Papers by Jan Skov Pedersen
Small-angle neutron scattering study of the structure of protein / detergent complexes
Biopolymers, 1990
ABSTRACT
Journal of Biological Chemistry, Jul 1, 2016
Hepatocyte growth factor activator inhibitor-1 (HAI-1) is a type I transmembrane protein and inhi... more Hepatocyte growth factor activator inhibitor-1 (HAI-1) is a type I transmembrane protein and inhibitor of several serine proteases, including hepatocyte growth factor activator and matriptase. The protein is essential for development as knockout mice die in utero due to placental defects caused by misregulated extracellular proteolysis. HAI-1 contains two Kunitz-type inhibitor domains (Kunitz), which are generally thought of as a functionally self-contained protease inhibitor unit. This is not the case for HAI-1, where our results reveal how interdomain interactions have evolved to stimulate the inhibitory activity of an integrated Kunitz. Here we present an x-ray crystal structure of an HAI-1 fragment covering the internal domain and Kunitz-1. The structure reveals not only that the previously uncharacterized internal domain is a member of the polycystic kidney disease domain family but also how the two domains engage in interdomain interactions. Supported by solution small angle x-ray scattering and a combination of site-directed mutagenesis and functional assays, we show that interdomain interactions not only stabilize the fold of the internal domain but also stimulate the inhibitory activity of Kunitz-1. By completing our structural characterization of the previously unknown N-terminal region of HAI-1, we provide new insight into the interplay between tertiary structure and the inhibitory activity of a multidomain protease inhibitor. We propose a previously unseen mechanism by which the association of an auxiliary domain stimulates the inhibitory activity of a Kunitz-type inhibitor (i.e. the first structure of an intramolecular interaction between a Kunitz and another domain). * This work was supported by the Danish Cancer Society. The authors declare that they have no conflicts of interest with the contents of this article. The atomic coordinates and structure factors (code 5EZD) have been deposited in the Protein Data Bank ().
Scientific Reports, Jul 24, 2020
Bio-inspired synthetic calcium phosphate (cap) nanoparticles (nps), mimicking the mineral compone... more Bio-inspired synthetic calcium phosphate (cap) nanoparticles (nps), mimicking the mineral component of bone and teeth, are emergent materials for sustainable applications in agriculture. these sparingly soluble salts show self-inhibiting dissolution processes in undersaturated aqueous media, the control at the molecular and nanoscale levels of which is not fully elucidated. Understanding the mechanisms of particle dissolution is highly relevant to the efficient delivery of macronutrients to the plants and crucial for developing a valuable synthesis-by-design approach. it has also implications in bone (de)mineralization processes. Herein, we shed light on the role of size, morphology and crystallinity in the dissolution behaviour of cap nps and on their nitrate doping for potential use as (p,n)-nanofertilizers. Spherical fully amorphous nps and apatite-amorphous nanoplatelets (npLs) in a core-crown arrangement are studied by combining forefront Small-Angle and Wide-Angle X-ray total Scattering (SAXS and WAXtS) analyses. ca 2+ ion release rates differ for spherical nps and npLs demonstrating that morphology plays an active role in directing the dissolution kinetics. Amorphous nps manifest a rapid loss of nitrates governed by surface-chemistry. npLs show much slower release, paralleling that of ca 2+ ions, that supports both detectable nitrate incorporation in the apatite structure and dissolution from the core basal faces. Biomineralization, the process by which living organisms generate organic/inorganic hybrids with unique properties, has long been used as an unceasing stimulus for the development of materials with new functionalities 1,2 . Among them, calcium orthophosphate (CaP) nanoparticles (NPs), the most important inorganic constituents of bone and teeth, have attracted a great deal of attention 3-6 . In vertebrates, CaP NPs appear in the form of very thin nanoplates (NPLs) of a highly structurally defective and calcium-deficient (hydroxy)apatite phase crystallizing in the hexagonal P6 3 /m space group 7 (or subtle deformation thereof 8-10 ), likely grown from an amorphous metastable precursor . Synthetic CaP NPs prepared in close to physiological conditions or mimicking bone mineral structure or function (so called "biomimetic") are remarkably biocompatible, non-toxic and biodegradable . Additionally, they show high chemical and thermal stability, aptitude to either cation or anion doping, high adsorption capacity for organics (drugs and proteins), and pH-responsive solubility that opens the way to a controlled release of calcium and phosphate ions 6 . Owing to these remarkable properties, CaP has been used
Nano Letters, Oct 15, 2019
The microgel shell syntheses were done under the same amount of water but with different amount o... more The microgel shell syntheses were done under the same amount of water but with different amount of monomers. The reaction conditions are described in the main text and the used weights of each chemical for the synthesis of each system are listed in Table .
