Faculty of Science

Delen

Publications 2006 - 2012

  • Fast production of homogeneous recombinant RNA - towards large-scale production of RNA
    F.H. Nelissen, E.H. Leunissen, L. van de Laar, M. Tessari, H.A. Heus, S.S. Wijmenga
    Nucleic Acids Research (2012) 40, e102
  • NMR and pattern recognition methods in metabolomics: from data acquisition to biomarker discovery: a review
    A. Smolinska, L. Blanchet, L.M. Buydens, S.S. Wijmenga
    Anal Chim Acta (2012) 750, 82-97
  • Chemical shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment
    J.M. Fonville, M. Swart, Z. Vokacova, V. Sychrovsky, J.E. Sponer, J. Sponer, C.W. Hilbers, F.M. Bickelhaupt, S.S. Wijmenga
    Chemistry (2012) 18, 12372-87
  • Force spectroscopy of Rev-peptide-RRE interaction from HIV-1
    J. Zivkovic, L. Janssen, F. Alvarado, S. Speller, H.A. Heus
    Soft Matter (2012) 8, 2103-2109
  • Simultaneous analysis of plasma and CSF by NMR and hierarchical models fusion
    A. Smolinska, J.M. Posma, L. Blanchet, K.A.M. Ampt, A. Attali, T. Tuinstra, T. Luider, M. Doskocz, P.J. Michiels, F.C. Girard, L.M.C. Buydens, S.S. Wijmenga
    Anal Bioanal Chem (2012), 403, 947-959
  • Interpretation and visualization of non-linear data fusion in kernel space: study on metabolomic characterization of progression of Multiple Sclerosis
    A. Smolinska, L. Blanchet, L. Coulier, K.A.M. Ampt, T. Luider, R.Q. Hintzen, S.S. Wijmenga, L.M.C. Buydens
    PLoS One (2012) 7, e38163

  • Using indirect covariance processing for structure elucidation of small molecules in cases of spectral crowding
    R.L.E.G. Aspers, P.E.T.J. Geutjes, M. Honing and M. Jaeger
    Magn Reson Chem (2011) 49, 425-436

  • Determination of size and sign of hetero-nuclear coupling constants from 2D 19F-13C correlation spectra
    K.A.M. Ampt, Aspers, R.L.E.G., Dvortsak, P., Werf, R.M. van der, Wijmenga, S.S., Jaeger, M.
    J Magn Resonan (2012) 215, 27-33

  • Regioselective 16-b Hydoxylation of steroids by rational redesign of the active site of Cytochrome P450 BM3
    V. Rea, A.J. Kolkman, Vottero, E. Stronks, E., Vermeulen, N.P.E., Wijmenga, S.S., Commandeur, J.N.M.
    Biochemistry (2012) 51, 750-60

  • A 10,000-fold nuclear hyperpolarization of a membrane protein in the liquid phase via a solid-state mechanism
    E. Daviso, G. J. Janssen, A. Alia, G. Jeschke, J. Matysik and M. Tessari
    J Am Chem Soc (2011) 133, 16754-7

  • Active site substitution A82W improves regioselectivity of steroid hydroxylation by cytochrome P450 BM3 mutants as rationalised by spin relaxation NMR studies
    V. Rea, A. J. Kolkman, E. R. Vottero, E. J. Stronks, K. A. Ampt, M. Honing, N. P. Vermeulen, S. S. Wijmenga and J. N. Commandeur
    Biochem (2012) 51, 750-760

  • Unusual loop-sequence flexibility of the proximal RNA replication element in EMCV
    J. Zoll, M. M. Hahn, P. Gielen, H. A. Heus, W. J. Melchers and F. J. van Kuppeveld
    PLoS One (2011) 6, e24818

