Jan Skov Pedersen

Self-assembly of a nanoscale DNA box with a controllable lid

The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a ‘bottom-up’ approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA ‘origami’ method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 × 36 × 36 nm3 in size that can be opened in the presence of externally supplied DNA ‘keys’. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.

Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA.

In higher eukaryotes, a multiprotein exon junction complex is deposited on spliced messenger RNAs. The complex is organized around a stable core, which serves as a binding platform for numerous factors that influence messenger RNA function. Here, we present the crystal structure of a tetrameric exon junction core complex containing the DEAD-box adenosine triphosphatase (ATPase) eukaryotic initiation factor 4AIII (eIF4AIII) bound to an ATP analog, MAGOH, Y14, a fragment of MLN51, and a polyuracil mRNA mimic. eIF4AIII interacts with the phosphate-ribose backbone of six consecutive nucleotides and prevents part of the bound RNA from being double stranded. The MAGOH and Y14 subunits lock eIF4AIII in a prehydrolysis state, and activation of the ATPase probably requires only modest conformational changes in eIF4AIII motif I.

Small-angle neutron scattering study of structural changes in temperature sensitive microgel colloids

The structure of temperature-sensitive poly(N-isopropylacrylamide) microgels in dilute suspension was investigated by means of small-angle neutron scattering. A direct modeling expression for the scattering intensity distribution was derived which describes very well the experimental data at all temperatures over an extensive q range. The overall particle form as well as the internal structure of the microgel network is described by the model. The influence of temperature, cross-linking density, and particle size on the structure was revealed by radial density profiles and clearly showed that the segment density in the swollen state is not homogeneous, but gradually decays at the surface. The density profile reveals a box profile only when the particles are collapsed at elevated temperatures. An increase of the cross-linking density resulted in both an increase of the polymer volume fraction in the inner region of the particle and a reduction of the smearing of the surface. The polymer volume fraction inside the colloid decreased with increasing particle size. The structural changes are in good agreement with the kinetics of the emulsion copolymerization used to prepare the microgel colloids.

Analytical treatment of the resolution function for small-angle scattering

Analytical expression for the resolution function for small-angle scattering in pinhole geometry are derived. The contributions to the resolution function due to wavelength spread, finite collimation and detector resolution are determined separately using Gaussian functions to approximate the contributions. A general resolution function is derived which is the result of the combined effect of the three contributions. An azimuthal-integrated resolution function, which can be applied to scattering from a material with a circular symmetric scattering cross section, is calculated. This resolution function contains in addition a contribution from the averaging procedure itself. The analytical results are compared with the results of computer simulations. The comparison shows that Gaussian functions give a good description of the resolution function and that the widths agree with those calculated by the analytical expressions. The resolution function is applied in the analysis of two experimental examples: neutron scattering from latex particles [Wignall, Christen & Ramakrishnan (1988). J. Appl. Cryst. 21, 438–451] and neutron scattering from lamellar structures of bilayer lipid membranes (Mortensen, Pfeiffer, Sackmann & Knoll, unpublished). The analytical expressions for the resolution function allow a least-squares analysis to be performed and excellent agreement between experimental and theoretical scattering patterns are obtained.

Self-healing mussel-inspired multi-pH-responsive hydrogels.

Self-healing hydrogels can be made using either reversible covalent cross-links or coordination chemistry bonds. Here we present a multi-pH-responsive system inspired by the chemistry of blue mussel adhesive proteins. By attaching DOPA to an amine-functionalized polymer, a multiresponsive system is formed upon reaction with iron. The degree of polymer cross-linking is pH controlled through the pH-dependent DOPA/iron coordination chemistry. This leads to the formation of rapidly self-healing high-strength hydrogels when pH is raised from acidic toward basic values. Close to the pK(a) value, or more precisely the pI value, of the polymer, the gel collapses due to reduced repulsion between polymer chains. Thereby a bistable gel-system is obtained. The present polymer system more closely resembles mussel adhesive proteins than those previously reported and thus also serves as a model system for mussel adhesive chemistry.

A flux- and background-optimized version of the NanoSTAR small-angle X-ray scattering camera for solution scattering

A commercially available small-angle X-ray scattering camera, NanoSTAR from Bruker AXS, has been modified to optimize its use for weakly scattering solution samples. The original NanoSTAR is a pinhole camera with two Gobel mirrors for monochromating and making the beam parallel, and with a two-dimensional position-sensitive gas detector (HiSTAR) for data collection. The instrument has one integrated vacuum. It was constructed for position-resolved studies and thus has a small beam size at the sample position. In the present work, the instrumental configuration has been optimized by numerical calculations based on phase-space analysis and Monte Carlo simulations in order to obtain a higher flux. This has led to a setup in which the beam at the sample is larger and the collimation part of the instrument is longer, so that divergence of the beam is similar to that of the original camera. An extra pinhole is included after the Gobel mirrors to make the beam size well defined after the mirrors. The camera thus has genuine three-pinhole collimation. The use of electron-microscope pinholes minimizes parasitic scattering. At the University of Aarhus, the modified camera is installed on a powerful rotating-anode X-ray source (MacScience 6 kW Cu with a 0.3 × 0.3 mm effective source size). Measurements have been performed on a wide variety of weakly scattering samples, such as surfactant micelles, homopolymer solutions, block copolymer micelles, proteins etc. The data are routinely converted to absolute scale using the scattering from water as a primary standard. The standard configuration covers the range of scattering vectors from 0.01 to 0.35 A−1 with a flux of 1.7 × 107 photons s−1 for Cu Kα radiation at a generator power of 4.05 kW. The camera is easily converted to a high-resolution version covering 0.0037 to 0.22 A−1 with a loss of flux of about a factor of 10, as well as to a position-resolved version.