Journal of Chemical Physics, Apr 21, 2012
Recently we developed a formalism for the scattering from linear and acyclic branched structures ... more Recently we developed a formalism for the scattering from linear and acyclic branched structures build of mutually non-interacting sub-units.[C. Svaneborg and J. S. Pedersen, J. Chem. Phys. 136, 104105 (2012)] We assumed each sub-unit has reference points associated with it. These are well defined positions where sub-units can be linked together. In the present paper, we generalize the formalism to the case where each reference point can represent a distribution of potential link positions. We also present a generalized diagrammatic representation of the formalism. Scattering expressions required to model rods, polymers, loops, flat circular disks, rigid spheres and cylinders are derived. and we use them to illustrate the formalism by deriving the generic scattering expression for micelles and bottle brush structures and show how the scattering is affected by different choices of potential link positions.
A Monte Carlo study on the effect of excluded volume interactions on the scattering from block copolymer micelles
Journal of Chemical Physics, Jun 1, 2000
Effects of excluded volume interaction on the form factor of a block copolymer micelle model have... more Effects of excluded volume interaction on the form factor of a block copolymer micelle model have been investigated by performing Monte Carlo simulations. The micelles are modeled as a corona of semi-flexible chains tethered to a spherical core. Simulated form factors are analyzed using the model proposed by Pedersen and Gerstenberg. A slightly modified model is presented, in which chains consists of a radially pointing rigid rod, onto which a Gaussian chain is attached. The straight section emulates chain stretching near the micelle core. Both models are fitted to the simulation data using two parameters, that describes the individual chains: the radius of gyration, and the average center-of-mass distance to the micelle core. Based on a comparison between parameters obtained from fits, and those obtained directly from the simulation, it is concluded that the models provide good estimates for the radius of gyration and the chain center-of-mass distance for a low surface coverage, while systematic deviations are observed for high surface coverage, where chains begin to overlap, and excluded volume interactions becomes significant.
Physical review, Jun 27, 2001
Chain-chain interactions in a corona of polymers tethered to a spherical core under good solvent ... more Chain-chain interactions in a corona of polymers tethered to a spherical core under good solvent conditions are studied using Monte Carlo simulations. The total scattering function of the corona as well as different partial contributions are sampled. By combining the different contributions in a self-consistent approach, it is demonstrated that the corona can be regarded as a quasi-two-dimensional polymer solution, with a concentration dependence analogous to that of an ordinary polymer solution. Scattering due to the corona profile and density fluctuation correlations are separated in this approach. The osmotic compressibility is extracted from the latter, and it is shown to be a universal function of surface coverage, with some deviations at high coverage due to surface curvature effects.
Monte Carlo simulations and analysis of scattering from neutral and polyelectrolyte polymer and polymer-like systems
Current Opinion in Colloid and Interface Science, Apr 1, 2004
Methods for analyzing small-angle scattering data from complex liquids with particles with many i... more Methods for analyzing small-angle scattering data from complex liquids with particles with many internal degrees of freedom have progressed substantially during the past years. This is mainly due to the use of Monte Carlo simulation techniques for obtaining scattering functions and ...
