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Tomasz Róg

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Sanja Pöyry; Marcin Sarewicz; Ilpo Vattulainen; Oana Cramariuc; Karol Kaszuba; Artur Osyczka; Pekka A Postila; Tomasz Róg
Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex.
Pekka A Postila; Karol Kaszuba; Artur Osyczka; Marcin Sarewicz; Ilpo Vattulainen; Tomasz Róg
Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations.
Hector Martinez-Seara; Tomasz Róg
Molecular dynamics simulations of lipid bilayers: simple recipe of how to do it.

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2013: Sanja Pöyry; Marcin Sarewicz; Ilpo Vattulainen; Oana Cramariuc; Karol Kaszuba; Artur Osyczka; Pekka A Postila; Tomasz Róg
Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex.
Biochimica et biophysica acta 2013;1827(6):769-78.
2013: Pekka A Postila; Karol Kaszuba; Artur Osyczka; Marcin Sarewicz; Ilpo Vattulainen; Tomasz Róg
Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations.
Biochimica et biophysica acta 2013;1827(6):761-8.
2013: Hector Martinez-Seara; Tomasz Róg
Molecular dynamics simulations of lipid bilayers: simple recipe of how to do it.
Methods in molecular biology (Clifton, N.J.) 2013;924():407-29.
2012: Adam Orłowski; Marta Pasenkiewicz-Gierula; alex bunker; Michał Grzybek; Pekka T Männistö; Ilpo Vattulainen; Tomasz Róg
Strong preferences of dopamine and l-dopa towards lipid head group: importance of lipid composition and implication for neurotransmitter metabolism.
Journal of neurochemistry 2012;122(4):681-90.
2012: Yen-Chin Li; Sabir Mirza; Sami Rissanen; Tomasz Róg; Michał Stepniewski; Magdalena Wytrwal; Henri Xhaard; Oana Cramariuc; Mariusz Kepczynski; alex bunker
Study of interaction between PEG carrier and three relevant drug molecules: piroxicam, paclitaxel, and hematoporphyrin.
The journal of physical chemistry. B 2012;116(24):7334-41.
2012: Julia Lehtinen; Aniket Magarkar; Tomasz Róg; Michał Stepniewski; Arto Urtti; Marjo Yliperttula; Mathias Bergman; Satu Hakola; alex bunker
Analysis of cause of failure of new targeting peptide in PEGylated liposome: molecular modeling as rational design tool for nanomedicine.
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences 2012;46(3):121-30.
2012: Karol Kaszuba; Pekka T Männistö; Tomasz Róg; J-F St Pierre; Zoltán Szeltner; Peter Canning; Reinis Danne; Vilmos Fülöp; Arturo García-Horsman; Jyrki Hokkanen; Tünde Juhász; mikko karttunen; alex bunker
Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase.
Biochimie 2012;94(6):1398-411.
2012: Aniket Magarkar; Tomasz Róg; Michał Stepniewski; Esra Karakas; alex bunker
Molecular dynamics simulation of PEGylated bilayer interacting with salt ions: a model of the liposome surface in the bloodstream.
The journal of physical chemistry. B 2012;116(14):4212-9.
2012: Astrid Subrizi; Eva Tuominen; Maxim Antopolsky; alex bunker; Tomasz Róg; Arto Urtti
Tat(48-60) peptide amino acid sequence is not unique in its cell penetrating properties and cell-surface glycosaminoglycans inhibit its cellular uptake.
Journal of controlled release : official journal of the Controlled Release Society 2012;158(2):277-85.
2012: Jean-François St-Pierre; Tomasz Róg; Alex Bunker; Mikko Karttunen; Normand Mousseau
Molecular dynamics simulations of the bacterial ABC transporter SAV1866 in the closed form.
The journal of physical chemistry. B 2012;116(9):2934-42.
2011: Adam Orłowski; Marta Pasenkiewicz-Gierula; Alex Bunker; Aniket Magarkar; Jean-François St-Pierre; Ilpo Vattulainen; Tomasz Róg
Properties of the membrane binding component of catechol-O-methyltransferase revealed by atomistic molecular dynamics simulations.
