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Interdisciplinary Nanoscience Center

Danish Center for Ultrahigh Field NMR Spectroscopy

Publications

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Yoshimura, Y., Kulminskaya, N. V. & Mulder, F. A. A. (2015). Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone (15)N or (13)C' chemical shifts of multiple contiguous residues in highly resolved 3D spectra. Journal of Biomolecular N M R, 61(2), 109-121. https://doi.org/10.1007/s10858-014-9890-7

Yoshimura, Y., Oktaviani, N. A., Yonezawa, K., Kamikubo, H. & Mulder, F. A. A. (2017). Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy. Angewandte Chemie International Edition, 56(1), 239–242. Advance online publication. https://doi.org/10.1002/anie.201609605

Yoshimura, Y., Holmberg, M., Kukic, P., Andersen, C. B., Mata-Cabana, A., Falsone, S. F., Vendruscolo, M., Nollen, E. A. A. & Mulder, F. (2017). MOAG-4 promotes the aggregation of α-synuclein by competing with self-protective electrostatic interactions. Journal of Biological Chemistry, 292(20), 8269-8278. https://doi.org/10.1074/jbc.M116.764886

Yoshimura, Y. & Mulder, F. A. A. (2020). Sensitive and simplified: a combinatorial acquisition of five distinct 2D constant-time ¹³C− ¹H NMR protein correlation spectra. Journal of Biomolecular NMR, 74(12), 695-706. Advance online publication. https://doi.org/10.1007/s10858-020-00341-x

Xue, M., Kitahara, R., Yoshimura, Y. & Mulder, F. A. A. (2016). Aberrant increase of NMR signal in hydrogen exchange experiments. Observation and explanation. Biochemical and Biophysical Research Communications, 478(3), 1185-1188. https://doi.org/10.1016/j.bbrc.2016.08.092

Xue, M., Wakamoto, T., Kejlberg, C., Yoshimura, Y., Nielsen, T. A., Risør, M. W., Sanggaard, K. W., Kitahara, R. & Mulder, F. A. A. (2019). How internal cavities destabilize a protein. Proceedings of the National Academy of Sciences, 116(42), 21031-21036. https://doi.org/10.1073/pnas.1911181116

Wood, K., Paz, A., Dijkstra, K., Scheek, R. M., Otten, R., Silman, I., Sussman, J. L. & Mulder, F. A. A. (2012). Backbone and side chain NMR assignments for the intrinsically disordered cytoplasmic domain of human neuroligin-3. Biomolecular N M R Assignments, 6(1), 15-8. https://doi.org/10.1007/s12104-011-9315-4

Wood, K., Gallat, F-X., Otten, R., van Heel, A. J., Lethier, M., van Eijck, L., Moulin, M., Haertlein, M., Weik, M. & Mulder, F. A. A. (2013). Protein Surface and Core Dynamics Show Concerted Hydration-Dependent Activation. Angewandte Chemie International Edition, 52(2), 665-668. https://doi.org/10.1002/anie.201205898

Wood, K., Tobias, D. J., Kessler, B., Gabel, F., Oesterhelt, D., Mulder, F. A. A., Zaccai, G. & Weik, M. (2010). The low-temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation: Direct evidence using isotope labeling and molecular dynamics simulations. Journal of the American Chemical Society, 132(14), 4990-4991. https://doi.org/10.1021/ja910502g

van Tilborg, P. J., Czisch, M., Mulder, F. A. A., Folkers, G. E., Bonvin, A. M., Nair, M., Boelens, R. & Kaptein, R. (2000). Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site. Biochemistry, 39(30), 8747-8757. https://doi.org/10.1021/bi991550g

van Tilborg, P. J., Mulder, F. A. A., de Backer, M. M., Nair, M., van Heerde, E. C., Folkers, G., van der Saag, P. T., Karimi-Nejad, Y., Boelens, R. & Kaptein, R. (1999). Millisecond to microsecond time scale dynamics of the retinoid X and retinoic acid receptor DNA-binding domains and dimeric complex formation. Biochemistry, 38(7), 1951-1956. https://doi.org/10.1021/bi982526q

