Bijvoet Center for Biomolecular Research

Utrecht, Netherlands

Bijvoet Center for Biomolecular Research

Utrecht, Netherlands
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Raju S.,University Utrecht | Jastrzebski J.T.B.H.,University Utrecht | Lutz M.,Bijvoet Center for Biomolecular Research | Klein Gebbink R.J.M.,University Utrecht
ChemSusChem | Year: 2013

A bulky cyclopentadienyl (Cp)-based trioxorhenium compound was developed for the catalytic deoxydehydration of vicinal diols to olefins. The 1,2,4-tri(tert-butyl)cyclopentadienyl trioxorhenium (2) catalyst was synthesised in a two-step synthesis procedure. Dirhenium decacarbonyl was converted into 1,2,4-tri(tert-butyl)cyclopentadienyl tricarbonyl rhenium, followed by a biphasic oxidation with H2O2. These two new three-legged compounds with a 'piano-stool' configuration were fully characterised, including their single crystal X-ray structures. Deoxydehydration reaction conditions were optimised by using 2 mol % loading of 2 for the conversion of 1,2-octanediol into 1-octene. Different phosphine-based and other, more conventional, reductants were tested in combination with 2. Under optimised conditions, a variety of vicinal diols (aromatic and aliphatic, internal and terminal) were converted into olefins in good to excellent yields, and with minimal olefin isomerisation. A high turnover number of 1400 per Re was achieved for the deoxydehydration of 1,2-octanediol. Furthermore, the biomass-derived polyols (glycerol and erythritol) were converted into their corresponding olefinic products by 2 as the catalyst. In the bulk of it: Bulky 1,2,4-tri(tert-butyl)cyclopentadienyl trioxorhenium was studied as a catalyst for the deoxydehydration of different vicinal diols. Under optimised conditions, a variety of vicinal diols were converted into olefins in good to excellent yields, and with minimal olefin isomerisation. Biomass-derived polyols were also converted into their corresponding olefinic products. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mooibroek T.J.,Leiden Institute of Chemistry | Lutz M.,Bijvoet Center for Biomolecular Research | Spek A.L.,Bijvoet Center for Biomolecular Research | Bouwman E.,Leiden Institute of Chemistry
Dalton Transactions | Year: 2010

Complexes of the type [Pd(ligand)2](anion)2 were prepared with a series of bidentate di(o-methoxyphenyl)phosphine ligands with increasing steric bulk on the meta position of the phenyl groups: m-H (L1); m-MeO (L2); and m-Me (L3). The solid-state structure of [Pd(L2) 2](OTs)2 revealed that the two ligands are symmetrically coordinated to Pd2+. In the solid state structure of [Pd(L3) 2](OTs)2 however, the two ligands are unsymmetrically coordinated to Pd2+, yielding an unprecedented conformation of this bis-chelate P4Pd2+ complex. 1H- 1H-COSY and NOESY analysis and a 31P-NMR simulation showed that the asymmetric structure of [Pd(L3)2](OTs)2 is retained in solution. © The Royal Society of Chemistry 2010.

Munoz J.,Bijvoet Center for Biomolecular Research | Munoz J.,University Utrecht | Heck A.J.R.,Bijvoet Center for Biomolecular Research
Methods in Molecular Biology | Year: 2011

Understanding the signaling pathways governing pluripotency and self-renewal is a prerequisite for better controlling stem cell differentiation to specific fates. Reversible protein phosphorylation is one of the most important posttranslational modifications regulating signaling pathways in biological processes. Global analysis of dynamic changes in protein phosphorylation is, therefore, key to understanding signaling at the system level. Here, we describe a generic mass spectrometry (MS)-based phosphoproteomics strategy applied to monitor phosphorylation dynamics after bone morphogenetic protein 4 (BMP4)-induced differentiation of human embryonic stem cells (hESCs). Our method combines the use of strong cation exchange (SCX) and titanium dioxide (TiO 2) for phosphopeptide enrichment, high-resolution MS for peptide and protein identification, and stable isotope labeling by amino acids in cell culture (SILAC) for quantification. This approach allows us to identify thousands of phosphorylation sites and profile their relative abundance during differentiation. This systems-biology-based approach provides new insights into how human pluripotent stem cells exit the pluripotent state. © 2011 Springer Science+Business Media, LLC.

