Side Chain Density Research Articles

3.3 Å Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry

To achieve cell entry, many nonenveloped viruses must transform from a dormant to a primed state. In contrast to the membrane fusion mechanism of enveloped viruses (e.g., influenza virus), this membrane penetration mechanism is poorly understood. Here, using single-particle cryo-electron microscopy, we report a 3.3 A structure of the primed, infectious subvirion particle of aquareovirus. The density map reveals side-chain densities of all types of amino acids (except glycine), enabling construction of a full-atom model of the viral particle. Our structure and biochemical results show that priming involves autocleavage of the membrane penetration protein and suggest that Lys84 and Glu76 may facilitate this autocleavage in a nucleophilic attack. We observe a myristoyl group, covalently linked to the N terminus of the penetration protein and embedded in a hydrophobic pocket. These results suggest a well-orchestrated process of nonenveloped virus entry involving autocleavage of the penetration protein prior to exposure of its membrane-insertion finger.

Architecture of prototype copolymer brushes composed of alternating structure and intramolecular phase separation of side chains in solution

AbstractAtom transfer radical polymerization (ATRP) was applied to the synthesis of prototype copolymer brushes composed polystyrene/poly(t‐butyl methacrylate) (PS/PBMA) alternating structure. Dilute solution properties of prototype copolymer brush were investigated by static and dynamic light scattering (SLS and DLS) in tetrahydrofuran (THF). As a result, such prototype copolymer brush composed of short aspect ratio formed a star‐like single molecule in THF. To discuss the intramolecular phase separation of PS/PBMA brushes in solution, we determined the radius of gyration (Rg) and cross‐sectional radius of gyration (Rg,c) of prototype copolymer brush by small‐angle X‐ray scattering (SAXS) using Guinier's plots in THF and styrene. We used styrene as solvent to cancel each other out with the electron density of PS side chains. Both Rg and Rg,c obtained in styrene decreased drastically compared with those obtained in THF. These results indicated strongly that PS and PBMA side chains of prototype brushes formed intramolecular phase separation even in good solvent. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010

Bimetallomesogens: Synthesis and Mesomorphic Properties of Coppercomplexes of 3,3'-(2-hydroxypropane-1,3-diyl)bis(azan-1- yl-1-ylidene)bis(2-(4-alkoxyphenyl)prop-1-en-1-ol)

A new type of 3,3'-(2-hydroxypropane-1,3-diyl) bis(azan-1-yl-1-ylidene)bis(2-(4-alkoxy phenyl)prop-1-en-1-ol) and their copper complexes were prepared and mesomorphic properties characterized. The mesomorphic properties of these copper complexes were studied by differential scanning calorimetry (DSC), polarized optical microscopy (POM) and powder X-ray diffraction. X-ray structural crystallographic analysis showed that these bimetallic compounds have two copper centers coordinated with central square planar geometry. These molecules all have total two 1a or five alkoxy sidechains 1b appended around the central core. The mesomorphic behavior exhibited was found to be dependent on the sidechain density. All compounds in 1a exhibited smectic mesophases, however, compounds in 1b exhibited hexagonal columnar phases (Colh), which were characterized by optical textures and confirmed by powder x-ray diffraction.

Effect of substituted trifluoromethyl groups on thermal and mechanical properties of fluorine-containing epoxy resin

In this study, 2-diglycidylether of benzotrifluoride (2-DGEBTF) and 4-diglycidylether of benzotrifluoride (4-DGEBTF) epoxy resins, which contained fluorine groups in the main chain, were synthesized. The resins were characterized by FTIR,1H NMR,13C NMR and19F NMR spectroscopy. The 2-DGEBTF and 4-DGEBTF epoxy resins were cured with triethylene tetramine (TETA), and the effect of the fluorine group on the synthesized epoxy resin on the cure behavior, thermal, and mechanical properties was investigated. The 2-DGEBTF/TETA system was more reactive than the 4-DGEBTF/TETA system, whereas the thermal stability factor i.e., the decomposition activation energy (E d ), of 4-DGEBTF/TETA was higher than that of 2-DGEBTF/TETA. These results can be explained by the decrease in cross-linking density and decomposition of the short side chains, resulting in the CF3 group at the para position. However, theK IC value of 4-DGEBTF/TETA was higher than that of 2-DGEBTF/TETA. This was attributed to the increase in flexibility in the epoxy backbone, resulting in a difference in steric hindrance and polarlizability.

