroma bathing the thylakoids. The structural and organizational changes of grana stacks in turn are driven by physicochemical forces, including entropy, at work in the chloroplast. In response to light, attractive van der Waals interactions and screening of electrostatic repulsion between appressed grana thylakoids across the partition gap and most probably direct protein interactions across the granal lumen (PSII extrinsic proteins OEEp-OEEp, particularly PsbQ-PsbQ) contribute to the integrity of grana stacks. We propose that both the light-induced contraction of the partition gap and the granal lumen elicit maximisation of entropy in the chloroplast stroma, thereby enhancing carbon fixation and chloroplast protein synthesizing capacity. This spatiotemporal dynamic flexibility in the structure and function of active and inactive PSIIs within grana stacks in higher plant chloroplasts is vital for the optimization of photosynthesis under a wide range of environmental and developmental conditions.

Macromolecular crowding and its potential impact on nuclear function

It is well established, that biochemical reactions are dependent on pH, ionic strength, temperature and the concentration of reactants. However, the steric repulsion among bulky components of biological systems also affect biochemical behavior: The 'excluded volume effect of macromolecular crowding' drives bulky components into structurally compact organizations, increases their thermodynamic activities and slows down diffusion. The very special composition of the cell nucleus, which is packed with high-molecular chromatin, ribonucleo-particles and associated proteins, suggests that crowding-effects are part of nuclear functionality. Realizing that many nuclear processes, notably gene transcription, hnRNA splicing and DNA replication, use macromolecular machines, and taking into account that macromolecular crowding provides a cooperative momentum for the assembly of macromolecular complexes, we here elaborate why macromolecular crowding may be functionally important in supporting the statistical significance of nuclear activities.

Selective precipitation of proteins

Selective precipitation of proteins can be used as a bulk method to recover the majority of proteins from a crude lysate, as a selective method to fractionate a subset of proteins from a protein solution, or as a very specific method to recover a single protein of interest from a purification step. This unit describes a number of methods suitable for selective precipitation. In each of the protocols that are outlined, the physical or chemical basis of the precipitation process, the parameters that can be varied for optimization, and the basic steps for developing an optimized precipitation are described.

Use of Parsons-Lee and Onsager theories to predict nematic and demixing behavior in binary mixtures of hard rods and hard spheres

Parsons-Lee and Onsager theories are formulated for the isotropic-nematic transition in a binary mixture of hard rods and hard spheres. Results for the phase coexistence and for the equation of state in both phases for mixtures with different relative sizes and composition are presented. The two theories explain correctly the general behavior observed in experiments and computer simulations for these fluids. In particular, the theory accounts for the destabilization of the nematic phase when spherical or globular macromolecules are added to a system of rodlike colloids, and the entrance of the system into a demixed regime at high volume fractions of the spherical particles. Upon demixing a nematic state rich in rods coexists in equilibrium with an isotropic state much more diluted in the rodlike component. Onsager theory fails on quantitative grounds for aspect ratios of the rodlike molecules smaller than 100, and in the cases where the molar fractions of spheres becomes close to unity. On the contrary, the Parsons-Lee approximation remains accurate down to aspect ratios as small as 5. The spinodal analysis indicates that the isotropic-isotropic and nematic-nematic coexistences become feasible for sufficiently large spheres and long rods, respectively. The latter type of coexistence interferes partially with the isotropic-nematic coexistence regime of interest to the present work. Overall, the study serves to rationalize and control key aspects of the behavior of these binary nematogenic colloidal systems, which can be tuned with an appropriate choice of the relative size and molar fractions of the particles.

