Publikacje Zakładu

• Dongmei Wu, Michal Gucwa, Mateusz P. Czub, David R. Cooper, Ivan G. Shabalin, Remi Fritzen, Swati Arya, Ulrich Schwarz-Linek, Claudia A. Blindauer, Wladek Minor and Alan J. Stewart, Structural and biochemical characterisation of Co2+ -binding sites on serum albumins and their interplay with fatty acids. Chemical Science, 2023, 14, 6244.
• Michal Gucwa, Joanna Lenkiewicz, Heping Zheng, Marcin Cymborowski,  David R. Cooper,  Krzysztof Murzyn, Wladek Minor, CMM—An enhanced platform for interactive validation ofmetal binding sites. Protein Science. 2023;32:e4525.
• Madej E, Brożyna AA, Adamczyk A, Wronski N, Harazin-Lechowska A, Muzyk A, Makuch K, Markiewicz M, Wolnicka-Glubisz A, Vemurafenib and Dabrafenib Downregulates RIPK4 Level. Cancers, 2023, 15(3), 918.
• Radzin S, Wiśniewska-Becker A, Markiewicz M, Bętkowski S, Furso J, Waresiak J, Grolik J, Sarna T, Pawlak AM. Structural Impact of Selected Retinoids on Model Photoreceptor Membranes. Membranes, 2023, 13(6), 575.
• Hryc J, Markiewicz M, Pasenkiewicz-Gierula M. Stacks of monogalactolipid bilayers can transform into a lattice of water channels. Iscience, 2023, 26(10), 107863.
• Bijak V, Szczygiel M, Lenkiewicz J, Gucwa M, Cooper DR, Murzyn K, Minor W. The current role and evolution of X-ray crystallography in drug discovery and development. Expert Opin Drug Discov. 2023 Jul-Dec;18(11):1221-1230. doi: 10.1080/17460441.2023.2246881. Epub 2023 Aug 17. PMID: 37592849; PMCID: PMC10620067.
• Lenkiewicz J, Bijak V, Poonuganti S, Szczygiel M, Gucwa M, Murzyn K, Minor W. Structural biology and public health response to biomedical threats. Struct Dyn. 2023 Jun 5;10(3):034701. doi: 10.1063/4.0000186. PMID: 37350851; PMCID: PMC10284607.
• Bijak V, Gucwa M, Lenkiewicz J, Murzyn K, Cooper DR, Minor W. Continuous Validation Across Macromolecular Structure Determination Process. Nihon Kessho Gakkaishi. 2023 Feb 28;65(1):10-16. doi: 10.5940/jcrsj.65.10. Epub 2023 Mar 8. PMID: 37416056; PMCID: PMC10321142.
• Subczynski WK, Pasenkiewicz-Gierula M, Widomska J. Protecting the Eye Lens from Oxidative Stress through Oxygen Regulation. Antioxidants (Basel). 2023 Sep 20;12(9):1783. doi: 10.3390/antiox12091783. PMID: 37760086; PMCID: PMC10525422.

• Bilska B, Godlewska U, Damulewicz M, Murzyn K, Kwitniewski M, Cichy J, Pyza E. Antimicrobial Properties of a Peptide Derived from the Male Fertility Factor kl2 Protein of Drosophila melanogaster. Curr Issues Mol Biol. 2022 Feb 28;44(3):1169-1181. doi: 10.3390/cimb44030076. PMID: 35723299; PMCID: PMC8947439.
• Hryc J, Szczelina R, Markiewicz M, Pasenkiewicz-Gierula M. Lipid/water interface of galactolipid bilayers in different lyotropic liquid-crystalline phases. Front Mol Biosci. 2022 Aug 15;9:958537. doi: 10.3389/fmolb.2022.958537. PMID: 36046609; PMCID: PMC9423040.
• Kania A, Sarapata K. Multifarious aspects of the chaos game representation and its applications in biological sequence analysis. Comput Biol Med. 2022 Dec;151(Pt A):106243. doi: 10.1016/j.compbiomed.2022.106243. Epub 2022 Oct 25. PMID: 36335814.
• Kania A, Bratek M, Majta J, Sarapata K, Gałan W, Markiewicz M, Wójcik-Augustyn A. The importance of atomic partial charges in the reproduction of intermolecular interactions for the triacetin - a model of glycerol backbone. Chem Phys Lipids. 2022 Jul;245:105203. doi: 10.1016/j.chemphyslip.2022.105203. Epub 2022 Apr 7. PMID: 35398336.

