• E-postNathalie.Reuter@uib.no
  • Telefon+47 55 58 40 40
  • Besøksadresse
    Thormøhlensgt 55
    5008 Bergen
  • Postadresse
    Postboks 7803
    5020 Bergen

Protein Dynamics, Molecular Modeling, Amphitropic Proteins

MOL204 - Applied bioinformatics I
MOL217 - Applied bioinformatics II

  • Maximova, Ksenia; Venken, Tom; Reuter, Nathalie; Trylska, Joanna. 2018. D-peptides as inhibitors of PR3-membrane interactions. Biochimica et Biophysica Acta - Biomembranes. 1860: 458-466. doi: 10.1016/j.bbamem.2017.11.001
  • Tiwari, Sandhya Premnath; Reuter, Nathalie. 2018. Conservation of intrinsic dynamics in proteins-what have computational models taught us? Current opinion in structural biology. 50. doi: 10.1016/j.sbi.2017.12.001
  • Aksnes, Henriette; Goris, Marianne; Strømland, Øyvind; Drazic, Adrian; Waheed, Qaiser; Reuter, Nathalie; Arnesen, Thomas. 2017. Molecular determinants of the N-Terminal acetyltransferase Naa60 anchoring to the Golgi membrane. Journal of Biological Chemistry. 292: 6821-6837. doi: 10.1074/jbc.M116.770362
  • Venken, Tom; Schillinger, Anne-Sophie; Fuglebakk, Edvin; Reuter, Nathalie. 2017. Interactions stabilizing the C-terminal helix of human phospholipid scramblase 1 in lipid bilayers: A computational study. Biochimica et Biophysica Acta - Biomembranes. 1859: 1200-1210. doi: 10.1016/j.bbamem.2017.03.019
  • Khan, Hanif Muhammad; Grauffel, Cédric; Broer, Ria; MacKerell, Alexander D.; Havenith, Remco W.A.; Reuter, Nathalie. 2016. Improving the force field description of tyrosine-choline cation-π interactions: QM investigation of Phenol-N(Me)4 Interactions. Journal of Chemical Theory and Computation. 12: 5585-5595. doi: 10.1021/acs.jctc.6b00654
  • Khan, Hanif Muhammad; He, Tao; Fuglebakk, Edvin; Grauffel, Cédric; Yang, Boqian; Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie. 2016. A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding. Biophysical Journal. 110: 1367-1378. doi: 10.1016/j.bpj.2016.02.020
  • Martin, Katherine R; Kantari-Mimoun, Chahrazade; Yin, Min; Pederzoli-Ribeil, Magali; Angelot-Delettre, Fanny; Ceroi, Adam; Grauffel, Cédric; Benhamou, Marc; Reuter, Nathalie; Saas, Philippe; Frachet, Philippe; Boulanger, Chantal M; Wikto-sarsat, Veronique. 2016. Proteinase 3 is a phosphatidylserine-binding protein that affects the production and function of microvesicles. Journal of Biological Chemistry. 291: 10476-10489. doi: 10.1074/jbc.M115.698639
  • Tiwari, Sandhya Premnath; Reuter, Nathalie. 2016. Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes. PloS Computational Biology. 12. 26 sider. doi: 10.1371/journal.pcbi.1004834
  • Chon, Nara Lee; Osterberg, J. Ryan; Henderson, Jack; Khan, Hanif Muhammad; Reuter, Nathalie; Knight, Jefferson D.; Lin, Hai. 2015. Membrane docking of the synaptotagmin 7 C2A domain: computation reveals interplay between electrostatic and hydrophobic contributions. Biochemistry. 54: 5696-5711. doi: 10.1021/acs.biochem.5b00422
  • Fuglebakk, Edvin; Tiwari, Sandhya Premnath; Reuter, Nathalie. 2015. Comparing the intrinsic dynamics of multiple protein structures using elastic network models. Biochimica et Biophysica Acta - General Subjects. 1850: 911-922. doi: 10.1016/j.bbagen.2014.09.021
  • Myklebust, Line Merethe; Van Damme, Petra; Støve, Svein Isungset; Dörfel, Max J; Abboud, Angèle; Kalvik, Thomas Vikestad; Grauffel, Cédric; Jonckheere, Veronique; Wu, Yiyang; Swensen, Jeffrey; Kaasa, Hanna; Liszczak, Glen; Marmorstein, Ronen; Reuter, Nathalie; Lyon, Gholson J; Gevaert, Kris; Arnesen, Thomas. 2015. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Human Molecular Genetics. 24: 1956-1976. doi: 10.1093/hmg/ddu611
