Decrease In Radius Of Gyration Research Articles

Anti-polyelectrolyte and polyelectrolyte effects on conformations of polyzwitterionic chains in dilute aqueous solutions.

Polyzwitterions (PZs) are considered as model synthetic analogs of intrinsically disordered proteins. Based on this analogy, PZs in dilute aqueous solutions are expected to attain either globular (i.e. molten, compact) or random coil conformations. Addition of salt is expected to open these conformations. To the best of our knowledge, these hypotheses about conformations of PZs have never been verified. In this study, we test these hypotheses by studying effects of added salt [potassium bromide (KBr)] on gyration and hydrodynamic radii of poly(sulfobetaine methacrylate) in dilute aqueous solutions using dynamic light scattering and small-angle X-ray scattering, respectively. Effects of zwitteration are revealed by direct comparisons of the PZs with the polymers of the same backbone but containing (1) no explicit charges on side groups such as poly(2-dimethylaminoethyl methacrylate)s and (2) explicit cationic side groups with tertiary amino bromide pendants. Zeta-potential measurements, transmission electron microscopy, and ab initio molecular dynamics simulations reveal that the PZs acquire net positive charge in near salt-free conditions due to protonation but retain coiled conformations. Added KBr leads to nonmonotonic changes exhibiting an increase followed by a decrease in radius of gyration (and hydrodynamic radius), which are called antipolyelectrolyte and polyelectrolyte effects, respectively. Charge regulation and screening of charge-charge interactions are discussed in relation to the antipolyelectrolyte and polyelectrolyte effects, respectively, which highlight the importance of salt in affecting net charge and conformations of PZs.

Impact of PEGylation on the degradation and pore organization in mesoporous silica nanoparticles: A study of the inner mesoporous structure in physiologically relevant ionic conditions

The degradation of mesoporous silica nanoparticles (MSNs) in the biological milieu due to silica hydrolysis plays a fundamental role for the delivery of encapsulated drugs and therapeutics. However, little is known on the evolution of the pore arrangement in the MSNs in biologically relevant conditions. Small Angle X-ray scattering (SAXS) studies were performed on unmodified and PEGylated MSNs with a MCM-48 pore structure and average sizes of 140 nm, exposed to simulated body fluid solution (SBF) at pH 7.4 for different time intervals from 30 min to 24 h. Experiments were performed with silica concentrations below, at and over 0.14 mg/mL, the saturation concentration of silica in water at physiological temperature. At silica concentrations of 1 mg/mL (oversaturation), unmodified MSNs show variation in interpore distances over 6 h exposure to SBF, remaining constant thereafter. A decrease in radius of gyration is observed over the same time. Mesoporosity and radius of gyration of unmodified MSNs remain then unchanged up to 24 h. PEGylated MSNs at 1 mg/mL concentration show a broader diffraction peak but no change in the position of the peak is observed following 24 h exposure to SBF. PEGylated MSNs at 0.01 mg/mL show no diffraction peaks already after 30 min exposure to SBF, while at 0.14 mg/mL a small diffraction peak is present after 30 min exposure but disappears after 1 h.

Mesostructural study on graphenic-based carbon prepared from coconut shells by heat treatment and liquid exfoliation

In this study, the effect of heating temperature on the structure of graphenic-based carbon (GC) has been successfully investigated. A series of GC materials was prepared from coconut shells by a green synthesis method. The process includes heating at four temperatures (T = 400, 600, 800 and 1000 °C) followed by an exfoliation process assisted by hydrochloric acid (HCl). These materials were characterized by wide- and small-angle x-ray scattering (WAXS and SAXS), Fourier-transform infrared spectroscopy (FTIR), x-ray photoemission spectroscopy (XPS) and transmission electron microscopy (TEM). The WAXS analysis shows Braggs peaks corresponding to the reduced graphene oxide (rGO)-like phase. Investigations by FTIR and XPS methods show the presence of carbon-oxygen functional groups such as C=C (carbon with sp2 hybridization), C–C (carbon with sp3 hybridization), and C=O bonds. The sp2 bonds form a 2-dimensional (2D) network in hexagonal lattice, while carbon with sp3 bonds tends to form a 3-dimensional (3D) tetrahedral structure. The BET analysis revealed meso- and micro-pore structures in GC. Heating process reduces the specific surface area and increases pore size of GC. Moreover, increasing the heating temperature induces a decrease in radius of gyration (Rg) and an increase in the formation of 2D structures in GC. The fitting results of SAXS profiles, proved by TEM and XPS, yielded the structure of GC containing the mixture of 2D and 3D structures. Thus, it is suggested that the GC has a mesostructure.

