Publications

    Submitted

    2010

  1. S. Baoukina, S.J. Marrink, D.P. Tieleman. 2009. Lateral pressure profiles in lipid monolayers, Faraday Discussions 144, pp. 393 - 409

    2. 2009

  2. P.T. Vernier, Z.A. Levine, Y.-H. Wu, V. Joubert, M.J. Ziegler, L.M. Mir, D.P. Tieleman. 2009. Electroporating fields target oxidatively damaged areas in the cell membrane, PLoS ONE, in press
  3. C. Kandt, D.P. Tieleman. 2009. Holo-BtuF stabilizes the open conformation of the vitamin B12 ABC transporter BtuCD, PROTEINS Struct. Funct. Bioinf. in press. DOI: 10.1002/prot.22606
  4. W.L. Vos, M. Schor, A. Baumgaertner, D.P. Tieleman, M.A. Hemminga. 2009. Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins, Eur. Biophys. J., in press (special issue in honor of M. Hemminga)
  5. W.F.D. Bennet, J.L. MacCallum, M. Hinner, S.J. Marrink, D.P. Tieleman. 2009. A molecular view of cholesterol flip-flop and chemical potential in different membrane environments, J. Am. Chem. Soc. 131, pp. 12714-12720
  6. E. Crowley, M.L. O’Mara, C. Reynolds, D.P. Tieleman, J. Storm, I.D. Kerr, R. Callaghan. 2009. Transmembrane helix 12 modulates progression of the ATP catalytic cycle in ABCB1, Biochemistry 48, pp. 6249-6258
  7. W.F.D. Bennett, D.P. Tieleman. 2009. "Free energies of lipid-lipid interactions in membranes", in Annual Reports in Computational Chemistry, vol. 5, Wheeler ed., Elsevier/ACS, in press
  8. N. Sapay, W.F.D. Bennett, D.P. Tieleman. 2009. Thermodynamics of flip-flop and desorption for a systematic series of phosphatidylcholine lipids, Soft Matter 5, pp. 3295-3302
  9. J. Pan, D.P. Tieleman, J.F. Nagle, N. Kucerka, S. Tristram-Nagle. 2009. Alamethicin in lipid bilayers: combined use of X-ray scattering and MD Simulations, Biochim. Biophys. Acta 1788, pp. 1387-1397
  10. C. Laing, S. Baoukina, D.P. Tieleman. 2009. Molecular dynamics study of the effect of cholesterol on the properties of lipid monolayers at low surface tensions, Phys. Chem. Chem. Phys. 11, pp. 1916-1922
  11. G. Oancea , M.L. O'Mara , W.F.D. Bennett , D.P. Tieleman , R. Abele , R. Tampé. 2009. Structural arrangement of the transmission interface in the antigen ABC transport complex TAP, Proc. Natl. Acad. Sci. 106, pp. 5551-5556
  12. E. Procko, M.L. O'Mara, W.F.D. Bennett, D.P. Tieleman, R. Gaudet. 2009. The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter, FASEB J. 23, pp. 1287-1302
  13. W.F.D. Bennett, J.L. MacCallum, D.P. Tieleman. 2009. Thermodynamic analysis of the effect of cholesterol on dipalmitoylphosphatidylcholine lipid membranes., J. Am. Chem. Soc. 131, pp.1972-1978.
  14. S.J. Marrink, A.H. de Vries, D.P. Tieleman. 2009. Lipids on the move: simulations of membrane pores, domains, stalks and curves, Biochim. Biophys. Acta 1788, pp. 149-168
  15. S. Baoukina, S.J. Marrink, D.P. Tieleman. 2009. "Structure and dynamics of lipid monolayers: model systems and lung surfactant", in Handbook of Modern Biophysics - Frontiers in Biomembranes, Humana/Springer press

