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Interdisciplinary Nanoscience Center

Danish Center for Ultrahigh Field NMR Spectroscopy

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

Martin, J. R., Mulder, F. A. A., Karimi-Nejad, Y., van der Zwan, J., Mariani, M., Schipper, D. & Boelens, R. (1997). The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site. Structure, 5(4), 521-532. https://doi.org/10.1016/S0969-2126(97)00208-6

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

Helgstrand, M., Mandava, C. S., Mulder, F. A. A., Liljas, A., Sanyal, S. & Akke, M. (2007). The Ribosomal Stalk Binds to Translation Factors IF2, EF-Tu, EF-G and RF3 via a Conserved Region of the L12 C-terminal Domain. Journal of Molecular Biology, 365(2), 468-479. https://doi.org/10.1016/j.jmb.2006.10.025

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

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

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

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

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

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

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

Düx, P., Rubinstenn, G., Vuister, G. W., Boelens, R., Mulder, F. A. A., Hård, K., Hoff, W. D., Kroon, A. R., Crielaard, W., Hellingwerf, K. J. & Kaptein, R. (1998). Solution structure and backbone dynamics of the photoactive yellow protein. Biochemistry, 37(37), 12689-12699. https://doi.org/10.1021/bi9806652

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

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

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

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

André, I., Linse, S. & Mulder, F. A. A. (2007). Residue-specific pK_a determination of lysine and arginine side chains by indirect ¹⁵N and ¹³C NMR spectroscopy: Application to apo calmodulin. Journal of the American Chemical Society, 129(51), 15805-15813. https://doi.org/10.1021/ja0721824

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. (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

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

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

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

Lindman, S., Linse, S., Mulder, F. A. A. & André, I. (2007). pK_a Values for Side-Chain Carboxyl Groups of a PGB1 Variant Explain Salt and pH-Dependent Stability. Biophysical Journal, 92(1), 257-266. https://doi.org/10.1529/biophysj.106.088682

Lindman, S., Bauer, M. C., Lund, M., Diehl, C., Mulder, F. A. A., Akke, M. & Linse, S. (2010). PK_a values for the unfolded state under native conditions explain the pH-dependent stability of PGB1. Biophysical Journal, 99(10), 3365-3373. https://doi.org/10.1016/j.bpj.2010.08.078

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

Mäler, L., Mulder, F. A. A. & Kowalewski, J. (1995). Paramagnetic Cross-Correlation Effects in the Longitudinal Proton Relaxation ofcis-Chloroacrylic Acid in the Presence of Nickel(II) Ions. Journal of Magnetic Resonance, 117(2), 220-227. https://doi.org/10.1006/jmra.1995.0734

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

Brünger, A. T., Karimi-Nejad, Y., Mulder, F. A. A., Martin, J. R., Schipper, D. & Boelens, R. (1999). NMR Studies of the 269 Residue Serine Protease PB92 from Bacillus Alcalophilus. NMR in Supramolecular Chemistry, 526, 227-246. https://doi.org/10.1007/978-94-011-4615-9_14

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

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

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

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

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Lise Refstrup Linnebjerg Pedersen