Tampere University of Technology

TUTCRIS Research Portal

Tomasz Rog

  1. 2019
  2. Published

    Behavior of the DPH fluorescence probe in membranes perturbed by drugs

    Poojari, C., Wilkosz, N., Lira, R. B., Dimova, R., Jurkiewicz, P., Petka, R., Kepczynski, M. & Róg, T., 1 Sep 2019, In : Chemistry and Physics of Lipids. 223, 104784.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Published

    Complex Behavior of Phosphatidylcholine-Phosphatidic Acid Bilayers and Monolayers: Effect of Acyl Chain Unsaturation

    Kulig, W., Korolainen, H., Zatorska, M., Kwolek, U., Wydro, P., Kepczynski, M. & Róg, T., 30 Apr 2019, In : Langmuir. 35, 17, p. 5944-5956 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. 2018
  5. Published

    Glucosylceramide modifies the LPS-induced inflammatory response in macrophages and the orientation of the LPS/TLR4 complex in silico

    Mobarak, E., Håversen, L., Manna, M., Rutberg, M., Levin, M., Perkins, R., Rog, T., Vattulainen, I. & Borén, J., 1 Dec 2018, In : Scientific Reports. 8, 1, 13600.

    Research output: Contribution to journalArticleScientificpeer-review

  6. Published

    How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative

    Mobarak, E., Javanainen, M., Kulig, W., Honigmann, A., Sezgin, E., Aho, N., Eggeling, C., Rog, T. & Vattulainen, I., Nov 2018, In : Biochimica et Biophysica Acta - Biomembranes. 1860, 11, p. 2436-2445

    Research output: Contribution to journalArticleScientificpeer-review

  7. Published

    Physiologically-relevant levels of sphingomyelin, but not GM1, induces a β-sheet-rich structure in the amyloid-β(1-42) monomer

    Owen, M. C., Kulig, W., Poojari, C., Rog, T. & Strodel, B., Sep 2018, In : Biochimica et Biophysica Acta - Biomembranes. 1860, 9, p. 1709-1720

    Research output: Contribution to journalArticleScientificpeer-review

  8. Published

    The effect of light sensitizer localization on the stability of indocyanine green liposomes

    Lajunen, T., Nurmi, R., Wilbie, D., Ruoslahti, T., Johansson, N. G., Korhonen, O., Rog, T., Bunker, A., Ruponen, M. & Urtti, A., 28 Aug 2018, In : Journal of Controlled Release. 284, p. 213-223 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Published

    Negatively Charged Gangliosides Promote Membrane Association of Amphipathic Neurotransmitters

    Juhola, H., Postila, P. A., Rissanen, S., Lolicato, F., Vattulainen, I. & Róg, T., 1 Aug 2018, In : Neuroscience. 384, p. 214-223 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

    How Cardiolipin Peroxidation Alters the Properties of the Inner Mitochondrial Membrane?

    Vähäheikkilä, M., Peltomaa, T., Rog, T., Vazdar, M., Pöyry, S. & Vattulainen, I., Aug 2018, In : Chemistry and Physics of Lipids. 214, p. 15-23 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Published

    Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study

    Owen, M. C., Kulig, W., Rog, T., Vattulainen, I. & Strodel, B., Jun 2018, In : Journal of Membrane Biology. 251, 3, p. 521-534 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  12. Published

    Membrane bound COMT isoform is an interfacial enzyme: General mechanism and new drug design paradigm

    Magarkar, A., Parkkila, P., Viitala, T., Lajunen, T., Mobarak, E., Licari, G., Cramariuc, O., Vauthey, E., Róg, T. & Bunker, A., 11 Apr 2018, In : Chemical Communications. 54, 28, p. 3440-3443 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Published

    Bobbing of Oxysterols: Molecular Mechanism for Translocation of Tail-Oxidized Sterols through Biological Membranes

    Kulig, W., Mikkolainen, H., Olżyńska, A., Jurkiewicz, P., Cwiklik, L., Hof, M., Vattulainen, I., Jungwirth, P. & Rog, T., 1 Mar 2018, In : Journal of Physical Chemistry Letters. 9, 5, p. 1118-1123 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  14. 2017
  15. Published

    DoGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

    Danne, R., Poojari, C., Martinez-Seara, H., Rissanen, S., Lolicato, F., Róg, T. & Vattulainen, I., 23 Oct 2017, In : Journal of Chemical Information and Modeling. 57, 10, p. 2401-2406 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  16. Published

    Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles

    Mokkila, S., Postila, P. A., Rissanen, S., Juhola, H., Vattulainen, I. & Róg, T., 21 Jun 2017, In : ACS Chemical Neuroscience. 8, 6, p. 1242-1250 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  17. Published

    Phase partitioning of GM1 and its bodipy-labeled analog determine their different binding to Cholera Toxin

    Rissanen, S., Grzybek, M., Orlowski, A., Róg, T., Cramariuc, O., Levental, I., Eggeling, C., Sezgin, E. & Vattulainen, I., 9 May 2017, In : Frontiers in Physiology. 8, MAY, 252.

    Research output: Contribution to journalArticleScientificpeer-review

  18. Published

    Long-chain GM1 gangliosides alter transmembrane domain registration through interdigitation

    Manna, M., Javanainen, M., Martinez-Seara Monne, H., Gabius, H-J., Rog, T. & Vattulainen, I., 1 May 2017, In : Biochimica et Biophysica Acta: Biomembranes. 1859, 5, p. 870-878 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  19. Published

    Effect of piroxicam on lipid membranes: Drug encapsulation and gastric toxicity aspects

    Wilkosz, N., Rissanen, S., Cyza, M., Szybka, R., Nowakowska, M., Bunker, A., Róg, T. & Kepczynski, M., 30 Mar 2017, In : European Journal of Pharmaceutical Sciences. 100, p. 116-125 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition

    Bilkova, E., Pleskot, R., Rissanen, S., Sun, S., Czogalla, A., Cwiklik, L., Róg, T., Vattulainen, I., Cremer, P. S., Jungwirth, P. & Coskun, Ü., 22 Mar 2017, In : Journal of the American Chemical Society. 139, 11, p. 4019-4024 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

    Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis

    Euro, L., Haapanen, O., Róg, T., Vattulainen, I., Suomalainen, A. & Sharma, V., 7 Mar 2017, In : Biochemistry. 56, 9, p. 1227-1238 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    Glycosylation and Lipids Working in Concert Direct CD2 Ectodomain Orientation and Presentation

    Polley, A., Orłowski, A., Danne, R., Gurtovenko, A. A., Bernardino de La Serna, J., Eggeling, C., Davis, S. J., Róg, T. & Vattulainen, I., 2 Mar 2017, In : Journal of Physical Chemistry Letters. 8, 5, p. 1060-1066 7 p.

