Institute of Biomembranes

Utrecht, Netherlands

Institute of Biomembranes

Utrecht, Netherlands

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Ramadurai S.,Groningen Biomolecular science and Biotechnology Institute | Holt A.,Institute of Biomembranes | Schafer L.V.,University of Groningen | Krasnikov V.V.,Groningen Biomolecular science and Biotechnology Institute | And 4 more authors.
Biophysical Journal | Year: 2010

We investigated the effect of amino acid composition and hydrophobic length of α-helical transmembrane peptides and the role of electrostatic interactions on the lateral diffusion of the peptides in lipid membranes. Model peptides of varying length and composition, and either tryptophans or lysines as flanking residues, were synthesized. The peptides were labeled with the fluorescent label Alexa Fluor 488 and incorporated into phospholipid bilayers of different hydrophobic thickness and composition. Giant unilamellar vesicles were formed by electroformation, and the lateral diffusion of the transmembrane peptides (and lipids) was determined by fluorescence correlation spectroscopy. In addition, we performed coarsegrained molecular-dynamics simulations of single peptides of different hydrophobic lengths embedded in planar membranes of different thicknesses. Both the experimental and simulation results indicate that lateral diffusion is sensitive to membrane thickness between the peptides and surrounding lipids. We did not observe a difference in the lateral diffusion of the peptides with respect to the presence of tryptophans or lysines as flanking residues. The specific lipid headgroup composition of the membrane has a much less pronounced impact on the diffusion of the peptides than does the hydrophobic thickness. © 2010 by the Biophysical Society.


Zapun A.,CNRS Institute of Pharmacology and Structural Biology | Zapun A.,French National Center for Scientific Research | Zapun A.,CEA Grenoble | Philippe J.,CNRS Institute of Pharmacology and Structural Biology | And 11 more authors.
ACS Chemical Biology | Year: 2013

Understanding the molecular basis of bacterial cell wall assembly is of paramount importance in addressing the threat of increasing antibiotic resistance worldwide. Streptococcus pneumoniae presents a particularly acute problem in this respect, as it is capable of rapid evolution by homologous recombination with related species. Resistant strains selected by treatment with β-lactams express variants of the target enzymes that do not recognize the drugs but retain their activity in cell wall building, despite the antibiotics being mimics of the natural substrate. Until now, the crucial transpeptidase activity that is inhibited by β-lactams was not amenable to in vitro investigation with enzymes from Gram-positive organisms, including streptococci, staphylococci, or enterococci pathogens. We report here for the first time the in vitro assembly of peptidoglycan using recombinant penicillin-binding proteins from pneumococcus and the precursor lipid II. The two required enzymatic activities, glycosyl transferase for elongating glycan chains and transpeptidase for cross-linking stem-peptides, were observed. Most importantly, the transpeptidase activity was dependent on the chemical nature of the stem-peptide. Amidation of the second residue glutamate into iso-glutamine by the recently discovered amido-transferase MurT/GatD is required for efficient cross-linking of the peptidoglycan. © 2013 American Chemical Society.


Van Der Schaar H.M.,A-Life Medical | Van Der Linden L.,A-Life Medical | Van Der Linden L.,Rega Institute for Medical Research | Lanke K.H.W.,A-Life Medical | And 6 more authors.
Cell Research | Year: 2012