    16. 2008

  16. D.I. Chan, T. Stockner, D.P. Tieleman, H.J. Vogel. 2008. Molecular dynamics simulations of the apo, holo-, and acyl- forms of Escherichia coli acyl carrier protein, J. Biol. Chem. 283, pp. 33620-33629
  17. D.P. Tieleman, R.J. Turner, H.J. Vogel, J.H. Weiner. 2008. Structural proteomics of the cell envelope of Gram-negative bacteria, Biochim. Biophys. Acta 1778, p. 1697
  18. A. Moussatova, C. Kandt, M.L. O'Mara, D.P. Tieleman. 2008. ATP-binding cassette transporters in Escherichia coli, Biochim. Biophys. Acta 1778, pp. 1757-1771
  19. S. Baoukina, L. Monticelli, J. Risselada, S.J. Marrink, D.P. Tieleman. 2008. The molecular mechanism of lipid monolayer collapse, Proc. Natl. Acad. Sci. 105, pp. 10803-10808
  20. J. Wong-Ekkabut, S. Baoukina, W. Triampo, I-M. Tang, D.P. Tieleman, L. Monticelli. 2008. Computer simulation study of fullerene translocation through lipid membranes, Nature Nanotechnology 3, pp. 363 - 368 (cover image)
  21. L. Monticelli, S. Kandasamy, X. Periole, R. Larson, D.P. Tieleman, S.J. Marrink. 2008. The MARTINI coarse grained force field: extension to proteins, J. Chem. Theo. Comp. 4, pp. 819 - 834 (cover image)
  22. L. Monticelli, E.J. Sorin, D. P. Tieleman, V.S. Pande, G. Colombo. 2008. Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories, J. Comp. Chem. 29, pp. 1740–1752, (DOI: 10.1002/jcc.20935)
  23. J. Storm, S. Modok, M. O'Mara, D.P. Tieleman, I. Kerr, R. Callaghan. 2008. The cytosolic region of TM6 in P-glycoprotein: topographical analysis and functional perturbation by site directed labelling, Biochemistry 47, pp. 3615-3624
  24. C. Kandt, E. Mátyus, D.P. Tieleman. Protein Lipid Interactions from a Simulation Point of View. in "Structure & Dynamics of Membranous Interfaces", K. Nag, editor, John Wiley & Sons, Hoboken, NJ, USA, pp. 267-282
  25. E. Mátyus, K. Blaskó, F. Fidy, D.P. Tieleman. 2008. Structure and dynamics of the antifungal molecules syringotoxin-B and syringopeptin-25A from molecular dynamics simulation, Eur. Biophys. J. 37, pp. 495-502
  26. J.L. MacCallum, D.P. Tieleman. 2008. Interactions between small molecules and lipid bilayers, Curr. Top. Memb. 60, pp. 227-256
  27. N. Sapay, D.P. Tieleman. 2008. Molecular dynamics simulation of lipid-protein interactions, Curr. Top. Memb. 60, pp. 111-130
  28. J.L. MacCallum, W.F. D. Bennett, D. P. Tieleman. 2008. Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations, Biophys. J. 94, pp. 3393-3404