    Research output: Contribution to journalLetterScientificpeer-review

  23. Published

    Effects of Membrane PEGylation on Entry and Location of Antifungal Drug Itraconazole and their Pharmacological Implications

    Dzieciuch-Rojek, M., Poojari, C., Bednar, J., Bunker, A., Kozik, B., Nowakowska, M., Vattulainen, I., Wydro, P., Kepczynski, M. & Rog, T., 24 Feb 2017, In : Molecular Pharmaceutics. 14, 4, p. 1057-1070

    Research output: Contribution to journalArticleScientificpeer-review

  24. Published

    Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle

    Grabon, A., Orłowski, A., Tripathi, A., Vuorio, J., Javanainen, M., Róg, T., Lönnfors, M., McDermott, M. I., Siebert, G., Somerharju, P., Vattulainen, I. & Bankaitis, V. A., 2017, In : Journal of Biological Chemistry. 292, 35, p. 14438-14455 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    The Integrin Receptor in Biologically Relevant Bilayers: Insights from Molecular Dynamics Simulations

    Kalli, A. C., Rog, T., Vattulainen, I., Campbell, I. D. & Sansom, M. S. P., 2017, In : Journal of Membrane Biology. 250, p. 337-351 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  26. 2016
  27. Published

    Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

    Manna, M., Niemelä, M., Tynkkynen, J., Javanainen, M., Kulig, W., Müller, D. J., Rog, T. & Vattulainen, I., 29 Nov 2016, In : eLIFE. 5, e18432.

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    Stearylated cycloarginine nanosystems for intracellular delivery - simulations, formulation and proof of concept

    Dhawan, V., Magarkar, A., Joshi, G., Makhija, D., Jain, A., Shah, J., Reddy, B. V. V., Krishnapriya, M., Rog, T., Bunker, A., Jagtap, A. & Nagarsenker, M., 24 Nov 2016, In : RSC Advances. 6, 114, p. 113538-113550 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  29. Published

    Identifying involvement of Lys251/Asp252 pair in electron transfer and associated proton transfer at the quinone reduction site of Rhodobacter capsulatus cytochrome bc1

    Kuleta, P., Sarewicz, M., Postila, P., Róg, T. & Osyczka, A., 1 Oct 2016, In : Biochimica et Biophysica Acta: Bioenergetics. 1857, 10, p. 1661-1668 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  30. Published

    Lipid membranes: Theory and simulations bridged to experiments

    Vattulainen, I. & Róg, T., 1 Oct 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 10, p. 2251-2253 3 p.

    Research output: Contribution to journalEditorialScientificpeer-review

  31. Published

    Functionalized lipids and surfactants for specific applications

    Kepczynski, M. & Róg, T., Oct 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 10, p. 2362-2379

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

    Postila, P. A., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka, A. & Róg, T., 26 Sep 2016, In : Scientific Reports. 6, 33607.

    Research output: Contribution to journalArticleScientificpeer-review

  33. Published

    Distribution and dynamics of quinones in the lipid bilayer mimicking the inner membrane of mitochondria

    Kaurola, P., Sharma, V., Vonk, A., Vattulainen, I. & Róg, T., 1 Sep 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 9, p. 2116-2122 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  34. Published

    Effect of Calcium Ions on PI(4,5)P2 Presentation in Lipid Bilayers Revealed by MD Simulations

    Rissanen, S., Pleskot, R., Bilkova, E., Jungwirth, P., Rog, T. & Coskun, Ü., 16 Aug 2016.

    Research output: Other conference contributionPaper, poster or abstractScientific

  35. Published

    Design of cholesterol arabinogalactan anchored liposomes for asialoglycoprotein receptor mediated targeting to hepatocellular carcinoma: In silico modeling, in vitro and in vivo evaluation

    Pathak, P., Dhawan, V., Magarkar, A., Danne, R., Govindarajan, S., Ghosh, S., Steiniger, F., Chaudhari, P., Gopal, V., Bunker, A., Róg, T., Fahr, A. & Nagarsenker, M., 25 Jul 2016, In : International Journal of Pharmaceutics. 509, 1-2, p. 149-158 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  36. Published

    Indocyanine Green-Loaded Liposomes for Light-Triggered Drug Release

    Lajunen, T., Kontturi, L-S., Viitala, L., Manna, M., Cramariuc, O., Róg, T., Bunker, A., Laaksonen, T., Viitala, T., Murtomäki, L. & Urtti, A., 6 Jun 2016, In : Molecular Pharmaceutics. 13, 6, p. 2095-2107 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  37. Published

    Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

    Róg, T., Orłowski, A., Llorente, A., Skotland, T., Sylvänne, T., Kauhanen, D., Ekroos, K., Sandvig, K. & Vattulainen, I., 1 Jun 2016, In : Data in Brief. 7, p. 1171-1174 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  38. Published

    Oxidation of Cholesterol Changes the Physical Properties of Lipid Membranes

    Kulig, W., Olzynska, A., Jurkiewicz, P., Kantola, A. M., Manna, M., Pourmousa, M., Vazdar, M., Cwiklik, L., Rog, T., Khelashvili, G., Harries, D., Telkki, V-V., Hof, M., Vattulainen, I. & Jungwirth, P., 16 Feb 2016, In : Biophysical Journal. 110, 3, Supplement 1, p. 84a 1 p.

    Research output: Contribution to journalArticleScientific

  39. Published

    Protocol to Avoid Possible Artifacts in Atomistic Simulation of GPCR Proteins whose Crystal Structure is Heavily Engineered

    Manna, M., Kulig, W., Javanainen, M., Tynkkynen, J., Hensen, U., Müller, D. J., Rog, T. & Vattulainen, I., 16 Feb 2016, In : Biophysical Journal. 110, 3, Supplement 1, p. 59a 1 p.

    Research output: Contribution to journalArticleScientific

  40. Published

    Selective effect of cell membrane on synaptic neurotransmission

    Postila, P. A., Vattulainen, I. & Róg, T., 19 Jan 2016, In : Scientific Reports. 6, 19345.

    Research output: Contribution to journalArticleScientificpeer-review

  41. Published

    Cholesterol oxidation products and their biological importance

    Kulig, W., Cwiklik, L., Jurkiewicz, P., Rog, T. & Vattulainen, I., 2016, In : Chemistry and Physics of Lipids. 199, p. 144-160 17 p.

    Research output: Contribution to journalArticleScientificpeer-review

  42. Published

    Cis and Trans Unsaturated Phosphatidylcholine Bilayers: A Molecular Dynamics Simulation Study

    Kulig, W., Pasenkiewicz-Gierula, M. & Róg, T., 2016, In : Chemistry and Physics of Lipids. 195, p. 12-20

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    Interdigitation of long-chain sphingomyelin induces coupling of membrane leaflets in a cholesterol dependent manner

    Rog, T., Orlowski, A., Llorente, A., Skotland, T., Sylvänne, T., Kauhanen, D., Ekroos, K., Sandvig, K. & Vattulainen, I., 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 2, p. 281-288

    Research output: Contribution to journalArticleScientificpeer-review

  44. Published

    The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations

    Rog, T. & Koivuniemi, A., 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 1, p. 97-103 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  45. 2015
  46. Published

    Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol

    Kulig, W., Pasenkiewicz-Gierula, M. & Róg, T., 5 Dec 2015, In : Data in Brief. 5, p. 333-336 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    PIP2 and Talin Join Forces to Activate Integrin

    Orlowski, A., Kukkurainen, S., Pöyry, A., Rissanen, S., Vattulainen, I., Hytönen, V. P. & Róg, T., 24 Sep 2015, In : Journal of Physical Chemistry Part B. 119, 38, p. 12381-12389 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  48. Published

    Redox-induced activation of the proton pump in the respiratory complex I

    Sharma, V., Belevich, G., Gamiz-Hernandez, A. P., Róg, T., Vattulainen, I., Verkhovskaya, M. L., Wikström, M., Hummer, G. & Kaila, V. R. I., 15 Sep 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 37, p. 11571-11576 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  49. Published

    Building synthetic sterols computationally: unlocking the secrets of evolution?