RNA viruses can rapidly mutate and acquire resistance to drugs that directly target viral enzymes, which poses serious problems in a clinical context. Therefore, there is a growing interest in the development of antiviral drugs that target host factors critical for viral replication, since they are unlikely to mutate in response to therapy. We recently demonstrated that phosphatidylinositol-4-kinase IIIβ (PI4KIIIβ) and its product phosphatidylinositol-4-phosphate (PI4P) are essential for replication of enteroviruses, a group of medically important RNA viruses including poliovirus (PV), coxsackievirus, rhinovirus, and enterovirus 71. Here, we show that enviroxime and GW5074 decreased PI4P levels at the Golgi complex by directly inhibiting PI4KIIIβ. Coxsackievirus mutants resistant to these inhibitors harbor single point mutations in the non-structural protein 3A. These 3A mutations did not confer compound-resistance by restoring the activity of PI4KIIIβ in the presence of the compounds. Instead, replication of the mutant viruses no longer depended on PI4KIIIβ, since their replication was insensitive to siRNA-mediated depletion of PI4KIIIβ. The mutant viruses also did not rely on other isoforms of PI4K. Consistently, no high level of PI4P could be detected at the replication sites induced by the mutant viruses in the presence of the compounds. Collectively, these findings indicate that through specific single point mutations in 3A, CVB3 can bypass an essential host factor and lipid for its propagation, which is a new example of RNA viruses acquiring resistance against antiviral compounds, even when they directly target host factors. © 2012 IBCB, SIBS, CAS All rights reserved.


PubMed | University of Florida, CNR Institute of Protein Biochemistry, Tel Aviv University, The FIRC Institute of Molecular Oncology and 2 more.
Type: Journal Article | Journal: International journal of molecular sciences | Year: 2015

Membrane organelles often have complicated shapes and differ in their volume, surface area and membrane curvature. The ratio between the surface area of the cytosolic and luminal leaflets (trans-membrane area asymmetry (TAA)) determines the membrane curvature within different sites of the organelle. Thus, the shape of the organelle could be critically dependent on TAA. Here, using mathematical modeling and stereological measurements of TAA during fast transformation of organelle shapes, we present evidence that suggests that when organelle volume and surface area are constant, TAA can regulate transformation of the shape of the Golgi apparatus, endosomal multivesicular bodies, and microvilli of brush borders of kidney epithelial cells. Extraction of membrane curvature by small spheres, such as COPI-dependent vesicles within the Golgi (extraction of positive curvature), or by intraluminal vesicles within endosomes (extraction of negative curvature) controls the shape of these organelles. For instance, Golgi tubulation is critically dependent on the fusion of COPI vesicles with Golgi cisternae, and vice versa, for the extraction of membrane curvature into 50-60 nm vesicles, to induce transformation of Golgi tubules into cisternae. Also, formation of intraluminal ultra-small vesicles after fusion of endosomes allows equilibration of their TAA, volume and surface area. Finally, when microvilli of the brush border are broken into vesicles and microvilli fragments, TAA of these membranes remains the same as TAA of the microvilli. Thus, TAA has a significant role in transformation of organelle shape when other factors remain constant.


Bryde S.,Institute of Biomembranes | Bryde S.,French National Center for Scientific Research | Hennrich H.,Institute of Biomembranes | Verhulst P.M.,Institute of Biomembranes | And 4 more authors.
Journal of Biological Chemistry | Year: 2010

Members of the P4 subfamily of P-type ATPases catalyze phospholipid transport and create membrane lipid asymmetry in late secretory and endocytic compartments. P-type ATPases usually pump small cations and the transport mechanism involved appears conserved throughout the family. How this mechanism is adapted to flip phospholipids remains to be established. P 4-ATPases form heteromeric complexes with CDC50 proteins. Dissociation of the yeast P4-ATPase Drs2p from its binding partner Cdc50p disrupts catalytic activity (Lenoir, G., Williamson, P., Puts, C. F., and Holthuis, J. C. (2009) J. Biol. Chem. 284, 17956-17967), suggesting that CDC50 subunits play an intimate role in the mechanism of transport by P 4-ATPases. The human genome encodes 14 P4-ATPases while only three human CDC50 homologues have been identified. This implies that each human CDC50 protein interacts with multiple P4-ATPases or, alternatively, that some human P4-ATPases function without a CDC50 binding partner. Here we show that human CDC50 proteins each bind multiple class-1 P4-ATPases, and that in all cases examined, association with a CDC50 subunit is required for P4-ATPase export from the ER. Moreover, we find that phosphorylation of the catalytically important Asp residue in human P 4-ATPases ATP8B1 and ATP8B2 is critically dependent on their CDC50 subunit. These results indicate that CDC50 proteins are integral part of the P4-ATPase flippase machinery. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.