    29. 2007

  29. G. Choudhary, M.P. Aliste, D. P. Tieleman, R.J. French, S.C. Dudley, Jr. 2007. Docking orientation of mu-Conotoxin GIIIA in the sodium channel outer vestibule, Channels 1(5), pp. e1-e9 (cover image)
  30. S. Baoukina, L. Monticelli, S.J. Marrink, D.P. Tieleman. 2007. The pressure-area isotherm of a lipid monolayer from molecular dynamics simulations, Langmuir 23, pp. 12617-12623
  31. E. Matyus, C. Kandt, D.P. Tieleman. 2007. Computer simulation of antimicrobial peptides, Curr. Med. Chem. 14, pp. 2789-2798
  32. M.L. O'Mara, D.P. Tieleman. 2007. P-glycoprotein models of the apo and ATP-bound states based on homology with Sav1866 and MalK, FEBS Letters 581, pp. 4217-4222
  33. S. Baoukina, L. Monticelli, M.W. Amrein, D.P. Tieleman. 2007. The molecular mechanism of monolayer-bilayer transformations of lung surfactant from molecular dynamics simulations, Biophys. J. 93, pp. 3775-3782 (cover image)
  34. J. Wong-ekkabut, Z. Xu, W. Triampo, I-M. Tang, D.P. Tieleman, L. Monticelli. 2007. Effect of lipid peroxidation on the properties of lipid bilayers: a molecular dynamics study, Biophys. J. 93, pp. 4225-4236
  35. J. Storm, M. O'Mara, E. Crowley, J. Peall, D.P. Tieleman, I. Kerr, R. Callaghan. 2007. Residue G346 in transmembrane segment six is involved in inter-domain communication in P-glycoprotein, Biochemistry 46, pp. 9899-9910
  36. E.P. Coll, C. Kandt, D. Bird, A. L. Samuels, D. P. Tieleman. 2007. The distribution and conformation of long-chain plant wax components in a lipid bilayer, J. Phys. Chem. B 111, pp. 8702-8704
  37. C.S. Chan, M.R. Zlomislic, D.P. Tieleman, R.J. Turner. 2007. The TatA subunit of Escherichia coli Twin-Arginine Translocase has an N-in topology, Biochemistry 46, pp. 7396-7404
  38. S.J. Marrink, J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. 2007. The MARTINI force field: coarse grained model for biomolecular simulations, J. Phys. Chem. B. 111, pp. 7812-7824
  39. J.L. MacCallum, W.F.D. Bennett, D.P. Tieleman. 2007. Partitioning of amino acid sidechains into lipid bilayers: results from computer simulations and comparison to experiment, J. Gen. Physiol. 129, pp. 371-377
  40. C. Kandt, E.O. Oloo, D.P. Tieleman. 2007. Domain coupling in the ABC transporter system BtuCD/BtuF: molecular dynamics simulation, normal mode analysis and protein-protein docking, HPCS2007 proceedings (IEEE press)
  41. J.L. MacCallum, M.S. Moghaddam, H.S. Chan, D.P. Tieleman. 2007. Hydrophobic association of alpha-helices, steric de-wetting and enthalpic barriers to protein folding, Proc. Natl. Acad. Sci. 104, pp. 6206-6210
  42. E.E. Kooijman, D.P. Tieleman, C. Testerink, T. Munnik, D.T. Rijkers, K.N. Burger, B. de Kruijff. 2007. An electrostatic/hydrogen bond switch as basis for the specific interaction of phosphatidic acid with proteins, J. Biol. Chem. 282, pp. 11356-11364
  43. Z. Xu, H.H. Luo, D.P. Tieleman. 2007. Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues, J. Comp. Chem. 28, pp. 689-697
  44. J. Sonne, C. Kandt, G.H. Peters, F.Y. Hansen, M.Ø. Jensen, D.P. Tieleman. 2007. Simulation of the coupling between nucleotide binding and transmembrane domains in the ABC transporter BtuCD, Biophys. J. 92, pp. 2727-2734
  45. C. Kandt, W.L. Ash, D.P. Tieleman. 2007. Setting up and running membrane protein simulations, Methods 41, pp. 475-488