• Markiewicz M, Szczelina R, Pasenkiewicz-Gierula M. Data for molecular dynamic simulations in the OPLSAA force field: Partial charges of cholesterol, C7-hydroxycholesterol and C7-hydroperoxycholesterol, torsional parameters for the hydroperoxy group of C7-hydroperoxycholesterol. Data Brief. 2021 Oct 14;39:107483. doi: 10.1016/j.dib.2021.107483. PMID: 34712759; PMCID: PMC8528686.
• Makuch K, Hryc J, Markiewicz M, Pasenkiewicz-Gierula M. Lutein and Zeaxanthin in the Lipid Bilayer-Similarities and Differences Revealed by Computational Studies. Front Mol Biosci. 2021 Oct 26;8:768449. doi: 10.3389/fmolb.2021.768449. PMID: 34765645; PMCID: PMC8575744.
• Markiewicz M, Szczelina R, Milanovic B, Subczynski WK, Pasenkiewicz-Gierula M. Chirality affects cholesterol-oxysterol association in water, a computational study. Comput Struct Biotechnol J. 2021 Jul 26;19:4319-4335. doi: 10.1016/j.csbj.2021.07.022. PMID: 34429850; PMCID: PMC8361299.
• Kania A. Harnessing the information theory and chaos game representation for pattern searching among essential and non-essential genes in Bacteria. J Theor Biol. 2021 Dec 21;531:110917. doi: 10.1016/j.jtbi.2021.110917. Epub 2021 Sep 23. PMID: 34563550.
• Kania A, Sarapata K. The robustness of the chaos game representation to mutations and its application in free-alignment methods. Genomics. 2021 May;113(3):1428-1437. doi: 10.1016/j.ygeno.2021.03.015. Epub 2021 Mar 11. PMID: 33713823.
• Kania A, Sarapata K, Gucwa M, Wójcik-Augustyn A. Optimal Solution to the Torsional Coefficient Fitting Problem in Force Field Parametrization. J Phys Chem A. 2021 Apr 1;125(12):2673-2681. doi: 10.1021/acs.jpca.0c10845. Epub 2021 Mar 24. PMID: 33759532; PMCID: PMC8041298

• Subczynski WK, Pasenkiewicz-Gierula M. Hypothetical Pathway for Formation of Cholesterol Microcrystals Initiating the Atherosclerotic Process. Cell Biochem. Biophys. 2020 78:241-247
• Szczelina R, Baczynski K, Markiewicz M, Pasenkiewicz-Gierula M. Network of lipid interconnections at the interfaces of galactolipid and phospholipid bilayers. J. Mol. Liquids 2020 298:112002
• Bratek M, Wójcik-Augustyn A, Kania A, Majta J, Murzyn K. Condensed phase properties of n-pentadecane emerging from application of biomolecular force fields. Acta Biochem. Polon. 2020 67:309-318

• Makuch K, Markiewicz M, Pasenkiewicz-Gierula M. Asymmetric Spontaneous Intercalation of Lutein into a Phospholipid Bilayer, a Computational Study. Comput. Struct. Biotechn. J. 2019 17:516-526
• Bratek L, Markiewicz M, Baczynski K, Jalocha-Bratek J, Pasenkiewicz-Gierula M. Inverse hexagonal phase of poly-unsaturated monogalactolipids: a computer model and analysis. J. Mol. Liquids 2019 290:111189

• Plesnar E, Szczelina R, Subczynski WK, Pasenkiewicz-Gierula M. Is the cholesterol bilayer domain a barrier to oxygen transport into the eye lens? Biochim. Biophys. Acta – Biomembr. 2018 1860:434-441

• M. Markiewicz, T. Librowski, A. Lipkowska, P. Serda, K. Baczynski a, M. Pasenkiewicz-Gierula, Assessing gastric toxicity of xanthone derivatives of anti-inflammatory activity using simulation and experimental approaches, Biophysical Chemistry 220: 20–33, 2017.

