Department of Chemistry

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 Department of Chemistry Research Research areas and groups Theoretical chemistry Biomodelling Publications

Publications

Papers

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Koldsø, H., B. Christiansen, A., Sinning, S. & Schiøtt, B. (2013). Comparative Modelling of the Human Monoamine Transporters. ACS Chemical Neuroscience, 4, 295-309. https://doi.org/10.1021/cn300148r
Koldsø, H., Noer, P. R., Grouleff, J., Autzen, H. E., Sinning, S. & Schiøtt, B. (2011). Unbiased simulations reveal the inward-facing conformation of the human serotonin transporter and Na+ ion release. PLoS Computational Biology, 7(10), e1002246. https://doi.org/10.1371/journal.pcbi.1002246
Koldsø, H., Severinsen, K., Tran, TT., Celik, L., Jensen, H. H., Wiborg, O., Schiøtt, B. & Sinning, S. (2010). The two enantiomers of citalopram bind to the human serotonin transporterin reverse orientations. Journal of American Chemical Society, 132(4), 1311-22.
Koldsø, H., Autzen, H. E., Grouleff, J. & Schiøtt, B. (2013). Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations. PLoS One, 8(6), Article e63635. https://doi.org/10.1371/journal.pone.0063635
Koldsø, H., Andersen, O. J., Nikolajsen, C. L., Scavenius, C., Sørensen, C. S., Underhaug, J., Runager, K., Nielsen, N. C., Enghild, J. J. & Schiøtt, B. (2015). Early Events in the Amyloid Formation of the A546T Mutant of Transforming Growth Factor Beta Induced Protein (TGFBIp) in Corneal Dystrophies Compared to the Non-Fibrillating R555W and R555Q Mutants. Biochemistry, 54(36), 55546-5556. https://doi.org/10.1021/acs.biochem.5b00473
Koldsø, H., Grouleff, J. & Schiøtt, B. (2015). Insights to ligand binding to the monoamine transporters-from homology modeling to LeuBAT and dDAT. Frontiers in Pharmacology, 6, Article 208. https://doi.org/10.3389/fphar.2015.00208
Kold, D., Dauter, Z., Laustsen, A., M. Brzozowski, A., P. Turkenburg, J., D. Nielsen, A., Koldsø, H., Petersen, E., Schiøtt, B., De Maria, L., S. Wilson, K., Svendsen, A. & Wimmer, R. (2014). Thermodynamic and structural investigation of the specific SDS binding of humicola insolens cutinase. Protein Science, 23(8), 1023-1035. https://doi.org/10.1002/pro.2489
Kjølbye, L. R., De Maria, L., Wassenaar, T. A., Abdizadeh, H., Marrink, S. J., Ferkinghoff-Borg, J. & Schiøtt, B. (2021). General Protocol for Constructing Molecular Models of Nanodiscs. Journal of Chemical Information and Modeling, 61(6), 2869-2883. https://doi.org/10.1021/acs.jcim.1c00157
Kjølbye, L. R., Sørensen, L., Yan, J., Berglund, N. A., Ferkinghoff-Borg, J., Robinson, C. V. & Schiøtt, B. (2022). Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4,5)P2 Lipids. Journal of Chemical Information and Modeling, 62(24), 6788-6802. https://doi.org/10.1021/acs.jcim.2c00635
Kjolbye, L. R., Laustsen, A., Vestergaard, M., Periole, X., De Maria, L., Svendsen, A., Coletta, A. & Schiott, B. (2019). Molecular Modeling Investigation of the Interaction between Humicola insolens Cutinase and SDS Surfactant Suggests a Mechanism for Enzyme Inactivation. Journal of Chemical Information and Modeling, 59(5), 1977-1987. https://doi.org/10.1021/acs.jcim.8b00857
Jorgensen, C., Linville, R. M., Galea, I., Lambden, E., Vögele, M., Chen, C., Troendle, E. P., Ruggiu, F., Ulmschneider, M. B., Schiøtt, B. & Lorenz, C. D. (2025). Permeability Benchmarking: Guidelines for Comparing in Silico, in Vitro, and in Vivo Measurements. Journal of Chemical Information and Modeling, 65(3), 1067-1084. https://doi.org/10.1021/acs.jcim.4c01815
Jensen, J. K., Malmendal, A., Schiøtt, B., Skeldal, S., Pedersen, K. E., Celik, L., Nielsen, N. C., Andreasen, P. & Wind, T. (2006). Inhibition of plasminogen activator inhibitor-1 binding to endocytosis receptors of the low density lipoprotein receptor family by a peptide isolated from a phage displayed library. Biochemical Journal, 399, 387-396.