Steady state sedimentation of ultrasoft colloids.

The structural and dynamical properties of ultra-soft colloids-star polymers-exposed to a uniform external force field are analyzed by applying the multiparticle collision dynamics technique, a hybrid coarse-grain mesoscale simulation approach, which captures thermal fluctuations and long-range hydrodynamic interactions. In the weak-field limit, the structure of the star polymer is nearly unchanged; however, in an intermediate regime, the radius of gyration decreases, in particular transverse to the sedimentation direction. In the limit of a strong field, the radius of gyration increases with field strength. Correspondingly, the sedimentation coefficient increases with increasing field strength, passes through a maximum, and decreases again at high field strengths. The maximum value depends on the functionality of the star polymer. High field strengths lead to symmetry breaking with trailing, strongly stretched polymer arms and a compact star-polymer body. In the weak-field-linear response regime, the sedimentation coefficient follows the scaling relation of a star polymer in terms of functionality and arm length.

Molecular dynamics study of coil-to-globule transition in a thermo-responsive oligomer bound to various surfaces: hydrophilic surfaces stabilize the coil form.

The structural and dynamical properties of 40-mer of thermo-responsive polymer PNIPAM covalently bound to different surfaces have been studied, at different temperatures, by means of molecular dynamics simulations. Evolution of the radius of gyration, Rg, of the polymer chain and radial distribution functions (RDFs) calculated for the carbon atoms of the PNIPAM backbone with water oxygens and for the hydrogen atom of the amide groups with water oxygens indicate that functionalized surfaces affect the coil-to-globule transition of PNIPAM, by means of electrostatic interactions, increasing the lower critical solution temperature (LCST) of the polymer. Such interactions, mainly represented by a H-bond, hinder the transition in the globular form while hydrophobic groups on the surface, such as -OCH3, contribute to the globular collapse. A significant alteration in the arrangement of water molecules around the polymer is testified by: (i) the absence of the second peak in the RDF between the C atoms of the PNIPAM backbone and the O atoms of water at the same temperature at which the radius of gyration decreases; (ii) the height of both the first and the second peak of the RDF between the H atom of the amide groups and water O atoms decreases when the temperature increases above the LCST. Finally, the H-bond autocorrelation function indicates that: (i) hydrogen bonds between the bound-to-surface PNIPAM acceptor groups (O[double bond, length as m-dash]C[double bond splayed right]) and the H atoms of water molecules are less persistent than H-bonds formed between the free PNIPAM acceptor groups and water; (ii) H-bonds between the PNIPAM acceptor groups and hydroxyl groups on the quartz surface are longer lived than those formed on graphene oxide.

BIM (BCL-2 interacting mediator of cell death) SAHB (stabilized α helix of BCL2) not always convinces BAX (BCL-2-associated X protein) for apoptosis

The interaction of BAX (BCL-2-associated X protein) with BIM (BCL-2 interacting mediator of cell death) SAHB (stabilized α helix of BCL2) directly initiates BAX-mediated mitochondrial apoptosis. This molecular dynamics study reveals that BIM SAHB forms a stable complex with BAX but it remains in a non-functional conformation. N terminal of BAX folds towards the core which has been reported exposed in the functional monomer. The α1-α2 loop, which has been reported in open conformation in functional BAX, acquires a closed conformation during the simulation. BH3/α2 remains less exposed as compared to initial structure. The hydrophobic residues of BIM accommodates in the rear pocket of BAX during the simulation. A steep decrease in radius of gyration and solvent accessible surface area (SASA) indicates the complex folding to acquire a more stable but inactive conformation. Further the covariance matrix reveals that the backbone atoms’ motions favour the inactive conformation of the complex. This is the first report on the non-functional BAX-BIM SAHB complex by molecular dynamics simulation in the best of our knowledge.