• Pasenkiewicz-Gierula M, Baczynski K, Markiewicz M, Murzyn K. Computer modelling studies of the bilayer/water interface. Biochim. Biophys. Acta – Biomembr. 2016 1858:2305-2321.
• W. Kulig, M. Pasenkiewicz-Gierula, T. Róg, Cis and trans unsaturated phosphatidylcholine bilayers: A molecular dynamics simulation study, Chemistry and Physics of Lipids 195: 12–20, 2016.
• P. J. Porebski, M. Cymborowski, M. Pasenkiewicz-Gierula W. Minor, Fitmunk : improving protein structures by accurate, automatic modeling of side-chain conformations, Acta Cryst. D72: 266–280, 2016.

• Murzyn K, Pasenkiewicz-Gierula M. Structural Properties of the Water/Membrane Interface of a Bilayer Built of the E. coli Lipid A. J. Phys. Chem. B 2015 119:5846-5856.
• W. Kulig, M. Pasenkiewicz-Gierula, T. Róg, Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field : DPPC, POPC, DOPC, PEPC, and cholesterol, Data in Brief 2015, 5: 333-336, 2015.
• M. Markiewicz, K. Baczynski, M. Pasenkiewicz-Gierula, Properties of water hydrating the galactolipid and phospholipid bilayers: a Molecular dynamics simulation study, Acta Biochimica Polonica 2015, 62:475-481, 2015.
• K. Baczynski, M. Markiewicz, M. Pasenkiewicz-Gierula, A computer model of a polyunsaturated monogalactolipid bilayer, Biochimie 2015, 118:129-140, 2015.

• Maciejewski A, Pasenkiewicz-Gierula M, Cramariuc O, Vattulainen I, Rog T. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration. J. Phys. Chem. B 2014 118:4571-4581
• B.A. Zabel, M. Kwitniewski, M. Banas, K. Zabieglo, K. Murzyn, J. Cichy, Chemerin regulation and role in host defense. American Journal of Clinical and Experimental Immunology, 3, 1-19, 2014.
• A. Wójcik, E. Broclawik, P.E.M. Siegbahn, M. Lundberg, G. Moran, T. Borowski, The role of substrate positioning in the catalytic reaction of 4-hydroxyphenylpyruvate dioxygenase – a QM/MM study. Journal of the American Chemical Society, 136, 14472-14485, 2014.
• R. Szczelina, K. Murzyn, DMG-alpha-A Computational Geometry Library for Multimolecular Systems. Journal of Chemical Information and Modeling, 54, 3112-3123, 2014.
• M. Pasenkiewicz-Gierula, M. Markiewicz. Computer Modelling of the Lipid Matrix of Biomembranes. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes – from bioinformatics to molecular quantum mechanics. Ed. A. Liwo, Springer Verlag, Berlin, Heidelberg, 2014, 317-356.

• Murzyn K, Bratek M, Pasenkiewicz-Gierula M. Refined OPLS All-Atom Force Field Parameters for n-Pentadecane, Methyl Acetate, and Dimethyl Phosphate. J. Phys. Chem. B 2013 117:16388-16396
• M. Zdzalik, M. Kalinska, M. Wysocka, J. Stec-Niemczyk, P. Cichon, N. Stach, N. Gruba, H. R. Stennicke, A. Jabaiah, M. Markiewicz, S. Kedracka-Krok, B. Wladyka, P. S. Daugherty, A. Lesner, K. Rolka, A. Dubin, J. Potempa, G. Dubin, Biochemical and structural characterization of SplD protease from Staphylococcus aureus, PLOS-One, 2013.
• P. Kolesinski, P. Golik, P. Grudnik, J. Piechota, M. Markiewicz, M. Tarnawski, G. Dubin, A. Szczepaniak, Insights into eukaryotic Rubisco assembly — Crystal structures of RbcX chaperones from Arabidopsis thaliana. BBA - General Subjects, 1830(4), 2899–2906, 2013.
• M. Banas, K. Zabieglo, G. Kasetty, M. Kapinska-Mrowiecka, J. Borowczyk, J. Drukala, K. Murzyn, B. A. Zabel, E. C. Butcher, J. M. Schroeder, A. Schmidtchen, J. Cichy. Chemerin Is an Antimicrobial Agent in Human Epidermis. PLOS ONE, 8, 2013.
• E. Plesnar, W. K. Subczynski, M. Pasenkiewicz-Gierula. Comparative Computer Simulation Study of Cholesterol in Hydrated Unary and Binary Lipid Bilayers and in an Anhydrous Crystal. The Journal of Physical Chemistry B, 8758−8769, 117, 2013.

