Structure of and influence of a tick complement inhibitor on human complement component 5.

To provide insight into the structural and functional properties of human complement component 5 (C5), we determined its crystal structure at a resolution of 3.1 A. The core of C5 adopted a structure resembling that of C3, with the domain arrangement at the position corresponding to the C3 thioester being very well conserved. However, in contrast to C3, the convertase cleavage site in C5 was ordered and the C345C domain flexibly attached to the core of C5. Binding of the tick C5 inhibitor OmCI to C5 resulted in stabilization of the global conformation of C5 but did not block the convertase cleavage site. The structure of C5 may render possible a structure-based approach for the design of new selective complement inhibitors.

Controlling the morphology of microgels by ionic stimuli.

Stimuli-responsive microgels have attracted much interest for their use as vehicles for drug delivery or as the building blocks of adaptive materials. Ionic microgel particles, including popular poly(NIPAM-co-acrylic acid), show strong mechanical responsiveness to many external stimuli, including changes in ionic strength or acidity. In this work, we demonstrate that combining multiple ionic stimuli can enable detailed control over the morphology of microgels. To this extent, we analyze the particle morphology in various surroundings with light-scattering techniques. First, we find strong indications of an inverted density profile in the core of the particles. Secondly, we show that the swelling of this hydrogel core and the corona of dangling polymer ends can be targeted separately by a combination of deionization and deprotonation steps. Hence, this work represents an advance in tailoring particle morphologies after synthesis in a predictable fashion.

α-Synucleins from Animal Species Show Low Fibrillation Propensities and Weak Oligomer Membrane Disruption.

The intrinsically disordered protein α-synuclein (aSN) forms insoluble aggregates in the brains of Parkinson's disease (PD) patients. Cytotoxicity is attributed to a soluble aSN oligomeric species that permeabilizes membranes significantly more than monomers and fibrils. In humans, the A53T mutation induces early onset PD and increases the level of aSN oligomerization and fibrillation propensity, but Thr53 occurs naturally in aSNs of most animals. We compared aSNs from elephant, bowhead whale, and pig with human aSN. While all three animal aSNs showed significantly weakened fibrillation, elephant aSN formed much more oligomer, and pig aSN much less, than human aSN did. However, all animal aSN oligomers showed weakened permeabilization toward anionic lipid vesicles, indicative of decreased cytotoxicity. These animal aSNs share three substitutions compared to human aSN: A53T, G68E, and V95G. We analyzed aggregation and membrane binding of all eight mutants combining these three mutations. While the G68E mutation is particularly important in weakening fibrillation and possible toxicity, the strongest effect is seen when all three mutations are present. Thus, a small number of mutations can significantly decrease aSN toxicity.

The Use of Liprotides To Stabilize and Transport Hydrophobic Molecules.

Recently, it has been shown that different complexes consisting of protein and fatty acids, which we call liprotides, have common functional and structural features. Liprotides can transfer their fatty acid content to membranes, highlighting the potential to incorporate other small molecules and help transfer them to membranes. In this study, this potential was explored with regard to the poorly water-soluble vitamin E compound α-tocopherol (Toc). Uptake into liprotides increased Toc solubility and chemical stability. The liprotide-Toc complexes retained the characteristic liprotide structure with a core of fatty acid surrounded by protein. Toc and fatty acid could be transferred to artificial vesicles upon being incorporated into the liprotide complex. Extending this work, we found that free tryptophan and the vitamin A precursor retinaldehyde could also be incorporated in the liprotides; however, other small molecules failed to be taken up, and we conclude that successful incorporation requires a hydrophobic terminal moiety that can be accommodated within the micelle interior of the liprotides. Nevertheless, our work suggests that liprotides are able to stabilize and transport a number of otherwise insoluble small molecules with significant potential health benefits.

How epigallocatechin gallate can inhibit α-synuclein oligomer toxicity in vitro.