  • Liquid state NMR spectroscopy as a tool to obtain structural and binding information of drug molecules metabolized by P450BM3 enzymes
    A.J. Kolkman, V. Rea, J. Draaisma, M. Tessari, E.V. Vottero, K.A.M. Ampt, J.N.M. Commandeur, H. Irth, N.P.E. Vermeulen, M. Honing,and S.S. Wijmenga
    J. Biomol. Struct. Dyn. (2011), 1007
  • The impact of delayed storage on the proteome and metabolome of human cerebrospinal fluid (CSF)
    T. Rosenling, M.P. Stoop, A. Smolinska, L. Coulier, S. Shi, C. Christin, F. Suits, P.L. Horvatovich, S. Wijmenga, L. Buydens, R. Vreeken, T. Hankemeier, A.J. van Gool, T.M. Luider and R. Bisschoff
    Clinical Chem. (2011), doi:10.1373/clinchem.2011.167601

  • Isotape labeling of larger DNA for NMR structural studies
    S.S. Wijmenga, F. Nelissen, H.A. Heus and M. Tessari
    In: Advances in biomedical spectroscopy, advances in bioNMR spectroscopy, (2011) Eds.: S. Pascal & A. Dingley
  • NMR and Pattern Recognition Can Distinguish Neuroinflammation and Peripheral Inflammation
    A. Smolinska, A. Attali, L. Blanchet, K. Ampt, T. Tuinstra, H. van Aken, E. Suidgeest, A. J. van Gool, T. Luider, S. S. Wijmenga and L. M. Buydens
    J Proteome Res (2011) 10, 4428 - 4438

  • Atomic force microscope-based single-molecule force spectroscopy of RNA unfolding
    H. A. Heus, E. M. Puchner, A. J. van Vugt-Jonker, J. L. Zimmermann and H. E. Gaub
    Anal Biochem (2011) 414, 1-6

  • NMR at earth's magnetic field using para-hydrogen induced polarization,
    B. C. Hamans, A. Andreychenko, A. Heerschap, S. S. Wijmenga and M. Tessari
    J Magn Reson 212 (2011) 224-8

  • Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis
    L. Blanchet, A. Smolinska, A. Attali, M. P. Stoop, K. A. Ampt, H. van Aken, E. Suidgeest, T. Tuinstra, S. S. Wijmenga, T. Luider and L. M. Buydens
    BMC Bioinformatics (2011) 12,  254

  • Application of fluorine NMR for structure identification of steroids
    K. A. Ampt, R. L. Aspers, M. Jaeger, P. E. Geutjes, M. Honing and S. S. Wijmenga
    Magn Reson Chem (2011) 49, 221-30