    46. 2006

  46. E.O. Oloo, C. Kandt, M.L. O'Mara, D.P. Tieleman. 2006. Computer simulations of ABC transporter components, Biochem. Cell Biol. 84, pp. 900-911
  47. P.T. Vernier, M.J Ziegler, Y. Sun, M.A. Gundersen, D.P. Tieleman. 2006. Nanopore-facilitated, voltage-driven phosphatidylserine translocation in lipid bilayers — in cells and in silico, Phys. Biol. 3, pp. 233-247
  48. C. Kandt, Z. Xu, D.P. Tieleman. 2006. Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF, Biochemistry 45, pp. 13284-13292
  49. D.P. Tieleman. 2006. Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters, Clin. Exp. Pharmacol. Physiol. 33, pp. 893-903
  50. M.R. Zlomislic, D.P. Tieleman. "Protein modeling", in Proteins: From Analytics to Structural Genomics, Wiley-VCH (reprinted from Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2nd edition, Volume 11, pp. 133-159).
  51. D.P. Tieleman, S.J. Marrink. 2006. Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop, J. Am. Chem. Soc. 128, pp. 12462 - 12467
  52. E.O. Oloo, E.Y. Fung, D.P. Tieleman. 2006. The dynamics of the MgATP-driven closure of MalK, the energy-transducing subunit of the maltose ABC transporter, J. Biol. Chem. 281, pp. 28397-28407 (cover image)
  53. E. Mátyus, L. Monticelli, K. E. Kövér, Z. Xu, K. Blaskó, J. Fidy, D. P. Tieleman. 2006. Structural investigation of syringomycin-E using molecular dynamics simulation and NMR, Eur. Biophys. J. 35, pp. 459 - 467
  54. D.P. Tieleman, J.L. MacCallum, W.L. Ash, C. Kandt, Z. Xu, L. Monticelli. 2006. Membrane protein simulations with a united atom lipid and all atom protein model: side chain transfer free energies and model proteins, J. Phys. Cond. Matt. 18, pp. S1221-S1234
  55. D.P. Tieleman. 2006. Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters, Proc. Austr. Phys. Soc. 37, pp. 15-27
  56. P.T. Vernier, M.J. Ziegler, Y. Sun, W.V. Chang, M.A. Gundersen, D.P. Tieleman. 2006. Nanopore formation and phosphatidylserine externalization in a phospholipid Bilayer at high transmembrane potential, J. Am. Chem. Soc. 128, pp. 6288-6289
  57. J.L. MacCallum, D.P. Tieleman. 2006. Computer simulation of the distribution of hexane in a lipid bilayer: spatially resolved free energy, entropy, and enthalpy profiles. J. Am. Chem. Soc. 128, pp. 125-130
  58. S.H. Chung, D.P. Tieleman. 2006. "Computational and Theoretical Approaches to Unraveling the Permeation Dynamics in Biological Nanotubes", in Handbook of theoretical and computational nanotechnology, M. Rieth and W. Schommers (eds), American Scientific Publishers. Volume 6, pp. 567-618

    59. 2005

  59. M.P. Aliste, D.P. Tieleman. 2005. Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces. BMC Biochemistry 6:30
  60. M. Ulmschneider, D.P. Tieleman, M.S.P. Sansom. 2005. The role of extra-membranous inter-helical loops in helix-helix interactions. Protein Eng. Des. Sel. 18, pp. 563-570
  61. L. Monticelli, D.P. Tieleman, G. Colombo. 2005. Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations. J. Phys. Chem. B. 109, pp. 20064-20067
  62. E. Sparr, W.L. Ash, P.V. Nazarov, D.T.S. Rijkers, M.A. Hemminga, D.P. Tieleman, J.A. Killian. 2005. Self-association of transmembrane alpha-helices in model membranes: importance of helix orientation and role of hydrophobic mismatch, J. Biol. Chem. 280, pp. 39324-39331
  63. E. Kelly, G.G. Prive, D.P. Tieleman. 2005. Molecular models of lipopeptide detergents: large coiled-coils with hydrocarbon interiors. J. Am. Chem. Soc. 127, pp. 13446-13447
  64. T. Stockner, H.J. Vogel, D.P. Tieleman. 2005. A salt-bridge motif involved in ligand binding and large scale domain motions of the maltose binding protein. Biophys. J. 89, pp. 3362-3371
  65. M.R. Zlomislic, D.P. Tieleman. 2005. "Protein modeling", Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2nd edition, Volume 11, pp. 133-159. Wiley-VCH.
  66. B. Hoff, E. Strandberg, A.S. Ulrich, D.P. Tieleman, C. Posten. 2005. 2H-NMR study and molecular dynamics simulation of the location, alignment and mobility of pyrene in POPC bilayers. Biophys. J. 88, pp. 1818-1827.
  67. H. Ahumada, R. Montecinos, D. P. Tieleman, B.E. Weiss-López. 2005. Dynamics of benzyl alcohol and benzyl alkyl ethers dissolved in nematic lyotropic liquid crystals. 2H-NMR and MD simulations. J. Phys. Chem. A 109, pp. 6644-6651.