Oligomeric species of various proteins are linked to the pathogenesis of different neurodegenerative disorders. Consequently, there is intense focus on the discovery of novel inhibitors, e.g. small molecules and antibodies, to inhibit the formation and block the toxicity of oligomers. In Parkinson disease, the protein α-synuclein (αSN) forms cytotoxic oligomers. The flavonoid epigallocatechin gallate (EGCG) has previously been shown to redirect the aggregation of αSN monomers and remodel αSN amyloid fibrils into disordered oligomers. Here, we dissect EGCG's mechanism of action. EGCG inhibits the ability of preformed oligomers to permeabilize vesicles and induce cytotoxicity in a rat brain cell line. However, EGCG does not affect oligomer size distribution or secondary structure. Rather, EGCG immobilizes the C-terminal region and moderately reduces the degree of binding of oligomers to membranes. We interpret our data to mean that the oligomer acts by destabilizing the membrane rather than by direct pore formation. This suggests that reduction (but not complete abolition) of the membrane affinity of the oligomer is sufficient to prevent cytotoxicity.

Dendrimer nanofluids in the concentrated regime: from polymer melts to soft spheres.

Understanding dendrimer structures and their interactions in concentrated solutions is important to a wide range of applications, such as drug delivery and lubrication. However, controversy has persisted concerning whether, when confined to proximity, dendrimers would entangle as observed for polymer systems, or act as deformable spheres. Furthermore, how such behavior may be related to their size-dependent molecular architecture remains unclear. Using small-angle X-ray scattering (SAXS), the intermolecular interactions and structures in aqueous nanofluids containing three generations of carboxyl-terminated poly(amidoamine) (PAMAM) dendrimers (G0.5, Rg = 9.3 Å; G3.5, Rg = 22.6 Å; G5.5, Rg = 39.9 Å, where Rg is the radius of gyration) over a mass fraction range 0.005 ≤ x ≤ 0.316 have been studied. In the highly concentrated regime (x ≥ 0.157), we observe that the solution properties depend on the dendrimer generation. Our results suggest that the smaller G0.5 dendrimers form a highly entangled polymer melt, while the larger dendrimers, G3.5 and G5.5, form densely packed and ordered structures, in which the individual dendrimers exhibit some degree of mutual overlap or deformation. Our results demonstrate the tunability of interdendrimer interactions via their molecular architecture, which in turn may be harnessed to control and tailor the physical properties of dendrimer nanofluids.

The shapes of Z-α1-antitrypsin polymers in solution support the C-terminal domain-swap mechanism of polymerization.

Emphysema and liver cirrhosis can be caused by the Z mutation (Glu342Lys) in the serine protease inhibitor α1-antitrypsin (α1AT), which is found in more than 4% of the Northern European population. Homozygotes experience deficiency in the lung concomitantly with a massive accumulation of polymers within hepatocytes, causing their destruction. Recently, it was proposed that Z-α1AT polymerizes by a C-terminal domain swap. In this study, small-angle x-ray scattering (SAXS) was used to characterize Z-α1AT polymers in solution. The data show that the Z-α1AT trimer, tetramer, and pentamer all form ring-like structures in strong support of a common domain-swap polymerization mechanism that can lead to self-terminating polymers.

The role of nanometer-scaled ligand patterns in polyvalent binding by large mannan-binding lectin oligomers.

Mannan-binding lectin (MBL) is an important protein of the innate immune system and protects the body against infection through opsonization and activation of the complement system on surfaces with an appropriate presentation of carbohydrate ligands. The quaternary structure of human MBL is built from oligomerization of structural units into polydisperse complexes typically with three to eight structural units, each containing three lectin domains. Insight into the connection between the structure and ligand-binding properties of these oligomers has been lacking. In this article, we present an analysis of the binding to neoglycoprotein-coated surfaces by size-fractionated human MBL oligomers studied with small-angle x-ray scattering and surface plasmon resonance spectroscopy. The MBL oligomers bound to these surfaces mainly in two modes, with dissociation constants in the micro to nanomolar order. The binding kinetics were markedly influenced by both the density of ligands and the number of ligand-binding domains in the oligomers. These findings demonstrated that the MBL-binding kinetics are critically dependent on structural characteristics on the nanometer scale, both with regard to the dimensions of the oligomer, as well as the ligand presentation on surfaces. Therefore, our work suggested that the surface binding of MBL involves recognition of patterns with dimensions on the order of 10-20 nm. The recent understanding that the surfaces of many microbes are organized with structural features on the nanometer scale suggests that these properties of MBL ligand recognition potentially constitute an important part of the pattern-recognition ability of these polyvalent oligomers.