  • Enzymatic stereospecific preparation of fluorescent S-adenosyl-L-methionine analogs
    O. M. Ottink, F. H. T. Nelissen, Y. Derks, S. S. Wijmenga and H. A. Heus
    Anal Biochem (2010) 396, 280-283
  • (1)H and (13)C resonance assignments of a guanine sensing riboswitch's terminator hairpin
    O. M. Ottink, I. M. Westerweele, M. Tesssari, F. H. Nelissen, H. A. Heus and S. S. Wijmenga
    Biomol NMR Assign. (2010) 4, 89-91
  • Network theory approach for data evaluation in the dynamic force spectroscopy of biomolecular interactions
    J. Zivkovic, M. Mitrovic, L. Janssen, H. A. Heus, B. Tadic and S. Speller 
    Epl (2010) 89, 68004
  • Quantitative Proteomics and Metabolomics Analysis of Normal Human Cerebrospinal Fluid Samples
    M. P. Stoop, L. Coulier, T. Rosenling, S. Shi, A. M. Smolinska, L. Buydens, K. Ampt, C. Stingl, A. Dane, B. Muilwijk, R. L. Luitwieler, P. A. E. S. Smitt, R. Q. Hintzen, R. Bischoff, S. S. Wijmenga, T. Hankemeier, A. J. van Gool and T. M. Luider
    Mol Cell Prot (2010) 9, 2063-2075
  • Determination and identification of estrogenic compounds generated with biosynthetic enzymes using hyphenated screening assays, high resolution mass spectrometry and off-line NMR
    J. S. B. de Vlieger, A. J. Kolkman, K. A. M. Ampt, J. N. M. Commandeur, N. P. E. Vermeulen, J. Kool, S. S. Wijmenga, W. M. A. Niessen, H. Irth and M. Honing
    Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences (2010) 878, 667-674
  • Cytochrome P450 BM3 Mutants as NOVEL Biocatalytic TOOLS for Regioselective Hydroxylation of Steroids
    V. Rea, A. J. Kolkman, E. Vottero, M. Honing, S. S. Wijmenga, N. P. E. Vermeulen and J. N. M. Commandeur
    Drug Metabol Rev (2010) 42, 285-286
  • Functional analysis of the SRV-1 RNA frameshifting pseudoknot
    R. C. L. Olsthoorn, R. Reumerman, C. W. Hilbers, C. W. A. Pleij and H. A. Heus
    Nucleic Acids Res (2010) 38, 7665-7672
  • The unstable part of the apical stem of duck hepatitis B virus epsilon shows enhanced base pair opening but not pico- to nanosecond dynamics and is essential for reverse transcriptase binding
    K. A. Ampt, R. M. van der Werf, F. H. Nelissen, M. Tessari and S. S. Wijmenga
    Biochemistry (2009) 48, 10499-508
  • The structure-function relationship of the enterovirus 3'-UTR
    J. Zoll, H. A. Heus, F. J. van Kuppeveld and W. J. Melchers
    Virus Res (2009) 139, 209-16
  • A microfluidic high-resolution NMR flow probe
    J. Bart, A. J. Kolkman, A. J. Oosthoek-de Vries, K. Koch, P. J. Nieuwland, H. J. Janssen, J. P. van Bentum, K. A. Ampt, F. P. Rutjes, S. S. Wijmenga, H. J. Gardeniers and A. P. Kentgens
    J Am Chem Soc (2009) 131, 5014-5
  • Preparation of selective and segmentally labeled single-stranded DNA for NMR by self-primed PCR and asymmetrical endonuclease double digestion
    F. H. Nelissen, F. C. Girard, M. Tessari, H. A. Heus and S. S. Wijmenga
    Nucleic Acids Res (2009) 37, e114
  • 1H, 13C and 15N NMR assignments of Duck HBV apical stem loop of the epsilon encapsidation signal
    K.A.M Ampt, O.M. Ottink, F.C. Girard, F. Nelissen, M. Tessari and S.. Wijmenga
    Biomol NMR Assign (2008) 2, 143-5
  • Cartilage-hair hypoplasia-associated mutations in the RNase MRP P3 domain affect RNA folding and ribonucleoprotein assembly
    T. J. Welting, S. Mattijssen, F. M. Peters, N. L. van Doorn, L. Dekkers, W. J. van Venrooij, H. A. Heus, L. Bonafe and G. J. Pruijn
    Biochim Biophys Acta (2008) 1783, 455-66
  • Dependence of the size of a protein-SDS complex on detergent and Na+ concentrations
    C. S. Gangabadage, A. Najda, D. Bogdan, S. S. Wijmenga and M. Tessari
    J Phys Chem B 1(2008) 12, 4242-45
  • Multiple segmental and selective isotope labeling of large RNA for NMR structural studies