  • Yang, Boqian; Pu, Mingming; Khan, Hanif Muhammad; Friedman, Larry; Reuter, Nathalie; Roberts, Mary F.; Gershenson, Anne. 2015. Quantifying transient interactions between bacillus phosphatidylinositol-specific phospholipase-C and phosphatidylcholine-rich vesicles. Journal of the American Chemical Society. 137: 14-17. doi: 10.1021/ja508631n
  • Budnjo, Adnan; Narawane, Shailesh; Grauffel, Cédric; Schillinger, Anne-Sophie; Fossen, Torgils; Reuter, Nathalie; Haug, Bengt Erik. 2014. Reversible ketomethylene-based inhibitors of human neutrophil proteinase 3. Journal of Medicinal Chemistry. 57: 9396-9408. doi: 10.1021/jm500782s
  • Narawane, Shailesh; Budnjo, Adnan; Grauffel, Cédric; Haug, Bengt Erik; Reuter, Nathalie. 2014. In silico design, synthesis, and assays of specific substrates for proteinase 3: Influence of fluorogenic and charged groups. Journal of Medicinal Chemistry. 57: 1111-1115. doi: 10.1021/jm401559r
  • Perica, Tina; Kondo, Yasushi; Tiwari, Sandhya Premnath; McLaughlin, Stephen H; Kemplen, Katherine R; Zhang, Xiuwei; Steward, Annette; Reuter, Nathalie; Clarke, Jane; Teichmann, Sarah A. 2014. Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science. 346. doi: 10.1126/science.1254346
  • Schillinger, Anne-Sophie; Grauffel, Cédric; Khan, Hanif Muhammad; Halskau, Øyvind; Reuter, Nathalie. 2014. Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter. Biochimica et Biophysica Acta - Biomembranes. 1838: 3191-3202. doi: 10.1016/j.bbamem.2014.09.003
  • Taxt, Arne Michael; Diaz, Yuleima; Bacle, Amélie; Grauffel, Cédric; Reuter, Nathalie; Aasland, Rein; Sommerfelt, Halvor; Puntervoll, Pål. 2014. Characterization of immunological cross-reactivity between enterotoxigenic Escherichia coli heat-stable toxin and human guanylin and uroguanylin. Infection and Immunity. 82: 2913-2922. doi: 10.1128/IAI.01749-14
  • Tiwari, Sandhya Premnath; Fuglebakk, Edvin; Hollup, Siv Midtun; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn Helge; Tekle, Kidane M; Reuter, Nathalie. 2014. WEBnm@ v2.0: Web server and services for comparing protein flexibility. BMC Bioinformatics. 15. doi: 10.1186/s12859-014-0427-6
  • Cheng, Jiongjia; Karri, Sashank; Grauffel, Cédric; Wang, Fang; Reuter, Nathalie; Roberts, Mary F.; Wintrode, Patrick L.; Gershenson, Anne. 2013. Does changing the predicted dynamics of a phospholipase C alter activity and membrane binding? Biophysical Journal. 104: 185-195. doi: 10.1016/j.bpj.2012.11.015
  • De Chiara, Alessia; Pederzoli-Ribeil, Magali; Mocek, Julie; Candalh, Céline; Mayeux, Patrick; Reuter, Nathalie; Witko-Sarsat, Veronique. 2013. Characterization of cytosolic proliferating cell nuclear antigen (PCNA) in neutrophils: anti-apoptotic role of monomeric PCNA. European Journal of Clinical Investigation. 43: 20-20.
  • Fuglebakk, Edvin; Reuter, Nathalie; Hinsen, Konrad. 2013. Evaluation of protein elastic network models based on an analysis of collective motions. Journal of Chemical Theory and Computation. 9: 5618-5628. doi: 10.1021/ct400399x
  • Fuglebakk, Edvin; Tiwari, Sandhya; Hollup, Siv Midtun; Skjærven, Lars; Cragnolini, Tristan; Tekle, Kidane M; Grindhaug, Svenn Helge; Reuter, Nathalie. 2013. Comparing normal modes of protein structures using Webnm@ 2.0. Biophysical Journal. 104: 228A-228A.