Synthesis and Characterization of Alternating and Random Copolymer Brushes

AbstractAlternating free‐radical copolymerization of vinylbenzyl‐ and methacryloyl‐terminated macromonomers in the presence of Lewis acid was applied to the synthesis of prototype copolymer brushes composed of polystyrene/poly(ethylene oxide) (PS/PEO) alternating structure. Random copolymer brushes were also prepared by radical copolymerization of both macromonomers in the absence of Lewis acid. It was found from dilute solution properties that both copolymer brushes composed of short aspect ratio formed an ellipsoid‐like single molecule in solution. To discuss the intramolecular phase separation of PS/PEO brushes in solution, we determined the radius of gyration (Rg) and cross‐sectional radius of gyration (Rg,c) of copolymer brushes by small‐angle X‐ray scattering (SAXS) using Guinier's plots in DMF and styrene. We used styrene as a solvent to cancel each other out with the electron density of PS side chains. We made also clear the effect of branching topology on polymer crystallinity to be examined by comparing the copolymer brushes with corresponding linear PEO or PEO‐block‐PS block copolymer.magnified image

Ion-Induced Formation of Charge-Transfer States in Conjugated Polyelectrolytes

We use time-resolved optical spectroscopy to demonstrate that the luminescence quenching observed when ions are incorporated in films of conjugated polymers can be explained by the formation of charge-transfer (CT) states that are stabilized by the Coulomb field of ions. Our investigation is focused on a conjugated polyelectrolyte (CPE) derived from F8BT (poly(9,9'-dioctylfluorene-alt-benzothiadiazole)). The statistical copolymer contains tetra-alkyl ammonium moieties and BF(4)(-) counteranions attached to a moderate (approximately 7%) density of polymer alkyl side chains, providing a film morphology comparable to F8BT but with ions distributed on the length scale of exciton diffusion. The ionic substituents have little influence over the polymers electronic absorption and emission properties in solution, however photoluminescence (PL) quantum efficiency (approximately 6%) is considerably lower for the polyelectrolyte compared with F8BT (approximately 60%) in thin films. Time-resolved PL spectroscopy reveals that the primary exciton lifetime is shortened in the polyelectrolyte and a red-shifted CT emission peak with a longer lifetime emerges. Transient absorption spectroscopy of thin films enables us to detect CT states that persist beyond the primary decay and are found to be immobile. The PL intensity of the partially ionic film is found to increase with decreasing temperature, consistent with thermally activated exciton hopping (E(act) = 28 meV) prior to formation of CT states at ionic regions. We suggest that ion-induced stabilization of CT states is a general phenomenon in CPEs, which raises the possibility that ions might be arranged to direct the flow of excitons toward charge-separating interfaces in polymer photovoltaic devices.

Effect of the length of the side chains of comb-like copolymer dispersants on dispersion and rheological properties of concentrated cement suspensions

Two different groups of comb-like copolymer dispersants with side chain lengths ranging from 8 to 48 were synthesized and characterized: one group with the carboxylic content per mole molecule constant and the other group with the carboxylic contents per gram polymer constant. The effects of side chain length on comb-like copolymers on adsorption, dispersion, rheological behavior, and zeta potential for cement suspensions were investigated systematically to elucidate the governing dispersing mechanism. The adsorption of comb-like copolymer on the cement surfaces, controlled by COO − content in copolymer backbones, side chain length, and also polymer conformation in solution, governs the dispersion and rheological behavior of the cementitious system. The dispersion effect increases with the adsorbed amount; especially the adsorbed side chain density increases. But the dispersion power of comb-like copolymers varies depending on the side chain length in comb-like copolymer. The long side chain polymer has higher dispersion power than the shorter ones due to the stronger steric hindrance effect of the former; for the short side chain polymer with high ionic content, the electrostatic repulsion and steric hindrance together should be responsible for its dispersion effect. Such information also suggests that their exists the geometrical balance between the main chain and the side chains in comb-like copolymer dispersants which should be very useful in designing optimum molecular structures of high efficient dispersants.

Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization

AMPA and kainate receptors mediate fast synaptic transmission. AMPA receptor ligand-binding domains form dimers, which are key functional units controlling ion-channel activation and desensitization. Dimer stability is inversely related to the rate and extent of desensitization. Kainate and AMPA receptors share common structural elements, but functional measurements suggest that subunit assembly and gating differs between these subtypes. To investigate this, we constructed a library of GluR6 kainate receptor mutants and directly measured changes in kainate receptor dimer stability by analytical ultracentrifugation, which, combined with electrophysiological experiments, revealed an inverse correlation between dimer stability and the rate of desensitization. We solved crystal structures for a series of five GluR6 mutants, to understand the molecular mechanisms for dimer stabilization. We demonstrate that the desensitized state of kainate receptors acts as a deep energy well offsetting the stabilizing effects of dimer interface mutants, and that the deactivation of kainate receptor responses is dominated by entry into desensitized states. Our results show how neurotransmitter receptors with similar structures and gating mechanisms can exhibit strikingly different functional properties.