Association behavior of native beta-lactoglobulin.

The association behavior of beta-lactoglobulin has been studied by small-angle neutron scattering as a function of protein concentration, temperature, pH, and NaCl concentration of the solution. By indirect Fourier transformation of the spectra, pair-distance distribution functions for the various samples were obtained. These functions provided information on the maximum size, the weight-averaged molecular mass, and the z-averaged radius of gyration of the beta-lactoglobulin particles. At room temperature and pH values below 4 and above 5.2 the protein consists predominantly of monomers and dimers, consistent with literature. In these pH regimes the formation of dimers is favored upon increasing ionic strength and decreasing protein charge (pH values closer to the isoelectric point of the protein). Around pH 4.7, larger oligomeric structures are formed, enhanced by a decrease in temperature and a decrease in ionic strength. beta-Lactoglobulin A associates more strongly than beta-lactoglobulin B. Surprisingly, at pH 6.9 larger structures than dimers seem to be formed at high protein concentrations (> 30 mg mL-1).

Form factors of block copolymer micelles with spherical, ellipsoidal and cylindrical cores

The form factor of a micelle model with a spherical core and Gaussian polymer chains attached to the surface has previously been calculated analytically by Pedersen and Gerstenberg [(1996). Macromolecules 29, 1363-1665.]. Non-penetration of the chains into the core region was mimicked in the analytical calculations by moving the center of mass of the chains Rg away from the surface of the core, where Rg is the radius of gyration of the chains. In the present work, the calculations have been extended to micelles with ellipsoidal and cylindrical cores. Non-penetration was also for these taken into account by moving the center of mass of the chains Rg away from the core surface. In addition results for worm-like micelles, disk-shape micelles and micelles with a vesicle shape are given.

Structure of the haptoglobin–haemoglobin complex

Red cell haemoglobin is the fundamental oxygen-transporting molecule in blood, but also a potentially tissue-damaging compound owing to its highly reactive haem groups. During intravascular haemolysis, such as in malaria and haemoglobinopathies, haemoglobin is released into the plasma, where it is captured by the protective acute-phase protein haptoglobin. This leads to formation of the haptoglobin–haemoglobin complex, which represents a virtually irreversible non-covalent protein–protein interaction. Here we present the crystal structure of the dimeric porcine haptoglobin–haemoglobin complex determined at 2.9 Å resolution. This structure reveals that haptoglobin molecules dimerize through an unexpected β-strand swap between two complement control protein (CCP) domains, defining a new fusion CCP domain structure. The haptoglobin serine protease domain forms extensive interactions with both the α- and β-subunits of haemoglobin, explaining the tight binding between haptoglobin and haemoglobin. The haemoglobin-interacting region in the αβ dimer is highly overlapping with the interface between the two αβ dimers that constitute the native haemoglobin tetramer. Several haemoglobin residues prone to oxidative modification after exposure to haem-induced reactive oxygen species are buried in the haptoglobin–haemoglobin interface, thus showing a direct protective role of haptoglobin. The haptoglobin loop previously shown to be essential for binding of haptoglobin–haemoglobin to the macrophage scavenger receptor CD163 (ref. 3) protrudes from the surface of the distal end of the complex, adjacent to the associated haemoglobin α-subunit. Small-angle X-ray scattering measurements of human haptoglobin–haemoglobin bound to the ligand-binding fragment of CD163 confirm receptor binding in this area, and show that the rigid dimeric complex can bind two receptors. Such receptor cross-linkage may facilitate scavenging and explain the increased functional affinity of multimeric haptoglobin–haemoglobin for CD163 (ref. 4).

SDS-Induced Fibrillation of α-Synuclein: An Alternative Fibrillation Pathway

A structural investigation of the sodium dodecyl sulfate (SDS)-induced fibrillation of alpha-synuclein (alphaSN), a 140-amino-acid protein implicated in Parkinsons disease, has been performed. Spectroscopic analysis has been combined with isothermal titration calorimetry, small-angle X-ray scattering, and transmission electron microscopy to elucidate a fibrillation pathway that is remarkably different from the fibrillation pathway in the absence of SDS. Fibrillation occurs most extensively and most rapidly (starting within 45 min) under conditions where 12 SDS molecules are bound per alphaSN molecule, which is also the range where SDS binding is associated with the highest enthalpy. Fibrillation is only reduced in proportion to the fraction of SDS below 25 mol% SDS in mixed surfactant mixtures with nonionic surfactants and is inhibited by formation of bulk micelles and induction of alpha-helical structure. In this fibrillogenic complex, 4 alphaSN molecules initially associate with 40-50 SDS molecules to form a shared micelle that gradually grows in size. The complex initially exhibits a mixture of random coil and alpha-helix, but incubation results in a structural conversion into beta-sheet structure and concomitant formation of thioflavin-T-binding fibrils over a period of several hours. Based on small-angle X-ray scattering, the aggregates elongate as a beads-on-a-string structure in which individual units of ellipsoidal SDS-alphaSN are bridged by strings of the protein, so that aggregates nucleate around the surface of protein-stabilized micelles. Thus, fibrillation in this case occurs by a process of continuous accretion rather than by the rate-limiting accumulation of a distinct nucleus. The morphology of the SDS-induced fibrils does not exhibit the classical rod-like structures formed by alphaSN when aggregated by agitation in the absence of SDS. The SDS-induced fibrils have a flexible worm-like appearance, which can be converted into classical straight fibrils by continuous agitation. SDS-induced fibrillation represents an alternative and highly reproducible mechanism for fibrillation where protein association is driven by the formation of shared micelles, which subsequently allows the formation of beta-sheet structures that presumably link individual micelles. This illustrates that protein fibrillation may occur by remarkably different mechanisms, testifying to the versatility of this process.