    Róg, T., Pöyry, S. & Vattulainen, I., 21 Aug 2015, In : Frontiers in Bioengineering and Biotechnology. 3, 00121.

    Research output: Contribution to journalArticleScientificpeer-review

  50. Published

    Effect of Phosphatidic Acid on Biomembrane: Experimental and Molecular Dynamics Simulations Study

    Kwolek, U., Kulig, W., Wydro, P., Nowakowska, M., Róg, T. & Kepczynski, M., 6 Aug 2015, In : Journal of Physical Chemistry Part B. 119, 31, p. 10042-10051 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  51. Published

    Cholesterol under oxidative stress: How lipid membranes sense oxidation as cholesterol is being replaced by oxysterols

    Kulig, W., Olzyńska, A., Jurkiewicz, P., Kantola, A. M., Komulainen, S., Manna, M., Pourmousa, M., Vazdar, M., Cwiklik, L., Rog, T., Khelashvili, G., Harries, D., Telkki, V. V., Hof, M., Vattulainen, I. & Jungwirth, P., 1 Jul 2015, In : Free Radical Biology and Medicine. 84, p. 30-41 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  52. Published

    How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: beta(2)-Adrenergic Receptor in the Spotlight

    Manna, M., Kulig, W., Javanainen, M., Tynkkynen, J., Hensen, U., Mueller, D. J., Rog, T. & Vattulainen, I., Jul 2015, In : Journal of Chemical Theory and Computation. 11, 7, p. 3432-3445 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  53. Published

    PEGylated liposomes as carriers of hydrophobic porphyrins

    Dzieciuch, M., Rissanen, S., Szydłowska, N., Bunker, A., Kumorek, M., Jamróz, D., Vattulainen, I., Nowakowska, M., Róg, T. & Kepczynski, M., 4 Jun 2015, In : Journal of Physical Chemistry Part B. 119, 22, p. 6646-6657 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  54. Published

    Sec14-nodulin proteins and the patterning of phosphoinositide landmarks for developmental control of membrane morphogenesis

    Ghosh, R., De Campos, M. K. F., Huang, J., Huh, S. K., Orlowski, A., Yang, Y., Tripathi, A., Nile, A., Lee, H-C., Dynowski, M., Schäfer, H., Róg, T., Lete, M. G., Ahyayauch, H., Alonso, A., Vattulainen, I., Igumenova, T. I., Schaaf, G. & Bankaitis, V. A., 1 May 2015, In : Molecular Biology of the Cell. 26, 9, p. 1764-1781 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

  55. Published

    Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase

    Sharma, V., Ala-Vannesluoma, P., Vattulainen, I., Wikström, M. & Róg, T., 17 Apr 2015, In : Biochimica et Biophysica Acta: Bioenergetics. 1847, 8, p. 690-697 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  56. Published

    N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes

    Kaszuba, K., Grzybek, M., Orłowski, A., Danne, R., Róg, T., Simons, K., Coskun, Ü. & Vattulainen, I., 7 Apr 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 14, p. 4334-4339 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  57. Published

    Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

    Sharma, V., Enkavi, G., Vattulainen, I., Róg, T. & Wikström, M., 17 Feb 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 7, p. 2040-2045 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  58. Published

    Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate

    Kulig, W., Jurkiewicz, P., Olzyńska, A., Tynkkynen, J., Javanainen, M., Manna, M., Rog, T., Hof, M., Vattulainen, I. & Jungwirth, P., 2015, In : Biochimica et Biophysica Acta: Biomembranes. 1848, 2, p. 422-432 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  59. Published

    How endoglucanase enzymes act on cellulose nanofibrils: role of amorphous regions revealed by atomistic simulations

    Orłowski, A., Róg, T., Paavilainen, S., Manna, M., Heiskanen, I., Backfolk, K., Timonen, J. & Vattulainen, I., 2015, In : Cellulose. 22, 5, p. 2911-2925 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  60. Published

    Insights into the molecular mechanism of complex I from atomistic molecular dynamics simulations

    Sharma, V., V. R. I., K., Mårten, W., Vattulainen, I. T. & Rog, T., 2015, European Biophysics Journal . Suppl. 1 ed. Springer International Publishing, Vol. 44. p. S91 (European Biophysics Journal; vol. 44, no. Supplement 1).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  61. Published

    Insights into the molecular mechanism of complex I from atomistic molecular dynamics simulations.

    Sharma, V., Kaila, V., Wikström, M., Vattulainen, I. T. & Rog, T., 2015, European Biophysics Journal.

    Research output: Other contributionScientificpeer-review

  62. Published

    Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions

    Botan, A., Favela-Rosales, F., Fuchs, P. F. J., Javanainen, M., Kanduč, M., Kulig, W., Lamberg, A., Loison, C., Lyubartsev, A., Miettinen, M. S., Monticelli, L., Määttä, J., Ollila, O. H. S., Retegan, M., Róg, T., Santuz, H. & Tynkkynen, J., 2015, In : Journal of Physical Chemistry Part B. 119, 49, p. 15075-15088 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  63. 2014
  64. Published

    Cholesterol level affects surface charge of lipid membranes in saline solution

    Magarkar, A., Dhawan, V., Kallilnteri, P., Viitala, T., Elmowafy, M., Rog, T. & Bunker, A., 2014, In : Scientific Reports. 4, p. 1-5 5 p., 5005.

    Research output: Contribution to journalArticleScientificpeer-review

  65. Published

    Cholesterol, sphingolipids and glycolipids: What do we know about their role in raft-like membranes?

    Rog, T. & Vattulainen, I., 2014, In : Chemistry and Physics of Lipids. 184, p. 82-104 22 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  66. Published

    Co-exposure with fullerene may strengthen health effects of organic industrial chemicals

    Lehto, M., Karilainen, T., Rog, T., Cramariuc, O., Vanhala, E., Yornaeus, J., Taberman, H., Jänis, J., Alenius, H., Vattulainen, I. & Laine, O., 2014, In : PLoS ONE. 9, 12, p. 1-24 24 p., e114490.

    Research output: Contribution to journalArticleScientificpeer-review

  67. Published

    Dehydroergosterol as an Analogue for Cholesterol: Why It Mimics Cholesterol So Well - or Does It?

    Pourmousa, M., Rog, T., Mikkeli, R., Vattulainen, I., Solanko, L. M., Wustner, D., Holmgaard List, N., Kongsted, J. & Karttunen, M., 2014, In : Journal of Physical Chemistry Part B. 118, 26, p. 7345-7357 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  68. Published

    Effect of PEGylation on Drug Entry into Lipid Bilayer

    Rissanen, S., Kumorek, M., Martinez-Seara, H., Li, Y-C., Jamroz, D., Bunker, A., Nowakowska, M., Vattulainen, I., Kepczynski, M. & Rog, T., 2014, In : Journal of Physical Chemistry Part B. 118, 1, p. 144-151 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  69. Published

    Enzymatic oxidation of cholesterol: Properties and functional effects of cholestenone in cell membranes

    Neuvonen, M., Manna, M., Mokkila, S., Javanainen, M., Rog, T., Liu, Z., Bittman, R., Vattulainen, I. & Ikonen, E., 2014, In : PLoS ONE. 9, 8, 13 p., e103743.