Experimental evidence for the influence of molecular crowding on nuclear architecture

Many compounds in the cell nucleus are structurally organized. To assess the influence of structural organization on nuclear function, we investigated the physical mechanisms of structure formation by using molecular crowding as a parameter for nuclear integrity. Molecular crowding promotes compaction of macromolecular compounds depending on their size and shape without the need for site-specific interactions. HeLa and MCF7 cells were incubated with hypertonic medium to increase crowding of their macromolecular content as a result of the osmotic loss of water. Supplementation of sucrose, sorbitol or NaCl to the growth medium shifted nuclear organization, observed by fluorescence and electron microscopy, towards compaction of chromatin and segregation of other nuclear compounds. With increasing hypertonic load and incubation time, this nuclear re-organization proceeded gradually, irrespective of the substances used, and reversibly relaxed to a regular phenotype upon re-incubation of cells in isotonic growth medium. Gradual and reversible re-organization are major features of controlled de-mixing by molecular crowding. Of fundamental importance for nuclear function, we discuss how macromolecular crowding could account for the stabilization of processes that involve large, macromolecular machines.

Nucleation of Self-Associating Fluids: Free versus Activated Association

We use the density functional theory of statistical mechanics in a square gradient approximation to analyze the structure, size, and work of formation of critical nuclei in self-associating fluids where association reduces the strength of the interactions between bonded particles. This effect is expected in systems of strongly dipolar particles that associate into chains. In this work we analyze the nucleation behavior of two types of self-associating fluids: a system comprised of particles that can freely associate, and a system in which the association process involves a thermally activated initiation step. For the first case, we explore the properties of critical nuclei in fluids that exhibit a metastable critical point between a vapor phase and a highly associated liquid phase. In fluids where the association dynamics involves an initiation step, we investigate the nucleation behavior in the vicinity of the polymerization transition. In both cases critical nuclei undergo a structural transition that shares many of the features of the coil-globule transition reported in Monte Carlo simulations of strongly dipolar Stockmayer fluids. Our results suggest that the sharp structural transition observed in these simulations is evidence of the existence of a second-order or nearly second-order association transition in these model fluids.

Spontaneous assembly of viruses on multilayered polymer surfaces

The idea that randomly arranged supermolecular species incorporated in a network medium can ultimately create ordered structures at the surface may be counterintuitive. However, such order can be accommodated by regulating dynamic and equilibrium driving forces. Here, we present the ordering of M13 viruses, highly complex biomacromolecules, driven by competitive electrostatic binding, preferential macromolecular interactions and the rigid-rod nature of the virus systems during alternating electrostatic assembly. The steric constraints inherent to the competitive charge binding between M13 viruses and two oppositely charged weak polyelectrolytes leads to interdiffusion and the virtual 'floating' of viruses to the surface. The result is the spontaneous formation of a two-dimensional monolayer structure of viruses atop a cohesive polyelectrolyte multilayer. We demonstrate that this viral-assembled monolayer can be a biologically tunable scaffold to nucleate, grow and align nanoparticles or nanowires over multiple length scales. This system represents an interface that provides a general platform for the systematic incorporation and assembly of organic, biological and inorganic materials.

Electrochemical structure of the crowded cytoplasm

The current view of the cytoplasm as a 'bustling and well-organized metropolitan city' raises the issue of how physicochemical forces control the macromolecular interactions and transport of metabolites and energy in the cell. Motivated by studies on bacterial osmosensors, we argue that charged cytoplasmic macromolecules are stabilized electrostatically by their ionic atmospheres. The high cytoplasmic crowding (25-50% of cell volume) shapes the remaining cell volume (50-75%) into transient networks of electrolyte pathways and pools. The predicted 'semi-conductivity' of the electrolyte pathways guides the flow of biochemical ions throughout the cytoplasm. This metabolic and signaling current is powered by variable electrochemical gradients between the pools. The electrochemical gradients are brought about by cellular biochemical reactions and by extracellular stimuli. The cellular metabolism is thus vectorial not only across the membrane but also throughout the cytoplasm.

