Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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The supramolecular organization of a peptide-based nanocarrier at high molecular detail
Rad-Malekshahi, M. ; Visscher, K.M. ; Rodrigues, J.P.G.L.M. ; Vries, R.J. de; Hennink, W.E. ; Baldus, M. ; Bonvin, A.M.J.J. ; Mastrobattista, E. - \ 2015
Journal of the American Chemical Society 137 (2015)24. - ISSN 0002-7863 - p. 7775 - 7784.
solid-state nmr - protein secondary structure - chemical-shift index - force-field - polypeptide vesicles - drug-delivery - beta-sheet - dynamics - nanovesicles - spectroscopy
Nanovesicles self-assembled from amphiphilic peptides are promising candidates for applications in drug delivery. However, complete high-resolution data on the local and supramolecular organization of such materials has been elusive thus far, which is a substantial obstacle to their rational design. In the absence of precise information, nanovesicles built of amphiphilic “lipid-like” peptides are generally assumed to resemble liposomes that are organized from bilayers of peptides with a tail-to-tail ordering. Using the nanocarrier formed by the amphiphilic self-assembling peptide 2 (SA2 peptide) as an example, we derive the local and global organization of a multimega-Dalton peptide-based nanocarrier at high molecular detail and at close-to physiological conditions. By integrating a multitude of experimental techniques (solid-state NMR, AFM, SLS, DLS, FT-IR, CD) with large- and multiscale MD simulations, we show that SA2 nanocarriers are built of interdigitated antiparallel ß-sheets, which bear little resemblance to phospholipid liposomes. Our atomic level study allows analyzing the vesicle surface structure and dynamics as well as the intermolecular forces between peptides, providing a number of potential leads to improve and tune the biophysical properties of the nanocarrier. The herein presented approach may be of general utility to investigate peptide-based nanomaterials at high-resolution and at physiological conditions.
Structural and functional characterization of a novel, host penetration-related pectate lyase from the potato cyst nematode Globodera rostochiensis
Kudla, U. ; Milac, A. ; Qin Ling, ; Overmars, H.A. ; Roze, E.H.A. ; Holterman, M.H.M. ; Petrescu, A.J. ; Goverse, A. ; Bakker, J. ; Helder, J. ; Smant, G. - \ 2007
Molecular Plant Pathology 8 (2007)3. - ISSN 1464-6722 - p. 293 - 305.
subventral esophageal glands - protein secondary structure - heterodera-glycines - developmental expression - erwinia-chrysanthemi - structure prediction - new-generation - agrobacterium - identification - transformation
The cell wall, a strong extraprotoplasmic layer surrounding plant cells that mainly consists of a variety of polysaccharides, constitutes a major barrier for potential parasites. Plant-parasitic nematodes are well equipped to overcome this barrier as they produce and secrete cell-wall-degrading enzymes. Expression profiling of various life stages of the potato cyst nematode Globodera rostochiensis revealed a novel pectate lyase gene (Gr-pel2, 759 bp). The Gr-PEL2 protein showed highest similarity to pectate lyases from the facultative plant-parasitic nematodes Bursaphelenchus mucronatus and B. xylophilus and the soil-inhabiting saprophytic Streptomyces and Frankia species (i.e. 40-42% identity and 58-60% similarity), whereas only a remote relatedness to the previously identified Gr-PEL1 was observed (i.e. 28% identity and 43% similarity). Transient expression of Gr-pel2 in leaves of Nicotiana benthamiana resulted in severe malformations of the infiltrated tissues, not relating to maceration and soft rot symptoms. Ca2+ is known to be essential for pectate lyase activity, and the most likely calcium-binding site was identified in the Gr-PEL2 protein by combining homology modelling of the three-dimensional structure, site-directed mutagenesis and transient expression in leaves. A highly charged cleft in Gr-PEL2, which is likely to be involved in substrate binding and which is also significantly more hydrophobic in Gr-PEL1, was shown to be essential for protein activity. Our results underline the broad spectrum of pectate lyases and cell-wall-degrading enzymes necessary for successful parasitism by cyst nematodes
Structure and localization of an essential transmembrane segment of the proton translocation channel of yeast H+-ATPase
Duarte, A.M. ; Wolfs, C.J.A.M. ; Nuland, N.A.J. van; Harrison, M.A. ; Findlay, J.B.C. ; Mierlo, C.P.M. van; Hemminga, M.A. - \ 2007
Biochimica et Biophysica Acta. Biomembranes 1768 (2007)2. - ISSN 0005-2736 - p. 218 - 227.
