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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. 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. 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 (PNAS), 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

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

Sette, M., Johnson, L. A., Jimenez, R. & Mulder, F. A. A. (2023). Backbone ¹H, ¹⁵N and ¹³C resonance assignments of the 27kDa fluorescent protein mCherry. Biomolecular NMR Assignments, 17(2), 243-247. https://doi.org/10.1007/s12104-023-10149-z

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

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

Olsen, W. P., Courtade, G., Peña-Díaz, S., Nagaraj, M., Sønderby, T. V., Mulder, F. A. A., Malle, M. G. & Otzen, D. E. (2024). CsgA gatekeeper residues control nucleation but not stability of functional amyloid. Protein Science, 33(10), Article e5178. https://doi.org/10.1002/pro.5178

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., 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. (2018). Fuzzy and fast nuclear transport. Journal of Biological Chemistry, 293(12), 4564-4565. https://doi.org/10.1074/jbc.H118.002129

Mulder, F. A. A., Tenori, L. & Luchinat, C. (2019). Fast and Quantitative NMR Metabolite Analysis Afforded by a Paramagnetic Co-Solute. Angewandte Chemie - International Edition, 58(43), 15283-15286. https://doi.org/10.1002/anie.201908006

Mulder, F. A. A. (2021). NMR spectroscopy charges into protein surface electrostatics. Proceedings of the National Academy of Sciences (PNAS), 118(30), Article 2110176118. https://doi.org/10.1073/pnas.2110176118

Mulder, F. A. A., Tenori, L., Licari, C. & Luchinat, C. (2023). Practical considerations for rapid and quantitative NMR-based metabolomics. Journal of Magnetic Resonance, 352, Article 107462. https://doi.org/10.1016/j.jmr.2023.107462

Møller, K. V., Nguyen, H. T. T., Mørch, M. G. M., Hesselager, M. O., Mulder, F. A. A., Fuursted, K. & Olsen, A. (2022). A Lactobacilli diet that confers MRSA resistance causes amino acid depletion and increased antioxidant levels in the C. elegans host. Frontiers in Microbiology, 13, Article 886206. https://doi.org/10.3389/fmicb.2022.886206

Meinema, A. C., Laba, J. K., Hapsari, R. A., Otten, R., Mulder, F. A. A., Kralt, A., van den Bogaart, G., Lusk, C. P., Poolman, B. & Veenhoff, L. M. (2011). Long unfolded linkers facilitate membrane protein import through the nuclear pore complex. Science, 333(6038), 90-3. https://doi.org/10.1126/science.1205741

Maeno, A., Sindhikara, D., Hirata, F., Otten, R., Dahlquist, F. W., Yokoyama, S., Akasaka, K., Mulder, F. A. A. & Kitahara, R. (2015). Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme. Biophysical Journal, 108(1), 133-45. https://doi.org/10.1016/j.bpj.2014.11.012

Madl, T. & Mulder, F. A. A. (2018). Small Paramagnetic Co-solute Molecules. In C. Luchinat, G. Parigi & E. Ravera (Eds.), Paramagnetism in Experimental Biomolecular NMR (Vol. 2018/16, pp. 283-309). Royal Society of Chemistry. https://doi.org/10.1039/9781788013291-00283

Lorenzen, N., Nielsen, S. B., Yoshimura, Y., Vad, B. S., Andersen, C. B., Betzer, C., Kaspersen, J. D., Christiansen, G., Pedersen, J. S., Jensen, P. H., Mulder, F. A. A. & Otzen, D. E. (2014). How epigallocatechin gallate can inhibit α-synuclein oligomer toxicity in vitro. Journal of Biological Chemistry, 289(31), 21299-21310. https://doi.org/10.1074/jbc.M114.554667

Lenard, A. J., Mulder, F. A. A. & Madl, T. (2022). Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. Progress in Nuclear Magnetic Resonance Spectroscopy, 132-133, 113-139. https://doi.org/10.1016/j.pnmrs.2022.09.001