Rocking Motion of the Equatorial Domains of a Group II Chaperonin between Two Biochemical States Revealed by Single‐Particle Cryo‐EM at Near‐atomic and Subnanometer Resolutions

Chaperonins consist of two rings which are stacked back‐to‐back, forming folding cavities where substrates are encapsulated. The closure of the chaperonin cavity is triggered by ATP binding or hydrolysis. We report four single‐particle cryo‐EM structures of both wildtype and mutant Mm‐cpn, an Archaeal chaperonin in the nucleotide free and nucleotide bound states. The 4.3‐4.8Å resolution maps of the Mm‐cpn closed, nucleotide‐bound state, clearly show pitches of α‐helices and separation of β‐strands. More than 56% non‐small sidechain densities are visible in the 4.3Å resolution map of the wildtype Mm‐cpn. Protein backbones are modeled for both of the closed conformations. Models are built with geometry‐constrained flexible fitting to the 8‐10Å maps of the nucleotide free Mm‐cpn which exhibits an open conformation. The open and closed structures reveal a rocking motion in the equatorial domain of all subunits which results in different molecular contacts between the two rings in these two states. We observe a ~40° tilting of the region containing the N and C termini, as mm‐cpn switches from the closed to open state. This swinging movement of the N and C termini induced by the nucleotide hydrolysis may suggest their role in the substrate folding and/or release.Research is supported by NIH Nanomedicine Roadmap grant (PN2EY016525)

Selective G-quadruplex ligands: The significant role of side chain charge density in a series of perylene derivatives

The human telomeric G-quadruplex structure is a promising target for the design of cancer drugs. The selectivity of G-quadruplex ligands with respect to duplex genomic DNA is of especial importance. The high selectivity of polyamine conjugated perylene derivatives appears to be regulated by side-chain charge density, as indicated by data from a FRET melting assay and induced CD spectroscopy.

The structural basis for peptide selection by the transport receptor OppA

Oligopeptide-binding protein A (OppA) from Lactococcus lactis binds peptides of an exceptionally wide range of lengths (4-35 residues), with no apparent sequence preference. Here, we present the crystal structures of OppA in the open- and closed-liganded conformations. The structures directly explain the protein's phenomenal promiscuity. A huge cavity allows binding of very long peptides, and a lack of constraints for the position of the N and C termini of the ligand is compatible with binding of peptides with varying lengths. Unexpectedly, the peptide's amino-acid composition (but not the exact sequence) appears to have a function in selection, with a preference for proline-rich peptides containing at least one isoleucine. These properties can be related to the physiology of the organism: L. lactis is auxotrophic for branched chain amino acids and favours proline-rich caseins as a source of amino acids. We propose a new mechanism for peptide selection based on amino-acid composition rather than sequence.

Interaction of polycarboxylate-based superplasticizers with cements containing different C3A amounts

This parametric study links the molecular structure of a carboxylate-type of superplasticizer with their performance in cement pastes with different C3A-contents. Beside the variation of the C3A-content, the experimental synthesized superplasticizers have been varied by polyethylene-oxide side chain density and length. The connection between the superplasticizers, their effect on workability properties and retardation phenomenon and the dependency of C3A-content in the cement paste has been investigated. The characteristic interaction phenomenons between different PCE-architectures and different C3A-contents have been examined by calorimetric, rheological, adsorption, and zeta potential measurements. This study shows that with decreasing side chain density the PCE molecules adsorb stronger and thus, lower the yield stress of a cement paste by steric stabilization. It is also shown that PCE molecules with long side chains delaying the setting of the cement paste to less extend than PCE molecules with shorter side chains. Consequently, in terms of optimization of the molecular architecture, good workability can be achieved by addition of highly charged PCE with long side chains. The latter minimizes undesired retardation phenomena.

Molecular structure and phase behaviour of hairy-rod polymers

Using dissipative particle dynamics simulations the relationship between molecular architecture and phase behaviour in model hairy-rod polymers is studied. In agreement with experimental and theoretical studies the phase behaviour is controlled by changes to the molecular structure, particularly the sidechain length and density, and the molecular interactions. For dense sidechains a lamellar structure is found, which becomes an inverted cylindrical phase when the sidechain density is lowered. The ordered phases become more stable on increasing sidechain length and on increasing the repulsion strength between the backbone and sidechains. In the absence of torsional potentials the structures are double-walled, i.e. layers are two polymer backbones thick, while single-walled structures are observed for polymers with torsional potentials.