• A. Orłowski, M. Grzybek, A. Bunker, M. Pasenkiewicz-Gierula, I. Vattulainen, P.T. Mannisto, T. Róg. Strong preferences of dopamine and L-dopa towards lipid head group: importance of lipid composition and implication for neurotransmitter metabolism. Journal of Neurochemistry, 122, 681-690, 2012.
• M. Pasenkiewicz-Gierula, K. Baczyński, K. Murzyn, M. Markiewicz. Orientation of lutein in a lipid bilayer — revisited. Acta Biochimica Polonica, 59, 105-108, 2012.
• E. Plesnar, W. K. Subczynski, M. Pasenkiewicz-Gierula. Saturation with cholesterol increases vertical order and smoothes the surface of the phosphatidylcholine bilayer: A molecular simulation study. Biochimica et Biophysica Acta, 1818, 520–529, 2012.

• Kneller G, Baczynski K, Pasenkiewicz-Gierula M. Consistent picture of lateral subdiffusion in lipid bilayers: Molecular dynamics simulation and exact results. J. Chem. Phys. 2011 135:141105.
• A. Orłowski, J.F. St-Pierre, A. Magarkar, A. Bunker, M. Pasenkiewicz-Gierula, I. Vattulainen, T. Róg. Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations. J. Phys. Chem. B 115, 13541–13550, 2011.
• M.M. Klimecka, M. Chruszcz, J. Font, T. Skarina, I. Shumilin, O. Onopryienko, P.J. Porebski, M. Cymborowski, M.D. Zimmerman, J. Hasseman, I.J. Glomski, L. Lebioda, A. Savchenko, A. Edwards, W. Minor. Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis. J. Mol. Biol. 410, 411–423, 2011.
• M. Markiewicz, M. Pasenkiewicz-Gierula. Comparative Model Studies of Gastric Toxicity of Nonsteroidal Anti-Inflammatory Drugs. Langmuir, 27, 6950–6961, 2011.
• M. Stepniewski, M. Pasenkiewicz-Gierula, T. Róg, R. Danne, A. Orlowski, M. Karttunen, A. Urtti, M. Yliperttula, E. Vuorimaa, A. Bunker. Study of PEGylated Lipid Layers as a Model for PEGylated Liposome Surfaces: Molecular Dynamics Simulation and Langmuir Monolayer Studies. Langmuir 27, 7788–7798, 2011.

• G. Neunert, P. Polewski, M. Markiewicz et al. Partition of tocopheryl glucopyranoside into liposome membranes studied by fluorescence methods. Biophys. Chem., 146, 92-97, 2010.
• M. Stępniewski, A. Bunker, M. Pasenkiewicz-Gierula, M. Karttunen, T. Róg. Effects of the lipid bilayer phase state on the water membrane interface. J. Phys. Chem. B., 114, 11784-11792, 2010.

• Rog T, Murzyn K, Milhaud J, Karttunen M, Pasenkiewicz-Gierula M. Water isotope effect on the phosphatidylcholine bilayer properties: a molecular dynamics simulation study. J. Phys. Chem. B. 2009;113:2378-2387.
• Rog T, Pasenkiewicz-Gierula M, Vattulainen I, Karttunen M. Ordering effects of cholesterol and its analogues. Biochim. Biophys. Acta – Biomembr. 2009 1788:97-121.
• P. Górnas, G. Neunert, K. Baczyński, K. Polewski. Beta-cyclodextrin complexes with chlorogenic and caffeic acids from coffee brew: Spectroscopic, thermodynamic and molecular modelling study. Food Chemistry. 114, 190-196, 2009.
• G. Neunert, P. Polewski, M. Markiewicz, P. Walejko, S. Witkowski, K. Polewski. Glycosidic moiety changes spectroscopic properties of DL-á-tocopherol in DMSO/water solution and in organic solvents. Spectrochim. Acta A: Molecular and Biomolecular Spectroscopy, 73, 301-308, 2009.

