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Reuter group

Publications

Peer-reviewed journals (including review articles, marked with ••)

2016

56. Improving the Force Field Description of Tyrosine–Choline Cation−π Interactions: QM Investigation of Phenol–N(Me)4+ Interactions. H.M.Khan, C.Grauffel, R.Broer, A.D. MacKerell, R.W.A. Havenith, N.Reuter*. J Chem Theory Comput. 2016 (in press) doi: 10.1021/acs.jctc.6b00654

55. A role for weak electrostatic interactions in peripheral membrane protein binding. H.M.Khan, T.He, E.Fuglebakk, C.Grauffel, B.Yang, M.F.Roberts, A.Gershenson, N.Reuter*.  Biophys J. 2016. 110(6): 1367-78. doi: 10.1016/j.bpj.2016.02.020

54. Similarity in shape dictates signature intrinsic dynamics despite no functional conservation in TIM Barrel enzymes. S.P.Tiwari, N.Reuter*. PLoS Comp Biol. 2016. 12(3):e1004834 doi: 10.1371/journal.pcbi.1004834

53. Proteinase 3 is a phosphatidylserine binding protein which affects the production and function of microvesicles. K.R. Martin, C. Kantari-Mimoun, M.Yin, M.Pederzoli-Ribeil, F.Angelot-Delettre, A.Ceroi, C.Grauffel, M.Benhamou, N.Reuter, P.Saas, P.Frachet, C.M.Boulanger, V.Witko-Sarsat*. J Biol Chem. 2016. 291(20):10476-89 doi: 10.1074/jbc.M115.698639

 

2015

52. Membrane docking of the synaptotagmin 7 C2A domain: computation reveals interplay between electrostatic and hydrophobic contributions. N.L.Chon, J.R.Osterberg, J.Henderson, H.M.Khan, N.Reuter, J.D.Knight*, H.Lin*. Biochemistry. 2015 54(37): 5696-711 doi:10.1021/acs.biochem.5b00422      

51. Biochemical and cellular analysis of Ogden syndrome reveals downstream N-acetylation defects. L.M.Myklebust, P.Van Damme*, S.I. Støve, M.J. Dörfel, A.Abboud, T.V.Kalvik, C. Grauffel, V.Jonckheere, Y.Wu, J.Swensen, H.Kaasa, G.Liszczak, R.Marmorstein, N.Reuter, G.J.Lyon*, K.Gevaert, T.Arnesen*. Human Molecular Genetics 2015 24(7):1956-1976 10.1093/hmg/ddu611

50.      •• Comparing the Intrinsic Dynamics of Multiple Protein Structures Using Elastic Network Models E. Fuglebakk, S.P. Tiwari, N. Reuter*. Biochim Biophys Acta - General Subjects (2015) 1850(5): 911-922 10.1016/j.bbagen.2014.09.021 

49.       Quantifying Transient Interactions between Bacillus Phosphatidylinositol-Specific Phospholipase-C and Phosphatidylcholine-Rich Vesicles. B.Yang, M.Pu, H.F.Khan, L.Friedman, N.Reuter, M.F.Roberts, A.Gershenson*. J Am Chem Soc (2015) 137(1):14-17 10.1021/ja508631n 

 

2014

48.       WEBnm@ v2.0: Web server and services for comparing protein flexibility.  S.P. Tiwari, E.Fuglebakk*, S.M.Hollup, L.Skjaerven, T.Cragnolini, S.H.Grindhaug, K.M.Tekle, N.Reuter*. BMC Bioinformatics (2014) 15: 6597 10.1186/s12859-014-0427-6

47.       Evolution of oligomeric state through allosteric pathways that mimic ligand binding. T.Perica,Y.Kondo,S.P.Tiwari, S.H.McLaughlin, K.R.Kemplen, X.Zhang, A.Steward, N.Reuter, J.Clarke, S.A.Teichmann*. Science. (2014), 346(6216) 10.1126/science.1254346

46.        Reversible Ketomethylene-Based Inhibitors of Human Neutrophil Proteinase 3 A.Budnjo, S.Narawane, C.Grauffel, A.S. Schillinger, T. Fossen, N.Reuter*, B.E.Haug*. Journal of Medicinal Chemistry (2014) 57(22):9396–9408 10.1021/jm500782s