nuclear-magnetic-resonance - sarcoplasmic-reticulum ca2+-atpase - protein secondary structure - circular-dichroism spectra - sodium dodecyl-sulfate - m13 coat protein - v-atpase - vacuolar (h+)-atpases - membrane-proteins - nmr-spectroscopy
Vacuolar (H+)-ATPase (V-ATPase) is a proton pump present in several compartments of eukaryotic cells to regulate physiological processes. From biochemical studies it is known that the interaction between arginine 735 present in the seventh transmembrane (TM7) segment from subunit a and specific glutamic acid residues in the subunit c assembly plays an essential role in proton translocation. To provide more detailed structural information about this protein domain, a peptide resembling TM7 (denoted peptide MTM7) from Saccharomyces cerevisiae (yeast) V-ATPase was synthesized and dissolved in two membrane-mimicking solvents: DMSO and SDS. For the first time the secondary structure of the putative TM7 segment from subunit a is obtained by the combined use of CD and NMR spectroscopy. SDS micelles reveal an ¿-helical conformation for peptide MTM7 and in DMSO three ¿-helical regions are identified by 2D 1H-NMR. Based on these conformational findings a new structural model is proposed for the putative TM7 in its natural environment. It is composed of 32 amino acid residues that span the membrane in an ¿-helical conformation. It starts at the cytoplasmic side at residue T719 and ends at the luminal side at residue W751. Both the luminal and cytoplasmatic regions of TM7 are stabilized by the neighboring hydrophobic transmembrane segments of subunit a and the subunit c assembly from V-ATPase
Calcium-induced tertiary structure modifications of endo-B-1,3-glucanase form Pyrococcus furiosus in 7.9 M guanidinium chloride
Chiaraluce, R. ; Gianese, G. ; Angelaccio, S. ; Florio, R. ; Lieshout, J.F.T. van; Oost, J. van der; Consalvi, V. - \ 2005
Biochemical Journal 386 (2005)3. - ISSN 0264-6021 - p. 515 - 524.
transform infrared-spectroscopy - protein secondary structure - 3-dimensional structures - ftir spectroscopy - free-energy - recognition - database - endo-beta-1,3-glucanase - intermediate - alignments
The family 16 endo-b-1,3 glucanase from the extremophilic archaeon Pyrococcus furiosus is a laminarinase, which in 7.9 M GdmCl (guanidinium chloride) maintains a significant amount of tertiary structure without any change of secondary structure. The addition of calcium to the enzyme in 7.9 M GdmCl causes significant changes to the near-UV CD and fluorescence spectra, suggesting a notable increase in the tertiary structure which leads to a state comparable, but not identical, to the native state. The capability to interact with calcium in 7.9 M GdmCl with a consistent recovery of native tertiary structure is a unique property of this extremely stable endo-b-1,3 glucanase. The effect of calcium on the thermodynamic parameters relative to the GdmCl-induced equilibrium unfolding has been analysed by CD and fluorescence spectroscopy. The interaction of calcium with the native form of the enzyme is studied by Fourier-transform infrared spectroscopy in the absorption region of carboxylate groups and by titration in the presence of a chromophoric chelator. A homology-based model of the enzyme is generated and used to predict the putative binding site(s) for calcium and the structural interactions potentially responsible for the unusual stability of this protein, in comparison with other family 16 glycoside hydrolases
Origin, distribution and 3D-modeling of Gr-EXPB1, an expansin from the potato cyst nematode Globodera rostochiensis
Kudla, U. ; Qin Ling, ; Milac, A. ; Kielak, A. ; Maissen, C. ; Overmars, H.A. ; Popeijus, H.E. ; Roze, E.H.A. ; Petrescu, A.J. ; Smant, G. ; Bakker, J. ; Helder, J. - \ 2005
FEBS Letters 579 (2005)11. - ISSN 0014-5793 - p. 2451 - 2457.
