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Biomedical subjects

Jan Skov Pedersen

Publications and source records attributed to Jan Skov Pedersen.

15 recordsLinked to original sources
PubMed2007

Rupturing polymeric micelles with cyclodextrins.

Small-angle neutron scattering has been used to investigate the associative structures formed by triblock copolymers of poly(ethylene oxide) (PEO)-polypropylene oxide (PPO)-poly(ethylene oxide) (PEO) (also known as Pluronics) and to monitor the structural changes occurring upon complexation with heptakis(2,6-di-O-methyl)-beta-cyclodextrin (hbeta-CD) over the temperature range from 5 to 70 degrees C. At low temperature, the Pluronics are dispersed as unimers. Close to ambient temperature, the hydrophobicity of PPO causes the aggregation of the polymers into spherical micelles with core sizes between 40 and 50 A and a high inclusion of solvent. The aggregation number increases with temperature as the hydrophobicity of the core is gradually enhanced. hbeta-CD spontaneously forms pseudopolyrotaxanes with the triblock copolymers either when in their unimer form or micellized. The complexation results in an increase in the effective critical micellar concentration. It is suggested that the cyclodextrins thread onto the polymer backbone to localize preferentially on the central PPO block, therefore improving its water solubility. At temperatures where the polymers exist in micellar form, complexation with hbeta-CD gives rise to a complete disruption of the aggregates. These processes are highly temperature-dependent. Above 50 degrees C, the break-up of the aggregates is inhibited, and large-scale aggregation is observed.

Journal Article↗
PubMed2006

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.

Adenosine Triphosphate↗
PubMed2006

Structure of eEF3 and the mechanism of transfer RNA release from the E-site.

Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aminoacyl-tRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate the clearance of deacyl-tRNA from the E-site. Here we present the crystal structure of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains, with a chromodomain inserted in ABC2. Moreover, we present the cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release.

Adenosine Diphosphate↗
PubMed2006

Mechanism of oligomerisation of cyclase-associated protein from Dictyostelium discoideum in solution.

Cyclase-associated protein (CAP) is a highly conserved modular protein implicated in the regulation of actin filament dynamics and a variety of developmental and morphological processes. The protein exists as a high molecular weight complex in cell extracts and purified protein possesses a high tendency to aggregate, a major obstacle for crystallisation. Using a mutagenesis approach, we show that two structural features underlie the mechanism of oligomerisation in Dictyostelium discoideum CAP. Positively charged clusters on the surface of the N-terminal helix-barrel domain are involved in inter-molecular interactions with the N or C-terminal domains. Abolishing these interactions mainly renders dimers due to a domain swap feature in the extreme C-terminal region of the protein that was previously described. Based on earlier studies with yeast CAP, we also generated constructs with mutations in the extreme N-terminal region of Dictyostelium CAP that did not show significantly altered oligomerisation behaviour. Constructs with mutations in the earlier identified protein-protein interaction interface on the N-terminal domain of CAP could not be expressed as soluble protein. Assessment of the soluble proteins indicates that the mutations did not affect their overall fold. Further studies point to the correlation between stability of full-length CAP with its multimerisation behaviour, where oligomer formation leads to a more stable protein.

Actins↗
PubMed2006

Nanostructure of the neurocentral growth plate: Insight from scanning small angle X-ray scattering, atomic force microscopy and scanning electron microscopy.

In this study, the experimental techniques scanning electron microscopy (SEM) including energy-dispersive X-ray analysis, atomic force microscopy (AFM) and scanning small angle X-ray scattering (SAXS) have been exploited to characterize the organization of large molecules and nanocrystallites in and around the neurocentral growth plate (NGP) of a pig vertebrae L4. The techniques offer unique complementary information on the nano- to micrometer length scale and provide new insight in the changes in the matrix structure during endochondral bone formation. AFM and SEM imaging of the NGP reveal a fibrous network likely to consist of collagen type II and proteoglycans. High-resolution AFM imaging shows that the fibers have a diameter of approximately 100 nm and periodic features along the fibers with a periodicity of 50-70 nm. This is consistent with the SAXS analysis that yields a cross-sectional diameter of the fibers in the range of 90 to 112 nm and a predominant orientation in the longitudinal direction of the NGP. Furthermore, we find inhomogeneities around 7 nm in the NGP by SAXS analysis. Moving towards the bone in the direction perpendicular to the growth plate, a systematic change in apparent thickness is observed, while the large-scale structural features remain constant. In the region of bone, the apparent thickness equals the mean mineral thickness and increases from 2 nm to approximately 3.5 nm as a function distance from the NGP. The mineral particles are organized as plates in a rather compact network structure. We have demonstrated that SEM, AFM and SAXS are valuable tools for the investigation of the organization of large molecules and nanocrystallites in the NGP and adjacent trabecular bone. Our findings will be an important basis for future work into identifying the defects on nanometer length scale responsible for idiopathic scoliosis and other growth-plate-related diseases.

