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

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