Macromolecules, Dec 27, 2001
The scattering of a diblock copolymer micelle has been simulated using Monte Carlo techniques. Th... more The scattering of a diblock copolymer micelle has been simulated using Monte Carlo techniques. The scattering is analyzed using a novel model, where the corona is represented as a dilute/ semidilute polymer solution with a radial profile. This approach decouples the scattering due to interaction and connectivity induced density fluctuations and scattering due to the radial profile of the corona. Three different profiles have been used to fit the simulated corona scattering: a box with a Gaussian tail and two maximum entropy (ME) profiles; chain penetration into the core region is not allowed for any of the profiles. Excellent fits are obtained, especially for a ME profile with three parameters. An excludedvolume parameter and the corona compressibility are obtained and show a strong dependence on surface coverage. The derived expressions for the form factor provides a new approach for analyzing experimental data obtained by neutron or X-ray small-angle scattering for block copolymer micelles with significant intra-and interchain excluded-volume interactions.
Scattering from block copolymer micelles
Current Opinion in Colloid and Interface Science, Aug 1, 2002
Block copolymers consist of two different types of polymer chains, which are covalently bonded to... more Block copolymers consist of two different types of polymer chains, which are covalently bonded together. When dissolved in a solvent, which is a good solvent for one block and a poor solvent for the other, micelles are formed. They have a compact core constituted by the insoluble ...
Structural and colloidal changes of casein micelles induced by membrane concentration and their dependence on the milieu exchange conditions
Colloids and Surfaces A: Physicochemical and Engineering Aspects
A model on an absolute scale for the small-angle X-ray scattering from bovine casein micelles
Soft Matter
The scattering from casein micelles made up of colloidal calcium phosphate particles (CCPs) in a ... more The scattering from casein micelles made up of colloidal calcium phosphate particles (CCPs) in a protein network is modelled on absolute scale, and the individual contributions to the scattering are identified.
Nanomaterials, 2022
Calcium silicate hydrate (C-S-H) is the main binding phase in Portland cement. The addition of C-... more Calcium silicate hydrate (C-S-H) is the main binding phase in Portland cement. The addition of C-S-H nanoparticles as nucleation seeds has successfully been used to accelerate the hydration process and the precipitation of binding phases either in conventional Portland cement or in alternative binders. Indeed, the modulation of the hydration kinetics during the early-stage dissolution-precipitation reactions, by acting on the nucleation and growth of binding phases, improves the early strength development. The fine-tuning of concrete properties in terms of compressive strength and durability by designed structural modifications can be achieved through the detailed description of the reaction products at the atomic scale. The nano-sized, chemically complex and structurally disordered nature of these phases hamper their thorough structural characterization. To this aim, we implement a novel multi-scale approach by combining forefront small-angle X-ray scattering (SAXS) and synchrotron...
During the last two decades, there has been a tremendeous development of small-angle x-ray scatte... more During the last two decades, there has been a tremendeous development of small-angle x-ray scattering (SAXS) instrumentation, at synchrotrons as well as at home sources. In particular the development of more powerful home sources and advanced optics means that even weakly scattering samples can be measured at home, and the commercialization of the instruments has led to a large increase in capacity, so that the use has become much more widespread. Simultaneous development of analysis and modelling methods means that more detailed structural information can be extraxted from the SAXS data. At Aarhus University we have in 2014 installed a SAXS instrument from Bruker AXS [1], which uses a powerful Ga metal jet X-ray source from Excillum, and which employs an optimized geometry with homebuilt scatterless slits [2]. In this contribution a recent application of this SAXS instrument for investigating the structure of low-density lipoprotein (LDL) particles [3] as a function of temperature ...
