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Publications

2024

  1. M. Jurkowski, M. Kogut, S. Sappati, J. Czub Why Are Left-Handed G-Quadruplexes Scarce? The Journal of Physical Chemistry Letters 2024, 15, 3142-3148
  2. J. Jędrychowska, V. Vardanyan, M. Wieczor, A. Marciniak, J. Czub, R. Amini, ... & V. Korzh Mutant analysis of Kcng4b reveals how the different functional states of the voltage-gated potassium channel regulate ear development. Developmental Biology 2024, (in press)
  3. J. Słabońska, S. Sappati, A. Marciniak, J. Czub, Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline ACS Medicinal Chemistry Letters 2024, 15(2), 265-269
  4. A. Shiroudi, J. Czub, M. Altarawneh, Chemical Investigation on the Mechanism and Kinetics of the Atmospheric Degradation Reaction of Trichlorofluoroethene by OH⋅ and Its Subsequent Fate in the Presence of O2/NOx ChemPhysChem 2024, 25(3), e202300665

2023

  1. M. Jelen, I. Grochowina, A. Grabinska-Rogala, S. J. Ciesielski, K. Dabrowska, B. Tomiczek, L. Nierzwicki, W. Delewski, B. Schilke, J. Czub, M. Dadlez, R. Dutkiewicz, E. A. Craig, J. Marszalek, Analysis of Reconstituted Tripartite Complex Supports Avidity-Based Recruitment of Hsp70 by Substrate Bound J-Domain Protein Journal of Molecular Biology 2023, 435(21), 168283
  2. O. Grabowska, K. Żamojć, M. Olewniczak, L. Chmurzyński, D. Wyrzykowski, Can sodium 1-alkylsulfonates participate in the sodium dodecyl sulfate micelle formation? Journal of Molecular Liquids 2023, 377, 121568.
  3. K. A. Hossain, M. Kogut, J. Słabońska, S. Sappati, M. Wieczór, J. Czub, How acidic amino acid residues facilitate DNA target site selection Proc. Natl. Acad. Sci. USA 2023, 120, 3, e2212501120
  4. J. Borzyszkowska-Bukowska, J. Czub, P. Szczeblewski, T. Laskowski, Antibiotic-sterol interactions provide insight into the selectivity of natural aromatic analogues of amphotericin B and their photoisomers Sci. Rep. 2023, 13(1), 762
  5. M. Badocha, M. Wieczór, A. Marciniak, C. Kleist, H. Grubmuller, J. Czub, Molecular mechanism and energetics of coupling between substrate binding and product release in the F1-ATPase catalytic cycle Proc. Natl. Acad. Sci. USA 2023, 120, 8, e2215650120

2022

  1. M. Szadkowska, M. Olewniczak, A. Kloska, E. Jankowska, M. Kapusta, B. Rybak, ... & M. Plotka, A Novel Cryptic Clostridial Peptide That Kills Bacteria by a Cell Membrane Permeabilization Mechanism Microbiology Spectrum 2022, e01657-22
  2. S. Makurat, Q. Yuan, J. Czub, L. Chomicz-Mańka, W. Cao, X.B. Wang, J. Rak, Guanosine Dianions Hydrated by One to Four Water Molecules  J. Phys. Chem. Lett. 2022, 13, XXX, 3230–3236
  3. A. Marciniak, P. Chodnicki, K.A. Hossain, J. Slabonska, J. Czub, Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution  J. Phys. Chem. Lett. 2022, 13, 1, 387–392