Synergistic activation of eIF4A by eIF4B and eIF4G.

eIF4A is a key component in eukaryotic translation initiation; however, it has not been clear how auxiliary factors like eIF4B and eIF4G stimulate eIF4A and how this contributes to the initiation process. Based on results from isothermal titration calorimetry, we propose a two-site model for eIF4A binding to an 83.5 kDa eIF4G fragment (eIF4G-MC), with a high- and a low-affinity site, having binding constants KD of ∼50 and ∼1000 nM, respectively. Small angle X-ray scattering analysis shows that the eIF4G-MC fragment adopts an elongated, well-defined structure with a maximum dimension of 220 Å, able to span the width of the 40S ribosomal subunit. We establish a stable eIF4A-eIF4B complex requiring RNA, nucleotide and the eIF4G-MC fragment, using an in vitro RNA pull-down assay. The eIF4G-MC fragment does not stably associate with the eIF4A-eIF4B-RNA-nucleotide complex but acts catalytically in its formation. Furthermore, we demonstrate that eIF4B and eIF4G-MC act synergistically in stimulating the ATPase activity of eIF4A.

Mechanics and dynamics of triglyceride-phospholipid model membranes: Implications for cellular properties and function.

We demonstrate here that triolein alters the mechanical properties of phospholipid membranes and induces extraordinary conformational dynamics. Triolein containing membranes exhibit fluctuations up to size range of 100µm and with the help of these are e.g. able to squeeze through narrow passages between neighbouring structures. Triolein-phosphatidylcholine membranes were found to have bending rigidity significantly lower than that of corresponding pure phosphatidylcholine membrane. Moreover, the triolein containing membranes were found to be reluctant to fuse, which is in good accordance with larger lamellar distances observed in the TOPOPC membranes. These findings suggest repulsion between adjacent membranes. We provide a comprehensive discussion on the possible explanations for the observed mechanics and dynamics in the TOPOPC system and on their potential cellular implications.

Deducing the Relation between Viscosity and Oil-Induced Structural Changes of Viscoelastic Surfactants Using a Kinetic Approach.

The present study relates viscosity reduction with time of a wormlike micellar solution to the micellar transitions that occur with time in the presence of three n-alkanes, namely, n-decane, n-dodecane, and n-hexadecane. Steady-shear rheology and small-angle X-ray scattering were used to deduce the relationship. The effect of n-alkane concentration was tested only with n-decane. There were at most three stages of viscosity reduction, which appeared in the following order: (i) the rising viscosity stage, (ii) the fast viscosity reduction stage, and (iii) the low-viscosity stage. The stages and rates of viscosity transition depended on the type of micelles present and the degree of micelle entanglement. Moreover, the rate of transition increased when the n-alkane concentration was increased and when the n-alkane molecular mass was reduced. n-Hexadecane induced only the first two stages of transition at a slower rate compared to the other oils.

Strontium and bone nanostructure in normal and ovariectomized rats investigated by scanning small-angle X-ray scattering.

The effect of SrCl(2) treatment on bone nanostructure in a rat ovariectomy model was studied using scanning small-angle X-ray scattering (sSAXS). Twelve 6-month-old female Wistar rats were used. Six animals were ovariectomized (+ovx) and six were left intact after sham surgery (-ovx). Six animals, three +ovx and three -ovx, were treated with 4 mmol SrCl(2) (aq)/kg/day (+Sr), whereas the remaining six received placebo (-Sr) for 140 days. Rats were labeled with flourochromes at days 7, 126, and 136. Femoral cross sections were studied using fluorescence microscopy, scanning electron microscopy including energy-dispersive X-ray analysis, and sSAXS. The SAXS data comprised about 5,500 measurements and provided information about mineral crystal thickness and orientation in new and old bone. The newly formed bone contained higher levels of Sr(2+) in +Sr than in -Sr animals, indicating that the Sr(2+) was incorporated into the new bone. Mineral plates were significantly thicker in old bone, 2.62 nm (95% CI 2.58-2.66), than in new bone, 2.41 nm (95% CI 2.36-2.46). Surprisingly, mineral plates in new bone were significantly thicker (2.52 [95% CI 2.47-2.57] nm vs. 2.41 [95% CI 2.36-2.46] nm, P = 0.017) in +ovx rats than in -ovx rats. However, no significant effect of SrCl(2) on mineral plate thicknesses in new bone was observed. The statistical model yielded estimates of the difference in bone mineral plate thickness induced by Sr. The estimated effect of Sr was -0.09 (95% CI -0.21 to 0.03) and 0.02 (95% CI -0.10 to 0.14) nm for new bone in -ovx and +ovx rats, respectively.