45.      Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter. A.S. Schillinger, C. Grauffel, H.M. Khan, O. Halskau, N. Reuter*. Biochim Biophys Acta - Biomembranes (2014) 1838(12): 3191-3202 10.1016/j.bbamem.2014.09.003

44.      Characterization of Immunological Cross-Reactivity between Enterotoxigenic Escherichia coli Heat-Stable Toxin and Human Guanylin and Uroguanylin. A.M.Taxt, Y.Diaz, A.Bacle, C.Grauffel, N.Reuter, R.Aasland, H.Sommerfelt, P.Puntervoll*. Infection and Immunity (2014) 82(7):2913-2922 10.1128/IAI.01749-14

43.      In silico design, synthesis and assays of specific substrates for Proteinase 3: influence of fluorogenic and charged groups. S.Narawane, A.Budnjo, C.Grauffel, B.E.Haug*, N.Reuter*. Journal of Medicinal Chemistry (2014) 57(3):1111-1115 10.1021/jm401559r

 

2013

42.      Evaluation of protein elastic network models based on an analysis of collective motions. E.Fuglebakk*, N.Reuter, K.Hinsen*. Journal of Chemical Theory and Computation (2013) 9(12): 5618–5628 10.1021/ct400399x

41.      Visual cavity analysis in molecular simulations. J.Parulek*, C.Turkay, N.Reuter and I.Viola. BMC Bioinformatics (2013) 14(Suppl 19):S4 10.1186/1471-2105-14-S19-S4

40.      Cation-pi interactions as lipid-specific anchors for phosphatidylinositol-specific phospholipase-C. C.Grauffel, B.Yang, T.He, M.F. Roberts, A.Gershenson, N.Reuter*,  Journal of the American Chemical Society (2013) 135(15):5740-50  10.1021/ja312656v

39.      Does changing the predicted dynamics of a phospholipase C alter activity and membrane binding? J.Cheng, S. Karri, C.Grauffel, F.Wang, N.Reuter, M.F. Roberts, P.L.Wintrode, A.Gershenson*, Biophysical Journal (2013) 104: 1-11 10.1016/j.bpj.2012.11.015

38.      Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes. J.Romanowska, N.Reuter and J.Trylska*, Proteins: Structure, Function and Bioinformatics(2013) 81(1): 63-80. 10.1002/prot.24163

 

2012

37.      Specificity and versatility of substrate binding sites in four catalytic domains of human N-terminal acetyltransferases. C.Grauffel, A.Abboud, G.Liszczak, R.Marmorstein, T.Arnesen, N.Reuter*, PLoS ONE(2012) 7(12): e52642 10.1371/journal.pone.0052642

36.      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 anti-apoptotic activity in mature neutrophils. D. Bouayad, M. Pederzoli-Ribeil, J.Mocek, C.Candalh,J.-B. Arlet, O.Hermine, N.Reuter, N.Davezac, and V.Witko-Sarsat*, Journal of Biological Chemistry (2012), 287, 33812-33825 10.1074/jbc.M112.367839

35.      Measuring and comparing structural fluctuation patterns in large protein datasets. E.Fuglebakk, J.Echave, N.Reuter*. Bioinformatics (2012) 28(19):2431-40 10.1093/bioinformatics/bts445

34.      A dynamic model of long-range conformational adaptations triggered by nucleotide binding in groel-groes. L.Skjaerven*, A.Muga, N.Reuter, A.Martinez.  Proteins: Structure, Function and Bioinformatics (2012) 80(10):2333-46 10.1002/prot.24113

 

2011

33.      Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach. L.Skjaerven*, N. Reuter, A. Martinez. Future Medicinal Chemistry (2011) 3(16), 2079-2100

32.      Molecular analysis of the membrane insertion domain of proteinase 3, the Wegener's autoantigen, in RBL cells: implication for its pathogenic activity. C.Kantari, A.Millet A, J.Gabillet, E.Hajjar, T.Broemstrup, P.Pluta, N.Reuter, V.Witko-Sarsat*. Journal of Leukocyte Biology (2011) 90(5), 941-50

31.      Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by molecular dynamics simulations. L.Skjaerven, B.Grant, K.Teigen, A.McCammon, N.Reuter, A. Martinez*. PLoS Computational Biology (2011) 7(3):e1002004