    Research output: Contribution to journalArticleScientificpeer-review

  70. Published

    How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations

    Äijänen, T., Koivuniemi, A., Javanainen, M., Rissanen, S., Rog, T. & Vattulainen, I., 2014, In : PLoS Computational Biology. 10, 11, p. 1-14 14 p., e1003987.

    Research output: Contribution to journalArticleScientificpeer-review

  71. Published

    How To Tackle the Issues in Free Energy Simulations of Long Amphiphiles Interacting with Lipid Membranes: Convergence and Local Membrane Deformations

    Filipe, H. A. L., Moreno, M. J., Rog, T., Vattulainen, I. & Loura, L. M. S., 2014, In : Journal of Physical Chemistry Part B. 118, 13, p. 3572-3581 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  72. Published

    How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers?

    Kulig, W., Tynkkynen, J., Javanainen, M., Manna, M., Rog, T., Vattulainen, I. & Jungwirth, P., 2014, In : Journal of Molecular Modeling. 20, 2, p. 1-9 9 p., 2121.

    Research output: Contribution to journalArticleScientificpeer-review

  73. Published

    Molecular Dynamics Simulation of Inverse-Phosphocholine Lipids

    Magarkar, A., Rog, T. & Bunker, A., 2014, In : Journal of Physical Chemistry C. 118, 33, p. 19444-19449 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  74. Published

    Molecular Dynamics Simulation of PEGylated Membranes with Cholesterol: Building Toward the DOXIL Formulation

    Magarkar, A., Rog, T. & Bunker, A., 2014, In : Journal of Physical Chemistry C. 118, 28, p. 15541-15549 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  75. Published

    Molecular nature of the conformational and electrostatic coupling in the proton pumping mechanism of complex I

    Sharma, V., Wikström, M., Vattulainen, I. T. & Rog, T., 2014, BBA Bioenergetics.

    Research output: Other contributionScientificpeer-review

  76. Published

    Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration

    Maciejewski, A., Pasenkiewicz-Gierula, M., Cramariuc, O., Vattulainen, I. & Rog, T., 2014, In : Journal of Physical Chemistry C. 118, 17, p. 4571-4581 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  77. Published

    The challenges of understanding glycolipid functions: An open outlook based on molecular simulations

    Manna, M., Rog, T. & Vattulainen, I., 2014, In : Biochimica et Biophysica Acta: Molecular and Cell Biology of Lipids. 1841, 8, p. 1130-1145 16 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  78. 2013
  79. Published

    A computational QM/MM insight on the iron-sulphur cluster in cytocrhome BC1

    Cramariuc, O., Iglesias-Fernandez, J., Kaszuba, K., Rog, T., Rovira, C. & Vattulainen, I., 2013, Physics Days 2013 - Fysiikan päivät 2013, the 47th annual meeting of the Finnish Physical Society, Otaniemi, Espoo, March 14-16, 2013. 1 p. (Physics Days / Fysiikan päivät : Annual Meeting of the Finnish Physical Society).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  80. Published

    Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex

    Pöyry, S., Cramariuc, O., Postila, P. A., Kaszuba, K., Sarewicz, M., Osycza, A., Vattulainen, I. & Rog, T., 2013, In : Biochimica et Biophysica Acta: Bioenergetics. 1827, 6, p. 769-778 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  81. Published

    Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations

    Postila, P. A., Kaszuba, K., Sarewicz, M., Osycza, A., Vattulainen, I. & Rog, T., 2013, In : Biochimica et Biophysica Acta: Bioenergetics. 1827, 6, p. 761-768 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  82. Published

    Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It

    Martinez-Seara, H. & Rog, T., 2013, Biomolecular Simulations: Methods and Protocols. Monticelli, L. & Salonen, E. (eds.). New York: Humana Press, p. 407-429 (Methods in Molecular Biology; vol. 924).

    Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  83. Published

    Molecular lipidomics of exosomes released by PC-3 prostate cancer cells

    Llorente, A., Skotland, T., Sylvänne, T., Kauhanen, D., Rog, T., Orlowski, A., Vattulainen, I., Ekroos, K. & Sandvig, K., 2013, In : Biochimica et Biophysica Acta: Molecular and Cell Biology of Lipids. 1831, 7, p. 1302-1309 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  84. Published

    Molecular modeling of the PEGylated bilayer as a model for the PEGylated liposome surface in the bloodstream

    Magarkar, A., Stepniewski, M., Karakas, E., Rog, T., Yliperttula, M., Urtti, A. & Bunker, A., 2013, Technical Proceedings of the 2013 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech 2013. Vol. 2. p. 576-578 3 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  85. Published

    Parameterization of the prosthetic redox centers of the bacterial cytochrome bc1 complex for atomistic molecular dynamics simulations

    Kaszuba, K., Postila, P. A., Cramariuc, O., Sarewicz, M., Osyczka, A., Vattulainen, I. & Rog, T., 2013, In : Theoretical Chemistry Accounts. 132, 6, p. 1-13 13 p., UNSP 1370.

    Research output: Contribution to journalArticleScientificpeer-review

  86. 2012
  87. Published

    Analysis of cause of failure of new targeting peptide in PEGylated liposome: Molecular modeling as rational design tool for nanomedicine

    Lehtinen, J., Magarkar, A., Stepniewski, M., Hakola, S., Bergman, M., Rog, T., Yliperttula, M., Urtti, A. & Bunker, A., 2012, In : European Journal of Pharmaceutical Sciences. 46, 3, p. 121-130

    Research output: Contribution to journalArticleScientificpeer-review

  88. Published

    Drug-lipid membrane interaction mechanisms revealed through molecular simulations

    Cramariuc, O., Rog, T. & Vattulainen, I., 2012, In : Current Physical Chemistry. 2, 4, p. 379-400

    Research output: Contribution to journalReview ArticleScientificpeer-review

  89. Published

    Interaction of hematoporphyrin with lipid membranes

    Stepniewski, M., Kepczynski, M., Jamorz, D., Nowakowska, M., Rissanen, S., Vattulainen, I. & Rog, T., 2012, In : Journal of Physical Chemistry Part B. 116, 16, p. 4889-4897

    Research output: Contribution to journalArticleScientificpeer-review

  90. Published

    Mechanical properties of cellulose nanofibrils determined through atomistic molecular dynamics simulations

    Paavilainen, S., McWhirter, J. L., Rog, T., Järvinen, J., Vattulainen, I. & Ketoja, J. A., 2012, In : Nordic Pulp and Paper Research Journal. 27, 2, p. 282-286

    Research output: Contribution to journalArticleScientificpeer-review

  91. Published

    Mechanism for translocation of fluoroquinolones across lipid membranes

    Cramariuc, O., Rog, T., Javanainen, M., Monticelli, L., Polishchuk, A. & Vattulainen, I., 2012, In : Biochimica et Biophysica Acta: Biomembranes. 1818, 11, p. 2563-2571

    Research output: Contribution to journalArticleScientificpeer-review

  92. Published

    Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase

    Kaszuba, K., Rog, T., Danne, R., Canning, P., Fulöp, V., Juhasz, T., Szeltner, Z., St.Pierre, J-F., Garcia-Horsman, A., Männistö, P. T., Karttunen, M., Hokkanen, J. & Bunker, A., 2012, In : Biochimie. 94, 6, p. 1398-1411