Effect of macromolecular crowding agents on human immunodeficiency virus type 1 capsid protein assembly in vitro

Previous studies on the self-assembly of capsid protein CA of human immunodeficiency virus type 1 (HIV-1) in vitro have provided important insights on the structure and assembly of the mature HIV-1 capsid. However, CA polymerization in vitro was previously observed to occur only at very high ionic strength. Here, we have analyzed the effects on CA assembly in vitro of adding unrelated, inert macromolecules (crowding agents), aimed at mimicking the crowded (very high macromolecular effective concentration) environment within the HIV-1 virion. Crowding agents induced fast and efficient polymerization of CA even at low (close to physiological) ionic strength. The hollow cylinders thus assembled were indistinguishable in shape and dimensions from those formed in dilute protein solutions at high ionic strength. However, two important differences were noted: (i) disassembly by dilution of the capsid-like particles was undetectable at very high ionic strength, but occurred rapidly at low ionic strength in the presence of a crowding agent, and (ii) a variant CA from a presumed infectious HIV-1 with mutations at the CA dimerization interface was unable to assemble at any ionic strength in the absence of a crowding agent; in contrast, this mutation allowed efficient assembly, even at low ionic strength, when a crowding agent was used. The use of a low ionic strength and inert macromolecules to mimic the crowded environment inside the HIV-1 virion may lead to a better in vitro evaluation of the effects of conditions, mutations or/and other molecules, including potential antiviral compounds, on HIV-1 capsid assembly, stability and disassembly.

Equilibrium polymerization in the Stockmayer fluid as a model of supermolecular self-organization

A diverse range of molecular self-organization processes arises from a competition between directional and isotropic van der Waals intermolecular interactions. We conduct Monte Carlo simulations of the Stockmayer fluid (SF) with a large dipolar interaction as a minimal self-organization model and focus on basic thermodynamic properties that are needed to characterize the polymerization transition that occurs in this fluid. In particular, we determine the polymerization transition lines from the maximum in the specific heat, C(v), and the inflection point in the extent of polymerization, Phi. We also characterize the geometry (radius of gyration R(g), chain length L, chain topology) of the clusters that form in this associating fluid as a function of temperature, T, and concentration, rho . The pressure, P, and the second virial coefficient, B2, were determined, since these properties contain essential information about the strength of the isotropic (van der Waals) interactions. Our simulations indicate that the locations of the polymerization lines are quantitatively consistent with a model of equilibrium polymerization with the enthalpy of polymerization ("sticking energy") fixed by the minimum in the intermolecular potential. The polymerization transition in the SF is accompanied by a topological transition from predominantly linear to ring polymers upon cooling that is driven by the minimization of the dipolar energy of the clusters. We also find that the basic interaction parameters describing polymerization and phase separation in the SF can be estimated based on the existing theory of equilibrium polymerization, but the theory must be refined to account for ring formation in order to accurately describe the configurational properties of this model self-organizing fluid.

Phase equilibria in solutions of platelike particles: systems with steric and dispersive interactions between the platelets

Our statistical thermodynamics model of solution of stiff, platelike, biaxial particles interacting solely via repulsion on contact (athermal limit) [Phys. Rev. E 62, 5011 (2000)] is extended to incorporate dispersion interactions between the particles. Dispersion forces between anisotropic particles are accounted for using the Imura-Okano approach. Numerical calculations specialized to solutions of either rods or disks show that besides the isotropic-nematic biphasic coexistence range, inclusion of attractive forces resulted in the appearance of nematic-nematic coexistence in both, disks and rods, solutions. The critical divergence of the difference between the order parameters and concentrations of the two nematics is observed while approaching the critical temperature. The minimum aspect ratio of rods or disks for the formation of the nematic phase is also discussed.

Essential cell division protein FtsZ assembles into one monomer-thick ribbons under conditions resembling the crowded intracellular environment

Experimental conditions that simulate the crowded bacterial cytoplasmic environment have been used to study the assembly of the essential cell division protein FtsZ from Escherichia coli. In solutions containing a suitable concentration of physiological osmolytes, macromolecular crowding promotes the GTP-dependent assembly of FtsZ into dynamic two-dimensional polymers that disassemble upon GTP depletion. Atomic force microscopy reveals that these FtsZ polymers adopt the shape of ribbons that are one subunit thick. When compared with the FtsZ filaments observed in vitro in the absence of crowding, the ribbons show a lag in the GTPase activity and a decrease in the GTPase rate and in the rate of GTP exchange within the polymer. We propose that, in the crowded bacterial cytoplasm under assembly-promoting conditions, the FtsZ filaments tend to align forming dynamic ribbon polymers. In vivo these ribbons would fit into the Z-ring even in the absence of other interactions. Therefore, the presence of mechanisms to prevent the spontaneous assembly of the Z-ring in non-dividing cells must be invoked.

