Publications

2024

121. Małgorzata Lobka, Izabela Siekierska, Piotr Chyży, Michał Burmistrz, Julia Macyszyn, Monika Wojciechowska, Joanna Trylska, Novel Amphipathic Linear and Hydrocarbon-Stapled Peptides for Antibacterial Applications, submitted

120. Izabela Siekierska, Michał Burmistrz, Joanna Trylska, Evaluating delivery of peptide nucleic acids to gram-negative bacteria using differently linked membrane-active peptides and their stapled analogs, Bioorg. Med. Chem. Lett., 114:129993, 2024, doi: 10.1016/j.bmcl.2024.129993

119. Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska, Molecular dynamics in multi-dimensional space explains how mutations affect the association path of neomycin to a riboswitch, Proc. Natl. Acad. Sci., 121 (15) e2317197121, 2024, doi: 10.1073/pnas.2317197121

118. Uladzislava Tsylents, Michał Burmistrz, Monika Wojciechowska, Jan Stępień, Piotr Maj, Joanna Trylska, Iron uptake pathway of Escherichia coli as an entry route for peptide nucleic acids conjugated with a siderophore mimic, Front. Microbiol., 15:1331021, 2024, doi: 10.3389/fmicb.2024.1331021

2023

117. Julia Macyszyn, Piotr Chyży, Michał Burmistrz, Małgorzata Lobka, Joanna Miszkiewicz, Monika Wojciechowska, Joanna Trylska, Structural dynamics influences the antibacterial activity of a cell-penetrating peptide (KFF)3K, Sci. Rep., 13, 14826, 2023, 10.1038/s41598-023-38745-y

116. Julia Macyszyn, Michał Burmistrz, Adam Mieczkowski, Monika Wojciechowska, Joanna Trylska, Conjugates of aminoglycosides with stapled peptides as a way to target antibiotic resistant bacteria, ACS Omega, 8:19047−19056, 2023, doi: 10.1021/acsomega.3c02071

115. Uladzislava Tsylents, Izabela Siekierska, Joanna Trylska, Peptide nucleic acid conjugates and their applications – a mini-review, Eur. Biophys. J., 52(6-7):533-544, 2023, doi: 10.1007/s00249-023-01673-w

114. Natalia Ostrowska, Michael Feig, Joanna Trylska, Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease, PLoS Comp. Biol., 19(4): e1011054, 2023, doi: 10.1371/journal.pcbi.1011054

113. Alicja Dyzma, Beata Wielgus-Kutrowska, Agnieszka Girstun, Zoe Jelić Matošević, Krzysztof Staroń, Branimir Bertoša, Joanna Trylska, Agnieszka Bzowska, Trimeric architecture ensures the stability and biological activity of the calf purine nucleoside phosphorylase: in silico and in vitro studies of monomeric and trimeric forms of the enzyme, Int. J. Mol. Sci., 24(3), 2157, 2023, doi:10.3390/ijms24032157

2021

112. Fabio Trovato, Joanna Trylska, Peter J. Bond, Peter G. Wolynes, Editorial: Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events, Front. Mol. Biosci., 8:797754, 2021, doi: 10.3389/fmolb.2021.797754

111. Monika Wojciechowska, Julia Macyszyn, Joanna Miszkiewicz, Renata Grzela, Joanna Trylska, Stapled anoplin as an antibacterial agent, Frontiers in Microbiology, 12:772038, 2021, doi: 10.3389/fmicb.2021.772038

110. Magdalena Chrabąszczewska, Maria Winiewska-Szajewska, Natalia Ostrowska, Elżbieta Bojarska, Janusz Stępiński, Łukasz Mancewicz, Maciej Łukaszewicz, Joanna Trylska, Michał Taube, Maciej Kozak, Edward Darżynkiewicz, Renata Grzela, Insight into the binding and hydrolytic preferences of hNudt16 based on nucleotide diphosphate substrates, Int. J. Mol. Sci.,22(20), 10929, 2021, doi: 10.3390/ijms222010929

109. Natalia Ostrowska, Michael Feig, Joanna Trylska, Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex, Biophys. J, 20:3795–3806, 2021, doi: 10.1016/j.bpj.2021.07.008