Jensen, J. K., Malmendal, A., Schiøtt, B., Skeldal, S., Pedersen, K. E., Celik, L., Nielsen, N. C., Andreasen, P. A. & Wind, T. (2006). Inhibition of plasminogen activator inhibitor-1 binding to endocytosis receptors of the low-density-lipoprotein receptor family by a peptide isolated from a phage display library. Biochemical Journal, 399(3), 387-96. https://doi.org/10.1042/BJ20060533
Jensen, M. R., Bajic, G., Zhang, X., Laustsen, A. K., Koldsø, H., Skeby, K. K., Schiøtt, B., Andersen, G. R. & Vorup-Jensen, T. (2016). Structural basis for simvastatin competitive antagonism of complement receptor 3. Journal of Biological Chemistry, 291(33), 16963-16976. https://doi.org/10.1074/jbc.M116.732222
Ingólfsson, H. I., Bhatia, H., Zeppelin, T., Bennett, W. F. D., Carpenter, K. A., Hsu, P. C., Dharuman, G., Bremer, P. T., Schiøtt, B., Lightstone, F. C. & Carpenter, T. S. (2020). Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity. The journal of physical chemistry. B, 124(36), 7819-7829. https://doi.org/10.1021/acs.jpcb.0c03368
Hansen, S. K., Vestergaard, M., Thøgersen, L., Schiøtt, B., Nielsen, N. C. & Vosegaard, T. (2014). Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations. Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 118(19), 5119-5129. https://doi.org/10.1021/jp5000304
Halland, N., Lie, M. A., Jensen, A. K. K., Schiøtt, B. & Jørgensen, K. A. (2005). Mechanistic Insight Into the 2,5-Diphenylpyrrolidine Catalyzed Enantioselctive &alpha-Chlorination of Aldehydes. Chemistry: A European Journal, 11, 7083.
Grouleff, J., Søndergaard, S. & Schiøtt, B. (2013). Conformational Stability and Substrate Translocation: A Computational Study of the Leucine Transporter. Biophysical Journal, 104(2), 407a-408b. https://doi.org/10.1016/j.bpj.2012.11.2272
Grouleff, J., Sondergaard, S., Koldso, H. & Schiott, B. (2015). Properties of an Inward-Facing State of LeuT: Conformational Stability and Substrate Release. Biophysical Journal, 108(6), 1390-1399. https://doi.org/10.1016/j.bpj.2015.02.010
Grouleff, J., Ladefoged, L. K., Koldso, H. & Schiott, B. (2015). Monoamine transporters: insights from molecular dynamics simulations. Frontiers in Pharmacology, 6, Article 235. https://doi.org/10.3389/fphar.2015.00235
Grouleff, J., Irudayam, S. J., Skeby, K. K. & Schiøtt, B. (2015). The influence of cholesterol on membrane protein structure, function, and dynamics studied by molecular dynamics simulations. Biochimica et biophysica acta - Biomembranes, 1848(9), 1783-1795. https://doi.org/10.1016/j.bbamem.2015.03.029
Grouleff, J., Koldsø, H., Miao, Y. & Schiøtt, B. (2017). Ligand Binding in the Extracellular Vestibule of the Neurotransmitter Transporter Homologue LeuT. ACS Chemical Neuroscience, 8(3), 619-628. https://doi.org/10.1021/acschemneuro.6b00359
Friedman, R., Khalid, S., Aponte-Santamaría, C., Arutyunova, E., Becker, M., Boyd, K. J., Christensen, M. H., Coimbra, J. T. S., Concilio, S., Daday, C., van Eerden, F. J., Fernandes, P. A., Gräter, F., Hakobyan, D., Heuer, A., Karathanou, K., Keller, F., Lemieux, M. J., Marrink, S. J. ... Domene, C. (2018). Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. Journal of Membrane Biology, 251(5-6), 609-631. https://doi.org/10.1007/s00232-018-0050-y
Dupont, D. M., Hansen, M., Jensen, J. K., Kristiansen, S. K., Mathiasen, L., Pedersen, K. E., Skeldal, S., Wind, T., Malmendal, A., Schiøtt, B., Nielsen, N. C. & Andreasen, P. (2006). Novel conformational probes and activity regulators of plasminogen avtivator inhibitor-1, isolated from phage-displayed disulfide bridge constrained peptide libraries. Poster session presented at Annual Meeting of the "Cancer Degradome", København, Denmark.
Dittmer, J., Thøgersen, L., Underhaug, J., Bertelsen, K., Vosegaard, T., Pedersen, J. M., Schiøtt, H. B., Tajkhorshid, E., Skrydstrup, T. & Nielsen, N. C. (2009). Incorporation of Antimicrobial Peptides into Membranes: A Combined Liquid-State NMR and Molecular Dynamics Study of Alamethicin in DMPC/DHPC Bicelles. Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 113(19), 6928-6937. https://doi.org/10.1021/jp811494p

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Revised 13.06.2024