Strain rate dependence of the growth rate of grain boundary cavities during the high cycle high temperature fatigue of copper
High temperature fully reversed fatigue tests of high purity copper were made as a function of st... more High temperature fully reversed fatigue tests of high purity copper were made as a function of stress amplitude. A mean cavity volume V{sub p} and corresponding number density of cavities N{sub p} were determined from the total cavity volume fraction V{sub v} obtained from precision density measurements (PDM) and the total cavity surface area S{sub v} calculated from small angle neutron scattering (SANS) measurements. Under the range of stress amplitudes tested, the plastic strain rate d{epsilon}{sub p}/dt was found to cover three orders of magnitude. The results of these tests of the influence of stress amplitude on cavity growth were combined with previous results in which the frequency of cycling was varied. It was found that the cavity growth rate correlates well with the measured plastic strain and stress amplitude through the relation dV{sub p}/dt {proportional{underscore}to} (d{epsilon}{sub p}/dt){sup 0.45} {proportional{underscore}to} {Delta}{sigma}{sup 2}.
Nanomaterials, 2020
Nanotechnology is emerging as a very promising tool towards more efficient and sustainable practi... more Nanotechnology is emerging as a very promising tool towards more efficient and sustainable practices in agriculture. In this work, we propose the use of non-toxic calcium phosphate nanoparticles doped with urea (U-ACP) for the fertilization of Triticum durum plants. U-ACP nanoparticles present very similar morphology, structure, and composition than the amorphous precursor of bone mineral, but contain a considerable amount of nitrogen as adsorbed urea (up to ca. 6 wt % urea). Tests on Triticum durum plants indicated that yields and quality of the crops treated with the nanoparticles at reduced nitrogen dosages (by 40%) were unaltered in comparison to positive control plants, which were given the minimum N dosages to obtain the highest values of yield and quality in fields. In addition, optical microscopy inspections showed that Alizarin Red S stained nanoparticles were able to penetrate through the epidermis of the roots or the stomata of the leaves. We observed that the uptake thro...
IUCrJ, 2021
Mycobacterium tuberculosis (Mtb), which is responsible for more than a million deaths annually, u... more Mycobacterium tuberculosis (Mtb), which is responsible for more than a million deaths annually, uses lipids as the source of carbon and energy for its survival in the latent phase of infection. Mtb cannot synthesize all of the lipid molecules required for its growth and pathogenicity. Therefore, it relies on transporters such as the mammalian cell entry (Mce) complexes to import lipids from the host across the cell wall. Despite their importance for the survival and pathogenicity of Mtb, information on the structural properties of these proteins is not yet available. Each of the four Mce complexes in Mtb (Mce1–4) comprises six substrate-binding proteins (SBPs; MceA–F), each of which contains four conserved domains (N-terminal transmembrane, MCE, helical and C-terminal unstructured tail domains). Here, the properties of the various domains of Mtb Mce1A and Mce4A, which are involved in the import of mycolic/fatty acids and cholesterol, respectively, are reported. In the crystal struct...
Mixed liposomes containing gram-positive bacteria lipids: Lipoteichoic acid (LTA) induced structural changes
Colloids and Surfaces B: Biointerfaces, 2021
Lipoteichoic acid (LTA), a surface associated polymer amphiphile tethered directly to the Gram-po... more Lipoteichoic acid (LTA), a surface associated polymer amphiphile tethered directly to the Gram-positive bacterial cytoplasmic membrane, is a key structural and functional membrane component. Its composition in the membrane is regulated by bacteria under different physiological conditions. How such LTA compositional variations modulate the membrane structural stability and integrity is poorly understood. Here, we have investigated structural changes in mixed liposomes mimicking the lipid composition of Gram-positive bacteria membranes, in which the concentration of Bacillus Subtilis LTA was varied between 0-15 mol%. Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) measurements indicated formation of mixed unilamellar vesicles, presumably stabilized by the negatively charged LTA polyphosphates. The vesicle size increased with the LTA molar concentration up to ∼6.5 mol%, accompanied by a broadened size distribution, and further increasing the LTA concentration led to a decrease in the vesicle size. At 80 °C, SANS analyses showed the formation of larger vesicles with thinner shells. Complementary Cryo-TEM imaging confirmed the vesicle formation and the size increase with LTA addition, as well as the presence of interconnected spherical aggregates of smaller size at higher LTA concentrations. The results are discussed in light of the steric and electrostatic interactions of the bulky LTA molecules with increased chain fluidity at the higher temperature, which affect the molecular packing and interactions, and thus depend on the LTA composition, in the membrane.