30.      Exploring the factors determining the dynamics of different protein folds. S.M.Hollup, E.Fuglebakk, W.R.Taylor, N.Reuter*. Protein Science (2011) 20(1), 197-209

29.      Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. L.Skjaerven, A.Martinez, N.Reuter*. Proteins: Structure, Function and Bioinformatics (2011), 79(1), 232-43

 

2010

28.    Proliferating cell nuclear antigen acts as a cytoplasmic platform controlling human neutrophil survival. V.Witko-Sarsat, J.Mocek, D.Bouayad, N.Tamassia, J.A.Ribeil, C.Candalh, N.Davezac, N.Reuter, L.Mouthon, O.Hermine, M.Pederzoli-Ribeil, M.Cassatella. Journal of Experimental Medicine (2010), 207(12), 2631-45

27.      How does proteinase 3 interact with lipid bilayers? T.Broemstrup, N.Reuter, Physical Chemistry Chemical Physics (2010), 12, 7487-96.

26.      Molecular dynamics simulations of mixed acidic/zwitterionic phospholipid bilayers. T.Broemstrup, N.Reuter, Biophysical Journal (2010), 99(3), 825-33

25.      •• Structures of human proteinase 3 and neutrophil elastase--so similar yet so different. E.Hajjar, T.Broemstrup, C.Kantari, V.Witko-Sarsat, N.Reuter, Febs Journal (2010), 277, 2238-54.

24.      •• Interaction of proteinase 3 with its associated partners: implications in the pathogenesis of Wegener's granulomatosis V.Witko-Sarsat, N.Reuter, L.Mouthon, Current Opinion in Rheumathology (2010), 22(1),1-7.

 

2009

23.      Challenges in pKa predictions for proteins: the case of Asp213 in human proteinase 3. E.Hajjar, A.Dejaegere, N.Reuter. J Phys Chem A (2009), 113, 11783-92

22. •• Normal mode analysis for proteins. L.Skjaerven, S.M.Hollup, N.Reuter. Theochem: Journal of Molecular Structure (2009), 898(1-3), 42-48

 

1999-2008

21.      Computational prediction of the binding of Proteinase3 to lipid bilayers. E.Hajjar, M.Mihajlovic, V.Witko-Sarsat, T.Lazaridis, and N.Reuter. Proteins: Structure, Function and Bioinformatics (2008), 71(4): 1655-69.

20.      Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase. E.Hajjar, B.Korkmaz and N.Reuter. FEBS Letters (2007), 581(29): 5685-5690

19.      Two-Level Approach to Efficient Visualization of Protein Dynamics. O.Daae Lampe, I.Viola, N.Reuterand H.Hauser. IEEE Transactions on Visualization and Computer Graphics (2007)13(6): 1616-23

18.      tmm@: a web application for the analysis of transmembrane helix mobility. L.Skjærven, I.Jonassen and N.Reuter. BMC Bioinformatics (2007), 8:232

17.      Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase: a kinetic and molecular modelling analysis. B.Korkmaz, E.Hajjar, T.Kalupov, N.Reuter, M.Brillard-Bourdet, T.Moreau, L.Juliano and F.Gauthier. Journal of Biological Chemistry (2006), 282(3), 1989-1997

16. A novel locust (Schistocerca gregaria) serine protease inhibitor with a high affinity for neutrophil elastase. M.Brillard-Bourdet, A.Hamdaoui, E.Hajjar, C.Boudier, N.Reuter, L.Ehret-Sabatier, J.G.Bieth, F.Gauthier. Biochemical Journal (2006), 400(3), 467-7

15.      Evaluation of models for the evolution of protein sequences and functions under structural constraint. S.Rastogi, N.Reuter and D.Liberles. Biophysical Chemistry (2006),124(2), p.134-44

14. Inspection of the binding sites of proteinase3 for the design of a highly specific substrate. E.Hajjar, B.Korkmaz, B.O.Brandsdal, V.Witko-Sarsat and N.ReuterJournal of Medicinal Chemistry (2006), 49(4), p.1248-60