Control of the Geometry of the Adsorbed Thin Layer by the Depletion Interaction

The depletion interaction was reported to drive the mixtures of rodlike colloids and polymer coils into a variety of phase transitions such as isotropic-nematic, nematic-smectic, and so forth. We describe in this Communication a convenient preparation of the self-assembled monolayer of the platelike porphyrin molecules by the depletion interaction between the absorbent and the metal substrates. After the depletant, low molecular weight poly(ethylene oxide) (PEO), was added into the porphyrin/ethanol solution, random oriented porphyrin was then regulated to lie parallel to the adjacent metal substrates, forming the self-assembled monolayer.

Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance

Crowding, which characterizes the interior of all living cells, has been shown to dramatically affect biochemical processes, leading to stabilization of compact morphologies, enhanced macromolecular associations, and altered reaction rates. Due to the crowding-mediated shift in binding equilibria toward association, crowding agents were proposed to act as a metabolic buffer, significantly extending the range of intracellular conditions under which interactions occur. Crowding may, however, impose a liability because, by greatly and generally enhancing macromolecular association, it can lead to irreversible interactions. To better understand the physical determinants and physiological consequences of crowding-mediated buffering, we studied the effects of crowding, or excluded volume, on DNA structures. Results obtained from isothermal titration calorimetry (ITC) and UV melting experiments indicate that crowding-induced effects are marginal under conditions that a priori favor association of DNA strands but become progressively larger when conditions deteriorate. As such, crowding exerts "genuine" buffering activity. Unexpectedly, crowding-mediated effects are found to include enthalpy terms that favorably contribute to association processes. We propose that these enthalpy terms and preferential stabilization derive from a reconfiguration of DNA hydration that occurs in dense DNA-rich phases obtained in crowded environments.

Circular dichroism and Fourier transform infrared spectroscopic studies on self-assembly of tetrapeptide derivative in solution and solvated film

Aggregation of the hydrophobic peptide derivative Boc-Ala-Ile-Ile-Gly-OMe (1) was examined in methanol solution and in solvated film states. Formation of the peptide by self-assembly was evidenced using fluorescence [Mg salt of 8-anilino-naphthalenesulfonic acid (ANS) as an external probe] and circular dichroism (CD) spectroscopic techniques. In solution, peptide 1 formed as a stable aggregate at a concentration around 3 x 10(-4)m. The peptide gelled into a thin film for which we carried out CD and Fourier transform infrared (FTIR) measurements. Our spectroscopic study on peptide films at differing methanol concentrations indicates that the helical content of the peptide decreases with decreasing methanol concentration in solvated films. However, by reducing the methanol concentration we were able to observe a conformational transition from a predominantly helical turn to a beta-sheet structure via a random coil conformation. Our study focused on the aggregation of the alpha-helical turn-forming peptide derivative, which shows conformational transition on changing solvent concentration in the film form.

Relating interactions between neurofilaments to the structure of axonal neurofilament distributions through polymer brush models

Neurofilaments (NFs) have been proposed to interact with one another through mutual steric exclusion of their unstructured C-terminal "sidearm" domains, producing order in axonal NF distributions and conferring mechanical strength to the axon. Here we apply theory developed for polymer brushes to examine the relationship between the brush properties of the sidearms and NF organization in axons. We first measure NF-NF radial distribution functions and occupancy probability distributions for adult mice. Interpreting the probability distributions using information theory, we show that the NF distributions may be represented by a single pair potential of mean force. Then, to explore the relationship between model parameters and NF architecture, we conduct two-dimensional Monte Carlo simulations of NF cross-sectional distributions. We impose purely repulsive interaction potentials in which the sidearms are represented as neutral and polyelectrolyte chains. By treating the NFs as telechelic polymer brushes, we also incorporate cross-bridging interactions. Both repulsive potentials are capable of reproducing NF cross-sectional densities and their pair correlations. We find that NF structure is sensitive to changes in brush thickness mediated by chain charge, consistent with the experimental observation that sidearm phosphorylation regulates interfilament spacing. The presence of attractive cross-bridging interactions contributes only modestly to structure for moderate degrees of cross-bridging and leads to NF aggregation for extensive cross-bridging.