    Research output: Contribution to journalArticleScientificpeer-review

  93. Published

    Molecular dynamics simulation of PEGylated bilayer interacting with salt ions: A model of the liposome surface in the bloodstream

    Magarkar, A., Karakas, E., Stepniewski, M., Rog, T. & Bunker, A., 2012, In : Journal of Physical Chemistry Part B. 116, 14, p. 4212-4219

    Research output: Contribution to journalArticleScientificpeer-review

  94. Published

    Molecular dynamics simulations of the bacterial ABC transporter SAV1866 in the closed form

    St-Pierre, J-F., Bunker, A., Rog, T., Karttunen, M. & Mousseau, N., 2012, In : Journal of Physical Chemistry Part B. 116, 9, p. 2934-2942

    Research output: Contribution to journalArticleScientificpeer-review

  95. Published

    Molecular modeling of the PEGylated bilayer as a model for the PEGylated liposome surface in the bloodstream

    Magarkar, A., Stepniewski, M., Karakas, E., Rog, T., Yliperttula, M., Urtti, A. & Bunker, A., 2012, Nanotechnology 2012: Bio Sensors, Instruments, Medical, Environment and Energy - 2012 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech 2012, Santa Clara, CA, USA, 18-21 June 2012. Nano Science and Technology Institute NSTI, p. 293-295 (Nanotechnology Conference and Expo Nanotech).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  96. Published

    Strong preferences of dopamine and L-dopa towards lipid head group: importance of lipid composition and implication for neurotransmitter metabolism

    Orlowski, A., Crzybek, M., Bunker, A., Pasenkiewicz-Gierula, M., Rog, T., Vattulainen, I. & Männistö, P. T., 2012, In : Journal of Neurochemistry. 122, 4, p. 681-690

    Research output: Contribution to journalArticleScientificpeer-review

  97. Published

    Study of Interaction Between PEG Carrier and Three Relevant Drug Molecules: Piroxicam, Paclitaxel, and Hematoporphyrin

    Li, Y-C., Rissanen, S., Stepniewski, M., Cramariuc, O., Rog, T., Mirza, S., Xhaard, H., Wytrwal, M., Kepczynski, M. & Bunker, A., 2012, In : Journal of Physical Chemistry Part B. 116, 24, p. 7334-7341

    Research output: Contribution to journalArticleScientificpeer-review

  98. Published

    Tat(48-60) peptide amino acid sequence is not unique in its cell penetrating properties and cell-surface glycosaminoglycans inhibit its cellular uptake

    Subrizi, A., Tuominen, E., Bunker, A., Rog, T., Antopolsky, M. & Urtti, A., 2012, In : Journal of Controlled Release. 158, 2, p. 277-285

    Research output: Contribution to journalArticleScientificpeer-review

  99. 2011
  100. Published

    Analysis of twisting of cellulose nanofibrils in atomistic molecular dynamics simulations

    Paavilainen, S., Rog, T. & Vattulainen, I., 2011, In : Journal of Physical Chemistry Part B. 115, 14, p. 3747-3755

    Research output: Contribution to journalArticleScientificpeer-review

  101. Published

    Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans

    Pietiläinen, K., Rog, T., Seppänen-Laakso, T., Virtue, S., Gopalacharyulu, P., Tang, J., Rodriguez-Cuenca, S., Maciejewski, A., Naukkarinen, J., Ruskeepää, A-L., Niemelä, P., Yetukuri, L., Tan, C. Y., Velagapudi, V., Castillo, S., Nygren, H., Hyötyläinen, T., Rissanen, A., Kaprio, J., Yki-Järvinen, H., Vattulainen, I., Vidal-Puig, A. & Oresic, M., 2011, In : PLoS Biology. 9, 6, p. 1-14 14 p., e1000623.

    Research output: Contribution to journalArticleScientificpeer-review

  102. Published

    Cholesterol modulates glycolipid conformation and receptor activity

    Lingwood, D., Binnington, B., Rog, T., Vattulainen, I., Grzybek, M., Coskun, U., Lingwood, C. & Simons, K., 2011, In : Nature Chemical Biology. 7, p. 260-262

    Research output: Contribution to journalArticleScientificpeer-review

  103. Published

    Effect of galactosylceramide on the dynamics of cholesterol-rich lipid membranes

    Hall, A., Rog, T. & Vattulainen, I., 2011, In : Journal of Physical Chemistry Part B. 115, 49, p. 14424-14434

    Research output: Contribution to journalArticleScientificpeer-review

  104. Published

    Lateral sorting in model membranes by cholesterol-mediated hydrophobic matching

    Kaiser, H-J., Orlowski, A., Rog, T., Nyholm, T., Chai, W., Feizl, T., Lingwood, D., Vattulainen, I. & Simons, K., 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 40, p. 16628-16633

    Research output: Contribution to journalArticleScientificpeer-review

  105. Published

    Lipid simulations: a perspective on lipids in action

    Vattulainen, I. & Rog, T., 2011, In : Cold Spring Harbor Perspectives in Biology. 3, 4, p. 1-13 13 p., a004655.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  106. Published

    N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol

    Björkholm, A., Rog, T., Kankaanpää, P., Lindroos, D., Kaszuba, K., Kurita, M., Yamaguchi, S., Yamamoto, T., Jaikishan, S., Paavolainen, L., Päivärinne, J., Nyholm, T., Katsumura, S., Vattulainen, I. & Slotte, P. J., 2011, In : Biochimica et Biophysica Acta: Biomembranes. 1808, 4, p. 1179-1186

    Research output: Contribution to journalArticleScientificpeer-review

  107. Published

    Properties of the membrane binding component of catechol-O-methyltransferase revealed by atomistic molecular dynamics simulations

    Orlowski, A., St-Pierre, J-F., Magarkar, A., Bunker, A., Pasenkiewicz-Gierula, M., Vattulainen, I. & Rog, T., 2011, In : Journal of Physical Chemistry Part B. 115, 46, p. 13541-13550

    Research output: Contribution to journalArticleScientificpeer-review

  108. Published

    Study of PEGylated Lipid Layers as a Model for PEGylated Liposome Surfaces: Molecular Dynamics Simulation and Langmuir Monolayer Studies

    Stepniewski, M., Pasenkiewicz-Gierula, M., Rog, T., Danne, R., Orlowski, A., Karttunen, M., Urtti, A., Yliperttula, M., Vuorimaa, E. & Bunker, A., 2011, In : Langmuir. 27, 12, p. 7788-7798

    Research output: Contribution to journalArticleScientificpeer-review

  109. Published

    Use of umbrella sampling to calculate the entrance/exit pathway for Z-pro-prolinal inhibitor in prolyl oligopeptidase

    St-Pierre, J-F., Karttunen, M., Mousseau, N., Rog, T. & Bunker, A., 2011, In : Journal of Chemical Theory and Computation. 7, 6, p. 1583-1594

    Research output: Contribution to journalArticleScientificpeer-review

  110. 2010
  111. Published

    Behavior of 2,6-Bis(decyloxy)naphthalene inside lipid bilayer

    Kepczynski, M., Kumorek, M., Stepniewski, M., Rog, T., Kozik, B., Jamroz, D., Bednar, J. & Nowakowska, M., 2010, In : Journal of Physical Chemistry Part B. 114, 47, p. 15483-15494