Animals↗
PubMed2006

Influence of shell thickness and cross-link density on the structure of temperature-sensitive poly-N-isopropylacrylamide-poly-N-isopropylmethacrylamide core-shell microgels investigated by small-angle neutron scattering.

Swelling properties of doubly temperature sensitive core-shell microgels consisting of two thermosensitive polymers with lower critical solution temperatures (LCTS) at, respectively, 34 degrees C in the core and 44 degrees C in the shell have been investigated by small-angle neutron scattering (SANS). A core-shell form factor has been employed to evaluate the structure, and the real space particle structure is expressed by radial density profiles. By this means, the influences of both shell/core mass composition and shell cross-linker content on the internal structure have been revealed at temperatures above, between, and below the LCSTs. Higher shell/core mass ratios lead to an increased expansion of the core at temperatures between the LCSTs, whereas a variation of cross-linker in the shell mainly effects the dimensions of the shell. The influence on the core structure was interpreted as resulting from an elastic force developed from the swollen shell. At temperatures below the core LCST, the core cannot swell to its native size (i.e., in the absence of a shell), because the maximum expanded shell network prohibits further swelling. Thus, depending on temperature, the shell either expands or compresses the core.

Journal Article↗
PubMed2005

Silver nanoparticle formation in microemulsions acting both as template and reducing agent.

A novel method of making silver nanoparticles in water-in-oil microemulsions using the surfactants as both the reducing agent and as the structure-directing agent is presented. Since no external strong reducing agent is used the kinetics of the formation is slow, which makes it possible to study the silver nanoparticle formation in situ. The microemulsions used were based on either the nonionic surfactant Brij30 (C12E4), which reduces the silver ion to metallic silver and is thereby partly oxidized, or mixtures of Brij30 and AOT (sodium bis(2-ethylhexyl) sulfosuccinate, where the latter does not reduce the silver ions. The influences of silver ion and nonionic surfactant concentrations on the formation kinetics of the nanoparticles were followed in situ using UV-vis spectroscopy, and both parameters were found to have a big influence. The microemulsion droplet's size, size distribution, and shape were examined by small-angle X-ray scattering (SAXS), and the formed silver nanoparticles were studied using both transmission electron microscopy and SAXS. The SAXS measurements showed that the presence of silver nitrate does not affect the microemulsion systems noticeably and that the droplet's size and shape are retained during the particle formation. It is shown that the size and morphology of the particles do not directly follow the shape and size of the microemulsion droplets even though there is a relation between the droplet size and the radii of the formed particles.

Journal Article↗
PubMed2005

Preparation temperature dependence of size and polydispersity of alkylthiol monolayer protected gold clusters.

The influence of preparation temperature on the size and size distribution of dodecylthiol monolayer protected gold clusters was studied. The monolayer protected clusters (MPCs) were synthesized by two different variations of the Brust-Schiffrin procedure. In all of the experiments, the stoichiometry of the reactants dodecylthiol, HAuCl(4), and sodium borohydride was kept constant, while the temperature was varied in the range of -18 to +90 degrees C. Two series were performed in which an aqueous solution of NaBH(4) was either added over 30 s or all in one portion. The size and size distribution of the MPCs were determined by small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). It has been demonstrated that in general the MPC size increases with elevated preparation temperatures.

Letter↗
PubMed2005

Structure of multiresponsive "intelligent" core-shell microgels.

A doubly temperature-sensitive core-shell microgel composed of two temperature-sensitive polymers with different lower critical solution temperatures (LCSTs) in the core and shell has been studied by small-angle neutron scattering (SANS). The application of a novel universal form factor model in the analysis of the SANS data reveals that the radial density profile at temperatures above the LCSTs of both polymers can be well described by a two-box profile with narrow interfaces. At temperatures between the LCSTs, the radial density profile reveals that the core in the core-shell microgel has larger dimensions than the naked core. Thus the swollen shell pulls the core apart. At temperatures below both LCSTs, however, the shell restricts the core swelling, and the core is found to be smaller than in its native state. This clearly demonstrates the mutual influence of core and shell swelling.

Journal Article↗
PubMed2005

Structure and interactions of block copolymer micelles of Brij 700 studied by combining small-angle X-ray and neutron scattering.