The journal of physical chemistry. B 2011;115(46):13541-50.
2011: Monika Ostrowska; Tomasz Róg; Krzysztof Banaszkiewicz; Anna Kiławiec; Dieter Lütjohann; Andrzej Szczudlik
Cerebrotendinous xanthomatosis: a rare cause of spinocerebellar syndrome.
Neurologia i neurochirurgia polska 2011;45(6):600-3.
2011: Hermann-Josef Kaiser; Daniel Lingwood; Thomas K M Nyholm; Tomasz Róg; Wengang Chai; Ten Feizi; Ilpo Vattulainen; Adam Orłowski; Kai Simons
Lateral sorting in model membranes by cholesterol-mediated hydrophobic matching.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(40):16628-33.
2011: Kirsi H Pietiläinen; Aila Rissanen; Sergio Rodriguez-Cuenca; Tomasz Róg; Anna-Liisa Ruskeepää; Tuulikki Seppänen-Laakso; Chong Yew Tan; Jing Tang; Ilpo Vattulainen; Vidya Velagapudi; antonio vidal-puig; Sam Virtue; Laxman Yetukuri; Hannele Yki-Järvinen; Sandra Castillo; Peddinti Gopalacharyulu; Tuulia Hyötyläinen; Jaakko Kaprio; Arkadiusz Maciejewski; Jussi Naukkarinen; Perttu S Niemelä; Heli Nygren; Matej Orešič
Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans.
PLoS biology 2011;9(6):e1000623.
2011: Daniel Lingwood; Beth Binnington; Tomasz Róg; Ilpo Vattulainen; Michal Grzybek; Unal Coskun; Clifford A Lingwood; Kai Simons
Cholesterol modulates glycolipid conformation and receptor activity.
Nature chemical biology 2011;7(5):260-2.
2011: Sami Paavilainen; Tomasz Róg; Ilpo Vattulainen
Analysis of twisting of cellulose nanofibrils in atomistic molecular dynamics simulations.
The journal of physical chemistry. B 2011;115(14):3747-55.
2011: Anders Björkbom; Tomasz Róg; Pasi Kankaanpää; Daniel Lindroos; Karol Kaszuba; Mayuko Kurita; Shou Yamaguchi; Tetsuya Yamamoto; Shishir Jaikishan; Lassi Paavolainen; Joacim Päivärinne; Thomas K M Nyholm; Shigeo Katsumura; Ilpo Vattulainen; J Peter Slotte
N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol.
Biochimica et biophysica acta 2011;1808(4):1179-86.
2010: Mariusz Kepczynski; Marta Kumorek; Michał Stepniewski; Tomasz Róg; Bartłomiej Kozik; Dorota Jamróz; Jan Bednar; Maria Nowakowska
Behavior of 2,6-bis(decyloxy)naphthalene inside lipid bilayer.
The journal of physical chemistry. B 2010;114(47):15483-94.
2010: Anders Björkbom; Tomasz Róg; Karol Kaszuba; Mayuko Kurita; Shou Yamaguchi; Max Lönnfors; Thomas K M Nyholm; Ilpo Vattulainen; Shigeo Katsumura; J Peter Slotte
Effect of sphingomyelin headgroup size on molecular properties and interactions with cholesterol.
Biophysical journal 2010;99(10):3300-8.
2010: Michał Stepniewski; Alex Bunker; Marta Pasenkiewicz-Gierula; Mikko Karttunen; Tomasz Róg
Effects of the lipid bilayer phase state on the water membrane interface.
The journal of physical chemistry. B 2010;114(36):11784-92.
2010: Karol Kaszuba; Tomasz Róg; Krzysztof Bryl; Ilpo Vattulainen; mikko karttunen
Molecular dynamics simulations reveal fundamental role of water as factor determining affinity of binding of beta-blocker nebivolol to beta(2)-adrenergic receptor.