Tollinger, M., Skrynnikov, N. R., Mulder, F. A., Forman-Kay, J. D. & Kay, L. E. (2001). Slow dynamics in folded and unfolded states of an SH3 domain. Journal of the American Chemical Society, 123(46), 11341-11352. https://doi.org/10.1021/ja011300z

Tessari, M., Mulder, F. A. A., Boelens, R. & Vuister, G. W. (1997). Determination of Amide Proton CSA in ¹⁵N-Labeled Proteins Using ¹H CSA/¹⁵N-¹H Dipolar and ¹⁵N CSA/¹⁵N-¹H Dipolar Cross-Correlation Rates. Journal of Magnetic Resonance, 127(1), 128-133. https://doi.org/10.1006/jmre.1997.1199

Tamiola, K. & Mulder, F. A. A. (2012). Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins. Biochemical Society. Transactions, 40(5), 1014-20. https://doi.org/10.1042/BST20120171

Tamiola, K. & Mulder, F. A. A. (2011). ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. Bioinformatics (Online), 27(7), 1039-40. https://doi.org/10.1093/bioinformatics/btr054

Tamiola, K., Acar, B. & Mulder, F. A. A. (2010). Sequence-specific random coil chemical shifts of intrinsically disordered proteins. Journal of the American Chemical Society, 132(51), 18000-3. https://doi.org/10.1021/ja105656t

Tamiola, K., Scheek, R. M., Van Der Meulen, P. & Mulder, F. A. A. (2018). PepKalc: Scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides. Bioinformatics, 34(12), 2053-2060. https://doi.org/10.1093/bioinformatics/bty033

Stødkilde, K., Nielsen, J. T., Petersen, S. V., Paetzold, B., Brüggemann, H., Mulder, F. A. A. & Andersen, C. B. F. (2022). Solution Structure of the Cutibacterium acnes-Specific Protein RoxP and Insights Into Its Antioxidant Activity. Frontiers in cellular and infection microbiology, 12, Article 803004. https://doi.org/10.3389/fcimb.2022.803004

Skrynnikov, N. R., Mulder, F. A. A., Hon, B., Dahlquist, F. W. & Kay, L. E. (2001). Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: Application to methionine residues in a cavity mutant of T4 lysozyme. Journal of the American Chemical Society, 123(19), 4556-4566. https://doi.org/10.1021/ja004179p

Rubinstenn, G., Vuister, G. W., Mulder, F. A. A., Dux, P. E., Boelens, R., Hellingwerf, K. J. & Kaptein, R. (1998). Structural and dynamic changes of photoactive yellow protein during its photocycle in solution. Nature Structural Biology, 5(7), 568-570. https://doi.org/10.1038/823

Roodbeen, R., Paaske, B., Jiang, L., Jensen, J. K., Christensen, A., Nielsen, J. T., Huang, M., Mulder, F. A. A., Nielsen, N. C., Andreasen, P. & Jensen, K. J. (2013). Bicyclic Peptide Inhibitor of Urokinase-Type Plasminogen Activator: Mode of Action. ChemBioChem, 14(16), 2179–2188. https://doi.org/10.1002/cbic.201300335

Pool, T. J., Oktaviani, N. A., Kamikubo, H., Kataoka, M. & Mulder, F. A. A. (2013). ¹H, ¹³C, and ¹⁵N resonance assignment of photoactive yellow protein. Biomolecular N M R Assignments, 7(1), 97-100. https://doi.org/10.1007/s12104-012-9387-9

Paz, A., Zeev-Ben-Mordehai, T., Lundqvist, M., Sherman, E., Mylonas, E., Weiner, K. L., Haran, G., Svergun, D. I., Mulder, F. A. A., Sussman, J. L. & Silman, I. (2008). Biophysical characterization of the unstructured cytoplasmic domain of the human neuronal adhesion protein neuroligin 3. Biophysical Journal, 95(4), 1928-1944. https://doi.org/10.1529/biophysj.107.126995

Paquin, R., Ferrage, F., Mulder, F. A. A., Akke, M. & Bodenhausen, G. (2008). Multiple-timescale dynamics of side-chain carboxyl and carbonyl groups in proteins by ¹³C nuclear spin relaxation. Journal of the American Chemical Society, 130(47), 15805-15807. https://doi.org/10.1021/ja803794g