    68. 2004

  68. E.O. Oloo, D.P. Tieleman. 2004. Conformational transitions induced by the binding of MgATP to the vitamin B12 ABC-transporter BtuCD. J. Biol. Chem. 279, pp. 45013-45019.
  69. D.P. Tieleman, K.M. Robertson, J.L. MacCallum, L. Monticelli. 2004. Computer simulations of the voltage gated potassium channel KvAP. Int. J. Quant. Chem. 100, pp. 1071-1078.
  70. D.P. Tieleman. The molecular basis of electroporation. 2004. BMC Biochemistry 5:10.
  71. T. Stockner, W.L. Ash, J.L. MacCallum, D.P. Tieleman. 2004. Direct simulation of transmembrane helix association: role of asparagines. Biophys. J. 87, pp. 1650-1656.
  72. M.B. Ulmschneider, D.P. Tieleman, M.S.P. Sansom. 2004. Interaction of a transmembrane helix and a membrane: comparative simulations of bacteriorhodopsin helix A. J. Phys. Chem. B 108, pp. 10149-10159.
  73. W.L. Ash, T. Stockner, J.L. MacCallum, D.P. Tieleman. 2004. Computer modeling of polyleucine-based coiled coil dimers in a realistic membrane environment: insight into helix-helix interactions in membrane proteins. Biochemistry 43, pp. 9050-9060.
  74. B. Hoff, M. Herrenbauer, D.P. Tieleman, C. Posten. 2004. Molekulardynamische Simulationen zum Einfluss polyzyklischer aromatischer Kohlenwasserstoffe (PAK) auf Phospholipid-Membranen/Molecular-dynamics simulations pertaining to the influence of polycyclic aromatic hydrocarbons, Chemie Ingenieur Technik 76, pp. 1017-1021.
  75. R. Montecinos, H. Ahumada, R. Martinez, F.A. Olea, R. Araya-Maturana, M.P. Aliste, D. P. Tieleman, B.E. Weiss-Lopez. 2004. Structure and aggregation number of a lyotropic liquid crystal: a fluorescence quenching and molecular dynamics study. Langmuir 20, pp. 5703-5708.
  76. W.L. Ash, M.R. Zlomislic, E.O. Oloo, D.P. Tieleman. 2004. Computer simulations of membrane proteins. BBA - Reviews in Biomembranes 1666, pp. 158-189.
  77. M. Bachar, P. Brunelle, D.P. Tieleman, A. Rauk. 2004. Molecular dynamics simulation of a polyunsaturated lipid bilayer susceptible to lipid peroxidation. J. Phys. Chem. B 108, pp. 7170-7179.
  78. L. Monticelli, K.M. Robertson, J.L. MacCallum, D.P. Tieleman. 2004. Computer simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor. FEBS Letters 564, pp. 325-332.
  79. N. Zhou, D.P. Tieleman, H.J. Vogel. 2004. Molecular dynamics simulations of bovine lactoferricin: turning a helix into a sheet. Biometals 17, pp. 217-223.
  80. P. Mukhopadhyay, L. Monticelli, D.P. Tieleman. 2004. Molecular dynamics simulation of a almitoyloleoyl-phosphatidylserine bilayer with Na+ counterions and NaCl, Biophys. J. 86, pp. 1601-1609.
  81. P. Mukhopadhyay, H.J. Vogel, D.P. Tieleman. 2004. Distribution of pentachlorophenol in phospholipid bilayers: A molecular dynamics study, Biophys. J. 86, pp. 337-345
  82. A. Kessel, D.P. Tieleman, N. Ben-Tal. 2004. Implicit solvent model estimates of the stability of model structures of the alamethicin channel, Eur. Biophys. J. 33, pp. 16-28

