Interdisciplinary Nanoscience Center

Danish Center for Ultrahigh Field NMR Spectroscopy

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Publications

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Hansen, A. R. E., Enemark-Rasmussen, K., Mulder, F. A. A., Jensen, P. R. & Meier, S. (2022). Versatile Procedures for Reliable NMR Quantification of CO2 Electroreduction Products. Journal of Physical Chemistry C, 126(27), 11026-11032. https://doi.org/10.1021/acs.jpcc.2c03448
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
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
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
Chu, B. C. H., Otten, R., Krewulak, K. D., Mulder, F. A. A. & Vogel, H. J. (2014). The Solution Structure, Binding Properties, and Dynamics of the Bacterial Siderophore-binding Protein FepB. Journal of Biological Chemistry, 289(42), 29219-29234. https://doi.org/10.1074/jbc.M114.564021
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
Dass, R., Corlianò, E. & Mulder, F. A. A. (2021). The contribution of electrostatics to hydrogen exchange in the unfolded protein state. Biophysical Journal, 120(18), 4107-4114. https://doi.org/10.1016/j.bpj.2021.08.003
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
Hansen, B. K., Larsen, C. K., Nielsen, J. T., Svenningsen, E. B., Van, L. B., Jacobsen, K. M., Bjerring, M., Flygaard, R. K., Jenner, L. B., Nejsum, L. N., Brodersen, D. E., Mulder, F. A. A., Tørring, T. & Poulsen, T. B. (2020). Structure and Function of the Bacterial Protein Toxin Phenomycin. Structure, 28(5), 528-539.e9. https://doi.org/10.1016/j.str.2020.03.003
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
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
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
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
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
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
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
Buhl, J. M., Mahapatra, S., Kjærgaard, M. & Mulder, F. A. A. (2025). Quantification of Small Molecule Partitioning in a Biomolecular Condensate with 2D Nuclear Magnetic Resonance Spectroscopy. ChemBioChem, 26(17), Article e202500401. https://doi.org/10.1002/cbic.202500401
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
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
Ali, A. A. A. I., Hoffmann, F., Schäfer, L. V. & Mulder, F. A. . A. (2022). Probing Methyl Group Dynamics in Proteins by NMR Cross-Correlated Dipolar Relaxation and Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 18(12), 7722-7732. https://doi.org/10.1021/acs.jctc.2c00568
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
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
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
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
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
Dass, R. & Mulder, F. A. A. (2020). Paris-DÉCOR: A Protocol for the Determination of Fast Protein Backbone Amide Hydrogen Exchange Rates. In B. B. Kragelund & K. Skriver (Eds.), Intrinsically Disordered Proteins (pp. 337-344). Humana Press. https://doi.org/10.1007/978-1-0716-0524-0_17
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
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
Dass, R., Mulder, F. A. A. & Nielsen, J. T. (2020). ODiNPred: comprehensive prediction of protein order and disorder. Scientific Reports, 10(1), Article 14780. https://doi.org/10.1038/s41598-020-71716-1
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
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
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
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
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
Mulder, F. A. A. & Scheek, R. M. (2012). Multidimensional NMR spectroscopy. In G. C. K. Roberts (Ed.), Encyclopedia of Biophysics Springer.
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
Dass, R., Corlianò, E. & Mulder, F. A. A. (2019). Measurement of Very Fast Exchange Rates of Individual Amide Protons in Proteins by NMR Spectroscopy. ChemPhysChem, 20(2), 231-235. https://doi.org/10.1002/cphc.201801044
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
Andersen, C., Grønnemose, A. L., Pedersen, J. N., Nowak, J. S., Christiansen, G., Nielsen, J., Mulder, F. A. A., Otzen, D. E. & Jørgensen, T. J. D. (2021). Lipid Peroxidation Products HNE and ONE Promote and Stabilize Alpha-Synuclein Oligomers by Chemical Modifications. Biochemistry, 60(47), 3644-3658. https://doi.org/10.1021/acs.biochem.1c00478
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
Hoffmann, F., Mulder, F. A. A. & Schäfer, L. V. (2022). How Much Entropy Is Contained in NMR Relaxation Parameters? Journal of Physical Chemistry B, 126(1), 54-68. https://doi.org/10.1021/acs.jpcb.1c07786
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
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
Andersen, C. B., Yoshimura, Y., Nielsen, J., Otzen, D. E. & Mulder, F. A. A. (2021). How epigallocatechin gallate binds and assembles oligomeric forms of human alpha-synuclein. The Journal of Biological Chemistry, 296, Article 100788. https://doi.org/10.1016/j.jbc.2021.100788
Guo, X., Sarup, P. M., Jensen, J. D., Jihad, O., Kristensen, N. H., Mulder, F. A. A., Jahoor, A. & Jensen, J. (2020). Genetic Variance of Metabolomic Features and Their Relationship With Malting Quality Traits in Spring Barley. Frontiers in Plant Science, 11, Article 575467. https://doi.org/10.3389/fpls.2020.575467
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
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
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
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

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Revised 17.04.2023
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Lise Refstrup Linnebjerg Pedersen