108. Aleksandra J. Wierzba, Monika Wojciechowska, Joanna Trylska, Dorota Gryko, Vitamin B12: Peptide Nucleic Acid Conjugates, Peptide Conjugation: Methods and Protocols, in Methods in Molecular Biology, Springer Nature, 2021, vol. 2355, chapter 7, doi: 10.1007/978-1-0716-1617-8_7

107. Tomasz Pieńko, Jakub Czarnecki, Marcin Równicki, Monika Wojciechowska, Aleksandra J. Wierzba, Dorota Gryko, Dariusz Bartosik, Joanna Trylska, Vitamin B12-peptide nucleic acids use the BtuB receptor to pass through the E. coli outer membrane, Biophys. J., 120:725–737, 2021, doi: 10.1016/j.bpj.2021.01.004

106. Piotr Chyży, Marta Kulik, Suyong Re, Yuji Sugita, Joanna Trylska, Mutations of N1 riboswitch affect its dynamics and recognition by neomycin through conformational selection, Front. Mol. Biosciences, 8:633130, 2021, doi: 10.3389/fmolb.2021.633130

2020

105. Monika Wojciechowska, Joanna Miszkiewicz, Joanna Trylska, Conformational changes of anoplin, W-MreB1-9 and (KFF)3K peptides in proximity to membrane environments, Int. J. Mol. Sci., 21:9672, 2020, doi: 10.3390/ijms21249672

104. Anna Dobieżyńska, Joanna Miszkiewicz, Zbigniew M. Darżynkiewicz, Michał Tyras, Anna Stankiewicz-Drogoń, Joanna Trylska, Edward Darżynkiewicz, Renata Grzela, Development of bis-ANS-based modified fluorescence titration assay for IFIT/RNA studies, Biochem. Biophys. Res. Commun., 533(3):391-396, 2020, doi: 10.1016/j.bbrc.2020.09.006

103. Marcin Równicki, Robert Lasek, Joanna Trylska, Dariusz Bartosik, Targeting type II toxin-antitoxin systems as antibacterial strategies, Toxins, 12:568, 2020, doi: 10.3390/toxins12090568

102. Agnieszka Popielec, Natalia Ostrowska, Monika Wojciechowska, Michael Feig, Joanna Trylska, The effect of the crowded environment on the activity and inhibition of the NS3/4A protease, Biochimie, 176:169-180, 2020, doi: 10.1016/j.biochi.2020.07.009

101. Tomasz Pieńko, Joanna Trylska, Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli, PLoS Comput. Biol., 16(7): e1008024, 2020, doi: 10.1371/journal.pcbi.1008024, View Correction doi: 10.1371/journal.pcbi.1009696

100. Monika Wojciechowska, Marcin Równicki, Adam Mieczkowski, Joanna Miszkiewicz, Joanna Trylska, Antibacterial peptide nucleic acids – facts and perspectives, Molecules, 25(3), 559, 2020, Cover figure, doi: 10.3390/molecules25030559

99. Beata Miedziak, Anna Dobieżyńska, Zbigniew M. Darżynkiewicz, Julia Bartkowska, Joanna Miszkiewicz, Joanna Kowalska, Marcin Warmiński, Michal Tyras, Joanna Trylska, Jacek Jemielity, Edward Darzynkiewicz, Renata Grzela, Kinetic analysis of IFIT1 and IFIT5 interactions with different native and engineered RNAs and its consequences for designing mRNA-based therapeutics, RNA 26:58-68, 2020, doi: 10.1261/rna.073304.119

2019

98. Maciej Jasiński, Joanna Miszkiewicz, Michael Feig, Joanna Trylska, Thermal stability of peptide nucleic acid complexes, J. Phys. Chem. B, 123:8168−8177, 2019, doi: 10.1021/acs.jpcb.9b05168

97. Natalia Ostrowska, Michael Feig, Joanna Trylska, Modeling crowded environment in molecular simulations, Frontiers in Molecular Biosciences, 6:86, 2019, doi: 10.3389/fmolb.2019.00086

96. Ksenia Maximova, Jakub Wojtczak, Joanna Trylska, Enzymatic activity of human immunodeficiency virus type 1 protease in dilute and crowded solutions, Eur. Biophys. J., 48:685–689, 2019, doi: 10.1007/s00249-019-01392-1