• E. Falck, T. Róg, M. Karttunen, I. Vattulainen. 2008. Lateral diffusion in lipid membranes through collective flows. J. Am. Chem. Soc.130:44-45.
• A. Bunker, P. T. Männistö, J-F. St. Pierre, T. Róg, P. Pomorski, L. Stimson, M. Karttunen. 2008. Molecular Dynamics simulations of the enzyme Catechol-O-Methyl Transferase: Methodological issues. Sar. Qsar. Env. Res. 19:179-189.
• S. Poyry, T. Róg, M. Karttunen, I. Vattulainen. 2008. Significance of cholesterol methyl groups. J. Phys. Chem. B. 112:2922-2929.PDF
• W. Zhao, T. Róg, A. A. Gurtovenko, I. Vattulainen, M. Karttunen. 2008. Role of phosphatidylglycerols in the stability of bacterial membranes. Biochimie. 90:930-938.PDF
• H. Martinez-Seara, T. Róg, M. Karttunen, R. Reigada, I. Vattulainen. 2008. Influence of cis double bond parameterization on lipid membrane properties: How seemingly insignificant details in force field change even qualitative trends. J. Chem. Phys. 129: 105103.
• T. Róg, M. Karttunen, I. Vattulainen, M. Jansen, E. Ikonen. 2008. Comparison of cholesterol and its direct precursors on its biosynthetic pathway: desmosterol and 7-dehydrocholesterol effects on lipid bilayers. Chem. Phys. 129:154508
• T. Róg, L. M. Stimson, M. Pasenkiewicz-Gierula, I. Vattulainen, and M. Karttunen. 2008. Replacing the cholesterol hydroxyl group by the ketone group facilitates sterol flip-flop and promotes membrane fluidity. J. Phys. Chem. B. 112, 1946-1952.
• H. Martinez-Seara, T. Róg, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen, and R. Reigada. 2008. Interplay of Unsaturated Phospholipids and Cholesterol in Membranes: Effect of Double Bond Position. Biophys. J. 95, 3295-3305.

• L. Stimson, L. Dong, M. Karttunen, A. Wisniewska, M. Dutka, and T. Róg. 2007. Stearic acid spin labels in lipid bilayers: Insight through atomistic simulations. J. Phys. Chem. B 111, 12447-12453.
• T. Róg, K. Murzyn, M. Karttunen, and M. Pasenkiewicz-Gierula. 2008. Non-polar interactions between trans-membrane helical peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies. J. Pept. Sci. 14, 374-382.
• T. Róg, I. Vattulainen, A. Bunker, and M. Karttunen. 2007. Glycolipid membranes through atomistic simulations: Effect of glucose and glactose head groups on lipid bilayer properties. J. Phys. Chem. B 111, 10146-10154.
• H. Samuli Ollila, T. Róg, M. Karttunen, I. Vattulainen. 2007. Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterok, demosterol, 7-dehydrocholesterol and ketosterol. J. Struct. Biol. 159, 311-323.
• W. Zhao, T. Róg, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen. 2007. Atomic-scale structure and electrostatics of anionic palmitoyloleoylphosphatidylglycerol lipid bilayers with Na+ counterious. Biophys. J. 92, 1114-1124.
• P. Liguziński, B. Korzeniewski. 2007. Oxygen delivery by blood determines the maximal VO2 and work rate during whole body exercise in humans: In silico studies. Am. J. Physiol. - Heart and Circulatory Physiology. 293, H343-H353.
• M. Markiewicz, P. Serda, T. Librowski, S. Mogilski, H. Marona, M. Pasenkiewicz-Gierula, S. Hodorowicz, S. Funari. 2007. Interaction of nonsteroidal anti-inflammatory drugs with membrane. HASYLAB Jahresbericht 2006 – Annual Report 1, Editors: R. Gherke, U. Krell, J.R. Schneider, Publisher HASYLAB/DESY, Hamburg, 1293-1294.
• T. Róg, M. Pasenkiewicz-Gierula, I. Vattulainen, and M. Karttunen. 2007. What happens if cholesterol is made smoother: Importance of methyl substituents in cholesterol ring structure on phosphatidylcholine-sterol interaction. Biophys. J. 92, 3346-3357.
• H. Martinez-Seara, T. Róg, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen, and R. Reigada. 2007. Effect of double bond position on lipid bilayer properties: Insight through atomistic simulations. J. Phys. Chem. B. 111, 11162-11168.
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• Rog T, Pasenkiewicz-Gierula M. Cholesterol-sphingomyelin interactions: A molecular dynamics simulation study. Biophys. J. 2006 91:3756-3767.
• T. Róg, M. Pasenkiewicz-Gierula. 2006. Cholesterol effects on a mixed-chain phosphatidylcholine bilayer: a molecular dynamics simulation study. Biochimie. 88, 449-460.
• J. Aittoniemi, T. Róg, P. Niemela, M. Pasenkiewicz-Gierula, M. Karttunen, and I. Vattulainen. 2006. Tilt – major factor in sterols’ ordering capability in membranes. J. Phys. Chem. B. Letters. 110, 25562-25564.
• K. Murzyn, W. Zhao, M. Karttunen, M. Kurdziel, and T. Róg. 2006. Dynamics of water at membrane surfaces: Effect of headgroup structure. Biointerphases. 1(3):98-105.
• K. Murzyn, T. Róg, W. Blicharski, M. Dutka, J. Pyka, S. Szytula, W. Froncisz. 2006. Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c. Proteins. 62:1088-1100.
• S. Vainio, M. Jansen, M. Koivusalo, T. Róg, M. Karttunen, I. Vattulainen, E. Ikonen. 2006. Desmosterol cannot replace cholesterol in lipid rafts. J. Biol. Chem. 281:348-355.
• T. Murtola, T. Róg, E. Falck, M. Karttunen, I. Vattulainen. 2006. Transient ordered domains in pure phospholipid bilayers. Phys. Rev. Letters. 97, 238102.
• M. Markiewicz, P. Serda, T. Librowski, S. Mogilski, H. Marona, M. Pasenkiewicz-Gierula, S. Hodorowicz, S. Funari. 2007. Influence of xanthone derivatives on POPC membrane. HASYLAB Jahresbericht 2006 – Annual Report 1, Editors: R. Gherke, U. Krell, J.R. Schneider, Publisher HASYLAB/DESY, Hamburg, 1289-1290.