A Comprehensive Model for Packing and Hydration for Amyloid Fibrils of β2-Microglobulin

Volume can provide informative structural descriptions of macromolecules such as proteins in solution because a final volumetric outcome accompanies the exquisite equipoise of packing effects between residues, and residues and waters inside and outside proteins. Here we performed systematic investigations on the volumetric nature of the amyloidogenic conformations of beta2-microglobulin (beta2-m) and its amyloidogenic core peptide, K3, using a high precision densitometer. The transition from the acid-denatured beta2-m to the mature amyloid fibrils was accompanied by a positive change in the partial specific volume, which was larger than that observed for the transition from the acid-denatured beta2-m to the native structure. The data imply that the mature amyloid fibrils are more voluminous than the native structure because of a sparse packing density of side chains. In contrast, the formation of the mature amyloid-like fibrils of the K3 from the random coil was followed by a considerable decrease in the partial specific volume, suggesting a highly compact core structure. Interestingly, the immature amyloid-like fibrils of beta2-m exhibited a volume intermediate between those of the mature fibrils of beta2-m and K3, because of the core structure at their center and the relatively noncompact region around the core with much hydration. These volumetric differences would result from the nature of main-chain-dominated fibrillogenesis. We suggest comprehensive models for these three types of fibrils illustrating packing and hydrational states.

End-grafted Sugar Chains as Aqueous Lubricant Additives: Synthesis and Macrotribological Tests of Poly(l-lysine)-graft-Dextran (PLL-g-dex) Copolymers

Comb-like graft copolymers with carbohydrate side chains have been developed as aqueous lubricant additives for oxide-based tribosystems, in an attempt to mimic biological lubrication systems, whose surfaces are known to be covered with sugar-rich layers. As adopted in the previous studies of the graft copolymer poly(l-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG), which showed both excellent lubricating and antifouling properties, a similar approach was chosen to graft dextran chains onto the same backbone, thus generating PLL-g-dex. PLL-g-dex copolymers readily adsorb from aqueous solution onto negatively charged oxide surfaces. Tribological characterization at the macroscopic scale, either under pure sliding conditions or a mixed sliding/rolling contact regime, shows that PLL-g-dex is very effective for the lubrication of oxide-based tribosystems. The relative lubricating capabilities of PLL-g-dex copolymers compared with PLL-g-PEG copolymers were observed to be highly dependent on the molecular structure of the copolymers (in particular, side-chain density along the backbone) and the measurement conditions (in particular, time between tribocontacts); the PLL-g-dex copolymers with a low degree of grafted side chains (≤20% grafting of available protonated primary amine groups along the backbone) showed better lubricating performance than their PLL-g-PEG counterparts at high tribocontact frequency (≥ca. 0.32 Hz).

Well-Defined Brush Copolymers with High Grafting Density of Amphiphilic Side Chains by Combination of ROP, ROMP, and ATRP

This work reports a facile strategy for the preparation of a novel well-defined brush copolymer with two different grafts distributed on the same unit along the backbone via combination of three controlled polymerization methods, ring-opening polymerization (ROP), ring-opening metathesis polymerization (ROMP), and atom transfer radical polymerization (ATRP) based on the synthesis of the heterotrifunctional inimer, 2-hydroxymethyl-3-(2-bromoisobutyryloxymethyl)-5-norbornene (NBE-OH/Br). ROP of ε-caprolactone initiated by NBE-OH/Br was carried out to generate macroinimer, norbornene-graft-poly(ε-caprolactone)/Br (NBE-g- PCL/Br). The grafting-through strategy was then employed to construct the polymer backbone, poly(norbornene)-graft-poly(ε-caprolactone)/Br (PNBE-g-PCL/Br) via ROMP of the norbornene-terminated macroinimer NBE-g-PCL/Br. Finally, the grafting-from route was used for the synthesis of amphiphilic grafted brush copolymer, poly(norbornene)-graft-poly(ε-caprolactone)/poly(2-(dimethylamino)ethyl methacrylate) (PNBE-g-PCL/PDMAEMA) by ATRP of 2-(dimethylamino)ethyl methacrylate using bromo-functionalized ROMP product PNBE-g-PCL/Br as macroinitiators, containing one hydrophobic PCL graft and one hydrophilic PDMAEMA graft on each unit of the backbone.