Kondylis V.,University Utrecht | Kondylis V.,Institute of Biomembranes | Kondylis V.,University of Cologne | Van Nispen Tot Pannerden H.E.,University Utrecht | And 14 more authors.
Autophagy | Year: 2013

Activation of TLR signaling has been shown to induce autophagy in antigen-presenting cells (APCs). Using high-resolution microscopy approaches, we show that in LPS-stimulated dendritic cells (DCs), autophagosomes emerge from MHC class II compartments (MIIC s) and harbor both the molecular machinery for antigen processing and the autophagosome markers LC3 and ATG16L1. This ENdosome-Mediated Autophagy (ENMA) appears to be the major type of autophagy in DCs, as similar structures were observed upon established autophagy-inducing conditions (nutrient deprivation, rapamycin) and under basal conditions in the presence of bafilomycin A1. Autophagosome formation was not significantly affected in DCs expressing ATG4BC74A mutant and atg4b-/- bone marrow DCs, but the degradation of the autophagy substrate SQSTM1/p62 was largely impaired. Furthermore, we demonstrate that the previously described DC aggresome-like LPSinduced structures (DALIS) contain vesicular membranes, and in addition to SQSTM1 and ubiquitin, they are positive for LC3. LC3 localization on DALIS is independent of its lipidation. MIIC -driven autophagosomes preferentially engulf the LPS-induced SQSTM1-positive DALIS, which become later degraded in autolysosomes. DALIS-associated membranes also contain ATG16L1, ATG9 and the Q-SNARE VTI1B, suggesting that they may represent (at least in part) a membrane reservoir for autophagosome expansion. We propose that ENMA constitutes an unconventional, APC-specific type of autophagy, which mediates the processing and presentation of cytosolic antigens by MHC class II machinery, and/or the selective clearance of toxic by-products of elevated ROS/RNS production in activated DCs, thereby promoting their survival. © 2013 Landes Bioscience.


Puts C.F.,Institute of Biomembranes | Lenoir G.,Institute of Biomembranes | Lenoir G.,University Utrecht | Krijgsveld J.,Amherst College | And 3 more authors.
Journal of Proteome Research | Year: 2010

High-throughput analysis of protein-protein interactions can provide unprecedented insight into how cellular processes are integrated at the molecular level. Yet membrane proteins are often overlooked in these studies owing to their hydrophobic nature and low abundance. Here we used a proteomicsbased strategy with the specific intention of identifying membrane-associated protein complexes. One important aspect of our approach is the use of chemical cross-linking to capture transient and lowaffinity protein interactions that occur in living cells prior to cell lysis. We applied this method to identify binding partners of the yeast Golgi P4-ATPase Drs2p, a member of a conserved family of putative aminophospholipid transporters. Drs2p was endogeneously tagged with both a polyhistidine and a biotinylation peptide, allowing tandem-affinity purification of Drs2p-containing protein complexes under highly stringent conditions. Mass-spectrometric analysis of isolated complexes yielded one known and nine novel Drs2p binding partners. Binding specificity was verified by an orthogonal in vivo membrane protein interaction assay, confirming the efficacy of our method. Strikingly, three of the novel Drs2p interactors are involved in phosphoinositide metabolism. One of these, the phosphatidylinositol-4-phosphatase Sac1p, also displays genetic interactions with Drs2p. Together, these findings suggest that aminophospholipid transport and phosphoinositide metabolism are interconnected at the Golgi. © 2010 American Chemical Society.