• Murzyn K, Rog T, Pasenkiewicz-Gierula M. Phosphatidylethanolaminephosphatidylglycerol bilayer as a model of the inner bacterial membrane. Biophys. J. 2005 88:1091–1103.
• T. Róg, I. Vattulainen, M. Karttunen. 2005. Modeling glycolipids: take one. Cell. Biol. Mol. Lett. 10:625-630.
• L. M. Stimson, I. Vattulainen, T. Róg, M. Karttunen. 2005. Exploring the effect of xenon on biomembranes. Cell. Biol. Mol. Lett. 10:563-569
• M. Jemiola-Rzeminska, M. Pasenkiewicz-Gierula, K. Strzalka.2005.The behaviour of beta-carotene in the phosphatidylcholine bilayer as revealed by a molecular simulation study.Chem. Phys. Lipids 135 (1):27-37

• K. Murzyn, T. Róg, M. Pasenkiewicz-Gierula. 2004. Interactions of magainin-2 amide with membrane lipids. Lect. Notes Comput. Sc. 3037:325-331.
• T. Róg, K. Murzyn, R. Gurbiel, K. Kitamura, A. Kusumi, M. Pasenkiewicz-Gierula. 2004. Effects of phospholipid unsaturation on the structure and dynamics of the hydrocarbon core of the membrane. A Molecular Simulation Study. J. Lip. Res. 45:326-336.
• T. Róg, M. Pasenkiewicz-Gierula. 2004. Cholesterol-phospholipid hydrophobic interactions: a molecular simulation study. Biophys. Chem. 107:151-164. online

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• Gieldon A, Kazmierkiewicz R, Slusarz R, Pasenkiewicz-Gierula M, Ciarkowski J.2003. Molecular dynamics study of 4-OH-phenylacetyl-D-Y(Me)FQNRPR-NH2 selectivity to V1a receptor. J. Mol. Model 9 (6):372-378
• T. Róg, K. Murzyn, M. Pasenkiewicz-Gierula, Molecular dynamics simulation of charged and uncharged lipid bilayers : a treatment of electrostatic interactions. Acta Biochim. Polon. 2003.
• K. Murzyn, M. Pasenkiewicz-Gierula. 2003. Construction of a toroidal model for the magainin pore.J. Mol. Model. 9(4):217-224
• Róg, K. Murzyn, K. Hinsen, G. R. Kneller. NMoldyn: a program package for a neutron scattering analysis of molecular dynamics simulations. J. Comput. Chem. 24, 657-667, 2003.
• W.K. Subczyński, M. Pasenkiewicz-Gierula, R.N. McElhaney, J.S. Hyde, A. Kusumi. Molecular dynamics of 1-palmitoyl-2-oleoylphosphatidylcholine membranes containing transmembrane alpha-helical peptide with alternating leucine, alanine residues. Biochemistry. 42, 3939-3948, 2003.
• M. Pasenkiewicz-Gierula, T. Róg, J. Grochowski, P. Serda, R. Czarnecki, T. Librowski, S. Lochyński. Effects of a carane derivative local anesthetic on a phospholipid bilayer: a molecular dynamics simulation study. Biophys. J. 85(2), 2003.
• T. Róg, M. Pasenkiewicz-Gierula. Effects of epicholesterol on the phosphatidylcholine bilayer: a molecular simulation study. Biophys. J. 84, 1818-1226, 2003