The journal of physical chemistry. B 2010;114(25):8374-86.
2010: Anette Hall; Tomasz Róg; mikko karttunen; Ilpo Vattulainen
Role of glycolipids in lipid rafts: a view through atomistic molecular dynamics simulations with galactosylceramide.
The journal of physical chemistry. B 2010;114(23):7797-807.
2010: Hector Martinez-Seara; Tomasz Róg; mikko karttunen; Ilpo Vattulainen; Ramon Reigada
Cholesterol induces specific spatial and orientational order in cholesterol/phospholipid membranes.
PloS one 2010;5(6):e11162.
2009: Sanja Pöyry; Tomasz Róg; Mikko Karttunen; Ilpo Vattulainen
Mitochondrial membranes with mono- and divalent salt: changes induced by salt ions on structure and dynamics.
The journal of physical chemistry. B 2009;113(47):15513-21.
2009: Hector Martinez-Seara; Tomasz Róg; mikko karttunen; Ilpo Vattulainen; Ramon Reigada
Why is the sn-2 chain of monounsaturated glycerophospholipids usually unsaturated whereas the sn-1 chain is saturated? Studies of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (SOPC) and 1-oleoyl-2-stearoyl-sn-glycero-3-phosphatidylcholine (OSPC) membranes with and without cholesterol.
The journal of physical chemistry. B 2009;113(24):8347-56.
2009: Tomasz Róg; Hector Martinez-Seara; Nana Munck; Matej Oresic; Mikko Karttunen; Ilpo Vattulainen
Role of cardiolipins in the inner mitochondrial membrane: insight gained through atom-scale simulations.
The journal of physical chemistry. B 2009;113(11):3413-22.
2009: Tomasz Róg; Krzysztof Murzyn; Jeannine Milhaud; Mikko Karttunen; Marta Pasenkiewicz-Gierula
Water isotope effect on the phosphatidylcholine bilayer properties: a molecular dynamics simulation study.
The journal of physical chemistry. B 2009;113(8):2378-87.
2009: Tomasz Róg; Marta Pasenkiewicz-Gierula; Ilpo Vattulainen; Mikko Karttunen
Ordering effects of cholesterol and its analogues.
Biochimica et biophysica acta 2009;1788(1):97-121.
2008: Tomasz Róg; Ilpo Vattulainen; Maurice Jansen; Elina Ikonen; Mikko Karttunen
Comparison of cholesterol and its direct precursors along the biosynthetic pathway: effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers.
The Journal of chemical physics 2008;129(15):154508.
2008: Hector Martinez-Seara; Tomasz Róg; Marta Pasenkiewicz-Gierula; Ilpo Vattulainen; mikko karttunen; Ramon Reigada
Interplay of unsaturated phospholipids and cholesterol in membranes: effect of the double-bond position.
Biophysical journal 2008;95(7):3295-305.
2008: Hector Martinez-Seara; Tomasz Róg; mikko karttunen; Ramon Reigada; Ilpo Vattulainen
Influence of cis double-bond parametrization on lipid membrane properties: how seemingly insignificant details in force-field change even qualitative trends.
The Journal of chemical physics 2008;129(10):105103.
2008: Wei Zhao; Tomasz Róg; Andrey A Gurtovenko; Ilpo Vattulainen; mikko karttunen
Role of phosphatidylglycerols in the stability of bacterial membranes.
Biochimie 2008;90(6):930-8.
2008: Tomasz Róg; Krzysztof Murzyn; mikko karttunen; Marta Pasenkiewicz-Gierula
Nonpolar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies.
Journal of peptide science : an official publication of the European Peptide Society 2008;14(4):374-82.
2008: Sanja Pöyry; Tomasz Róg; mikko karttunen; Ilpo Vattulainen
Significance of cholesterol methyl groups.
The journal of physical chemistry. B 2008;112(10):2922-9.
2008: Tomasz Róg; Lorna M Stimson; Marta Pasenkiewicz-Gierula; Ilpo Vattulainen; mikko karttunen
Replacing the cholesterol hydroxyl group with the ketone group facilitates sterol flip-flop and promotes membrane fluidity.