95. Ksenia Maximova, Nathalie Reuter, Joanna Trylska, Peptidomimetic inhibitors targeting the membrane-binding site of the neutrophil proteinase 3, BBA – Biomembranes, 1861:1502-1509, 2019, doi: 10.1016/j.bbamem.2019.06.009

94. Tomasz Pieńko, Joanna Trylska, Computational methods used to explore transport events in biological systems, J. Chem. Inf. Model., 59, 5, 1772-1781, 2019, doi: 10.1021/acs.jcim.8b00974

93. Filip Leonarski, Joanna Trylska, Modeling nucleic acids at the residue-level resolution, In: Computational methods to study the structure and dynamics of biomolecules and biomolecular processes – from bioinformatics to molecular quantum mechanics, editor A. Liwo, Springer series on Bio- and Neurosystems, volume 8, second edition, 117-161, 2019, doi: 10.1007/978-3-642-28554-7_5

92. Marcin Równicki, Zofia Dąbrowska, Monika Wojciechowska, Aleksandra J. Wierzba, Ksenia Maximova, Dorota Gryko, Joanna Trylska, Inhibition of Escherichia coli growth by vitamin B12-peptide nucleic acid conjugates, ACS Omega, 4(1):819-824, 2019, doi: 10.1021/acsomega.8b03139

91. Maciej Giedyk, Agnieszka Jackowska, Marcin Równicki, Monika Kolanowska, Joanna Trylska, Dorota Gryko, Vitamin B12 transports modified RNA into E. coli and S. Typhimurium cells, Chem. Commun., 55:763-766, 2019, doi: 10.1039/c8cc05064c, cover figure, doi: 10.1039/c8cc05064c

90. Ksenia Maximova, Jakub Wojtczak, Joanna Trylska, Enzyme kinetics in crowded solutions from isothermal titration calorimetry, Anal. Biochem., 567, 96-105, 2019, doi: 10.1016/j.ab.2018.11.006

89. Boris Smolkin, Alina Khononov, Tomasz Pieńko, Michal Shavit, Valery Belakhov, Joanna Trylska, Timor Baasov, Towards catalytic antibiotics: redesign of aminoglycosides to catalytically disable bacterial ribosomes, ChemBioChem, 20:247-259, 2019, doi: 10.1002/cbic.201800549

88. Filip Leonarski, Maciej Jasiński, Joanna Trylska, Thermodynamics of the fourU RNA thermal switch derived from molecular dynamics simulations and spectroscopic techniques, Biochimie, 156:22-32, 2019, doi: 10.1016/j.biochi.2018.09.005

2018

87. Marcin Równicki, Tomasz Pieńko, Jakub Czarnecki, Monika Kolanowska, Dariusz Bartosik, Joanna Trylska, Artificial activation of Escherichia coli mazEF and hipBA toxin–antitoxin systems by antisense peptide nucleic acids as an antibacterial strategy, Front. Microbiol. 9:2870, 2018 doi: 10.3389/fmicb.2018.02870

86. Aleksandra J. Wierzba, Ksenia Maximova, Aleksandra Wincenciuk, Marcin Równicki, Monika Wojciechowska, Ebba Nexo, Joanna Trylska, Dorota Gryko, Does a conjugation site affect transport of vitamin B12-PNA conjugates into bacterial cells?, Chemistry – A European Journal, 24(70):18772-18778, 2018, doi: 10.1002/chem.201804304

85. Marta Kulik, Takaharu Mori, Yuji Sugita, Joanna Trylska, Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides, Nucl. Acids Res., 46(19): 9960–9970, 2018, doi: 10.1093/nar/gky833

84. Jaime Ivan Castillo, Marcin Równicki, Monika Wojciechowska, Joanna Trylska, Antimicrobial synergy between mRNA targeted peptide nucleic acid and antibiotics in E. coli, Bioorg. & Med. Chem. Lett.,  28: 3094–3098, 2018, doi: 10.1016/j.bmcl.2018.07.037

83. Maciej Jasiński, Michel Feig, Joanna Trylska, Improved force fields for peptide nucleic acids with optimized backbone torsion parameters, J. Chem. Theory Comput., 14 (7): 3603–3620, 2018, doi: 10.1021/acs.jctc.8b00291

82. Katarzyna Kulczycka-Mierzejewska, Joanna Sadlej, Joanna Trylska, Molecular dynamics simulations suggest why the A2058G mutation in 23S RNA results in bacterial resistance against clindamycin, J. Mol. Model., 24:191, 2018, doi: 10.1007/s00894-018-3689-5