    Research output: Contribution to journalArticleScientificpeer-review

  112. Published

    Cholesterol induces specific spatial and orientational order in cholesterol/phospholipid membranes

    Martinez-Seara, H., Rog, T., Karttunen, M., Vattulainen, I. & Reigada, R., 2010, In : PLoS ONE. 5, 6, e11162, p. 1-11 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  113. Published

    Deuteration of water enables self-organization of phospholipid-based reverse micelles

    Milhaud, J., Bouchemal, N., Rog, T. & Hanz, E., 2010, In : ChemPhysChem. 11, p. 590-598

    Research output: Contribution to journalArticleScientificpeer-review

  114. Published

    Effect of sphingomyelin headgroup size on molecular properties and interactions with cholesterol

    Bjorkbom, A., Rog, T., Kaszuba, K., Kurita, M., Yamaguchi, S., Lonnfors, M., Nyholm, T., Vattulainen, I., Katsumura, S. & Slotte, J. P., 2010, In : Biophysical Journal. 99, 10, p. 3300-3308

    Research output: Contribution to journalArticleScientificpeer-review

  115. Published

    Effects of the lipid bilayer phase state on the water membranes interface

    Stepniewski, M., Bunker, A., Pasenkiewicz-Gierula, M., Karttunen, M. & Rog, T., 2010, In : Journal of Physical Chemistry Part B. 114, 36, p. 11784-11792

    Research output: Contribution to journalArticleScientificpeer-review

  116. Published

    Molecular dynamics simulations reveal fundamental role of water as factor determining affinity of binding of b-blocker nebivolol to b2-adrenergic receptor

    Kaszuba, K., Rog, T., Bryl, K., Vattulainen, I. & Karttunen, M., 2010, In : Journal of Physical Chemistry Part B. 114, 25, p. 8374-8386

    Research output: Contribution to journalArticleScientificpeer-review

  117. Published

    Role of glycolipids in lipid rafts: A view through atomistic molecular dynamics simulations with galactosylceramide

    Hall, A., Rog, T., Karttunen, M. & Vattulainen, I., 2010, In : Journal of Physical Chemistry Part B. 114, p. 7797-7807

    Research output: Contribution to journalArticleScientificpeer-review

  118. Published

    Specific spatial and orientational order in phospholipid membranes induced by cholesterol

    Martinez-Seara, H., Rog, T., Karttunen, M., Reigada, R. & Vattulainen, I., 2010, Biophysical Society's 54th Annual Meeting 20.2-24.2.2010, San Fransisco, California, USA. Biophysical Journal. p. 668a-668a

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  119. 2009
  120. Published

    Mitochondrial membranes with mono- and divalent salt: Changes induced by salt ions on structure and dynamics

    Pöyry, S., Rog, T., Karttunen, M. & Vattulainen, I., 2009, In : Journal of Physical Chemistry Part B. 113, 47, p. 15513-15521

    Research output: Contribution to journalArticleScientificpeer-review

  121. Published

    Molecular dynamic simulations of nebivolol complexed with B1 and B2 adrenergic receptors - subtype specificity studies

    Kaszuba, K., Vattulainen, I., Karttunen, M. & Rog, T., 2009, Proceedings of the XLIII Annual Conference of The Finnish Physical Society, 12-14 March, 2009, Espoo, Finland, Helsinki University of Technology, Low Temperature Laboratory Publications. Laiho, P. (ed.). p. p. 307

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  122. Published

    Molecular dynamics simulations of cellulose nanofibrils

    Paavilainen, S., Rog, T. & Vattulainen, I., 2009, Proceedings of the XLIII Annual Conference of The Finnish Physical Society, 12-14 March, 2009, Espoo, Finland, Helsinki University of Technology, Low Temperature Laboratory Publications. Laiho, P. (ed.). p. p. 96

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  123. Published

    Molecular dynamics simulations of nebivolol complexed with B1 and B2 adrenergic receptors - subtype specificity studies

    Kaszuba, K., Vattulainen, I., Karttunen, M. & Rog, T., 2009, Fifth International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, 4-8 July 2009, Istanbul, Turkey. p. p. 107 1 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  124. Published

    Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity

    Kaszuba, K., Rog, T., St. Pierre, J-F., Männistö, P. T., Karttunen, M. & Bunker, A., 2009, In : SAR and QSAR in Environmental Research. 20, 7&8, p. 595-609

    Research output: Contribution to journalArticleScientificpeer-review

  125. Published

    Ordering effects of cholesterol and its analogues

    Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I. & Karttunen, M., 2009, In : Biochimica et Biophysica Acta: International Journal of Biochemistry and Biophysics. 1788, 1, p. 97-121

    Research output: Contribution to journalArticleScientificpeer-review

  126. Published

    Role of cardiolipins in the inner mitochondrial membrane: insight gained through atom-scale simulations

    Rog, T., Martinez-Seara, H., Munck, N., Oresic, M., Karttunen, M. & Vattulainen, I., 2009, In : Journal of Physical Chemistry Part B. 113, 11, p. 3413-3422

    Research output: Contribution to journalArticleScientificpeer-review

  127. Published

    The role of glycolipids in lipid rafts: molecular dynamics simulations of membranes with galactosylceramide

    Hall, A., Rog, T. & Vattulainen, I., 2009, Proceedings of the XLIII Annual Conference of The Finnish Physical Society, 12-14 March, 2009, Espoo, Finland, Helsinki University of Technology, Low Temperature Laboratory Publications. Laiho, P. (ed.). p. p. 350

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  128. Published

    Water isotope effect on phospholipid bilayer properties: molecular dynamics simulation study

    Rog, T., Milhaud, J., Karttunen, M. & Pasenkiewicz-Gierula, M., 2009, Proceedings of the XLIII Annual Conference of The Finnish Physical Society, 12-14 March, 2009, Espoo, Finland, Helsinki University of Technology, Low Temperature Laboratory Publications. Laiho, P. (ed.). p. p. 354

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  129. Published

    Water isotope effect on the phosphatidylcholilne bilayer properties: a molecular dynamics simulation study

    Rog, T., Murzyn, K., Milhaud, J., Karttunen, M. & Pasenkiewicz-Gierula, M., 2009, In : Journal of Physical Chemistry Part B. 113, 8, p. 2378-2387

    Research output: Contribution to journalArticleScientificpeer-review

  130. Published
  131. 2008
  132. Published

    Comparison of cholesterol and its direct precursors along the biosynthetic pathway: Effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers

    Rog, T., Vattulainen, I., Jansen, M., Ikonen, E. & Karttunen, M., 2008, In : Journal of Chemical Physics. 129, 154508, p. pp. 154508-1-10 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  133. Published

    Influence of cis douple-bond parametrization on lipid membrane properties: How seemingly insignificant details in force-field change even qualitative trends

    Martinez-Seara, H., Rog, T., Karttunen, M., Reigada, R. & Vattulainen, I., 2008, In : Journal of Chemical Physics. 129, 105103, p. pp. 105103-1-7 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  134. Published

    Interplay of unsaturated phospholipids and cholesterol in membranes: effect of the double-bond position

    Martinez-Seara, H., Rog, T., Pasenkeiwicz-Gierula, M., Vattulainen, I., Karttunen, M. & Reigada, R., 2008, In : Biophysical Journal. 95, p. 3295-3305