Hydrodynamic interactions of deformable polymeric nanocarriers and the effect of crosslinking.

We report theoretical as well as numerical investigations of deformable nanocarriers (NCs) under physiologically relevant flow conditions. Specifically, to model the deformable lysozyme-core/dextran-shell crosslinked polymer based NC with internal nanostructure and subject it to external hydrodynamic shear, we have introduced a coarse-grained model for the NC and have adopted a Brownian dynamics framework, which incorporates hydrodynamic interactions, in order to describe the static and dynamic properties of the NC. In order to represent the fluidity of the polymer network in the dextran brush-like corona, we coarse-grain the structure of the NC based on the hypothesis that Brownian motion, polymer melt reptations, and crosslinking density dominate their structure and dynamics. In our model, we specify a crosslinking density and employ the simulated annealing protocol to mimic the experimental synthesis steps in order to obtain the appropriate internal structure of the core-shell polymer. We then compute the equilibrium as well as steady shear rheological properties as functions of the Péclet number and the crosslinking density, in the presence of hydrodynamic interactions. We find that with increasing crosslinking, the stiffness of the nanocarrier increases, the radius of gyration decreases, and as a consequence the self-diffusivity increases. The nanocarrier under shear deforms and orients along the direction of the applied shear and we find that the orientation and deformation under shear are dependent on the shear rate and the crosslinking density. We compare various dynamic properties of the NC as a function of the shear force, such as orientation, deformation, intrinsic stresses etc., with previously reported computational and experimental results of other model systems. The computational approach described here serves as a powerful tool for the rational design of NCs by taking both the physiological as well as the hydrodynamic environments into consideration. Development of such models is essential in order to gain useful insights that may be translated into the optimal design of NCs for diagnostic as well as targeted drug delivery applications.

Inverse temperature transition of elastin like motifs in major ampullate dragline silk: MD simulations of short peptides and NMR studies of water dynamics

Using deuterium 2D T1 − T2 Inverse Laplace Transform (ILT) NMR, we have investigated the distribution, population, and dynamics of waters of hydration in major ampullate N. clavipes and A. aurantia silk as a function of temperature. In both samples studied, correlation times much larger than that of free water are measured, and in some cases, appear to increase with increasing temperature over the range of 5 to 60 °C (corresponding to reduced tumbling). In addition, the experimental data point to a reduction in the population of water localized in the silk with increasing temperature in the range of 20 to 50 °C. Molecular dynamics simulations were performed to probe the thermal characteristics of a variety of repeating motifs found in the two silk samples. The repeating motifs GLGSQ, GAAAAAAG, GPGGY, GPGQQ, GPSG, and GPSGPGS found in N. clavipes, GLGSQ, GYGSG, GPGSG, and GPGSQ found in A. aurantia silk were found to exhibit a thermal property observed in short elastin peptides known as the "inverse temperature transition". This is a well known characteristic exhibited by short peptides consisting of (VPGXG)n motifs (where X is any amino acid other than proline) found in elastin--a protein responsible for the elasticity of vertebrate tissues. In qualitative agreement with experimental measurements of water in the silks, all the peptides studied in simulation show evidence of an increase in sidechain contacts and peptide hydrogen bonds, concomitant with a decrease in radius of gyration and localized water as the temperature is raised from approximately 5 to 60 °C.