Laursen, K. R., Christensen, N. V., Mulder, F. A., Schullehner, J., Hoffmann, H. J., Jensen, A., Møller, P., Loft, S., Olin, A.-C., Rasmussen, B. B., Rosati, B., Strandberg, B., Glasius, M., Bilde, M., Sigsgaard, T. & Climate Chamber Group (2023). Airway and systemic biomarkers of health effects after short-term exposure to indoor ultrafine particles from cooking and candles: A randomized controlled double-blind crossover study among mild asthmatic subjects. Particle and Fibre Toxicology, 20(1), Article 26. https://doi.org/10.1186/s12989-023-00537-7

Kurnik, M., Sahin, C., Andersen, C. B., Lorenzen, N., Giehm, L., Mohammad-Beigi, H., Jessen, C. M., Pedersen, J. S., Christiansen, G., Petersen, S. V., Staal, R., Krishnamurthy, G., Pitts, K., Reinhart, P. H., Mulder, F. A. A., Mente, S., Hirst, W. D. & Otzen, D. E. (2018). Potent α-Synuclein Aggregation Inhibitors, Identified by High-Throughput Screening, Mainly Target the Monomeric State. Cell Chemical Biology, 25(11), 1389-1402. https://doi.org/10.1016/j.chembiol.2018.08.005

Kulminskaya, N. V., Yoshimura, Y., Runager, K., Sørensen, C. S., Bjerring, M., Andreasen, M., Otzen, D. E., Enghild, J. J., Nielsen, N. C. & Mulder, F. A. A. (2016). Near-complete ¹H, ¹³C, ¹⁵N resonance assignments of dimethylsulfoxide-denatured TGFBIp FAS1-4 A546T. Biomolecular N M R Assignments, 10(1), 25-29. https://doi.org/10.1007/s12104-015-9630-2

Kitahara, R. & Mulder, F. A. A. (2015). Is pressure-induced signal loss in NMR spectra for the Leu99Ala cavity mutant of T₄ lysozyme due to unfolding? Proceedings of the National Academy of Sciences (PNAS), 112(9), Article E923. https://doi.org/10.1073/pnas.1423279112

Kitahara, R., Yoshimura, Y., Xue, M., Kameda, T. & Mulder, F. A. A. (2016). Detecting O₂ binding sites in protein cavities. Scientific Reports, 6, Article 20534. https://doi.org/10.1038/srep20534

Kitahara, R., Sakuraba, S., Kameda, T., Okuda, S., Xue, M. & Mulder, F. A. A. (2018). Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities. Protein Science, 27(3), 769-779. https://doi.org/10.1002/pro.3371

Karasawa, A., Erkens, G. B., Berntsson, R. P.-A., Otten, R., Schuurman-Wolters, G. K., Mulder, F. A. A. & Poolman, B. (2011). Cystathionine β-synthase (CBS) domains 1 and 2 fulfill different roles in ionic strength sensing of the ATP-binding cassette (ABC) transporter OpuA. Journal of Biological Chemistry, 286(43), 37280-91. https://doi.org/10.1074/jbc.M111.284059

Hong, Z., Nowakowski, M., Spronk, C., Petersen, S. V., Andreasen, P., Koźmiński, W., Mulder, F. & Jensen, J. K. (2015). The solution structure of the MANEC-type domain from Hepatocyte Growth Factor Activator Inhibitor 1 reveals an unexpected PAN/apple domain-type fold. Biochemical Journal, 466(2), 299-309. https://doi.org/10.1042/BJ20141236

Hoffmann, F., Mulder, F. A. A. & Schaefer, L. V. (2018). Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. Journal of Physical Chemistry B, 122(19), 5038-5048. https://doi.org/10.1021/acs.jpcb.8b02769

Hoffmann, F., Xue, M., Schäfer, L. V. & Mulder, F. A. A. (2018). Narrowing the gap between experimental and computational determination of methyl group dynamics in proteins. Physical Chemistry Chemical Physics, 20(38), 24577-24590. https://doi.org/10.1039/c8cp03915a

Hoffmann, F., Mulder, F. A. A. & Schäfer, L. V. (2020). Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers. Journal of Chemical Physics, 152(8), Article 084102. https://doi.org/10.1063/1.5135379

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Lise Refstrup Linnebjerg Pedersen