Spherical micelles of the diblock copolymer/surfactant Brij 700 (C(18)EO(100)) in water (D(2)O) solution have been investigated by small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS). SAXS and SANS experiments are combined to obtain complementary information from the two different contrast conditions of the two techniques. Solutions in a concentration range from 0.25 to 10 wt % and at temperatures from 10 to 80 degrees C have been investigated. The data have been analyzed on absolute scale using a model based on Monte Carlo simulations, where the micelles have a spherical homogeneous core with a graded interface surrounded by a corona of self-avoiding, semiflexible interacting chains. SANS and SAXS data were fitted simultaneously, which allows one to obtain extensive quantitative information on the structure and profile of the core and corona, the chain interactions, and the concentration effects. The model describes the scattering data very well, when part of the EO chains are taken as a "background"contribution belonging to the solvent. The effect of this becomes non-negligible at polymer concentrations as low as 2 wt %, where overlap of the micellar coronas sets in. The results from the analysis on the micellar structure, interchain interactions, and structure factor effects are all consistent with a decrease in solvent quality of water for the PEO block as the theta temperature of PEO is approached.

Journal Article↗
PubMed2004

Are thermoresponsive microgels model systems for concentrated colloidal suspensions? A rheology and small-angle neutron scattering study.

The structure of concentrated temperature-sensitive poly(N-isopropylacrylamide) (PNiPAM) microgel suspensions has been investigated employing rheology and small-angle neutron scattering (SANS). A previously described model expression for the particle form factor P(inho)(q) is extended by a model hard sphere structure factor S(q), and the average radial density profiles phi(r) are calculated from the amplitude of the form factor A(q) and the structure factor S(q). By this procedure, a direct real space description of the spatial ordering in the neighborhood of a single particle is obtained. The overall particle size and the correlation length xi of the concentration fluctuations of the internal polymer network decrease with concentration, revealing the increasing compression of the spheres. Thus, the particle form factor P(inho)(q) of the swollen PNiPAM microgels depends on concentration. The particle-particle interaction potential does not change significantly between 25 and 32 degrees C. Even approximately 1 K below the lower critical solution temperature (LCST), the experimental scattering intensity distributions I(q)/c are described very well by the hard sphere structure factor when an equivalent hard sphere particle size R(HS) and volume fraction eta(HS) are used. Microgels with different degrees of cross-linking and particle size resemble true hard sphere behavior up to effective volume fractions of phi(eff) < 0.35. At higher effective volume fractions phi(eff) > 0.35 strong deviations from true hard spheres are observed. Interpenetration of the outer, less cross-linked regions of the soft spheres as well as particle compression occurred at higher concentrations. In agreement with this, the equilibrium colloidal phase behavior and rheology also has some features of soft sphere systems. At temperatures well above the LCST, the interaction potential becomes strongly attractive and the collapsed microgel spheres form aggregates consisting of flocculated particles without significant long-range order. Hence, an attractive interaction potential in concentrated suspensions of PNiPAM microgels leads to distinctively different structures as compared to attractive hard sphere colloids. When the peculiar structural properties of the PNiPAM microgels are considered, they can be used as model systems in colloidal science.

Journal Article↗
PubMed2004

Moments and distribution function of polyelectrolyte chains.

It is demonstrated that the moments R(2k) of the end-to-end distance distribution function f(r) of charged wormlike chains with excluded volume effects in solution with added salt, in the Debye-Huckel approximation, obey a remarkably simple relation. It is shown that the R(2k) can be expressed as weighted sums of the corresponding moments of ideal wormlike chains. As an application of this method, we show that the Fourier transform of f(r) can also be represented by a superposition of distribution functions of ideal chains. The quantities so calculated are compared with the results of Monte Carlo simulations. Excellent agreement between them is observed.

Journal Article↗
PubMed2004

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.

Acrylic Resins↗
PubMed2003

Small-angle x-ray scattering studies of metastable intermediates of beta-lactoglobulin isolated after heat-induced aggregation.

Small-angle x-ray scattering was used for studying intermediate species, isolated after heat-induced aggregation of the A variant of bovine beta-lactoglobulin. The intermediates were separated in two fractions, the heated metastable dimer and heated metastable oligomers larger than the dimer. The pair distance distribution functions for the two intermediate fractions as well as for the native protein have been obtained by indirect Fourier transformation. In addition, the scattering intensity data for samples of the native protein at different concentrations were fitted using a combination of monomer and dimer form factors, which provides an estimate of the amount of monomer in solutions. By subtracting the contribution from the monomer, the scattering intensity from the dimer of the native protein can be determined and compared with the results for the metastable dimer. An ellipsoidal model was used to fit the data for the metastable dimer, and for comparison the same analysis was performed on the dimer of the native protein. The results show that the metastable dimer is more elongated than the dimer of the native protein and it occupies a volume 1.4-fold larger, in agreement with a more loose, partially unfolded conformation. The same ellipsoidal model was used to analyze the data for the fraction of larger metastable oligomers. In this case, an even more elongated ellipsoid was obtained, suggesting a linear association of monomers in the oligomers.

Animals↗