13.      Molecular analysis of P21/Waf1/CIP1 cleavage by proteinase3: physiological implication in monocytic differentiation. B.Dublet, A.Ruello, M.Pederzoli, E.Hajjar, M.Courbebaisse, S.Canteloup, N.Reuter, and V.Witko-Sarsat. Journal of Biological Chemistry (2005), 280(34), p.30242-30253

12.      WEBnm@: a web application for normal mode analysis of proteins. S.M.Hollup, G.Sælensminde and N.Reuter. BMC Bioinformatics (2005), 6(1): 52

11.      Normal mode based fitting of atomic structure into electron density maps: application to SR Ca-ATPase. K.Hinsen, N.Reuter, J.Navaza, D.L.Stokes and J.-J.Lacapère. Biophysical Journal (2005), vol 88, p. 818-827

10. Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study. N.Reuter, K.Hinsen, J.-J.Lacapère. Biophysical Journal (2003), vol 85, p. 2186-2197

9. •• Orexins and their receptors: role in peripheral tissues. T.Voisin, P.Rouet-Benzineb, N.Reuter, M.Laburthe. Cellular and Molecular Life Sciences (2003), vol 60, n° 1, p. 72-87. Review

8. The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations. J.Schöneboom, H.Lin, N.Reuter, W.Thiel, S. Cohen, F.Ogliaro, S.Shaik. Journal of the American Chemical Society (2002), vol. 124, n° 27, p.8142-8151

7.      Green Fluorescent Proteins : Empirical force field for the neutral and deprotonated forms of the chromophore. Molecular dynamic simulations of the wild-type and S65T mutant. N.Reuter, H.Lin and W.Thiel. Journal of Physical Chemistry B (2001), vol. 106, n°24, p. 6310-6321

6.      The vibrational overtones of SiH4 isotopomers: experimental wavenumbers, assignment, ab initio dipole moment surfaces and intensities. H.Lin, S.-G.He, X.-G.Wang, L.-F.Yuan, H.Burger, J.-F.D’Eu, N.Reuter, W.Thiel. Physical Chemistry Chemical Physics (2001), vol. 3, n° 17, p. 3506-3517

5.      The search for a new model structure of b-factor XIIa. E.S.Henriques, A.Melo, J.A.N.F.Gomes, M. J.Ramos, W.B.Floriano, M.A.C.Nascimento, N.Reuter and B.Maigret. Journal of Computer Aided Molecular Design (2001), vol. 15, n° 4, p. 309-322

4.      Calibration of the quantum/classical hamiltonian in semi-empirical QM/MM AM1 and PM3 methods. F.J.Luque, N.Reuter, A.Cartier, and M.F.Ruiz-López. Journal of Physical Chemistry A (2000), vol. 104, n° 46, p. 10923-10931

3.      Frontier bonds in QM/MM methods: A comparison of different approaches. N.Reuter, A.Dejaegere, B.Maigret, M.Karplus. Journal of Physical Chemistry A (2000) , vol. 104, n° 8, p.1720-1735

2.      Theoretical study of arginine-carboxylate interactions. A.Melo, M.J.Ramos, W.B.Floriano, J.A.N.F.Gomes, J.F.R.Leao, A.L.Magalhaes, B.Maigret, M.C.Nascimento, N.Reuter. Journal of Molecular Structure (Theochem) (1999), vol. 463, n° 1-2, p. 81-90

1.      Modelling enzyme-inhibitor interactions.M.J.Ramos, A.Melo, E.S.Henriques, J.A.N.F.Gomes, N.Reuter, B.Maigret, W.B.FIoriano, M.A.C.Nascimento. International Journal of Quantum Chemistry (1999), vol. 74, n° 3, p. 299–314

 

  Book section • Slow dynamics of biomolecules: the normal mode analysis approach. N. Reuter In: Recent Adv in Prot Eng. Trivandrum, India. De Brevern A, editor. Research signpost (2008)

 

 Popular Science • Bioinformatikk platformen. I Jonassen, N. Reuter, E. Hovig, F. Drabløs. NBS Nytt (Norwegian biochem. Soc. newsletter), 2005 • Lokalanestetika og bioinformatikk. H. Lygre, N. Reuter og I. Rødland. Den Norske Tannlegeforenings Tidende (Journal of the Norwegian Dentistry Society), 2007, 117: 672-5 • Molecular Dynamics Simulations of proteins. N. Reuter. Meta2007, 117: 672-5