Otten, R., Villali, J., Kern, D. & Mulder, F. A. A. (2010). Probing microsecond time scale dynamics in proteins by methyl ¹H Carr-Purcell-Meiboom-Gill relaxation dispersion NMR measurements. Application to activation of the signaling protein NtrC^r. Journal of the American Chemical Society, 132(47), 17004-17014. https://doi.org/10.1021/ja107410x

Otten, R., Chu, B., Krewulak, K. D., Vogel, H. J. & Mulder, F. A. A. (2010). Comprehensive and cost-effective NMR spectroscopy of methyl groups in large proteins. Journal of the American Chemical Society, 132(9), 2952-2960. https://doi.org/10.1021/ja907706a

Otten, R., Wood, K. & Mulder, F. A. A. (2009). Comprehensive determination of ³J_HNHα for unfolded proteins using ¹³C′-resolved spin-echo difference spectroscopy. Journal of Biomolecular N M R, 45(4), 343-349. https://doi.org/10.1007/s10858-009-9382-3

O'Malley, T. T., Oktaviani, N. A., Zhang, D., Lomakin, A., O'Nuallain, B., Linse, S., Benedek, G. B., Rowan, M. J., Mulder, F. A. A. & Walsh, D. M. (2014). Aβ dimers differ from monomers in structural propensity, aggregation paths and population of synaptotoxic assemblies. Biochemical Journal, 461(3), 413-426. https://doi.org/10.1042/BJ20140219

Olesen, H. G., Mohr, D., Seweryn, P., Yoshimura, Y., Kutlubaeva, Z., Dolman, F., Chelchessa, B., Chetverin, A. B., Mulder, F. A. A., Brodersen, D. E. & Knudsen, C. R. (2015). Structural basis for RNA-genome recognition during bacteriophage Qβ replication. Nucleic Acids Research, 43(22), 10893-10906. https://doi.org/10.1093/nar/gkv1212

Oktaviani, N. A., Pool, T. J., Kamikubo, H., Slager, J., Scheek, R. M., Kataoka, M. & Mulder, F. A. A. (2012). Comprehensive determination of protein tyrosine pKa values for photoactive yellow protein using indirect 13C NMR spectroscopy. Biophysical Journal, 102(3), 579-86. https://doi.org/10.1016/j.bpj.2011.12.024

Oktaviani, N. A., Otten, R., Dijkstra, K., Scheek, R. M., Thulin, E., Akke, M. & Mulder, F. A. A. (2011). 100% complete assignment of non-labile (1)H, (13)C, and (15)N signals for calcium-loaded Calbindin D(9k) P43G. Biomolecular N M R Assignments, 5(1), 79-84. https://doi.org/10.1007/s12104-010-9272-3

Oktaviani, N. A., Risør, M. W., Lee, Y-H., Megens, R. P., de Jong, D. H., Otten, R., Scheek, R. M., Enghild, J. J., Nielsen, N. C., Ikegami, T. & Mulder, F. A. A. (2015). Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide. Journal of Biomolecular N M R, 62(2), 129-142. https://doi.org/10.1007/s10858-015-9925-8

Oktaviani, N. A., Pool, T. J., Yoshimura, Y., Kamikubo, H., Scheek, R. M., Kataoka, M. & Mulder, F. A. A. (2017). Active-Site pKa Determination for Photoactive Yellow Protein Rationalizes Slow Ground-State Recovery. Biophysical Journal, 112(10), 2109-2116. https://doi.org/10.1016/j.bpj.2017.04.008

Nielsen, J. T. & Mulder, F. A. A. (2016). There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order". Frontiers in Molecular Biosciences, 3(FEB), Article 4. https://doi.org/10.3389/fmolb.2016.00004

Nielsen, J. T. & Mulder, F. A. A. (2018). POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins. Journal of Biomolecular NMR, 70(3), 141-165. https://doi.org/10.1007/s10858-018-0166-5

Nielsen, J. T. & Mulder, F. A. A. (2019). Quality and bias of protein disorder predictors. Scientific Reports, 9, Article 5137. https://doi.org/10.1038/s41598-019-41644-w