Construction of a Polyhedral DNA 12-Arm Junction for Self-Assembly of Wireframe DNA Lattices.

A variety of different tiles for the construction of DNA lattices have been developed since the structural DNA nanotechnology field was born. The majority of these are designed for the realization of close-packed structures, where DNA helices are arranged in parallel and tiles are connected through sticky ends. Assembly of such structures requires the use of cation-rich buffers to minimize repulsion between parallel helices, which poses limits to the application of DNA nanostructures. Wireframe structures, on the other hand, are less susceptible to salt concentration, but the assembly of wireframe lattices is limited by the availability of tiles and motifs. Herein, we report the construction of a polyhedral 12-arm junction for the self-assembly of wireframe DNA lattices. Our approach differs from traditional assembly of DNA tiles through hybridization of sticky ends. Instead, the assembly approach presented here uses small polyhedral shapes as connecting points and branch points of wires in a lattice structure. Using this design principle and characterization techniques, such as transmission electron microscopy, single-particle reconstruction, patterning of gold nanoparticles, dynamic light scattering, UV melting analyses, and small-angle X-ray scattering among others, we demonstrated formation of finite 12-way junction structures, as well as 1D and 2D short assemblies, demonstrating an alternative way of designing polyhedral structures and lattices.

Tailoring Membrane Nanostructure and Charge Density for High Electrokinetic Energy Conversion Efficiency.

The electrokinetic energy conversion (EKEC) of hydraulic work directly into electrical energy has been investigated in charged polymeric membranes with different pore charge densities and characteristic diameters of the nanoporous network. The membranes were synthesized from blends of nitrocellulose and sulfonated polystyrene (SPS) and were comprehensively characterized with respect to structure, composition, and transport properties. It is shown that the SPS can be used as a sacrificial pore generation medium to tune the pore size and membrane porosity, which in turn highly affects the transport properties of the membranes. Furthermore, it is shown that very high EKEC efficiencies (>35%) are encountered in a rather narrow window of the properties of the nanoporous membrane network, that is, with pore diameters of ca. 10 nm and pore charge densities of 4.6 × 10(2) to 1.5 × 10(3) mol SO3(-) m(-3) for dilute solutions (0.03 M LiCl). The high absolute value of the efficiency combined with the determination of the optimal membrane morphology makes membrane-based EKEC devices a step closer to practical applications and high-performance membrane design less empirical.

A self-assembled nanopatch with peptide-organic multilayers and mechanical properties.

Peptides enable the construction of a diversity of one-dimensional (1D) and zero-dimensional (0D) nanostructures by molecular self-assembly. To date, it is a great challenge to construct two-dimensional (2D) nanostructures from peptides. Here we introduce an organic molecule to tune the amphiphilic-like peptide assembly to form a peptide-organic 2D nanopatch structure. The nanomechanical properties of the nanopatch were explored by quantitative nanomechanical imaging and force control manipulation. The peptide-organic patches are multilayers composed of several domains, which can be peeled off stepwise. The patch formation provides an approach towards constructing 2D nanostructures by peptide-organic assembly and it could be potentially utilized in a wide range of applications such as functional biomaterials.

Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites.

Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the ß-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.

NMR reveals two-step association of Congo Red to amyloid ß in low-molecular-weight aggregates.

Aggregation of the Amyloid ß peptide into amyloid fibrils is closely related to development of Alzheimer's disease. Many small aromatic compounds have been found to act as inhibitors of fibril formation, and have inspired the search for new drug candidates. However, the detailed mechanisms of inhibition are largely unknown. In this study, we have examined in detail the binding of the fibril-formation inhibitor Congo Red (CR) to monomeric Aß(1-40) using a combination of 1D, 2D, saturation transfer difference, and diffusion NMR, as well as dynamic light scattering experiments. Our results show that CR binds to the fibril forming stretches of Aß(1-40) monomers, and that complex formation occurs in two steps: An initial 1:1 CR:Aß(1-40) complex is formed by a relatively strong interaction (K(d) ≈ 5 µM), and a 2:1 complex is formed by binding another CR molecule in a subsequent weaker binding step (K(d) ≈ 300 µM). The size of these complexes is comparable to that of Aß(1-40) alone. The existence of two different complexes might explain the contradictory reports regarding the inhibitory effects of CR on the fibril-formation process.