Molecular crowding accelerates fibrillization of alpha-synuclein: could an increase in the cytoplasmic protein concentration induce Parkinson's disease?

Parkinson's disease (PD) is one of many neurodegenerative diseases that are characterized by amyloid fibril formation. Alpha-synuclein is a primary component of the fibrillar neuronal inclusions, known as Lewy bodies, that are diagnostic of PD. In addition, the alpha-synuclein gene is linked to familial PD. Fibril formation by alpha-synuclein proceeds via discrete beta-sheet-rich oligomers, or protofibrils, that are consumed as fibrils grow. Both FPD mutations accelerate formation of protofibrils, suggesting that these intermediates, rather than the fibril product, trigger neuronal loss. In idiopathic PD, other factors may be responsible for accelerating protofibril formation by wild-type alpha-synuclein. One possible factor could be molecular crowding in the neuronal cytoplasm. We demonstrate here that crowding using inert polymers significantly reduced the lag time for protofibril formation and the conversion of the protofibril to the fibril, but did not affect the morphology of either species. Physiologically realistic changes in the degree of in vitro crowding have significant kinetic consequences. Thus, nonspecific changes in the total cytoplasmic protein concentration, induced by cell volume changes and/or altered protein degradation, could promote formation of and stabilize the alpha-synuclein protofibril.

Beyond Flory-Huggins theory: new classes of blend miscibility associated with monomer structural asymmetry

Flory-Huggins (FH) theory is restricted to polymer mixtures whose monomers are structurally identical, a situation limited to isotopic blends and computer simulations. We investigate the influence of monomer structure on blend miscibility and scattering properties using the lattice cluster theory generalization of the FH model. Monomer structural asymmetry is shown to profoundly affect blend miscibility (T(c),phi(c)), chain swelling (T(theta)), and the scale (xi) and intensity [S(0)] of composition fluctuations. Four distinct blend miscibility classes are identified and experimental evidence for these classes is discussed.

Stirring effects on the spontaneous formation of chirality in the homoassociation of diprotonated meso-tetraphenylsulfonato porphyrins

Homoassociates of the achiral title porphyrins in acid solutions show spontaneous symmetry breaking, which can be detected by circular dichroism (CD). The CD spectra are due to differential scattering and differential absorption contributions, the relative significance of which is related to the shape and size of the homoassociate. When an earlier model, designed for the association of these diprotonated porphyrins (J aggregates with the geometry of stepped sheets of intramolecular-stabilised zwitterions), was applied to an exciton-coupling point-dipole approximation, the folding of the one-dimensional homoassociates explained the CD signals detected. An effect of the vortex direction, caused by stirring or rotary evaporation, upon the exciton chirality sign was detected. In the case of H2TPPS3, the number of experiments performed gave a statistical significance to this effect. This vortex effect can be attributed to enhancement of the chirality fluctuations that originate in the diffusion-limited aggregation to high-molecular-weight homoassociates. In this sense, the phenomenon could be general for supramolecular systems that are obtained under kinetic control, and its detection would be possible when inherent chiral chromophores were being generated in the association process.

Customizing model membranes and samples for NMR spectroscopic studies of complex membrane proteins

Both solution and solid state nuclear magnetic resonance (NMR) techniques for structural determination are advancing rapidly such that it is possible to contemplate bringing these techniques to bear upon integral membrane proteins having multiple transmembrane segments. This review outlines existing and emerging options for model membrane media for use in such studies and surveys the special considerations which must be taken into account when preparing larger membrane proteins for NMR spectroscopic studies.