  • Grauffel, Cédric; He, Tao; Yang, Boqian; Wintrode, Patrick L.; Gershenson, Anne; Roberts, Mary F.; Reuter, Nathalie. 2013. Cation-PI interactions as specific anchors for B. thurigiensis phosphoinositol-specific phospholipase-C binding to phosphatidylcholine bilayer. Biophysical Journal. 104: 536A-536A.
  • Grauffel, Cédric; Yang, Boqian; He, Tao; Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie. 2013. Cation-pi Interactions As Lipid-Specific Anchors for Phosphatidylinositol-Specific Phospholipase C. Journal of the American Chemical Society. 135: 5740-5750. doi: 10.1021/ja312656v
  • He, Tao; Yang, Boqian; Grauffel, Cédric; Reuter, Nathalie; Gershenson, Anne; Roberts, Mary F. 2013. Probing for pi-cation interactions in the binding of B. thuringiensis phohosphatidylinositol-specific phospholipase C phosphatidylcholine-rich vesicles. Biophysical Journal. 104: 363A-364A.
  • Parulek, Julius; Turkay, Cagatay; Reuter, Nathalie; Viola, Ivan. 2013. Visual cavity analysis in molecular simulations. BMC Bioinformatics. 14. Publisert 2013-11-12. doi: 10.1186/1471-2105-14-S19-S4
  • Romanowska, Julia; Reuter, Nathalie; Trylska, Joanna. 2013. Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes. Proteins: Structure, Function, and Genetics. 81: 63-80. doi: 10.1002/prot.24163
  • Tiwari, Sandhya; Reuter, Nathalie. 2013. Examining the flexibility of tim barrel proteins based on their structural topology. Biophysical Journal. 104: 227A-228A.
  • Bouayad, Dikra; Pederzoli-Ribeil, Magali; Mocek, Julie; Candalh, Céline; Arlet, Jean-Benoït; Hermine, Olivier; Reuter, Nathalie; Davezac, Noélie; Witko-Sarsat, Véronique. 2012. Nuclear-to-cytoplasmic Relocalization of the Proliferating Cell Nuclear Antigen (PCNA) during Differentiation Involves a Chromosome Region Maintenance 1 (CRM1)-dependent Export and Is a Prerequisite for PCNA Antiapoptotic Activity in Mature Neutrophils. Journal of Biological Chemistry. 287: 33812-33825. doi: 10.1074/jbc.M112.367839
  • Fuglebakk, Edvin; Echave, Julián; Reuter, Nathalie. 2012. Measuring and comparing structural fluctuation patterns in large protein datasets. Bioinformatics. 28: 2431-2440. doi: 10.1093/bioinformatics/bts445
  • Grauffel, Cédric; Abboud, Angele; Liszczak, Glen; Marmorstein, Ronen; Arnesen, Thomas; Reuter, Nathalie. 2012. Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases. PLoS ONE. 7. doi: 10.1371/journal.pone.0052642
  • Grauffel, Cédric; He, Tao; Yang, Boqian; Guo, Su; Wintrode, Patrick L.; Gershenson, Anne; Roberts, Mary F.; Reuter, Nathalie. 2012. Anchoring of PI-PLC to DMPC Bilayers Involves Specific Cation-PI Interactions. Biophysical Journal. 102: 78A-79A.
  • Schillinger, Anne-Sophie; Grauffel, Cédric; Halskau, Øyvind; Reuter, Nathalie. 2012. PR3 Interacts Directly to Lipid Bilayers: Evidence from MD Simulations and SPR Experiments. Biophysical Journal. 102: 497A-497A.