    Research output: Contribution to journalArticleScientificpeer-review

  135. Published

    Lateral diffusion in lipid membranes through collective flows

    Falck, E., Rog, T., Karttunen, M. & Vattulainen, I., 2008, In : Journal of the American Chemical Society. 130, p. 44-45

    Research output: Contribution to journalArticleScientificpeer-review

  136. Molecular dynamics simulations of the enzyme Catechol-O-Methyltransferase: methodological issues

    Bunker, A., Männistö, P. T., St. Pierre, J-F., Rog, T., Pomorski, P., Stimson, L. & Karttunen, M., 2008, In : SAR and QSAR in Environmental Research. 19, 1&2, p. 179-189

    Research output: Contribution to journalArticleScientificpeer-review

  137. Nonpolar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies

    Rog, T., Murzyn, K., Karttunen, M. & Pasenkiewicz-Gierula, M., 2008, In : Journal of Peptide Science. 14, p. 374-382

    Research output: Contribution to journalArticleScientificpeer-review

  138. Published

    Replacing the cholesterol hydroxyl group with the ketone group facilitates sterol flip-flop and promotes membrane fluidity

    Rog, T., Stimson, L. K., Pasenkiewicz-Gierula, M., Vattulainen, I. & Karttunen, M., 2008, In : Journal of Physical Chemistry Part B. 112, p. 1946-1952

    Research output: Contribution to journalArticleScientificpeer-review

  139. Published

    Role of glycolipids in lipid rafts: view through atomistic simulations

    Hall, A., Rog, T. & Vattulainen, I., 2008, GGS Annual Seminar, 5th Finnish Glycoscience Meeting, 23.-24.9.2008, University of Helsinki, Tvärminne Zoological Station. p. p. 23

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  140. Published

    Role of phosphatidylglycerols in the stability of bacterial membranes

    Zhao, W., Rog, T., Gurtovenko, A. A., Vattulainen, I. & Karttunen, M., 2008, In : Biochimie. 90, 6, p. 930-938

    Research output: Contribution to journalArticleScientificpeer-review

  141. Published

    Significance of cholesterol methyl groups

    Pöyry, S., Rog, T., Karttunen, M. & Vattulainen, I., 2008, In : Journal of Physical Chemistry Part B. 112, p. 2922-2929

    Research output: Contribution to journalArticleScientificpeer-review

  142. 2007
  143. Published

    Atomic-scale structure and electrostatics of anionic palmitoyloleoylphosphatidylglycerol lipid bilayers with Na+ counterions

    Zhao, W., Rog, T., Gurtovenko, A. A., Vattulainen, I. & Karttunen, M., 2007, In : Biophysical Journal. 92, 4, p. 1114-1124

    Research output: Contribution to journalArticleScientificpeer-review

  144. Published

    Cholesterol methyl groups - molecular fossils?

    Pöyry, S., Rog, T., Karttunen, M. & Vattulainen, I., 2007, Abstracts from the 48th International Conference on the Bioscience of Lipids, 4-8 September 2007, Turku, Finland. Chemistry and Physics of Lipids CPL. Kinnunen, P. K. J. (ed.). p. p. 41

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  145. Published

    Effect of double bond position on lipid bilayer properties: Insight through atomistic simulations

    Martinez-Seara, H., Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I., Karttunen, M. & Reigada, R., 2007, In : Journal of Physical Chemistry Part B. 111, 38, p. 11162-11168

    Research output: Contribution to journalArticleScientificpeer-review

  146. Published

    Effects of cholesterol, desmosterol and 7-dehydrocholesterol on lipid bilayers. Molecular dynamics simulation study

    Rog, T., Vattulainen, I., Ikonen, E. & Karttunen, M., 2007, Proceedings of the XLI Annual Conference of the Finnish Physical Society, March 15-17, 2007, Tallinn, Estonia. University of Helsinki. Report Series in Physics. Vainio, R. (ed.). p. p. 95

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  147. Published

    Glycolipid membranes through atomistic simulations: Effect of glucose and galactose head groups on lipid bilayer properties

    Rog, T., Vattulainen, I., Bunker, A. & Karttunen, M., 2007, In : Journal of Physical Chemistry Part B. 111, p. 10146-10154

    Research output: Contribution to journalArticleScientificpeer-review

  148. Published

    Lateral pressure profiles of lipid bilayers with different lipid compositions

    Ollila, S., Niemelä, P. S., Rog, T., Hyvönen, M. T., Karttunen, M. & Vattulainen, I., 2007, Proceedings of the XLI Annual Conference of the Finnish Physical Society, March 15-17, 2007, Tallinn, Estonia. University of Helsinki. Report Series in Physics. Vainio, R. (ed.). p. p. 87

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  149. Published

    Lateral pressure profiles of lipid membranes - Dependence on lipid composition

    Ollila, S., Niemelä, P. S., Rog, T., Hyvönen, M. T., Karttunen, M. & Vattulainen, I., 2007, Biophysical Society 51st Annual Meeting, March 3-7, 2007, Baltimore, Maryland, USA. Biophysical Journal. p. p. 234A

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  150. Published

    Multiscale simulations of domain formation in single-component phospholipid bilayers

    Murtola, T., Rog, T., Falck, E., Karttunen, M. & Vattulainen, I., 2007, Abstracts from the 48th International Conference on the Bioscience of Lipids, 4-8 September 2007, Turku, Finland. Chemistry and Physics of Lipids CPL. Kinnunen, P. K. J. (ed.). p. p. 15

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  151. Published

    Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol

    Ollila, S. O. H., Rog, T., Karttunen, M. & Vattulainen, I., 2007, In : Journal of Structural Biology. 159, p. 311-323

    Research output: Contribution to journalArticleScientificpeer-review

  152. Stearic acid spin labels in lipid bilayers: Insight through atomistic Simulations

    Stimson, L. M., Dong, L., Karttunen, M., Wisniewska, A., Dutka, M. & Rog, T., 2007, In : Journal of Physical Chemistry Part B. 111, 43, p. 12447-12453

    Research output: Contribution to journalArticleScientificpeer-review

  153. Published

    The significance of cholesterol methyl groups

    Pöyry, S., Rog, T., Karttunen, M. & Vattulainen, I., 2007, Proceedings of the XLI Annual Conference of the Finnish Physical Society, March 15-17, 2007, Tallinn, Estonia. University of Helsinki. Report Series in Physics. Vainio, R. (ed.). p. p. 94

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  154. Published

    What happens if cholesterol is made smoother: Importance of methyl substituents in cholesterol ring structure on phosphatidylcholine-sterol interaction

    Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I. & Karttunen, M., 2007, In : Biophysical Journal. 92, 10, p. 3346-3357

    Research output: Contribution to journalArticleScientificpeer-review

  155. 2006
  156. Cholesterol effects on a mixed-chain phosphatidylcholine bilayer: a molecular dynamics simulation study

    Rog, T. & Pasenkiewicz-Gierula, M., 2006, In : Biochimie. 88

    Research output: Contribution to journalArticleScientificpeer-review

  157. Cholesterol-sphingomyelin interactions: A molecular dynamics simulation study

    Rog, T. & Psenkiewicz-Gierula, M., 2006, In : Biophysical Journal. 91

    Research output: Contribution to journalArticleScientificpeer-review

  158. Dynamics of water at membrane surface: Effect of headgroup structure

    Murzyn, K., Zhao, W., Karttunen, M., Kurdziel, M. & Rog, T., 2006, In : Biointerphases. 1, 3, p. 8 p