Fibrils formed in vitro from alpha-synuclein and two mutant forms linked to Parkinson's disease are typical amyloid

Two missense mutations in the gene encoding alpha-synuclein have been linked to rare, early-onset forms of Parkinson's disease (PD). These forms of PD, as well as the common idiopathic form, are characterized by the presence of cytoplasmic neuronal deposits, called Lewy bodies, in the affected region of the brain. Lewy bodies contain alpha-synuclein in a form that resembles fibrillar Abeta derived from Alzheimer's disease (AD) amyloid plaques. One of the mutant forms of alpha-synuclein (A53T) fibrillizes more rapidly in vitro than does the wild-type protein, suggesting that a correlation may exist between the rate of in vitro fibrillization and/or oligomerization and the progression of PD, analogous to the relationship between Abeta fibrillization in vitro and familial AD. In this paper, fibrils generated in vitro from alpha-synuclein, wild-type and both mutant forms, are shown to possess very similar features that are characteristic of amyloid fibrils, including a wound and predominantly unbranched morphology (demonstrated by atomic force and electron microscopies), distinctive dye-binding properties (Congo red and thioflavin T), and antiparallel beta-sheet structure (Fourier transform infrared spectroscopy and circular dichroism spectroscopy). alpha-Synuclein fibrils are relatively resistant to proteolysis, a property shared by fibrillar Abeta and the disease-associated fibrillar form of the prion protein. These data suggest that PD, like AD, is a brain amyloid disease that, unlike AD, is characterized by cytoplasmic amyloid (Lewy bodies). In addition to amyloid fibrils, a small oligomeric form of alpha-synuclein, which may be analogous to the Abeta protofibril, was observed prior to the appearance of fibrils. This species or a related one, rather than the fibril itself, may be responsible for neuronal death.

Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area

Classical biochemistry is founded on several assumptions valid in dilute aqueous solutions that are often extended without question to the interior milieu of intact cells. In the first section of this chapter, we present these assumptions and briefly examine the ways in which the cell interior may depart from the conditions of an ideal solution. In the second section, we summarize experimental evidence regarding the physical properties of the cell cytoplasm and their effect on the diffusion and binding of macromolecules and vesicles. While many details remain to be worked out, it is clear that the aqueous phase of the cytoplasm is crowded rather than dilute, and that the diffusion and partitioning of macromolecules and vesicles in cytoplasm is highly restricted by steric hindrance as well as by unexpected binding interactions. Furthermore, the enzymes of several metabolic pathways are now known to be organized into structural and functional units with specific localizations in the solid phase, and as much as half the cellular protein content may also be in the solid phase.

Lateral organisation of membrane lipids. The superlattice view

Most biological membranes are extremely complex structures consisting of hundreds or even thousands of different lipid and protein molecules. The prevailing view regarding the organisation of these membranes is based on the fluid-mosaic model proposed by Singer and Nicholson in 1972. According to this model, phospholipids together with some other lipids form a fluid bilayer in which these lipids are diffusing very rapidly laterally. The idea of rapid lateral diffusion implies that, in general, the different lipid species would be randomly distributed in the plain of the membrane. However, there are recent data indicating that the components tend to adopt regular (superlattice-like) distributions in fluid, mixed bilayers. Based on this, a superlattice model of membranes has been proposed. This superlattice model is intriguing because it allows only a limited certain number of 'critical' compositions. These critical compositions could play a key role in the regulation of the lipid compositions of biological membranes. Furthermore, such putative critical compositions could explain how compositionally distinct organelles can exist despite of rapid inter-organelle membrane traffic. In this review, these intriguing predictions are discussed along with the basic principles of the model and the evidence supporting it.