Phenylene−Ethynylene Macrocycles as Model Systems of Interchromophoric Interactions in π-Conjugated Macromolecules

Unraveling the complex photophysics of macromolecular pi-conjugated systems requires both the development of suitable model systems to access a particular subset of a material's parameter space and the choice of matching spectroscopic techniques. We address the question of the strength of interchromophoric interactions in macromolecular systems by studying the fluorescence depolarization kinetics of a family of prototypical conjugated macrocycles. Shrinking the size of the molecular system decelerates fluorescence depolarization even though the radius of gyration decreases. Although the smaller macrocycles show faster rotational diffusion, the larger compounds exhibit an additional initial depolarization mechanism, attributed to intramolecular interchromophoric energy transfer. Comparison with fragments of the molecule illustrates that the larger macrocycles can be interpreted as bichromophoric systems, whereas the effectively parallel chromophoric elements of the smaller ring are indistinguishable in terms of polarization. The potential role of strong interchromophoric interaction is discussed. The results illustrate a subtle link between interchromophoric arrangement and ultrafast fluorescence depolarization, phenomena, which are often considered in the context of conjugated polymers: chromophoric alignment can potentially counteract the effect of polarization memory loss through energy transfer.

Thermodynamics of the first transition in writhe of a small circular DNA by Monte Carlo simulation

Monte Carlo simulations are employed to investigate the thermodynamics of the first transition in writhe of a circular model filament corresponding to a 468 base-pair DNA. Parameters employed in these simulations are the torsional rigidity, C = 2.0 x 10(-19) dyne cm2, and persistence length, P = 500 A. Intersubunit interactions are modeled by a screened Coulomb potential. For a straight line of subunits this accurately approximates the nonlinear Poisson-Boltzmann potential of a cylinder with the linear charge density of DNA. Curves of relative free energy vs writhe at fixed linking difference (delta l) exhibit two minima, one corresponding to slightly writhed circles and one to slightly underwrithed figure-8's, whenever delta l lies in the transition region. The free energies of the two minima are equal when delta lc = 1.35, which defines the midpoint of the transition. At this midpoint, the free energy barrier between the two minima is found to be delta Gbar = (0.20) kBT at 298 K. Curves of mean potential energy vs writhe at fixed linking difference similarly exhibit two minima for delta l values in the transition region, and the two minimum mean potential energies are equal when delta l = 1.50. At the midpoint writhe, delta lc = 1.35, the difference in mean potential energy between the minimum free energy figure-8 and circle states is (1.3) kBT, and the difference in their entropies is 1.3 kB. Thus, the entropy of the minimum free energy figure-8 state significantly exceeds that of the circle at the midpoint of the transition. The first transition in writhe is found to occur over a rather broad range of delta l values from 0.85 to 1.85. The twist energy parameter (ET), which governs the overall free energy of supercoiling, undergoes a sigmoidal decrease, while the translational diffusion coefficient undergoes a sigmoidal increase, over this same range. The static structure factor exhibits an increase, which reflects a decrease in radius of gyration associated with the circle to figure-8 transition.

Micellization of triblock copolymers in a solvent selective for the middle block: Influence of the molar mass

The micellization thermodynamics and micelle structural parameters for polystyrene- b -poly(ethylene/butylene) b -polystyrene copolymers (SEBS) in n -octane were studied. This solvent is selective for the middle poly(ethylene/butylene) block of the copolymer. The copolymer samples have similar chemical composition and different molar mass. Standard thermodynamic functions of micellization (Δ G °, Δ H ° and Δ S °) were determined by light scattering. All the functions showed more negative values for the SEBS copolymer with a larger molar mass. The structural parameters of micelles formed by different triblock copolymers were determined from static light scattering and viscosity measurements. Micelle molar mass, association number and viscometric hydrodynamic radius increase with the length of the copolymer chain for a constant copolymer composition; however, the radius of gyration decreases. Finally, the results found for SEBS micelles in n -octane are compared to those found for SEBS micelles in 4-methyl-2-pentanone. The different behaviour found supports the idea that the micelles of a triblock copolymer in a selective so vent of the middle block will show a shell formed by loops of the middle block in order that the two outer blocks go into the micelle core and even some poorly solvated outer blocks could be extended out of the micelle.