81. Monika Wojciechowska, Marta Dudek, Joanna Trylska, Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA, Biopolymers, 109(4):e23116, 2018, doi: 10.1002/bip.23116

80. Narayana Sabbavarapu, Tomasz Pieńko, Bat-Hen Zalman, Joanna Trylska, Timor Baasov, Exploring eukaryotic versus prokaryotic ribosomal RNA recognition with aminoglycoside derivatives, Med. Chem. Commun., 9:503-508, 2018, doi: 10.1039/c8md00001h

79. Maciej Jasiński, Marta Kulik, Monika Wojciechowska, Ryszard Stolarski, Joanna Trylska, Interactions of 2′-O-methyl Oligoribonucleotides with the RNA Models of the 30S Subunit A-site, PLoS ONE, 13(1):e0191138, 2018, doi: 10.1371/journal.pone.0191138

78. Ksenia Maximova, Tom Venken, Nathalie Reuter, Joanna Trylska, D-peptides as inhibitors of PR3-membrane interactions, BBA – Biomembranes, 1860:458-466, 2018, doi: 10.1016/j.bbamem.2017.11.001

2017

77. Marcin Równicki, Monika Wojciechowska, Aleksandra J. Wierzba, Jakub Czarnecki, Dariusz Bartosik, Dorota Gryko, Joanna Trylska, Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells, Sci. Rep., 7:7644, 2017, doi: 10.1038/s41598-017-08032-8

76. Marta Kulik, Agnieszka Markowska-Zagrajek, Monika Wojciechowska, Renata Grzela, Tomasz Wituła, Joanna Trylska, Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target, Biochimie, 138:32-42, 2017, doi: 10.1016/j.biochi.2017.04.001

75. Tomasz Pieńko, Aleksandra J. Wierzba, Monika Wojciechowska, Dorota Gryko, Joanna Trylska, Conformational dynamics of cyanocobalamin and its conjugates with peptide nucleic acids, J. Phys. Chem. B., 121:2968-2979, 2017, doi: 10.1021/acs.jpcb.7b00649

74. Marta Dudek, Joanna Trylska, Molecular dynamics simulations of L-RNA involving homo- and heterochiral complexes, J. Chem. Theory Comput., 13:1244-1253,2017, doi: 10.1021/acs.jctc.6b01075

73. Sapna G. Thoduka, Paul A. Zaleski, Zofia Dąbrowska, Marcin Równicki, Joanna Stróżecka, Anna Górska, Mikołaj Olejniczak, Joanna Trylska, Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides, Biopolymers,107:e23004, 2017, doi: 10.1002/bip.23004

2016

72. Joanna Trylska, Marta Kulik, Interactions of aminoglycoside antibiotics with rRNA, Biochem. Soc. Trans., 44(4):987-993, 2016, doi: 10.1042/BST20160087

71. Anna Górska, Agnieszka Markowska-Zagrajek, Marcin Równicki, Joanna Trylska, Scanning of 16S ribosomal RNA for peptide nucleic acid targets, J. Phys. Chem. B, 120(33):8369-8378,2016, doi: 10.1021/acs.jpcb.6b02081

70. Aleksandra Wierzba, Monika Wojciechowska, Joanna Trylska, Dorota Gryko, Vitamin B12 suitably tailored for disulfide-based conjugation, Bioconjugate Chemistry, 27:189-197, 2016, doi: 10.1021/acs.bioconjchem.5b00599

69. Katarzyna Kulczycka-Mierzejewska, Joanna Trylska, Joanna Sadlej, Conformational space of clindamycin studied by quantum and full-atom molecular dynamics, Journal of Molecular Modeling,22:20, 2016

68. Marta Kulik, Joanna Trylska, Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site, RAIRO-Operations Research, 50:375-386, 2016, doi: 10.1051/ro/2015041

2015

67. Anna Górska, Maciej Jasiński, Joanna Trylska, MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids, Nucl. Acids Res., 43(17):e114, 2015, doi: 10.1093/nar/gkv559

66. Ksenia Maximova, Joanna Trylska, Kinetics of trypsin catalyzed hydrolysis determined by isothermal titration calorimetry, Analytical Biochemistry, 486:24-34, 2015, doi: 10.1016/j.ab.2015.06.027