Dzik W.I.,University of Amsterdam | Calvo S.E.,University of Amsterdam | Reek J.N.H.,University of Amsterdam | Lutz M.,Bijvoet Center for Biomolecular Research | And 4 more authors.
Organometallics | Year: 2011

The binuclear iridium complex [(cod)(Cl)Ir(bpi)Ir(cod)]PF 6 (bpi = (pyridin-2-ylmethyl)(pyridin-2-ylmethylene)amine; cod = 1,5-cyclooctadiene) reveals a noteworthy asymmetric binuclear coordination geometry, wherein the bpi ligand acts as a heteroditopic ligand and has an unusual π-coordinated imine moiety. This species is an effective precatalyst for water oxidation. After a short incubation time the catalyst reveals a turnover frequency of 3400 mol mol -1 s -1 with an overall turnover number >1000. © 2011 American Chemical Society.

Karaca E.,Bijvoet Center for Biomolecular Research | Bonvin A.M.J.J.,Bijvoet Center for Biomolecular Research
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

Scoring, the process of selecting the biologically relevant solution from a pool of generated conformations, is one of the major challenges in the field of biomolecular docking. A prominent way to cope with this challenge is to incorporate information-based terms into the scoring function. Within this context, low-resolution shape data obtained from either ion-mobility mass spectrometry (IM-MS) or SAXS experiments have been integrated into the conventional scoring function of the information-driven docking program HADDOCK. Here, the strengths and weaknesses of IM-MS-based and SAXS-based scoring, either in isolation or in combination with the HADDOCK score, are systematically assessed. The results of an analysis of a large docking decoy set composed of dimers generated by running HADDOCK in ab initio mode reveal that the content of the IM-MS data is of too low resolution for selecting correct models, while scoring with SAXS data leads to a significant improvement in performance. However, the effectiveness of SAXS scoring depends on the shape and the arrangement of the complex, with prolate and oblate systems showing the best performance. It is observed that the highest accuracy is achieved when SAXS scoring is combined with the energy-based HADDOCK score. © 2013 International Union of Crystallography Printed in Singapore - all rights reserved.

Intemann J.,Stratingh Institute for Chemistry | Intemann J.,Friedrich - Alexander - University, Erlangen - Nuremberg | Lutz M.,Bijvoet Center for Biomolecular Research | Harder S.,Friedrich - Alexander - University, Erlangen - Nuremberg
Organometallics | Year: 2014

Multinuclear magnesium hydride complexes react with pyridine, forming 1,2- and 1,4-dihydropyridide (DHP) complexes. Reaction of PARA3Mg8H10 with pyridine initially formed 1,2-DHP and 1,4-DHP product mixtures which converted at 60 °C into PARA-[Mg(1,4-DHP)]2·(pyridine)2 (PARA = [(2,6-iPr2C6H3)NC(Me)C(H)C(Me)N]2-(p-C6H4)). Reaction of [NN-(MgH)2]2 with pyridine gave exclusive formation of the 1,2-DHP product NN-[Mg(1,2-DHP)]2·(pyridine)2 (NN = [(2,6-iPr2C6H3)NC(Me)CHC(Me)N-]2). Both products were characterized by crystal structure determinations. The unusual preference for 1,2-addition is likely caused by secondary intramolecular interactions based on mutual communication between the metal coordination geometries: an extended network of C-H···C π-interactions and π-stacking interactions is found. Whereas PARA3Mg8H10 is hardly active in magnesium-catalyzed hydroboration of pyridines with pinacolborane, [NN-(MgH)2]2 shows efficient coupling. However, the regioselectivity of the stoichiometric reaction is not translated to the catalytic regime. This result is taken as an indication for a potential alternative mechanism in which magnesium hydride intermediates do not play a role but the hydride is transferred from an intermediate borate complex. © 2014 American Chemical Society.

Scheidelaar S.,Bijvoet Center for Biomolecular Research | Koorengevel M.C.,Bijvoet Center for Biomolecular Research | Pardo J.D.,Bijvoet Center for Biomolecular Research | Meeldijk J.D.,University Utrecht | And 2 more authors.
Biophysical Journal | Year: 2015

