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OnderzoekZernike (ZIAM)

Refereed academic publications of 2010

Molecular Dynamics
  1. Apajalahti, T., Niemela, P., Govindan, P.N., Miettinen, M.S., Salonen, E., Marrink, S.J. & Vattulainen, I. Concerted diffusion of lipids in raft-like membranes. Faraday Discussions 144 411-430 (2010)

  2. Baoukina, S., Marrink, S.J. & Tieleman, D.P. Lateral pressure profiles in lipid monolayers. Faraday Discussions 144 393-409 (2010)

  3. Flemming Hansen, D., Neudecker, P., Vallurupalli, P. & Mulder, F.A.A. Determination of Leu Side-Chain Conformations in Excited Protein States by NMR Relaxation Dispersion. Journal of the American Chemical Society 132 42-43 (2010)

  4. Fuhrmans, M. & Marrink, S.J. A tool for the morphological analysis of mixtures of lipids and water in computer simulations. Journal of Nanoscience and Nanotechnology (2010)

  5. Fuhrmans, M., Sanders, B.P., Marrink, S.J. & de Vries, A.H. Effects of bundling on the properties of the SPC water model. Theoretical Chemistry Accounts 125 335-344 (2010)

  6. Horta, B., de Vries, A.H. & Hunenberger, P.H. Simulating the gel to liquid crystal phase transition of lipid bilayers: dependence of the transition temperature on the hydration level. Journal of Chemical Theory and Computation 6 2488-2500 (2010)

  7. Kucerka, N., Marquardt, D., Harroun, T.A., Nieh, M.P., Wassall, S.R., de Jong, D.H., Schafer, L.V., Marrink, S.J. & Katsaras, J. Cholesterol in bilayers with PUFA chains: Doping with DMPC or POPC results in sterol reorientation and membrane-domain formation. Biochemistry 49 (35) 7485-7493 (2010)

  8. Lindman, S., Bauer, M.C., Lund, M., Diehl, C., Mulder, F.A.A., Akke, M. & Linse, S. pK(a) values for the unfolded state under native conditions explain the pH-dependent stability of PGB1. Biophysical Journal 99 3365-3373 (2010)

  9. Louhivuori, M., Risselada, H.J., Van der Giessen, E. & Marrink, S.J. Release of content through mechano-sensitive gates in pressurized liposomes. Proceedings of the National Academy of Sciences of the United States of America 107 (46) 19856-19860 (2010)

  10. Lycklama, A.N.J., Bulacu, M., Marrink, S.J. & Driessen, A.J.M. Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation. Journal of Biological Chemistry 285 23747-23754 (2010)

  11. Marrink, S.J., Periole, X., Tieleman, D.P. & de Vries, A.H. Comment on "On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models'' by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934. Physical Chemistry Chemical Physics 12 (9) 2254-2256 (2010)

  12. Nijeholt, J.A.L.A., Bulacu, M., Marrink, S.J. & Driessen, A.J.M. Immobilization of the plug domain Inside the SecY channel allows unrestricted protein translocation. Journal of Biological Chemistry 285 (31) 23747-23754 (2010)

  13. Otten, R., Villali, J., Kern, D. & Mulder, F.A.A. Carr-Purcell-Meiboom-Gill Relaxation Dispersion NMR Measurements. Application to Activation of the Signaling Protein NtrCr. Journal of the American Chemical Society 132 17004-17014 (2010)

  14. Otten, R., Chu, B., Krewulak, K.D., Vogel, H.J. & Mulder, F.A.A. Comprehensive and cost-effective NMR spectroscopy of methyl groups in large proteins. Journal of the American Chemical Society 132 2952-2960 (2010)

  15. Polyansky, A.A., Ramaswamy, R., Volynsky, P.E., Sbalzarini, I.F., Marrink, S.J. & Efremov, R.G. Antimicrobial peptides induce growth of phosphatidylglycerol domains in a model bacterial membrane. Journal of Physical Chemistry Letters 1 (20) 3108-3111 (2010)

  16. Ramadurai, S., Holt, A., Schafer, L.V., Krasnikov, V.V., Rijkers, D.T.S., Marrink, S.J., Killian, J.A. & Poolman, B. Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides. Biophysical Journal 99 (5) 1447-1454 (2010)

  17. Rzepiela, A.J., Sengupta, D., Goga, N. & Marrink, S.J. Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions. Faraday Discussions 144 431-443 (2010)

  18. Rzepiela, A.J., Schafer, L.V., Goga, N., Risselada, H.J., de Vries, A.H. & Marrink, S.J. Software news and update reconstruction of atomistic details from coarse-grained structures. Journal of Computational Chemistry 31 (6) 1333-1343 (2010)

  19. Schafer, L.V. & Marrink, S.J. Partitioning of lipids at domain boundaries in model membranes. Biophysical Journal 99 (12) L91-L93 (2010)

  20. Sengupta, D. & Marrink, S.J. Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes. Physical Chemistry Chemical Physics 12 (40) 12987-12996 (2010)

  21. Smirnova, Y.G., Marrink, S.J., Lipowsky, R. & Knecht, V. Solvent-exposed tails as prestalk transition states for membrane fusion at low hydration. Journal of the American Chemical Society 132 (19) 6710-6718 (2010)

  22. Tamioka, K., Acar, B. & Mulder, F.A.A. Sequence-Specific Random Coil Chemical Shifts of Intrinsically Disordered Proteins. Journal of the American Chemical Society 132 18000-18003 (2010)

  23. Vuorela, T., Catte, A., Niemela, P.S., Hall, A., Hyvonen, M.T., Marrink, S.J., Karttunen, M. & Vattulainen, I. Role of lipids in spheroidal high density lipoproteins. Plos Computational Biology 6 (10) (2010)

  24. Wood, K., Tobias, D.J., Kessler, B., Gabel, F., Oesterhelt, S., Mulder, F.A.A., Zacci, G. & Weik, M. 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 4990-5001 (2010)

  25. Yesylevskyy, S.O., Schafer, L.V., Sengupta, D. & Marrink, S.J. Polarizable water model for the coarse-grained MARTINI force field. Plos Computational Biology 6 (6) (2010)

Last modified:22 October 2012 2.30 p.m.