• K. Murzyn, Woda w symulacjach dynamiki molekularnej. Postępy Biologii Komórki, 29, 87-101, 2002. (in Polish)
• J. Grochowski, P. Serda, M. Pasenkiewicz-Gierula, R. Czarnecki, T. Librowski, S. Lochyński, B. Frąckowiak. Structural characterization of carane derivative stereoisomers - potent local anesthetics. Acta Physica Polon. A 101, 665-674, 2002.
• T. Róg, K. Murzyn, M. Pasenkiewicz-Gierula. The dynamics of water at the phospholipid bilayer surface: a molecular dynamics simulation study. Chem. Phys. Lett. 352, 323-327, 2002.
• S. Lochyński, B. Frąckowiak, T. Librowski, R. Czarnecki, J. Grochowski, P. Serda, M. Pasenkiewicz-Gierula. Stereochemistry of terpene derivatives. Part 3. Hydrolytic kinetic resolution as a convenient approach to chiral aminohydroxyiminocaranes with local anaesthetic activity. Tetrahedron: Asymm. 13, 873-878, 2002

• K. Murzyn, T. Róg, G. Jezierski, Y. Takaoka, M. Pasenkiewicz-Gierula, Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study. Biophys. J. 81, 170-183, 2001.
• T. Róg, M. Pasenkiewicz-Gierula, Cholesterol effects on the phosphatidylcholine bilayer non-polar region: a molecular simulation study. Biophys. J. 81, 2190-2202, 2001.PDF
• S. Ohta-Iino, M. Pasenkiewicz-Gierula, Y. Takaoka, H. Miyagawa, K. Kitamura, A. Kusumi, Fast lipid disorientation at the onset of membrane fusion as revealed by molecular dynamics simulations. Biophys. J. 81, 217-224, 2001. online
• T. Róg, M. Pasenkiewicz-Gierula, Cholesterol effects on the phospholipid condensation and packing in the bilayer: a molecular simulation study. FEBS Letters, 502, 68-71, 2001.
• G. Jezierski, M. Pasenkiewicz-Gierula, The effect of the Glu342Lys mutation in alpha1-antitrypsin on its structure, studied by molecular modelling methods. Acta Biochim. Polon. 48, 1-11, 2001. online
• T. Librowski, R. Czarnecki, S. Lochyński, B. Frąckowiak, M. Pasenkiewicz-Gierula, J. Grochowski, P. Serda, Comparative investigations of hydroxyamine carane derivative and its R,S-diastereoisomers with strong local anesthetic activity]. Polish J. Pharmacol. 53, 535-539, 2001.
• T. Róg, M. Pasenkiewicz-Gierula, Oddziaływanie cholesterol z fosfolipidami w błonie - badania metodą symulacji dynamiki molekularnej. Postępy Biologii Komórki, 27, supl. 16, 277-283, 2001.
• W. K. Subczynski, M. Pasenkiewicz-Gierula, W. E Antholine. Zorientowana krystalizacja metaloporfiryn: wpływ pola magnetycznego i błon lipidowych. Postępy Biologii Komórki, 27, supl. 16, 285-296, 2001.
• M. Pasenkiewicz-Gierula, T. Róg, K. Murzyn, Molecular simulation studies of the interfacial region in lipid bilayers. Postępy Biologii Komórki, 27, supl. 16, 297-303, 2001.
• G. Jezierski, M. Pasenkiewicz-Gierula, Metoda symulowanego wyżarzania - zastosowanie do badania struktury i dynamiki białek. Postępy Biologii Komórki, 27, supl. 16, 305-317, 2001