A recent discovery in membrane research is the ability of styrene-maleic acid (SMA) copolymers to solubilize membranes in the form of nanodisks allowing extraction and purification of membrane proteins from their native environment in a single detergent-free step. This has important implications for membrane research because it allows isolation as well as characterization of proteins and lipids in a near-native environment. Here, we aimed to unravel the molecular mode of action of SMA copolymers by performing systematic studies using model membranes of varying compositions and employing complementary biophysical approaches. We found that the SMA copolymer is a highly efficient membrane-solubilizing agent and that lipid bilayer properties such as fluidity, thickness, lateral pressure profile, and charge density all play distinct roles in the kinetics of solubilization. More specifically, relatively thin membranes, decreased lateral chain pressure, low charge density at the membrane surface, and increased salt concentration promote the speed and yield of vesicle solubilization. Experiments using a native membrane lipid extract showed that the SMA copolymer does not discriminate between different lipids and thus retains the native lipid composition in the solubilized particles. A model is proposed for the mode of action of SMA copolymers in which membrane solubilization is mainly driven by the hydrophobic effect and is further favored by physical properties of the polymer such as its relatively small cross-sectional area and rigid pendant groups. These results may be helpful for development of novel applications for this new type of solubilizing agent, and for optimization of the SMA technology for solubilization of the wide variety of cell membranes found in nature. © 2015 Biophysical Society.

PubMed | FOM Institute for Atomic and Molecular Physics and Bijvoet Center for Biomolecular Research
Type: Journal Article | Journal: European biophysics journal : EBJ | Year: 2016

A promising tool in membrane research is the use of the styrene-maleic acid (SMA) copolymer to solubilize membranes in the form of nanodiscs. Since membranes are heterogeneous in composition, it is important to know whether SMA thereby has a preference for solubilization of either specific types of lipids or specific bilayer phases. Here, we investigated this by performing partial solubilization of model membranes and analyzing the lipid composition of the solubilized fraction. We found that SMA displays no significant lipid preference in homogeneous binary lipid mixtures in the fluid phase, even when using lipids that by themselves show very different solubilization kinetics. By contrast, in heterogeneous phase-separated bilayers, SMA was found to have a strong preference for solubilization of lipids in the fluid phase as compared to those in either a gel phase or a liquid-ordered phase. Together the results suggest that (1) SMA is a reliable tool to characterize native interactions between membrane constituents, (2) any solubilization preference of SMA is not due to properties of individual lipids but rather due to properties of the membrane or membrane domains in which these lipids reside and (3) exploiting SMA resistance rather than detergent resistance may be an attractive approach for the isolation of ordered domains from biological membranes.

PubMed | University Utrecht and Bijvoet Center for Biomolecular Research
Type: | Journal: Journal of extracellular vesicles | Year: 2016

Extracellular vesicles (EVs) in synovial fluid (SF) are gaining increased recognition as important factors in joint homeostasis, joint regeneration, and as biomarkers of joint disease. A limited number of studies have investigated EVs in SF samples of patients with joint disease, but knowledge on the role of EVs in healthy joints is lacking. In addition, no standardized protocol is available for isolation of EVs from SF. Based on the high viscosity of SF caused by high concentrations of hyaluronic acid (HA) - a prominent extracellular matrix component - it was hypothesized that EV recovery could be optimized by pretreatment with hyaluronidase (HYase). Therefore, the efficiency of EV isolation from healthy equine SF samples was tested by performing sequential ultracentrifugation steps (10,000g, 100,000g and 200,000g) in the presence or absence of HYase. Quantitative EV analysis using high-resolution flow cytometry showed an efficient recovery of EVs after 100,000g ultracentrifugation, with an increased yield of CD44+ EVs when SF samples were pretreated with HYase. Morphological analysis of SF-derived EVs with cryo-transmission-electron microscopy did not indicate damage by high-speed ultracentrifugation and revealed that most EVs are spherical with a diameter of 20-200 nm. Further protein characterization by Western blotting revealed that healthy SF-derived EVs contain CD9, Annexin-1, and CD90/Thy1.1. Taken together, these data suggest that EV isolation protocols for body fluids that contain relatively high amounts of HA, such as SF, could benefit from treatment of the fluid with HYase prior to ultracentrifugation. This method facilitates recovery and detection of CD44+ EVs within the HA-rich extracellular matrix. Furthermore, based on the findings presented here, it is recommended to sediment SF-derived EVs with at least 100,000g for optimal EV recovery.

Rubio M.,University of Amsterdam | Siegler M.A.,Bijvoet Center for Biomolecular Research | Spek A.L.,Bijvoet Center for Biomolecular Research | Reek J.N.H.,University of Amsterdam
Dalton Transactions | Year: 2010

New coordination polymers based on different combinations of silver atoms and pyridyl-substituted N-heterocyclic carbene moieties are described. The addition of Zn(ii) templates leads to Ag-Zn supramolecular assemblies via selective Zn⋯N interactions; a process that can be reverted. © 2010 The Royal Society of Chemistry.

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