65. Filip Leonarski, Joanna Trylska, RedMDStream: Parameterization and simulation toolbox for coarse-grained molecular dynamics models, Biophys. J., 108:1843-1847, 2015, doi: 10.1016/j.bpj.2015.03.023

64. Joanna Panecka, Jiri Sponer, Joanna Trylska, Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site, Biochimie, 112:96-110, 2015, doi: 10.1016/j.biochi.2015.02.021

63. Marta Kulik, Anna M. Goral, Maciej Jasiński, Paulina M. Dominiak, Joanna Trylska, Electrostatic interactions in aminoglycoside-RNA complexes, Biophys. J., 108(3):655-665, 2015 Cover figure, doi: 10.1016/j.bpj.2014.12.020

2014

62. Joanna Panecka, Cameron Mura, Joanna Trylska, Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: A molecular dynamics study, PLoS ONE, 9(11): e111811, 2014, doi: 10.1371/journal.pone.0111811

61. Agnieszka Markowska-Zagrajek, Marcin Równicki, Joanna Trylska, Inhibition of bacterial translation and growth by antisense peptide nucleic acids and their potential application in biotechnology (in Polish), Advances in Microbiology, 53(3): 255–263, 2014

60. Joanna Panecka, Marek Havrila, Kamila Reblova, Jiri Sponer, Joanna Trylska, The Role of S-turn2 in the Structure, Dynamics and Function of Mitochondrial Ribosomal A-site. A Bioinformatics and Molecular Dynamics Simulation Study, J. Phys. Chem. B, 118: 6687-6701, 2014, doi: 10.1021/jp5030685

59. Marta Dudek, Julia Romanowska, Tomasz Wituła, Joanna Trylska, Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies, Biochimie, 102: 188-202, 2014, doi: 10.1016/j.biochi.2014.03.009

58. Filip Leonarski, Joanna Trylska, Modeling Nucleic Acids at the Residue-Level Resolution, in: Computational methods to study the structure and dynamics of biomolecules and biomolecular processes – from bioinformatics to molecular quantum mechanics, Springer, 109-149, 2014, doi: 10.1007/978-3-642-28554-7_5

2013

57. Filip Leonarski, Fabio Trovato, Valentina Tozzini, Andrzej Leś, Joanna Trylska, Evolutionary algorithm in the optimization of a coarse-grained force field, J. Chem. Theory Comput., 9 (11): 4874–4889, 2013, doi: 10.1021/ct4005036

56. Joanna Trylska, Sapna Thoduka, Zofia Dąbrowska, Using sequence-specific oligonucleotides to inhibit bacterial ribosomal RNA, ACS Chem. Biol., 8(6): 1101–1109, 2013, doi: 10.1021/cb400163t

55. Julia Romanowska, Nathalie Reuter, Joanna Trylska, Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes, Proteins: Struct. Funct. Bioinf., 81(1):63-80, 2013, doi: 10.1002/prot.24163

2012

54. Julia Romanowska, Krzysztof Nowiński, Joanna Trylska, Determining geometrically stable domains in molecular conformation sets, J. Chem. Theory Comput., 8: 2588−2599, 2012, doi: 10.1021/ct300206j

53. Joanna Panecka, Joanna Trylska, Molecular Dynamics Techniques in the Studies of the Bacterial Ribosome, in: Theory and Applications in Computational Chemistry: The First Decade of the Second Millennium, AIP Conference Proceedings Series, 1456:207-214, 2012, doi: 10.1063/1.4730661

52. Maciej Długosz, Jan Antosiewicz, Paweł Zieliński, Joanna Trylska, Contributions of Far-Field Hydrodynamic Interactions to the Kinetics of Electrostatically-Driven Molecular Association, J. Phys. Chem. B., 116:5437-5447, 2012, doi: 10.1021/jp301265y

51. Karine Voltz, Joanna Trylska, Nicolas Calimet, Jeremy C. Smith, and Joerg Langowski, Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study, Biophys. J., 102: 849-858, 2012, doi: 10.1016/j.bpj.2011.11.4028

50. Katarzyna Kulczycka-Mierzejewska, Joanna Trylska, Joanna Sadlej, Quantum mechanical studies of lincosamides,  J. Mol. Model., 18:2727–2740, 2012, doi: 10.1007/s00894-011-1272-4