• M. Pasenkiewicz-Gierula, T. Róg, K. Kitamura, A. Kusumi, Cholesterol effects on the phosphatidylcholine bilayer polar region: a molecular simulation study. Biophys. J. 78, 1376-1389, 2000.
• Y. Takaoka, M. Pasenkiewicz-Gierula, H. Miyagawa, K. Kitamura, Y. Tamura, A. Kusumi, Generation of a liquid-crystalline phosphatidylcholine bilayer membrane from its crystal structure by molecular dynamics simulation. Biophys. J. 79, 3118-3138, 2000. online
• M. Pasenkiewicz-Gierula, K. Murzyn, T. Róg, C. Czaplewski, Molecular dynamics simulation studies of lipid bilayer systems. Acta Biochim. Polon. 47, 601-611, 2000.
• M. Pasenkiewicz-Gierula, G. Jezierski, K. Murzyn, T. Róg, C. Czaplewski, J. Ciarkowski, Biofizyczne badania błon i białek metodą symulacji dynamiki molekularnej. Biotechnologia, 49, 75-89, 2000. (In Polish)

• W.K. Subczyński, M. Pasenkiewicz-Gierula, W.E. Antholine, J.S. Hyde, Oriented self-association of copper(II) tetraphenylporphine in liquid-crystalline lipid bilayer membranes: an EPR study. J. Am. Chem. Soc. 16, 4045-4059, 1999.
• M. Pasenkiewicz-Gierula, Y. Takaoka, H. Miyagawa, K. Kitamura, A. Kusumi, Charge-pairing of headgroups in phosphatidylcholine membranes. A molecular dynamics simulation study. Biophys. J., 76, 1228-1240, 1999.
• C. Czaplewski, M. Pasenkiewicz-Gierula, J. Ciarkowski, Molecular dynamics of a vasopressin V2 receptor in a phospholipid bilayer membrane. J. Rec. Signal Transduction Res. 19, 355-367, 1999.
• C. Czaplewski, M. Pasenkiewicz-Gierula, J. Ciarkowski, G protein-coupled receptor - bioligand interactions modeled in a phospholipid bilayer. Int. J. Quantum Chem. 73, 61-70, 1999.
• K. Murzyn, M. Pasenkiewicz-Gierula, Construction and optimisation of a computer model for a bacterial membrane. Acta Biochim. Polon. 46, 631-639, 1999.
• K. Murzyn, T. Róg, M. Pasenkiewicz-Gierula, Comparison of the conformation and the dynamics of saturated and mono-unsaturated hydrocarbon chains of phospholipids. Curr. Top. Biophys. 23, 87-94, 1999.
• G. Jezierski, K. Murzyn, M. Pasenkiewicz-Gierula, T. Róg. Modelowanie molekularne biocząsteczek - ćwiczenia z podstaw i zastosowań. Red. M. Pasenkiewicz-Gierula. ISBN 83-909476-9-2, Wyd. IBM UJ, pp. 1-96, 1999.
• T. Róg, M. Pasenkiewicz-Gierula, T. Panz. Procesy nieliniowe. W: Biofizyka, ćwiczenia i seminaria. Red. T. Panz, K. Urbańska, P. Płonka. ISBN 83-90947-7-6, IBM UJ, Kraków, pp. 132-134, 1999.
• M. Pasenkiewicz-Gierula. Komputerowe modelowania biocząsteczek. W: Biofizyka, ćwiczenia i seminaria. Red. T. Panz, K. Urbańska, P. Płonka. ISBN 83-90947-7-6, Wyd. IBM UJ, pp. 178-188, 1999.

• J. Ciarkowski, C. Czaplewski, M. Pasenkiewicz-Gierula. Targets for majority of drugs: G protein-coupled receptors - their structure and interactions with bioligands. Task Quarterly. 4, 583-599, 1998.

• Pasenkiewicz-Gierula M, Takaoka Y, Miyagawa H, Kitamura K, Kusumi A. Hydrogen bonding of water to phosphatidylcholine in the membrane as studied by a molecular dynamics simulation: location, geometry, and lipid-lipid bridging via hydrogen-bonded water. J. Phys. Chem. A 1997 101:3677-3691
• M. Pasenkiewicz-Gierula, W.K. Subczyński, W.E. Antholine, Rotational motion of square planar copper complexes in solution and phospholipid bilayer membrane. J. Phys. Chem. B. 101, 5596-5606, 1997.
• M. Pasenkiewicz-Gierula, T. Róg, Conformations, orientations and time scales characterising dimyristoylphosphatidylcholine bilayer membrane. Molecular dynamics simulation studies. Acta Biochim. Polon. 44, 467-474, 1997.