    83. 2003

  83. MacCallum, J.L., and D.P. Tieleman. 2003. Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field, J. Comp. Chem. 24, 1930-1935.
  84. C. Anezo, A.H. de Vries, H.-D. Holtje, D.P. Tieleman, S.-J. Marrink. 2003. Methodological issues in lipid bilayer simulations, J. Phys. Chem. B 107, pp. 9424-9433.
  85. Aliste, M.P., MacCallum, J.L., and D.P. Tieleman. 2003. Molecular dynamics simulations of pentapeptides at interfaces: salt bridge and cation-pi interactions, Biochemistry 42, pp. 8976-8987.
  86. MacCallum, J.L., Mukhopadhyay, P., Luo, H., and D.P. Tieleman. 2003. Large scale molecular dynamics simulations of lipd-drug interactions, in Proceedings of the 17th Annual International Symposium on High Performance Computing Systems and Applications and the OSCAR Symposium, David Senechal (editor), NRC Research Press, Ottawa, Canada, pp. 115-122.
  87. D.P. Tieleman, H. Leontiadou, A.E. Mark, S.J. Marrink. 2003. Molecular dynamics simulation of pore formation in phospholipid bilayers by mechanical force and electric fields, J. Am. Chem. Soc. 125, pp. 6382-6383.
  88. D.P. Tieleman. 2003. "Atomistic simulations of ion channels". In: Computational neuroscience: a comprehensive approach, CRC Press.
  89. I. Chandrasekhar, M. Kastenholz, R.D. Lins, C. Oostenbrink, L.D. Schuler, D.P. Tieleman, W.F. van Gunsteren. 2003. A consistent potential energy parameter set for lipids - dipalmitoylphosphatidylcholine as a benchmark for the GROMOS96 45A3 force field, Eur. Biophys. J. 32, pp. 67-77.
  90. D.P. Tieleman. 2003. "Molecular motions in ion channels: a possible link to noise in single channels", in Unsolved problems in noise and fluctuations III, AIP Proceedings 665, pp. 298-304.
  91. D.P. Tieleman, V. Borisenko, M.S.P. Sansom, G.A. Woolley. 2003. Understanding pH-dependent selectivity of alamethicin K1 channels by computer simulations, Biophys. J. 84, pp. 1464-1469.
  92. C.M. Shepherd, H.J. Vogel, D.P. Tieleman. 2003. Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular dynamics simulations, Biochem.J. 370, pp. 233-243.
  93. R.J. Law, D.P. Tieleman, M.S.P. Sansom. 2003. Pores formed by the nicotinic receptor M2d peptide: a molecular dynamics study, Biophys. J. 84, pp. 14-27 2002.

    94. 2002

  94. J.L. MacCallum, D.P. Tieleman. 2002. Structure of neat and hydrated 1-octanol from computer simulations. J. Am. Chem. Soc. 124, pp. 15085-15093.
  95. D.P. Tieleman, B. Hess, M.S.P. Sansom. 2002. Analysis and evaluation of channel models: simulations of alamethicin, Biophys. J. 3, pp. 2393-2407.
  96. S.J. Marrink, D.P. Tieleman. 2002. Molecular dynamics simulation of spontaneous membrane fusion during a cubic-hexagonal phase transition, Biophys. J. 83, pp. 2386-2392.
  97. K.M. Robertson, D.P. Tieleman. 2002. Orientation and interaction of dipolar molecules during transport through OmpF porin, FEBS Lett. 528, pp. 53-57.
  98. K.M. Robertson, D.P. Tieleman. 2002. The molecular basis of voltage gating of OmpF porin, Biochem. Cell Biol. 80, pp. 517-523.
  99. D.P. Tieleman, J. Bentz. 2002. Molecular dynamics simulation of the evolution of hydrophobic defects in one monolayer of a phosphatidylcholine bilayer: Relevance for membrane fusion mechanisms, Biophys. J. 83, pp. 1501-1510.
  100. I.H. Shrivastava, D.P. Tieleman, P.C. Biggin, M.S.P. Sansom. 2002. K+ versus Na+ ions in a K channel selectivity filter: a simulation study, Biophys. J. 83, pp. 633-645.
  101. Mark S.P. Sansom, Peter Bond, Oliver Beckstein, Philip C. Biggin, Jose Faraldo-Gomez, Richard J. Law, George Patargias, D. Peter Tieleman. 2002. Water in ion channels and pores - simulation studies, Novartis Found. Sympos. 245, pp. 66-78.
  102. B.L. de Groot, D.P. Tieleman, P. Pohl, H. Grubmueller. 2002. Water permeation through gramicidin A: desformylation and the double helix; a molecular dynamics study, Biophys. J. 82, pp. 2934-2942.