    Research output: Contribution to journalArticleScientificpeer-review

  159. Published

    How sugar headgroups affect the properties of lipid bilayers: molecular dynamics simulation studies

    Rog, T., Vattulainen, I. & Karttunen, M., 2006, Proceedings of the XL Annual Conference of the Finnish Physical Society, 9-11 March, 2006, Tampere, Finland. Tampere University of Technology. Institute of Physics. Report. Kauranen, M. (ed.). Tampere, p. p. 347

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  160. Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome C

    Murzyn, K., Rog, T., Blicharski, W., Dutka, M., Pyka, J., Szytula, S. & Froncisz, W., 2006, In : Proteins: Structure Function and Bioinformatics. 62

    Research output: Contribution to journalArticleScientificpeer-review

  161. Published

    Significance of sterol structural specificity - Desmosterol cannot replace cholesterol in lipid rafts

    Vainio, S., Jansen, M., Koivusalo, M., Rog, T., Karttunen, M., Vattulainen, I. & Ikonen, E., 2006, In : Journal of Biological Chemistry. 281, 1, p. 348-355

    Research output: Contribution to journalArticleScientificpeer-review

  162. Published

    Systematic coarse-graining of phospholipid/cholesterol bilayer

    Murtola, T., Falck, E., Rog, T., Karttunen, M. & Vattulainen, I., 2006, Proceedings of the XL Annual Conference of the Finnish Physical Society, 9-11 March, 2006, Tampere, Finland. Tampere University of Technology. Institute of Physics. Report. Kauranen, M. (ed.). Tampere, p. p. 332

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  163. Published

    Tilt: major factor in sterols' ordering capability in membranes

    Aittoniemi, J., Rog, T., Niemelä, P., Pasenkiewicz-Gierula, M., Karttunen, M. & Vattulainen, I., 2006, In : Journal of Physical Chemistry Part B. 110, 51, p. 25562-25564

    Research output: Contribution to journalArticleScientificpeer-review

  164. Published

    Transient ordered domains in single-component phospholipid bilayers

    Murtola, T., Rog, T., Falck, E., Karttunen, M. & Vattulainen, I., 2006, In : Physical Review Letters. 97, 23, 238102, p. pp. 238102

    Research output: Contribution to journalArticleScientificpeer-review

  165. 2005
  166. Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane

    Murzyn, K., Rog, T. & Pasenkiewicz-Gierula, M., Feb 2005, In : Biophysical Journal. 88, 2, p. 1091-1103 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  167. Exploring the effect of xenon on biomembranes

    Stimson, L. M., Vattulainen, I., Rog, T. & Karttunen, M., 2005, In : Cellular and Molecular Biology Letters. 10, 4, p. 563-569

    Research output: Contribution to journalArticleScientificpeer-review

  168. Modeling glycolipids: Take one

    Rog, T., Vattulainen, I. & Karttunen, M., 2005, In : Cellular and Molecular Biology Letters. 10, 4, p. 625-630

    Research output: Contribution to journalArticleScientificpeer-review

  169. 2004
  170. Non-polar interactions between cholesterol and phospholipids: a molecular dynamics simulation study

    Rog, T. & Pasenkiewicz-Gierula, M., 1 Feb 2004, In : Biophysical Chemistry. 107, 2, p. 151-164 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  171. Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study

    Rog, T., Murzyn, K., Gurbiel, R., Takaoka, Y., Kusumi, A. & Pasenkiewicz-Gierula, M., Feb 2004, In : Journal of Lipid Research. 45, 2, p. 326-336 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  172. Interactions of magainin-2 amide with membrane lipids

    Murzyn, K., Rog, T. & Pasenkiewicz-Gierula, M., 2004, Computational Science - ICCS 2004, Pt 2, Proceedings. Bubak, M., VanAlbada, GD., Sloot, PMA. & Dongarra, JJ. (eds.). BERLIN: Springer-Verlag Berlin Heidelberg, p. 325-331 7 p. (LECTURE NOTES IN COMPUTER SCIENCE; vol. 3037).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  173. 2003
  174. Effects of a carane derivative local anesthetic on a phospholipid bilayer studied by molecular dynamics simulation

    Pasenkiewicz-Gierula, M., Rog, T., Grochowski, J., Serda, P., Czarnecki, R., Librowski, T. & Lochynski, S., Aug 2003, In : Biophysical Journal. 85, 2, p. 1248-1258 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  175. nMoldyn: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations

    Rog, T., Murzyn, K., Hinsen, K. & Kneller, GR., 15 Apr 2003, In : Journal of Computational Chemistry. 24, 5, p. 657-667 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  176. Effects of epicholesterol on the phosphatidylcholine bilayer: A molecular simulation study

    Rog, T. & Pasenkiewicz-Gierula, M., Mar 2003, In : Biophysical Journal. 84, 3, p. 1818-1826 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  177. Molecular dynamics simulations of charged and neutral lipid bilayers: Treatment of electrostatic interactions

    Rog, T., Murzyn, K. & Pasenkiewicz-Gierula, M., 2003, In : Acta Biochimica Polonica. 50, 3, p. 789-798 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  178. 2002
  179. Published

    The dynamics of water at the phospholipid bilayer surface: a molecular dynamics simulation study

    Rog, T., Murzyn, K. & Pasenkiewicz-Gierula, M., 6 Feb 2002, In : Chemical Physics Letters. 352, 5-6, p. 323-327 5 p.

    Research output: Contribution to journalArticleScientificpeer-review

  180. 2001
  181. Cholesterol effects on the phosphatidylcholine bilayer nonpolar region: A molecular simulation study

    Rog, T. & Pasenkiewicz-Gierula, M., Oct 2001, In : Biophysical Journal. 81, 4, p. 2190-2202 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  182. Cholesterol effects on the phospholipid condensation and packing in the bilayer: a molecular simulation study

    Rog, T. & Pasenkiewicz-Gierula, M., 27 Jul 2001, In : FEBS Letters. 502, 1-2, p. 68-71 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  183. Effects of phospholipid unsaturation on the membrane/water interface: A molecular simulation study

    Murzyn, K., Rog, T., Jezierski, G., Takaoka, Y. & Pasenkiewicz-Gierula, M., Jul 2001, In : Biophysical Journal. 81, 1, p. 170-183 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  184. 2000
  185. Cholesterol effects on the phosphatidylcholine bilayer polar region: A molecular simulation study

    Pasenkiewicz-Gierula, M., Rog, T., Kitamura, K. & Kusumi, A., Mar 2000, In : Biophysical Journal. 78, 3, p. 1376-1389 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  186. Molecular dynamics simulation studies of lipid bilayer systems

    Pasenkiewicz-Gierula, M., Murzyn, K., Rog, T. & Czaplewski, C., 2000, In : Acta Biochimica Polonica. 47, 3, p. 601-611 11 p.

    Research output: Contribution to journalLiterature reviewScientificpeer-review

  187. 1997
  188. Conformations, orientations and time scales characterising dimyristoylphosphatidylcholine bilayer membrane. Molecular dynamics simulation studies

    Pasenkiewicz-Gierula, M. & Rog, T., 1997, In : Acta Biochimica Polonica. 44, 3, p. 607-624 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

ID: 45237