The journal of physical chemistry. B 2008;112(7):1946-52.
2008: Emma Falck; Tomasz Róg; mikko karttunen; Ilpo Vattulainen
Lateral diffusion in lipid membranes through collective flows.
Journal of the American Chemical Society 2008;130(1):44-5.
2008: alex bunker; Pt Männistö; J-F St Pierre; Tomasz Róg; P Pomorski; L Stimson; mikko karttunen
Molecular dynamics simulations of the enzyme catechol-O-methyltransferase: methodological issues.
SAR and QSAR in environmental research 2008;19(1-2):179-89.
2007: Lorna Stimson; Lei Dong; mikko karttunen; Anna Wisniewska; Malgorzata Dutka; Tomasz Róg
Stearic acid spin labels in lipid bilayers: insight through atomistic simulations.
The journal of physical chemistry. B 2007;111(43):12447-53.
2007: Hector Martinez-Seara; Tomasz Róg; Marta Pasenkiewicz-Gierula; Ilpo Vattulainen; mikko karttunen; Ramon Reigada
Effect of double bond position on lipid bilayer properties: insight through atomistic simulations.
The journal of physical chemistry. B 2007;111(38):11162-8.
2007: Tomasz Róg; Ilpo Vattulainen; alex bunker; mikko karttunen
Glycolipid membranes through atomistic simulations: effect of glucose and galactose head groups on lipid bilayer properties.
The journal of physical chemistry. B 2007;111(34):10146-54.
2007: O H Samuli Ollila; Tomasz Róg; mikko karttunen; Ilpo Vattulainen
Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol.
Journal of structural biology 2007;159(2):311-23.
2007: Agnieszka Słowik; Wojciech Turaj; Grazyna Zwolińska; Tomasz Róg; Tomasz Dziedzic; Joanna Pera; Monika Rudzińska; Urszula Wyrwicz-Petkow; Katarzyna Kasprzyk; Agnieszka Kiełtyka; Andrzej Pajak; Andrzej Szczudlik
Stroke attack rates and case fatality in the Krakow Stroke Registry.
Neurologia i neurochirurgia polska 2007;41(4):291-5.
2007: Tomasz Róg; Marta Pasenkiewicz-Gierula; Ilpo Vattulainen; mikko karttunen
What happens if cholesterol is made smoother: importance of methyl substituents in cholesterol ring structure on phosphatidylcholine-sterol interaction.
Biophysical journal 2007;92(10):3346-57.
2007: Wei Zhao; Tomasz Róg; Andrey A Gurtovenko; Ilpo Vattulainen; mikko karttunen
Atomic-scale structure and electrostatics of anionic palmitoyloleoylphosphatidylglycerol lipid bilayers with Na+ counterions.
Biophysical journal 2007;92(4):1114-24.
2006: Jussi Aittoniemi; Tomasz Róg; Perttu S Niemelä; Marta Pasenkiewicz-Gierula; mikko karttunen; Ilpo Vattulainen
Tilt: major factor in sterols' ordering capability in membranes.
The journal of physical chemistry. B 2006;110(51):25562-4.
2006: Teemu Murtola; Tomasz Róg; Emma Falck; mikko karttunen; Ilpo Vattulainen
Transient ordered domains in single-component phospholipid bilayers.
Physical review letters 2006;97(23):238102.
2006: Tomasz Róg; Marta Pasenkiewicz-Gierula
Cholesterol-sphingomyelin interactions: a molecular dynamics simulation study.
Biophysical journal 2006;91(10):3756-67.
2006: Tomasz Róg; Marta Pasenkiewicz-Gierula
Cholesterol effects on a mixed-chain phosphatidylcholine bilayer: a molecular dynamics simulation study.
Biochimie 2006;88(5):449-60.
2006: Krzysztof Murzyn; Tomasz Róg; Wojciech Blicharski; Malgorzata Dutka; Janusz Pyka; Sebastian Szytula; Wojciech Froncisz
Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c.