Collapse of Isolated Chains in a Network

ABSTRACTIn this study we use small angle neutron scattering to investigate the conformation of linear deuterated polystyrene chains trapped in a crosslinked protonated polystyrene matrix. The second virial coefficient was obtained as a function of crosslink density for a wide range of crosslink density. It is shown that the second virial coefficient decreases with increasing crosslink density. By extrapolating the scattering to zero concentration of the linear chain at all values of q, the single chain scattering was obtained and radius of gyration was measured the function of network density. It was found that when the network density is low (NI < Nc where NI and Nc are the number of monomer units in the linear chain and the monomer units between crosslinks, respectively) the radius of gyration does not change. As the network density increases (NI > Nc ) radius of gyration decreases. In this region the inverse of the radius of gyration varies linearly with the inverse of Nc. When the crosslink density is very high (NI » Nc ), segregation of linear polymer chains occurs. These results are in agreement with prediction and computer simulation results of polymer chain conformation in a field of random obstacles where the crosslink junctions act as the effective obstacles.

Correlation between enzyme activity and hinge-bending domain displacement in 3-phosphoglycerate kinase.

Diffuse X-ray-scattering data give evidence for large-scale structural change in pig muscle 3-phosphoglycerate kinase upon substrate binding. Simultaneous binding of 3-phosphoglycerate and MgATP either to the unmodified enzyme or to its active methylated derivative leads to about an 0.1-nm decrease in radius of gyration. These data coincide well with the previous data for yeast 3-phosphoglycerate kinase. When, instead of methylation, the two reactive thiol groups of pig muscle 3-phosphoglycerate kinase are carboxamidomethylated, the enzyme becomes inactive and the radii of gyration of its 'apo' and 'holo' forms do not differ within limits of experimental error. Thus, a correlation exists between the activity of 3-phosphoglycerate kinase and its substrate-induced large-scale conformational change. This correlation is a strong argument in favor of the functional importance of domain locking in the reaction catalyzed by 3-phosphoglycerate kinase.

A neutron scattering study of the ternary complex EF-Tu.GTP-valyl-tRNAVal1A.

The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNAVal1A has been investigated in a hepes buffer of "pH" 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D2O where EF-Tu (42% D2O) and tRNA (71% D2O) are successively matched by the solvents. The results indicate that EF-Tu undergoes a conformational change and contracts as a result of the complex formation, since the radius of gyration decreases by 15% from 2.82 to 2.39 nm. tRNAVal1A, on the other hand, seems to mainly retain its conformation within the complex, since the radii of gyration for the free (after correction for interparticular scattering) and complexed form are essentially the same, 2.38 and 2.47 nm, respectively.

Conformational changes in arginine kinase upon ligand binding seen by small-angle X-ray scattering

Small-angle X-ray scattering is used to study the effects of substrate binding to lobster arginine kinase in solution. We measure the radius of gyration of the enzyme in the absence and in the presence of ligands. We find that the radius of gyration decreases by 1.20 ± 0.25 Å upon binding ADP-Mg and L-arginine to form the ternary complex. The same decrease is also observed upon binding ADP-Mg alone or ATP-Mg. These results indicate a large conformational change consistent with the hinge motion of domains observed in other phosphokinases.