  • Skjærven, Lars; Muga, Arturo; Reuter, Nathalie; Martinez, Aurora. 2012. A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES. Proteins: Structure, Function, and Genetics. 80: 2333-2346. doi: 10.1002/prot.24113
  • Hollup, Siv Midtun; Fuglebakk, Edvin; Taylor, William R.; Reuter, Nathalie. 2011. Exploring the factors determining the dynamics of different protein folds. Protein Science. 20: 197-209. doi: 10.1002/pro.558
  • Kantari, Chahrazade; Millet, Arnaud; Gabillet, Julie; Hajjar, Eric; Broemstrup, Torben; Pluta, Paulina Izabela; Reuter, Nathalie; Witko-Sarsat, Véronique. 2011. Molecular analysis of the membrane insertion domain of proteinase 3, the Wegener's autoantigen, in RBL cells: implication for its pathogenic activity. Journal of Leukocyte Biology. 90: 941-950. doi: 10.1189/jlb.1210695
  • Skjærven, Lars; Grant, Barry; Muga, Arturo; Teigen, Knut; McCammon, Andrew; Reuter, Nathalie; Martinez, Aurora. 2011. Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations. PloS Computational Biology. 7. doi: 10.1371/journal.pcbi.1002004
  • Skjærven, Lars; Martinez, Aurora; Reuter, Nathalie. 2011. Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins: Structure, Function, and Genetics. 79: 232-243. doi: 10.1002/prot.22875
  • Skjærven, Lars; Reuter, Nathalie; Martinez, Aurora. 2011. Dynamics, flexibility and ligand induced conformational changes in biological macromolecules: a computational approach. Future Medicinal Chemistry. 3: 2079-2100. doi: 10.4155/FMC.11.159
  • Turkay, Cagatay; Parulek, Julius; Reuter, Nathalie; Hauser, Helwig. 2011. Interactive Visual Analysis of Temporal Cluster Structures. Computer graphics forum (Print). 30: 711-720. doi: 10.1111/j.1467-8659.2011.01920.x
  • Broemstrup, Torben; Reuter, Nathalie. 2010. How does Proteinase 3 interact with lipid bilayers? Physical Chemistry, Chemical Physics - PCCP. 12: 7487-7496. doi: 10.1039/b924117e
  • Broemstrup, Torben; Reuter, Nathalie. 2010. Molecular Dynamics Simulations of Mixed Acidic/Zwitterionic Phospholipid Bilayers. Biophysical Journal. 99: 825-833. doi: 10.1016/j.bpj.2010.04.064
  • Hajjar, Eric; Broemstrup, Torben; Kantari, Chahrazade; Witko-Sarsat, Véronique; Reuter, Nathalie. 2010. Structures of human proteinase 3 and neutrophil elastase - so similar yet so different. The FEBS Journal. 277: 2238-2254. doi: 10.1111/j.1742-4658.2010.07659.x
  • Wikto-sarsat, Veronique; Mocek, J; Bouayad, Dikra; Tamassia, N; Ribeil, J.A.; Candahl, C; Davezac, N; Reuter, Nathalie; Mouton, Luc; Hermine, O; Pederzoli-Ribeil, M; Cassatella, M. 2010. Proliferating cell nuclear antigen acts as a cytoplasmic platform controlling human neutrophil survival. Journal of Experimental Medicine. 207: 2631-2645. doi: 10.1084/jem.20092241
  • Witko-Sarsat, Véronique; Reuter, Nathalie; Mouthon, Luc. 2010. Interaction of proteinase 3 with its associated partners: implications in the pathogenesis of Wegener's granulomatosis. Current Opinion in Rheumatology. 22: 1-7. doi: 10.1097/BOR.0b013e3283331594
  • Hajjar, Eric; Dejaegere, Annick; Reuter, Nathalie. 2009. Challenges in pK(a) Predictions for Proteins: The case of Asp213 in Human Proteinase 3. Journal of Physical Chemistry A. 113: 11783-11792. doi: 10.1021/jp902930u
  • Kantari, Chahrazade; Gabille, Julie; Hajjar, Eric; Reuter, Nathalie; Witko-Sarsat, Veronique. 2009. Mutagenesis analysis of the insertion domain of proteinase 3 into membrane: a potential target for anti-inflammatory therapy in vasculitis. APMIS : Acta pathologica, microbiologica et immunologica Scandinavica. Supplementum. 117: 121-121. doi: 10.1111/j.1600-0463.2009.02481.x
  • Skjærven, Lars; Hollup, Siv Midtun; Reuter, Nathalie. 2009. Normal mode analysis for proteins. Journal of Molecular Structure: THEOCHEM. 898: 42-48. doi: 10.1016/j.theochem.2008.09.024
  • Hajjar, Eric; Mihajlovic, Maja; Witko-Sarsat, Véronique; Lazaridis, Themis; Reuter, Nathalie. 2008. Computational prediction of the binding site of proteinase 3 to the plasma membrane. Proteins: Structure, Function, and Genetics. 71: 1655-1669. doi: 10.1002/prot.21853
  • Hajjar, Eric; Korkmaz, Baris; Reuter, Nathalie. 2007. Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase. FEBS Letters. 581: 5685-5690. doi: 10.1016/j.febslet.2007.11.029
  • Korkmaz, Baris; Hajjar, Eric; Kalupov, Timofey; Reuter, Nathalie; Brillard-Bourdet, Michele; Moreau, Thierry; Juliano, Luiz; Gauthier, Francis. 2007. Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase - A kinetic and molecular modeling analysis. Journal of Biological Chemistry. 282: 1989-1997. doi: 10.1074/jbc.M608700200
  • Lampe, Ove Daae; Viola, Ivan; Reuter, Nathalie; Hauser, Helwig. 2007. Two-Level Approach to Efficient Visualization of Protein Dynamics. IEEE Transactions on Visualization and Computer Graphics. 13: 1616-1623.