    103. 2001

  103. Craig M. Shepherd, Hans J. Vogel, D. Peter Tieleman. 2001. "Molecular modeling in membrane protein design and egineering", in Recent research developments in protein engineering, pp. 307-317.
  104. S.J. Marrink, D.P. Tieleman. 2001. Molecular dynamics simulation of a cubic membrane phase, J. Am. Chem. Soc. 123, pp. 12383-12391.
  105. Michael Herrenbauer, D. Peter Tieleman, Clemens Posten. 2001. Molecular modelling of diffusional motion and transfer of pyrene in lipid membranes, Computer Applications in Biotechnology 8, pp. 317-321.
  106. C.T. Choma, D.P. Tieleman, D. Cregut, L. Serrano, H.J.C. Berendsen. 2001. Design and computational characterization of a membrane protein, J. Mol. Graph. Mod. 20, pp. 219-234.
  107. D.P. Tieleman, G.R. Smith, P.C. Biggin, M.S.P. Sansom. 2001. Simulation approaches to ion channel structure-function relationships, Quart. Rev. Biophys. 34, pp. 473-561.
  108. D.P. Tieleman, I.H. Shrivastava, M.B. Ulmschneider, M.S.P. Sansom. 2001. Proline-induced hinges in trans-membrane helices: possible roles in ion-channel gating, PROTEINS: Struct. Func. Genet. 44, pp. 63-72.
  109. D.P. Tieleman, M.S.P. Sansom. 2001. Molecular dynamics simulations of antimicrobial peptides: from membrane binding to transmembrane channels, Int. J. Quantum Chem. 83, pp. 166-179.
  110. D.P. Tieleman, H.J.C. Berendsen, M.S.P. Sansom. 2001. Voltage-dependent insertion of a channel forming peptide: molecular dynamics simulations of alamethicin at phospholipid/water and octane/water interfaces, Biophys. J. 80, pp. 331-346. 2000.

    111. 2000

  111. S.J. Marrink, D.P. Tieleman, A.E. Mark. 2000. Molecular dynamics simulations of micellization kinetics, J. Phys. Chem. B 104, pp. 12165-12173.
  112. D. P. Tieleman, D. van der Spoel, H.J.C. Berendsen. 2000. Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: micellar structure and lipid chain relaxation, J. Phys. Chem. B 104, pp. 6380-6388.
  113. R.J. Law, L.R. Forrest, K.M. Ranatunga, P. La Rocca, D.P. Tieleman, M.S.P. Sansom. 2000. Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers and transbilayer bundles, PROTEINS: Struct. Func. Genet. 39, pp. 47-55.
  114. L.R. Forrest, A. Kukol, I.T. Arkin, D.P. Tieleman, M.S.P. Sansom. 2000. Exploring models of the Influenza M2 channel - MD simulations in a phospholipid bilayer, Biophys. J. 78, pp. 55-69.