Nielsen, J. T. & Mulder, F. A. A. (2020). Quantitative Protein Disorder Assessment Using NMR Chemical Shifts. In B. B. Kragelund & K. Skriver (Eds.), Intrinsically Disordered Proteins (pp. 303-317). Humana Press. https://doi.org/10.1007/978-1-0716-0524-0_15

Nielsen, J. T. & Mulder, F. A. A. (2021). CheSPI: chemical shift secondary structure population inference. Journal of Biomolecular NMR, 75(6-7), 273-291. https://doi.org/10.1007/s10858-021-00374-w

Mulder, F. A. A., Otten, R. & Scheek, R. M. (2011). Origin and removal of mixed-phase artifacts in gradient sensitivity enhanced heteronuclear single quantum correlation spectra. Journal of Biomolecular N M R, 51(1-2), 199-207. https://doi.org/10.1007/s10858-011-9554-9

Mulder, F. A. A. & Scheek, R. M. (2012). Multidimensional NMR spectroscopy. In G. C. K. Roberts (Ed.), Encyclopedia of Biophysics Springer.

Mulder, F. A. A. & Filatov, M. (2010). NMR chemical shift data and ab initio shielding calculations: Emerging tools for protein structure determination. Chemical Society Reviews, 39(2), 578-590. https://doi.org/10.1039/b811366c

Mulder, F. A. A., Bouakaz, L., Lundell, A., Venkataramana, M., Liljas, A., Akke, M. & Sanyal, S. (2004). Conformation and dynamics of ribosomal stalk protein L12 in solution and on the ribosome. Biochemistry, 43(20), 5930-5936. https://doi.org/10.1021/bi0495331

Mulder, F. A. A. & Akke, M. (2003). Carbonyl ¹³C transverse relaxation measurements to sample protein backbone dynamics. Magnetic Resonance in Chemistry, 41(10), 853-865. https://doi.org/10.1002/mrc.1252

Mulder, F. A. A., Hon, B., Mittermaier, A., Dahlquist, F. W. & Kay, L. E. (2002). Slow internal dynamics in proteins: Application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. Journal of the American Chemical Society, 124(7), 1443-1451. https://doi.org/10.1021/ja0119806

Mulder, F. A., Mittermaier, A., Hon, B., Dahlquist, F. W. & Kay, L. E. (2001). Studying excited states of proteins by NMR spectroscopy. Nature Structural and Molecular Biology, 8(11), 932-935. https://doi.org/10.1038/nsb1101-932

Mulder, F. A. A., Skrynnikov, N. R., Hon, B., Dahlquist, F. W. & Kay, L. E. (2001). Measurement of slow (μs-ms) time scale dynamics in protein side chains by ¹⁵N relaxation dispersion NMR spectroscopy: Application to Asn and Gln residues in a cavity mutant of T4 lysozyme. Journal of the American Chemical Society, 123(5), 967-975. https://doi.org/10.1021/ja003447g

Mulder, F. A. A., Hon, B., Muhandiram, D. R., Dahlquist, F. W. & Kay, L. E. (2000). Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR. Biochemistry, 39(41), 12614-12622. https://doi.org/10.1021/bi001351t

Mulder, F. A., Ayed, A., Yang, D., Arrowsmith, C. H. & Kay, L. E. (2000). Assignment of 1H(N), 15N, 13C(alpha), 13CO and 13C(beta) resonances in a 67 kDa p53 dimer using 4D-TROSY NMR spectroscopy. Journal of Biomolecular N M R, 18(2), 173-176. https://doi.org/10.1023/A:1008317825976

Mulder, F. A. A., Schipper, D., Bott, R. & Boelens, R. (1999). Altered flexibility in the substrate-binding site of related native and engineered high-alkaline Bacillus subtilisins. Journal of Molecular Biology, 292(1), 111-123. https://doi.org/10.1006/jmbi.1999.3034

Mulder, F. A. A., van Tilborg, P. J., Kaptein, R. & Boelens, R. (1999). Microsecond time scale dynamics in the RXR DNA-binding domain from a combination of spin-echo and off-resonance rotating frame relaxation measurements. Journal of Biomolecular N M R, 13(3), 275-288. https://doi.org/10.1023/A:1008354232281

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Lise Refstrup Linnebjerg Pedersen