2011

49. Maciej Długosz, Joanna Trylska, Secondary structures of native and pathogenic Huntingtin N-terminal fragments, J. Phys. Chem. B, 115: 11597–11608, 2011, doi: 10.1021/jp206373g

48. Maciej Jasiński, Maciej Długosz, Joanna Trylska, Molecular dynamics simulations of PNA oligomers, in: I National Conference of Biophysics Students Proceedings, Department of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, AT Group Ltd. 2010, 75 – 84, ISBN 978-83-61026-50-1, 2011

47. Julia Romanowska, Dariusz Ekonomiuk, Joanna Trylska, Computational studies of RNA dynamics and RNA-ligand interactions, in: Methods for Studying Nucleic Acid Drug Interactions, CRC Press, 337-360, ISBN 978-1439839737, 2011

46. Julia Romanowska, J. Andrew McCammon, Joanna Trylska, Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site, PLoS Computational Biology, 7(7):e1002099, 2011, doi: 10.1371/journal.pcbi.1002099

45. Maciej Długosz, Paweł Zieliński, Joanna Trylska, Brownian dynamics simulations on CPU and GPU with BD_BOX, J. Comput. Chem., 32:2734–2744, 2011, doi: 10.1002/jcc.21847

44. Maciej Długosz, Gary A. Huber, J. Andrew McCammon, Joanna Trylska, Brownian dynamics study of the association between the 70S ribosome and the elongation factor G, Biopolymers, 95 (9): 616-627, 2011 Cover figure , doi: 10.1002/bip.21619

43. Maciej Długosz, Joanna Trylska, Diffusion in crowded biological environments. Applications of Brownian dynamics, BMC Biophysics, 4:3, 2011, doi: 10.1186/2046-1682-4-3

42. Filip Leonarski, Fabio Trovato, Valentina Tozzini, Joanna Trylska, Genetic Algorithm Optimization of Force Field Parameters. Application to a Coarse-Grained Model of RNA, in: Lecture Notes in Computer Science, Springer, 6623: 147-152, 2011, doi: 10.1007/978-3-642-20389-3_15

41. Joanna Panecka, Cameron Mura, Joanna Trylska, Molecular Dynamics of Potential Ribosomal RNA Binders: Single-Stranded Nucleic Acids and some Analogues, J. Phys. Chem. B, 115 (3): 532–546, 2011, doi: 10.1021/jp106404u

40. Katarzyna Kulczycka, Maciej Długosz, Joanna Trylska, Molecular dynamics of ribosomal elongation factors G and Tu, Eur. Biophys. J., 40: 289–303, 2011, doi: 10.1007/s00249-010-0647-2

2010

39. Joanna Trylska, Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome,  J. Phys.: Condens. Matter, 22: 453101, 2010, doi: 10.1088/0953-8984/22/45/453101

38. Joanna Trylska, The Structure and Function of the Ribosome. Nobel Prize in Chemistry 2009, Kosmos, 1-2 (286-287): 9-16, 2010

2009

37. Joanna Trylska, Simulating Activity of the Bacterial Ribosome, Q. Rev. Biophys., 42:301-316, 2009, doi: 10.1017/S0033583510000028

36. Maciej Długosz, Jan M. Antosiewicz, Joanna Trylska, pH-Dependent Association of Proteins. The Test Case of Monoclonal Antibody HyHEL-5 and its Antigen Hen Egg White Lysozyme, J. Phys. Chem. B, 113:15662-15669, 2009, doi: 10.1021/jp906829z

35. Adam Gorecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska, RedMD – reduced molecular dynamics package, J. Comput. Chem., 30:2364-2373, 2009, doi: 10.1002/jcc.21223

34. Maciej Dlugosz, Joanna Trylska, Aminoglycoside Association Pathways with the 30S Ribosomal Subunit, J. Phys. Chem. B, 113:7322-7330, 2009, doi: 10.1021/jp8112914

33. Piotr Setny, Joanna Trylska; Search for Novel Aminoglycoside Derivatives by Combining Fragment-based Virtual Screening and 3D-QSAR Scoring, J. Chem. Inf. Model., 49:390-400, 2009, doi: 10.1021/ci800361a

32. Joanna Trylska, Computational Modeling of the Bacterial 70S Ribosome and Its Subunits, Biotechnologia, 1(84):36-47, 2009,