Conformational behaviour of poly(2,6-dimethyl-1,4-phenylene oxide) in solution—II. Sedimentation coefficients and permeabilities in the semi-dilute region as a function of temperature

Sedimentation and flotation coefficients of poly(2,6-dimethyl-1,4-phenylene oxide) (PPO) solutions have been measured as a function of temperature between 60 and 25°. The solvents were toluene and trichloroethane (TCE). Solvent permeabilities have been calculated from the sedimentation or flotation coefficients. PPO is less permeable to the solvents used than polystyrene of comparable molecular weight is to toluene and cyclohexane. Strong solvation of toluene and TCE by PPO molecules is proposed as an explanation for this finding. The measured permeabilities were used to check an earlier calculation of the change of radius of gyration with temperature from intrinsic viscosity data. A larger decrease in radius of gyration with increasing temperature has been calculated in this way than with the earlier assumption of essentially impermeable polymer coils, i.e. with the assumption of the value 2.5 × 10 23 for the universal viscosity parameter Φ 0.

Substrate binding closes the cleft between the domains of yeast phosphoglycerate kinase.

Using small angle x-ray scattering from solutions of yeast phosphoglycerate kinase, we have measured the radius of gyration of the enzyme both in the presence and in the abscence of ligands. We find that the radius of gyration decreases by 1.09 +/- 0.34 A upon binding both substrates MgATP and 3-phosphoglycerate to form the ternary complex. Smaller decreases, at the limit of the precision of the measurement, were found for the separate binding of MgATP (0.30 +/- 0.50 A). Using computer modeling, it has been estimated that a substrate-induced cleft closure in phosphoglycerate kinase resulting from one lobe rotating 8-14 degrees relative to the other lobe lobe is consistent with this observed change in radius of gyration. We suggest, therefore, that the conformational change that results in the smaller radius of gyration for the ternary complex is a hinge motion of the two lobes which produces a closing of the cleft between the two lobes. The apparent similarity of the ligand-induced change in phosphoglycerate kinase to the cleft closure in hexokinase suggests that this kind of conformational change may prove to be a rather general kinase phenomenon (Bennett, W.S., and Steitz T.A. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 4848-4852; Anderson, C.M., Zucker, F.H., and Steitz, T.A. (1979) Science 204, 375-380).

Conformation of hyaluronate in neutral and alkaline solutions

Increasing the pH of a neutral salt solution of sodium hyaluronate to 12.5 produces a rapid drop in viscosity which is reversible upon restoring the pH to neutrality. Light scattering data showing a decrease in radius of gyration with no change in molecular weight and negative results with chondroitin and other acidic glycosaminoglycans suggest that the conformational change is specific for hyaluronate molecules.

The initial stages of the heterogeneous degradation of alkali cellulose by oxygen in relation to the morphology of native cotton cellulose

AbstractTreatment of cotton cellulose with sodium hydroxide solutions of varying concentration over extended periods in the absence of oxygen markedly decreases the intrinsic viscosity of both the cellulose in cuoxam and its cellulose trinitrate derivative (CTN) in acetone. Light‐scattering measurements show that the molecular weight does not change while the radius of gyration decreases and the second virial coefficient increases. The narrow molecular weight distribution of the native cotton is still maintained. Mild oxidation first causes the intrinsic viscosity to increase. At more prolonged oxidation times the viscosity decreases. These results are interpreted by an intramolecular cross‐linking reaction in the folded cellulose chains with the formation of chemically resistent bonds. Cleavage of the resultant cyclic structures leads to molecules with a larger radius of gyration but the same molecular weight.

Lichtstreuung von hochmolekularen lösungen in abhängigkeit von temperatur und druck

The osmotic second virial coefficient and the radius of gyration of polystyrene in trans-decalin, cyclohexane, toluene and chloroform were measured by light scattering at pressures up to 750 Atm at temperatures between 15° and 50°. We obtained the following results: 1. (1) All the examined solvents become poorer with increasing pressure: the θ-point is increased and the systems become more endothermic. The statistical parameter β 0/ M 0 2 increases considerably with increasing pressure. 2. (2) The radius of gyration decreases, at temperatures between 15° and 40°, with increasing pressure for the systems polystyrene- trans-decalin and polystyrene-toluene. 3. (3) The excluded volume theory is applicable to pressure effects in polymer solutions. The unperturbed dimensions decrease with increasing pressure.