    115. 1999

  115. P. La Rocca, P. Biggin, D.P. Tieleman, M.S.P. Sansom. 1999. Simulation studies of the interaction of antimicrobial peptides and lipid bilayers, Biochim. Biophys. Acta 1462, pp. 185-200.
  116. M.S.P. Sansom, D.P. Tieleman, H.J.C. Berendsen. 1999. "The mechanism of channel formation by alamethicin as viewed by molecular dynamics simulations", in: Gramicidin and related ion channel forming peptides, Wiley: Chichester. Novartis Found. Symp. 225, pp. 128-145.
  117. L.R. Forrest, D.P. Tieleman, M.S.P. Sansom. 1999. Defining the transmembrane helix of M2 protein from Influenza A by molecular dynamics simulations in a lipid bilayer, Biophys. J. 76, pp. 1886-1896.
  118. D.P. Tieleman, H.J.C. Berendsen, M.S.P. Sansom. 1999. Surface binding of alamethicin stabilises its helical structure: molecular dynamics simulations, Biophys. J. 76, pp. 3186-3191 .
  119. D.P. Tieleman, H.J.C. Berendsen, M.S.P. Sansom. 1999. An alamethicin channel in a bilayer: molecular dynamics simulations, Biophys. J. 76, pp. 1757-1769.
  120. D.P. Tieleman, M.S.P. Sansom, H.J.C. Berendsen. 1999. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations, Biophys. J. 76, pp. 40-49.

    121. 1998

  121. D.P. Tieleman, J. Breed, H.J.C. Berendsen, M.S.P. Sansom. 1998. Alamethicin channels in a membrane: molecular dynamics simulations, Faraday Discuss. 111, pp. 209-223.
  122. D.P. Tieleman, L. Forrest, M.S.P. Sansom, H.J.C. Berendsen. 1998. Lipid properties and the orientation of aromatic residues in OmpF, Influenza M2 and Alamethicin systems: Molecular dynamics simulations, Biochemistry 37, pp. 17554-17561.
  123. D.P. Tieleman, H.J.C. Berendsen. 1998. A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylethanolamine bilayer, Biophys. J. 74, pp. 2786-2801. (see also New and Notable, same issue)
  124. M.S.P. Sansom, D.P. Tieleman, L.R. Forrest, H.J.C. Berendsen. 1998. Molecular dynamics simulations of membranes with embedded ion channels: porin, alamethicin, and influenza M2, Biochem. Soc. Transac. 26, pp. 438-443.
  125. M.S.P. Sansom, I.D. Kerr, R. Law, L. Davison, D.P. Tieleman. 1998. Modelling the packing of transmembrane helices: Application to Aquaporin 1, Biochem. Soc. Transac. 26, pp. 509-515.
  126. H.J.C. Berendsen, D.P. Tieleman. 1998. Molecular dynamics: Studies of lipid bilayers, Encyclopedia of Computational Chemistry, P. von Rague Schleyer (ed. in chief), volume 3, pp. 1639-1650, John Wiley & Sons.
  127. S.J. Marrink, O. Berger, D.P. Tieleman, F. Jaehnig. 1998. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations, Biophys. J. 74, pp. 931-943.

    128. 1997

  128. D.P. Tieleman, S.J. Marrink, H.J.C. Berendsen. 1997. A computer perspective of membranes: Molecular dynamics studies of lipid bilayers systems, Biochim. Biophys Acta 1331, pp. 235-270.

    129. 1996

  129. D. van der Spoel, A.R. van Buuren, D.P. Tieleman, H.J.C. Berendsen. 1996. Molecular dynamics simulations of peptides from BPTI: A closer look at amide-aromatic interactions, J. Biomol. NMR 8, pp. 229-238.
  130. S-J. Marrink, D.P. Tieleman, A.R. van Buuren, H.J.C. Berendsen. 1996. Membranes and water: An interesting relationship, Faraday Discuss. 103, pp. 191-200.
  131. A.R. van Buuren, D.P. Tieleman, J. de Vlieg, H.J.C. Berendsen. 1996. Cosurfactants lower surface tension of the diglyceride/water interface: A molecular dynamics study, Langmuir 12, pp. 2570-2579.
  132. D.P. Tieleman, H.J.C. Berendsen. 1996. Molecular dynamics simulations of fully hydrated DPPC with different macroscopic boundary conditions and parameters, J. Chem. Phys. 105, pp. 4871-4880.

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