2008

31. Julia Romanowska, Piotr Setny, Joanna Trylska; Molecular dynamics study of the ribosomal A-site, J. Phys. Chem. B., 112:15227-15243, 2008, doi: 10.1021/jp806814s

30. Maciej Dlugosz, Joanna Trylska; Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition, J. Chem. Phys., 129:015103, 2008, doi: 10.1063/1.2948414

29. Maciej Dlugosz, Jan M. Antosiewicz, Joanna Trylska; Association of Aminoglycosidic Antibiotics with the Ribosomal A-site Studied with Brownian Dynamics, J. Chem. Theory Comput., 4:549-559, 2008 Cover figure, doi: 10.1021/ct700210n

28. Magdalena Gruziel, Pawel Grochowski, Joanna Trylska; The Poisson-Boltzmann model for tRNA. Assessment of the calculation set-up and ionic concentration cutoff, J. Comput. Chem., 29:1970-1981, 2008, doi: 10.1002/jcc.20953

27. Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Joerg Langowski, Jeremy Smith; Coarse-grained Force Field for the Nucleosome from Self-consistent Multiscaling, J. Comput. Chem., 29:1429-1439, 2008, doi: 10.1002/jcc.20902

26. Pawel Grochowski, Joanna Trylska; Continuum Molecular Electrostatics, Salt Effects and Counterion Binding. A Review of the Poisson-Boltzmann Model and its Modifications, Biopolymers, 89:93-113, 2008, doi: 10.1002/bip.20877

25. Marcin Szypowski, Adam Gorecki, Joanna Trylska, RedMD – a New Package for Reduced Molecular Dynamics, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:389-392, ISBN 978-3-9810843-6-8, 2008

24. Katarzyna Kulczycka, Maciej Dlugosz, Joanna Trylska, Internal Dynamics of Elongation Factors G and Tu Studied with All-atom and Coarse-grained Molecular Dynamics, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:277-280, ISBN 978-3-9810843-6-8, 2008

23. Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jeremy Smith, Joerg Langowski, Global Motions in the Nucleosome Explored using a Coarse-grain Model, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:141-144, ISBN 978-3-9810843-6-8, 2008

22. Maciej Dlugosz, Joanna Trylska, Association of Neamine and its Derivative with the Ribosomal A-site RNA, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:81-84, ISBN 978-3-9810843-6-8, 2008

2007

21. Joanna Trylska, Valentina Tozzini, Chia-en Chang, J. Andrew McCammon; HIV-1 Protease Substrate Binding and Product Release Pathways Explored with Coarse-Grained Molecular Dynamics, Biophys. J., 92:4179-4187, 2007, doi: 10.1529/biophysj.106.100560

20. Chia-en Chang, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations, Chem. Biol. & Drug Design, 69:5-13, 2007 Cover figure, doi: 10.1111/j.1747-0285.2007.00464.x

19. Valentina Tozzini, Joanna Trylska, Chia-en Chang, J. Andrew McCammon; Flap Opening Dynamics in HIV-1 Protease Explored with a Coarse-Grained Model, J. Struct. Biol., 157:606-615, 2007, doi: 10.1016/j.jsb.2006.08.005

18. Magdalena Gruziel, Piotr Kmiec, Joanna Trylska, Bogdan Lesyng; Selected Microscopic and Mezoscopic Modelling Tools and Models – an Overview, In: Molecular Materials with Specific Interactions: Modeling and Design, Ed. A. W. Sokalski, Series Title: Challenges and Advances in Chemistry and Physics, Springer, Dordrecht, The Netherlands, 4:203-224, ISBN-10 1-4020- 5371-1 (HB), (2007), doi: 10.1007/1-4020-5372-X_3

2006

17. Grace Yang, Joanna Trylska, Yitzhak Tor, J. Andrew McCammon; Binding of Aminoglycosidic Antibiotics to the Oligonucleotide A-site Model and 30S Ribosomal Subunit: Poisson-Boltzmann Model, Thermal Denaturation and Fluorescence Studies, J. Med. Chem., 49:5478-5490, 2006, doi: 10.1021/jm060288o

16. Adam Gorecki, Joanna Trylska, Bogdan Lesyng; Causal Relations in Molecular Dynamics Investigated with Multi-Variable Autoregressive Model, Europhys. Lett., 75:503-509, 2006, doi: 10.1209/epl/i2006-10129-2