Experimental determination of the effective anionic charge density of polycarboxylate superplasticizers in cement pore solution

The specific anionic charge density of polycarboxylate superplasticizers can be determined experimentally by titration with a cationic polyelectrolyte. In this study, the anionic charge densities of several polycarboxylates based on methacrylate ester chemistry were measured in aqueous solution at pH 7 and 12.6, resp., and in cement pore solution. The anionic charge of the polycarboxylates increases with increasing pH value as a result of deprotonation of the carboxylate groups in the polymer backbone. Addition of Ca 2+ ions generally causes a decrease of the anionic charge density. The reduction in anionic charge varies and depends on the architecture of the polycarboxylate. The effect results from the binding of calcium ions by the carboxylate groups, both through complexation and counter-ion condensation. Consequently, the effective anionic charge density of polycarboxylates in cement pore solution can differ significantly from the charge density which is calculated based on the chemical composition. Generally the –COO − functionality may coordinate Ca 2+ as a monodentate or bidentate ligand. The type of coordination depends on the steric accessibility of the carboxyl group. In PC molecules possessing high side chain density, the –COO − group is shielded by the side chains and coordinates as bidentate ligand, producing a neutral Ca 2+–PC complex. Accordingly, this type of PC shows almost no anionic charge anymore in cement pore solution. In PCs possessing high amount of –COO −, Ca 2+ is coordinated monodentate, resulting in an anionic complex. Consequently, this type of PC shows significant anionic character in pore solution. Its adsorption behaviour is determined by a gain in enthalpy which derives from the electrostatic attraction between the PC and the surface of cement. This way, by utilizing the relatively simple method of charge titration, it is possible to assess the electrostatic attraction which, besides entropy gains, is the driving force behind the adsorption of polycarboxylates on the cement surface and thus determines their effectiveness as dispersing agent. The findings are generally applicable to other anionic admixtures used in cement.

Viscoelastic Properties of Adsorbed Bottle-brush Polymer Layers Studied by Quartz Crystal Microbalance — Dissipation Measurements

Adsorbed layers of a series of bottle-brush polyelectrolytes with 45 units long poly(ethylene oxide) [PEO], side chains have been investigated by the quartz crystal microbalance technique with dissipation monitoring. The data have been evaluated with three different models, the Sauerbrey model, the Johannsmann model, and the Voigt model. It is found that all three models predict the same trend in the variations of sensed mass and hydrodynamic layer thickness with polymer architecture, that is, with the backbone charge to side chain density ratio. However, the simple Sauerbrey model underestimates the sensed mass by a factor of 1.15−1.45 compared to the more accurate Voigt model. By following the evolution of the layer dissipation, elasticity, and viscosity with increasing surface coverage it was concluded that the layers formed by brush polymers with intermediate charge densities undergo a structural change as the coverage is increased. Initially, the polymers are anchored to the surface via the PEO side chains. However, as the adsorption proceeds a structural change that brings the backbone to the surface and forces the side chains to extend from it is observed. The layer elasticity and viscosity as a function of surface coverage go through a maximum in this transition region.

Polyvalent Display of Heme on Hepatitis B Virus Capsid Protein through Coordination to Hexahistidine Tags

The addition of a hexahistidine tag to the N terminus of the hepatitis B capsid protein gives rise to a self-assembled particle with 80 sites of high local density of histidine side chains. Iron protoporphyrin IX has been found to bind tightly at each of these sites, making a polyvalent system of well-defined spacing between metalloporphyrin complexes. The spectroscopic and redox properties of the resulting particle are consistent with the presence of 80 site-isolated bis(histidine)-bound heme centers, comprising a polyvalent b-type cytochrome mimic.

Adsorption Characteristics of Bottle-Brush Polymers on Silica: Effect of Side Chain and Charge Density

The adsorption behavior of bottle-brush polymers with different charge/PEO ratio on silica was studied using optical reflectometry and QCM-D. The results obtained under different solution conditions clearly demonstrate the existence of two distinct adsorption mechanisms depending on the ratio of charge/PEO. In the case of low-charge density brush polymers (0-10 mol %), the adsorption occurs predominantly through the PEO side chains. However, the presence of a small amount of charge along the backbone (as low as 2 mol %) increases the adsorption significantly above that of the uncharged bottle-brush polymer in pure water. As the charge density of the brush polymers is increased to 25 mol % or larger the adsorption occurs predominantly through electrostatic interactions. The adsorbed layer structure was studied by measuring the layer dissipation using QCM-D. The adsorbed layer formed by the uncharged brush polymer dissipates only a small amount of energy that indicates that the brush lie along the surface, the scenario in which the maximum number of PEO side chains interact with the surface. The adsorbed layers formed by the low-charge density brush polymers (2-10 mol %) in water are more extended, which results in large energy dissipation, whereas those formed by the high-charge density brush polymers (50-100 mol %) have their backbone relatively flat on the surface and the energy dissipation is again low.