Briegel A.,California Institute of Technology | Briegel A.,Howard Hughes Medical Institute | Chen S.,California Institute of Technology | Koster A.J.,Institute of Biomembranes | And 4 more authors.
Methods in Enzymology | Year: 2010

Light and electron cryo-microscopy have each proven to be powerful tools to study biological structures in a near-native state. Light microscopy provides important localization information, while electron microscopy provides the resolution necessary to resolve fine structural details. Imaging the same sample by both light and electron cryo-microscopy is a powerful new approach that combines the strengths of both techniques to provide novel insights into cellular ultrastructure. In this chapter, the methods and instrumentation currently used to correlate light and electron cryo-microscopy are described in detail. © 2010 Elsevier Inc.


Van Nispen Tot Pannerden H.,University Utrecht | Van Nispen Tot Pannerden H.,Institute of Biomembranes | De Haas F.,FEI Company | Geerts W.,Institute of Biomembranes | And 7 more authors.
Blood | Year: 2010

We have used (cryo) electron tomography to provide a 3-dimensional (3D) map of the intracellular membrane organization of human platelets at high spatial resolution. Our study shows that the open canalicular system and dense tubular system are highly intertwined and form close associations in specialized membrane regions. 3D reconstructions of individual α-granules revealed large heterogeneity in their membrane organization. On the basis of their divergent morphology, we categorized α-granules into the following subtypes: spherical granules with electron-denseandelectron-lucent zone containing 12-nm von Willebrand factor tubules, subtypes containing a multitude of luminal vesicles, 50-nm-wide tubular organelles, and a population with 18.4-nm crystalline cross-striations. Low-dose (cryo) electron tomography and 3D reconstruction of whole vitrified platelets confirmed the existence of long tubular granules with a remarkably curved architecture. Immunoelectron microscopy confirmed that these extended structures represent α-granule subtypes. Tubular α-granules represent approximately 16% of the total α-granule population and are detected in approximately half of the platelet population. They express membrane-bound proteins GLUT3 and αIIb-β3 integrin and contain abundant fibrinogen and albumin but low levels of β-thromboglobulin and no von Willebrand factor. Our 3D study demonstrates that, besides the existence of morphologically different α-granule subtypes, high spatial segregation of cargo exists within individual α-granules. © 2010 by The American Society of Hematology.


Van Nispen Tot Pannerden H.E.,Institute of Biomembranes | Van Nispen Tot Pannerden H.E.,University Utrecht | Geerts W.J.,Institute of Biomembranes | Geerts W.J.,University Utrecht | And 4 more authors.
Biology of the Cell | Year: 2010

Background information. DC (dendritic cells) continuously capture pathogens and process them into small peptides within the endolysosomal compartment, the MIIC (MHC class II-containing compartment). In MIICs peptides are loaded on to MHC class II and rapidly redistributed to the cell surface. This redistribution is accompanied by profound changes of the MIICs into tubular structures. An emerging concept is that MIIC tubulation provides a means to transport MHC class II-peptide complexes to the cell surface, either directly or through vesicular intermediates. To obtain spatial information on the reorganization of the MIICs during DC maturation, we performed electron tomography on cryo-immobilized and freeze-substituted mouse DCs after stimulation with LPS (lipopolysaccharide). Results. In non-stimulated DCs, MIICs are mostly spherical. After 3 h of LPS stimulation, individual MIICs transform into tubular structures. Three-dimensional reconstruction showed that the MIICs frequently display fusion profiles and after 6 h of LPS stimulation, MIICs become more interconnected, thereby creating large MIIC reticula. Microtubules and microfilaments align these MIICs and reveal physical connections. In our tomogramswe also identified a separate population of MIIC-like intermediates, particularly at extended ends of MIIC tubules and in close proximity to the trans-Golgi network. No fusion events were captured between reticular MIICs and the plasma membrane. Conclusions. Our results indicate that MIICs have the capacity to fuse together, whereby the cytoskeleton possibly provides a scaffold for the MIIC shape change and directionality. MIIC-like intermediates may represent MHC class II carriers. © The Authors.

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