protein secondary structure - cellulose-binding domains - plant-cell wall - beta-1,4-endoglucanase genes - meloidogyne-incognita - structure prediction - antibodies
Southern analysis showed that Gr-EXPB1, a functional expansin from the potato cyst nematode Globodera rostochiensis, is member of a multigene family, and EST data suggest expansins to be present in other plant parasitic nematodes as well. Homology modeling predicted that Gr-EXPB1 domain 1 (D1) has a flat ß-barrel structure with surface-exposed aromatic rings, whereas the 3D structure of Gr-EXPB1-D2 was remarkably similar to plant expansins. Gr-EXPB1 shows highest sequence similarity to two extracellular proteins from saprophytic soil-inhabiting Actinobacteria, and includes a bacterial type II carbohydrate-binding module. These results support the hypothesis that a number of pathogenicity factors of cyst nematodes is of procaryotic origin and were acquired by horizontal gene transfer
In situ FTIR assessment of desiccation-tolerant tissues
Wolkers, W.F. ; Hoekstra, F.A. - \ 2003
Spectroscopy: an international journal 17 (2003). - ISSN 0712-4813 - p. 297 - 313.
transform infrared-spectroscopy - protein secondary structure - electron-paramagnetic-resonance - typha-latifolia l - plant craterostigma-plantagineum - carrot somatic embryos - abscisic-acid - arabidopsis-thaliana - phase-transitions - seed development
This essay shows how Fourier transform infrared (FTIR) microspectroscopy can be applied to study thermodynamic parameters and conformation of endogenous biomolecules in desiccation-tolerant biological tissues. Desiccation tolerance is the remarkable ability of some organisms to survive complete dehydration. Seed and pollen of higher plants are well known examples of desiccation-tolerant tissues. FTIR studies on the overall protein secondary structure indicate that during the acquisition of desiccation tolerance, plant embryos exhibit proportional increases in alpha-helical structures and that beta-sheet structures dominate upon drying of desiccation sensitive-embryos. During ageing of pollen and seeds, the overall protein secondary structure remains stable, whereas drastic changes in the thermotropic response of membranes occur, which coincide with a complete loss of viability. Properties of the cytoplasmic glassy matrix in desiccation-tolerant plant organs can be studied by monitoring the position of the OH-stretching vibration band of endogenous carbohydrates and proteins as a function of temperature. By applying these FTIR techniques to maturation-defective mutant seeds of Arabidopsis thaliana we were able to establish a correlation between macromolecular stability and desiccation tolerance. Taken together, in situ FTIR studies can give unique information on conformation and stability of endogenous biomolecules in desiccation-tolerant tissues.
The role of the abundant phenylalanines in the mode of action of the antimicrobial peptide clavanin
Kan, E.J.M. van; Demel, R.A. ; Bent, A. van der; Kruijff, B. de - \ 2003
Biochimica et Biophysica Acta. Biomembranes 1615 (2003)1-2. - ISSN 0005-2736 - p. 84 - 92.
protein secondary structure - antibacterial peptides - hydrophobic moment - circular-dichroism - tunicate hemocytes - membrane-activity - charge - modulate - diastereomers - biomembranes
Clavanin A is a special antimicrobial peptide that acts at the level of the membrane via a pH-dependent mechanism. At neutral pH, clavanin disrupts biological and model membranes in a nonspecific manner, causing efflux of large molecules. At mildly acidic conditions, however, the peptide efficiently kills bacteria by permeabilizing their membrane most likely by interacting with proteins involved in proton translocation [Biochemistry 41 (2002) 7529]. Clavanin A is unusually rich in phenylalanines with 5 out of 23 residues, which suggests that these residues are functionally important. A set of mutants, in which all Phe residues are replaced by either Ile, Leu, Trp, or Tyr was used to investigate the role of these amino acids. The antimicrobial activities of the different peptides both at neutral and low pH show that the presence of phenylalanine is not essential nor optimal, as the Trp, Leu, and Ile mutant are equally or more active than the wild-type component. In general, at neutral pH, the biological activities correlate well with the peptides' ability to interact with membrane lipids. Correspondingly, the permeabilization efficiencies of biological and model membranes of the various derivatives were found to be closely related to their ability to adopt -helical structures, and follows the order 5L>5W>5I>5Y>wild type. The results suggest an important role for the Phe residues, in providing the peptide in a balanced manner with sufficient hydrophobicity, and therewith membrane affinity, as well as conformational flexibility
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