Acta Biomaterialia, 2020
The occurrence of an amorphous calcium phosphate layer covering the crystalline apatite core has ... more The occurrence of an amorphous calcium phosphate layer covering the crystalline apatite core has been suggested to be an intrinsic feature of both bone mineral and synthetic biomimetic analogs. However, an exahustive quantitative picture of the amorphous-crystalline relationship in these materials is still missing. Here, we present a multiple scale modelling that combines small-angle X-ray scattering (SAXS) and synchrotron wide-angle X-ray total scattering (WAXTS) analyses to investigate the amorphous-crystalline spatial interplay in bone sample and biomimetic carbonated nano-apatites. SAXS analysis indicates the presence of a single morphology consisting of tiny nanoplates (NPLs) and provides a measure of their thickness (falling in the 3-5 nm range). WAXTS analysis was performed by developing atomistic models of apatite NPLs incorporating lattice strain, mostly attributed to the carbonate content, and calculating the X-ray patterns using the Debye Scattering Equation. Upon model optimization, the size and strain parameters of the crystalline platelets were derived and the amorphous component, co-existing with the crystalline one, separated and quantified (in the 23-33 wt% range). Notably, the thickness of the apatite core was found to exhibit nearly null (bone) or minor ( < 0.5 nm, biomimetic samples) deviations from that of the entire NPLs, suggesting that the amorphous material remains predominantly distributed along the lateral sides of the NPLs, in a core-crown-like arrangement. The lattice strain analysis indicates a significant stiffness along the c axis, which is comparable in bone and synthetic samples, and larger deformations in the other directions. Current models of bone mineral and biomimetic nanoapatites suggest the occurrence of an amorphous layer covering the apatitic crystalline nanoplates in a core-shell arrangement. By combining X-ray scattering techniques in the small and wide angle regions, we propose a joint atomic-to-nanometre scale modelling to investigate the amorphous-crystalline interplay within the nanoplates. Estimates are extracted for the thickness of the entire nanoplates and the crystalline core, together with the quantification of the amorphous fraction and apatite lattice strain. Based on the thickness matching, the location of the amorphous material mostly along the edges of the nanoplates is inferred, with a vanishing or very thin layer in the thickness direction, suggesting a core-crown-like arrangement, with possible implications on the mineral surface reactivity.
Biochemical Journal, 2019
The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle... more The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in Escherichia coli, EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, whereas anEcTFE is expressed also under anaerobic conditions, with nitrate or fumarate as the ultimate electron acceptor. The anEcTFE subunits have higher sequence identity with the human mitochondrial TFE (HsTFE) than with the soluble EcTFE. Like HsTFE, here it is found that anEcTFE is a membrane-bound complex. Systematic enzyme kinetic studies show that anEcTFE has a preference for medium- and long-chain enoyl-CoAs, similar to HsTFE, whereas EcTFE prefers short chain enoyl-CoA substrates. The biophysical characterization of anEcTFE and EcTFE shows that EcTFE is heterotetrameric, whereas anEcTFE is purified as a complex of two heterotetrameric units, like HsTFE. The tetrameric assembly of anEcTFE resembles the HsTFE tetramer, although the arrangement of the two anEcTFE tetram...
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Papers by Jan Skov Pedersen