    F. H. Nelissen, A. J. van Gammeren, M. Tessari, F. C. Girard, H. A. Heus and S. S. Wijmenga
    Nucleic Acids Res 36 (2008) e89
  • Structure and dynamics of human apolipoprotein CIII
    C. S. Gangabadage, J. Zdunek, M. Tessari, S. Nilsson, G. Olivecrona and S. S. Wijmenga
    J Biol Chem (2008) 283, 17416-17427
  • Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns
    K. Petzold, E. Duchardt, S. Flodell, G. Larsson, K. Kidd-Ljunggren, S. Wijmenga and J. Schleucher
    Nucleic Acids Res (2007) 35, 6854-6861
  • Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined induced fit mechanism
    O. M. Ottink, S. M. Rampersad, M. Tessari, G. J. Zaman, H. A. Heus and S. S. Wijmenga
    RNA (2007) 13, 2202-12
  • Transcription and translation regulation riboswitches. Structure of the guanine sensing riboswitch in its guanine-free and -bound forms and comparison with the SAM riboswitch type II
    O. Ottink, S. Rampersad, M. Tessari, F. Nelissen, H. A. Heus and S. Wijmenga
    J Biomol Struct Dyn (2007) 24, 697
  • DNA and RNA branching: NMR structural studies
    S. Wijmenga, O. Ottink, S. Rampersad, M. Tessari, F. Nelissen, H. Heus, F. Girard, B. Wu, C.E. Pearson, R. van der Werf
    J Biomol Struct Dyn (2007) 24, 669
  • Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals
    F. C. Girard, O. M. Ottink, K. A. Ampt, M. Tessari and S. S. Wijmenga
    Nucleic Acids Res (2007) 35, 2800-11
  • Prediction of molecular alignment of nucleic acids in aligned media
    B. Wu, M. Petersen, F. Girard, M. Tessari and S. S. Wijmenga
    J Biomol NMR (2006) 35, 103-15
  • Nonspecific protein adsorption at the single molecule level studied by atomic force microscopy
    P. Schon, M. Gorlich, M. J. Coenen, H. A. Heus and S. Speller
    Langmuir (2007) 23, 9921-3
  • Breaking pseudo-twofold symmetry in the poliovirus 3'-UTR Y-stem by restoring Watson-Crick base pairs
    J. Zoll, M. Tessari, F. J. Van Kuppeveld, W. J. Melchers and H. A. Heus
    RNA (2007) 13, 781-92
  • Macroscopic hierarchical surface patterning of porphyrin trimers via self-assembly and dewetting
    R. van Hameren, P. Schon, A. M. van Buul, J. Hoogboom, S. V. Lazarenko, J. W. Gerritsen, H. Engelkamp, P. C. Christianen, H. A. Heus, J. C. Maan, T. Rasing, S. Speller, A. E. Rowan, J. A. Elemans and R. J. Nolte
    Science (2006) 314, 1433-6
  • An RNA conformational shift in recent H5N1 influenza A viruses
    A. P. Gultyaev, H. A. Heus and R. C. Olsthoorn
    Bioinformatics (2007) 23, 272-6
  • AFM Studies on beta-Sheet Block Copolymers at Solid Surfaces: High-Resolution Structures and Aggregation Dynamics
    P. Schön, J.M. Smeenk, S. Speller, H.A. Heus, and J.C.M. van Hest
    Australian J. of Chem. (2006), 59, 560 – 563.
  • Structural and functional integrity of the coxsackievirus ori/R: the spacing in-between coaxial RNA helices.
    M.J.M. van Ooij, D.H.R.F. Glaudemans, H.A. Heus, F.J.M. van Kuppeveld, and W.J.G. Melchers   
    J. Gen. Virol. (2006), 87, 689-895.
  • Chemical synthesis of picornaviral protein primers of RNA replication
    N. M. Kriek, N. J. Meeuwenoord, H. van den Elst, H. A. Heus, G. A. van der Marel and D. V. Filippov
    Org Biomol Chem (2006) 4, 3576-86
  • A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA
    W. J. Melchers, J. Zoll, M. Tessari, D. V. Bakhmutov, A. P. Gmyl, V. I. Agol and H. A. Heus
    RNA (2006) 12, 1671-82
  • CEESY: Characterizing the conformation of unobservable protein states
    H van Ingen, GW Vuister, S Wijmenga and M Tessari
    J Am Chem Soc (2006) 128, 3856-3857
  • Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal
    S. Flodell, M. Petersen, F. Girard, J. Zdunek, K. Kidd-Ljunggren, J. Schleucher and S. Wijmenga
    Nucleic Acids Res (2006) 34, 4449-4457
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