15. Chia-en Chang, Tongye Shen, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model, Biophys. J., 90:3880-3885, 2006, doi: 10.1529/biophysj.105.074575

14. David D. L. Minh, Chia-en Chang, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics J. Am. Chem. Soc., 128:6006-6007, 2006, doi: 10.1021/ja060483s

13. Kay Hamacher, Joanna Trylska, J. Andrew McCammon; Dependency Map of Proteins in the Small Ribosomal Subunit, PLoS Comp. Biol., 2:0080-0087, 2006, doi: 10.1371/journal.pcbi.0020010

12. Robert Konecny, Joanna Trylska, Florence Tama, Deqiang Zhang, Nathan A. Baker, Charles L. Brooks, III, J. Andrew McCammon; Electrostatic Properties of Cowpea Chlorotic Mottle Virus and Cucumber Mosaic Virus Capsids, Biopolymers, 82:106-120, 2006, doi: 10.1002/bip.20409

2005

11. Joanna Trylska, J. Andrew McCammon, Charles L. Brooks III; Exploring Assembly Energetics of the 30S Ribosomal Subunit Using an Implicit Solvent Approach, J. Am. Chem. Soc., 127:11125-11133, 2005, doi: 10.1021/ja052639e

10. Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Exploring Global Motions and Correlations in the Ribosome, Biophys. J., 89:1455-1463, 2005, doi: 10.1529/biophysj.104.058495

2004

9. Joanna Trylska, Robert Konecny, Florence Tama, Charles L. Brooks III, J. Andrew McCammon; Ribosome motions modulate electrostatic properties, Biopolymers, 74:423-431, 2004 Cover figure , doi: 10.1002/bip.20093

8. Joanna Trylska, Pawel Grochowski, J. Andrew McCammon; The Role of Hydrogen Bonding in the Enzymatic Reaction Catalyzed by HIV-1 Protease Protein Science, 13:513-528, 2004, doi: 10.1110/ps.03372304

2003

7. Joanna Trylska, Piotr Bala, Maciej Geller, Pawel Grochowski;  Quantum-Classical Molecular Dynamics Simulations in the Studies of the Reaction Catalyzed by HIV-1 Protease In: Simulation in Research and Development, Polish Association for Computer Simulation, p. 269-276, ISBN:83-7365-048-2, 2003

2002

6. Joanna Trylska, Piotr Bala, Maciej Geller, Pawel Grochowski; Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease Biophys. J., 83:794-807, 2002, doi: 10.1016/s0006-3495(02)75209-0

2001

5. Joanna Trylska, Pawel Grochowski, Maciej Geller; Parameterization of the Approximate Valence Bond (AVB) Method to Describe Potential Energy Surface in the Reaction Catalyzed by HIV-1 Protease Int. J. Quant. Chem., 82:86-103, 2001, doi: 10.1002/1097-461X(2001)82:2<86::AID-QUA1024>3.0.CO;2-E

2000

4. Roman Bogacewicz, Joanna Trylska, Maciej Geller; Ligand design package (LUDI – MSI) applied to known inhibitors of the HIV-1 protease. Test of performance, Acta Poloniae Pharmaceutica, 57:25-28, 2000

1999

3. Joanna Trylska, Jan Antosiewicz, Maciej Geller, C. N. Hodge, Ronald Klabe, Martha S. Head, Michael K. Gilson; Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease Protein Science, 8:180-195, 1999, doi: 10.1110/ps.8.1.180

2. Piotr Bala, Maciej Geller, Krzysztof Ginalski, Pawel Grochowski, Joanna Trylska, Bogdan Lesyng; Approximate Valence Bond Method – A Fast Generator of Quantum Potentials for Molecular Simulations In: Modelling and Simulation: A Tool for the Next Millenium, 13th European Simulation Multiconference, June 1-4, 1999, Warsaw, Poland, p. 181-183, Society for Computer Simulation International, 1999

1997

1. Maciej Geller, Joanna Trylska, Jan Antosiewicz; HIV-1 Protease and its Inhibitors In: Theoretical and Computational Methods in Genome Research, Sandor Suhai Plenum Press, p. 237-242, ISBN:030645503X, 1997, doi: 10.1007/978-1-4615-5903-0_18