Supramolecular ligands: monomer structure and protein ligation capability

The aim of this work was to define the chemical structure of compounds self-assembling in water solutions, which appear to interact with proteins as single ligands with their supramolecular nature preserved. For this purpose the ligation to proteins of bis azo dyes, represented by Congo red and its derivatives with designed structural alterations, were tested. The three parameters which characterize the reactivity of supramolecular material were determined in the same conditions for all studied dyes. These were: A) stability of the assembly products; B) binding to heat-denatured protein (human IgG); and C) binding to native protein (rabbit antibodies in the immune complex) measured by the enhancement of hemagglutination. The structural differences between the Congo red derivatives concerned the symmetry of the molecule and the structure of its non-polar component, which occupies the central part of the dye molecule and is thought to be crucial for self-assembly. Other dyes were also studied for the same purpose: Evans blue and Trypan blue, bis-ANS and ANS, as well as a group of compounds with a structural design unlike that of bis azo dyes. Compounds with rigid elongated symmetric molecules with a large non-polar middle fragment are expected to form a ribbon-like supramolecular organization in assembling. They appeared to have ligation properties related to their self-assembling tendency. The compounds with different structures, not corresponding to bis azo dyes, did not reveal ligation capability, at least in respect to native protein. The conditions of binding to denatured proteins seem less restrictive than the conditions of binding to native molecules. The molten hydrophobic protein interior becomes a new binding area allowing for complexation of even non-assembled molecules.

Laser light scattering evidence for a common wormlike growth structure of mixed micelles in bile salt- and straight-chain detergent-phosphatidylcholine aqueous systems: relevance to the micellar structure of bile

We employed quasielastic and static light scattering to measure apparent values of the mean hydrodynamic radii (Rh)app, molecular weights (Mapp), and radii of gyration (Rg)app in solutions containing mixed micelles composed of bile salts (cholate and taurochenodeoxycholate, both cholanoyl derivatives) and the glycoacyl chain detergent, octyl glucoside, with egg yolk phosphatidylcholine (EYPC) as functions of total lipid concentration (0.1-10 g/dL), EYPC/detergent molar ratio (0-1.2), and ionic strength (0.15-0.4 M NaCl) at 20 degreesC and 1 atm. As the mixed micellar phase boundaries were approached by dilution, (Rh)app, Mapp, and (Rg)app values increased markedly by up to 20-fold. For each micellar system, the scaling ratios (Rh)app/Mapp1/2 and (Rg)app/(Rh)app remained essentially constant at 0.018 nm/(g/mol)1/2 and 1.5 (dimensionless), respectively, despite large variations in total lipid concentration, detergent molecular species, and ionic strength. Refined data analysis is inconsistent with a flat "mixed-disc" model for bile salt-EYPC micelles [Mazer, N. A., Benedek, G. B., and Carey, M. C. (1980) Biochemistry 19, 601] and octyl glucoside-EYPC micelles principally because the numerical value of (Rh)app/Mapp1/2 corresponds to a hypothetical disk thickness of approximately 1 nm, which is 4-fold smaller than the bimolecular width of EYPC molecules, and for a disk, (Rg)app/(Rh)app ratios should be close to 1 at low total lipid concentrations. Assuming disc-shaped micelles, we show that intermicellar excluded volume interactions would have only a minor effect on Mapp and cannot account for the unrealistic disk thickness. Instead, locally cylindrical, semiflexible wormlike micelles of diameter d = 4 nm and persistence length xip = 17 nm in solution are compatible with the observed (Rh)app/Mapp1/2 and (Rg)app/(Rh)app values when intermicellar excluded-volume interactions are considered. With EYPC/taurochenodeoxycholate = 0.6 and EYPC/cholate = 1.0 in 0.15 M NaCl, independent micelles grow upon dilution and use of the second virial coefficient [Egelhaaf, S. U., and Schurtenberger, P. (1994) J. Phys. Chem. 98, 8560] is adequate for estimating micellar weights. The systems EYPC/cholate = 1.0 in 0.4 M NaCl, EYPC/cholate = 1.2 in 0.15 M NaCl, and EYPC/octyl glucoside = 0.13 in 0.15 M NaCl all form highly overlapping, semidilute polymer solutions, which mimic the observed scaling ratios. In such semidilute systems, use of the second virial coefficient alone to account for intermicellar interactions is inadequate for estimating micellar weights. The results of the present study, in combination with locations of known phase boundaries of the ternary bile salt-EYPC-water phase diagram at high dilution, suggest that elongation, as well as entanglement of wormlike mixed micelles may occur at concentrations approaching the micellar phase limit.