Proteins 2006;62(4):1088-100.
2006: Seppo Vainio; Maurice Jansen; Mirkka Koivusalo; Tomasz Róg; mikko karttunen; Ilpo Vattulainen; Elina Ikonen
Significance of sterol structural specificity. Desmosterol cannot replace cholesterol in lipid rafts.
The Journal of biological chemistry 2006;281(1):348-55.
2005: Krzysztof Murzyn; Tomasz Róg; Marta Pasenkiewicz-Gierula
Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane.
Biophysical journal 2005;88(2):1091-103.
2005: Lorna M Stimson; Ilpo Vattulainen; Tomasz Róg; mikko karttunen
Exploring the effect of xenon on biomembranes.
Cellular & molecular biology letters 2005;10(4):563-9.
2004: Tomasz Róg; Marta Pasenkiewicz-Gierula
Non-polar interactions between cholesterol and phospholipids: a molecular dynamics simulation study.
Biophysical chemistry 2004;107(2):151-64.
2004: Tomasz Róg; Krzysztof Murzyn; Ryszard Gurbiel; Yuji Takaoka; Akihiro Kusumi; Marta Pasenkiewicz-Gierula
Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study.
Journal of lipid research 2004;45(2):326-36.
2003: Marta Pasenkiewicz-Gierula; Tomasz Róg; Jacek Grochowski; Pawel Serda; Ryszard Czarnecki; Tadeusz Librowski; S Lochyński
Effects of a carane derivative local anesthetic on a phospholipid bilayer studied by molecular dynamics simulation.
Biophysical journal 2003;85(2):1248-58.
2003: Tomasz Róg; Krzysztof Murzyn; K Hinsen; GR Kneller
nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations.
Journal of computational chemistry 2003;24(5):657-67.
2003: Tomasz Róg; Marta Pasenkiewicz-Gierula
Effects of epicholesterol on the phosphatidylcholine bilayer: a molecular simulation study.
Biophysical journal 2003;84(3):1818-26.
2003: Tomasz Róg; Krzysztof Murzyn; Marta Pasenkiewicz-Gierula
Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.
Acta biochimica Polonica 2003;50(3):789-98.
2002: Jolanta Majka; Tomasz Róg; Peter C Konturek; Stanislaw J Konturek; Władysław Bielański; Marek Kowalsky; Andrzej Szczudlik
Influence of chronic Helicobacter pylori infection on ischemic cerebral stroke risk factors.
Medical science monitor : international medical journal of experimental and clinical research 2002;8(10):CR675-84.
2001: Tomasz Róg; Marta Pasenkiewicz-Gierula
Cholesterol effects on the phosphatidylcholine bilayer nonpolar region: a molecular simulation study.
Biophysical journal 2001;81(4):2190-202.
2001: Tomasz Róg; Marta Pasenkiewicz-Gierula
Cholesterol effects on the phospholipid condensation and packing in the bilayer: a molecular simulation study.
FEBS letters 2001;502(1-2):68-71.
2001: Krzysztof Murzyn; Tomasz Róg; G Jezierski; Yuji Takaoka; Marta Pasenkiewicz-Gierula
Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study.
Biophysical journal 2001;81(1):170-83.
2000: Marta Pasenkiewicz-Gierula; Tomasz Róg; K Kitamura; Akihiro Kusumi
Cholesterol effects on the phosphatidylcholine bilayer polar region: a molecular simulation study.
Biophysical journal 2000;78(3):1376-89.
2000: Marta Pasenkiewicz-Gierula; Krzysztof Murzyn; Tomasz Róg; Cezary Czaplewski
Molecular dynamics simulation studies of lipid bilayer systems.
Acta biochimica Polonica 2000;47(3):601-11.
1997: Marta Pasenkiewicz-Gierula; Tomasz Róg
Conformations, orientations and time scales characterising dimyristoylphosphatidylcholine bilayer membrane. Molecular dynamics simulation studies.
Acta biochimica Polonica 1997;44(3):607-24.