  • Lygre, Henning; Reuter, Nathalie; Rødland, Ingunn. 2007. Bioinformatikk anvendt på lokalanestetikas virkningsmekanisme. Den norske tannlegeforenings tidende. 117: 672-675.
  • Skjærven, Lars; Jonassen, Inge; Reuter, Nathalie. 2007. TMM@: a web application for the analysis of transmembrane helix mobility. BMC Bioinformatics. 8. 8 sider. doi: 10.1186/1471-2105-8-232
  • Brillard-Bourdet, Michele; Hamdaoui, Ahmed; Hajjar, Eric; Boudier, Christian; Reuter, Nathalie; Ehret-Sabatier, Laurence; Bieth, Joseph; Gauthier, Francis. 2006. A novel locust (Schistocerca gregaria) serine protease inhibitor with a high affinity for neutrophil elastase. Biochemical Journal. 400: 467-476.
  • Hajjar, E; Korkmaz, B; Gauthier, F; Brandsdal, Bjørn Olav; Witko-Sarsat, V; Reuter, N. 2006. Inspection of the binding sites of proteinase3 for the design of a highly specific substrate. Journal of Medicinal Chemistry. 49: 1248-1260.
  • Rastogi, Shruti; Reuter, Nathalie; Liberles, David A. 2006. Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophysical Chemistry. 124: 134-144.
  • Dublet, Bernard; Ruello, Antonella; Pederzoli, Magali; Hajjar, Eric; Courbebaisse, M; Courbebaisse, Marie; Canteloup, Sandrine; Reuter, Nathalie; Witko-Sarsat, Véronique. 2005. Cleavage of p21/WAF1/CIP1 by proteinase 3 modulates differentiation of a monocytic cell line. Journal of Biological Chemistry. 280: 30242-30253.
  • Hinsen, Konrad; Reuter, Nathalie; Navaza, Jorge; Stokes, David l.; Lacapere, Jean-Jacques. 2005. Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum Ca-ATPase. Biophysical Journal. 88: 818-827.
  • Hollup, Siv Midtun; Sælensminde, Gisle; Reuter, Nathalie. 2005. WEBnm@: a web application for normal mode analyses of proteins. BMC Bioinformatics. 6.
  • Tubiana, Thibault; Fuglebakk, Edvin; Reuter, Nathalie. 2013. Distribution des acides aminés aromatiques chez les protéines membranaires (Aromatic amino acid distribution in peripheral membrane proteins). Université Paris Diderot. 15 sider.
  • Parulek, Julius; Turkay, Cagatay; Reuter, Nathalie; Viola, Ivan. 2012. Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations. article, sider 115-123. I:
    • Roerdink, Jos; Hibbs, Matt. 2012. IEEE Symposium on Biological Data Visualization 2012. IEEE conference proceedings. 124 sider. ISBN: 978-1-4673-4730-3.
  • Turkay, Cagatay; Parulek, Julius; Reuter, Nathalie; Hauser, Helwig. 2011. Integrating Cluster Formation and Cluster Evaluation in Interactive Visual Analysis. 12, sider 107-114. I:
    • Nishita, Tomoyuki; Durikovic, Roman. 2011. Proceedings of the Spring Conference on Computer Graphics (SCCG 2011). 225 sider. ISBN: 978-80-223-3018-3.

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