2021

  1. L. Nierzwicki, K.W. East, U.N. Morzan, P.R. Arantes, V.S. Batista, G.P. Lisi, G. Palermo, Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9  eLife 2021, 10:e73601
  2. H. B. Belato, A. M. D'Ordine, Ł. Nierzwicki, P. R. Arantes, G. Jogl, G. Palermo, G. P. Lisi, Structural and Dynamic Insights into the HNH Nuclease of Divergent Cas9 Species  J. Struct. Biol. 2021, 107814
  3. G. da Rosa, L. Grille, V. Calzada, ..., J. Czub, ..., P. D. Dans, Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?  Biophys. Rev. 2021, 13, 995–1005
  4. J. Jurasz, M. Bagiński, J. Czub, M. Wieczór, Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE.  PLoS Comput. Biol. 2021, 17(10), e1009454
  5. Ł. Nierzwicki, M. Olewniczak, P. Chodnicki, J. Czub, Role of cholesterol in substrate recognition by γ-secretase.  Sci Rep 2021, 11, 15213
  6. R. Luchowski, W. Grudzinski, R. Welc, M.M.M. Pinto, A. Sek, J. Ostrowski, Ł. Nierzwicki, P. Chodnicki, M. Wieczor, K. Sowinski, R. Rejdak, A.G.M. Juenemann, G. Teresinski, J. Czub, and W.I. Gruszecki, Light-Modulated Sunscreen Mechanism in the Retina of the Human Eye.  J. Phys. Chem. B 2021, 125, 23, p. 6090–6102
  7. A. Piróg, F. Cantini, Ł. Nierzwicki, I. Obuchowski, B. Tomiczek, J. Czub, K. Liberek, Two bacterial small heat shock proteins, IbpA and IbpB, form a functional heterodimer.  J. Mol. Biol. 2021, 433, 15, p. 167054
  8. K.A. Hossain, M. Jurkowski, J. Czub, M. Kogut, Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations. Comput. Struct. Biotechnol. J. 2021, 19, p. 2526-2536
  9. K. Wegrzyn, E. Zabrocka, K. Bury, B. Tomiczek, M. Wieczor, J. Czub, U. Uciechowska, M. Moreno-del Alamo, U. Walkow, I. Grochowina, R. Dutkiewicz, J.M. Bujnicki, R. Giraldo, I. Konieczny, Defining a novel domain which provides an essential contribution to site-specific interaction of Rep protein with DNA. Nucleic Acids Res. 2021, 49, 6, p. 3394–3408
  10. Ł. Nierzwicki, G. Palermo, Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules. Front. Mol. Biosci. 2021, 8, 120
  11. J. Lica, M. Wieczór, G.J. Grabe, M. Heldt, M. Jancz, M. Misiak, K. Gucwa, W. Brankiewicz, N. Maciejewska, A. Stupak, M. Bagiński, K. Rolka, A. Hellmann, A. Składanowski, Effective Drug Concentration and Selectivity Depends on Fraction of Primitive Cells.  Int. J. Mol. Sci. 2021, 22(9), 4931
  12. N. Farag, R. Mattossovich, R. Merlo, Ł. Nierzwicki, G. Palermo, A. Porchetta, G. Perugino, F. Ricci, Folding‐upon‐repair DNA nanoswitches for monitoring DNA repair enzymes activity. Angew. Chem. Int. Ed. 2021, 10.1002/anie.202016223
  13. J. Zielińska, M. Wieczor, P. Chodnicki, E. Grela, R. Luchowski, Ł. Nierzwicki, T. Bączek, W. Gruszecki, J. Czub, Self-assembly, stability and conductance of amphotericin B channels: bridging the gap between structure and function. Nanoscale 2021, 13, 3686-3697

2020

  1. K. Hemine, A. Skwierawska, C. Kleist, M. Olewniczak, K. Szwarc-Karabyka, D. Wyrzykowski, A. Mieszkowska, J. Chojnacki, J. Czub, L. Nierzwicki, Effect of chemical structure on complexation efficiency of aromatic drugs with cyclodextrins: the example of dibenzazepine derivatives. Carbohydr. Polym. 2020, 250, 116957
  2. L. Casalino, Ł. Nierzwicki, M. Jinek, and G. Palermo, Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics. ACS Catal. 2020, 10, 22, 13596-13605
  3. Ł. Nierzwicki, P.R. Arantes, A. Saha and G. Palermo., Establishing the Allosteric Mechanism in CRISPR-Cas9. WIREs Comp. Mol. Biosci. 2020, e1503
  4. J.Y. Cui, F. Zhang, L. Nierzwicki, G. Palermo, R.J. Linhardt, G.P. Lisi, Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor. Biochemistry 2020, 59, 38, 3541-3553
  5. K. Butowska, K. Żamojć, M. Kogut, W. Kozak, D. Wyrzykowski, W. Wiczk, J. Czub, J. Piosik, J. Rak, The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA. Int. J. Mol. Sci. 2020, 21, 6923
  6. M. Wieczór, A. Hospital, G. Bayarri, J. Czub, M. Orozco, Molywood: streamlining the design and rendering of molecular movies. Bioinformatics 2020, 36, 4660–4661
  7. B. Tomiczek, W. Delewski, Ł. Nierzwicki, M. Stolarska, I. Grochowina, B. Schilke, R. Dutkiewicz, M. A. Uzarska, S. J. Ciesielski, J. Czub, E. A. Craig, J. Marszalek, Two-step mechanism of J-domain action in driving Hsp70 function. PLoS Comput. Biol. 2020, 16, e1007913
  8. M. Wieczór, J. Czub. Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models. Free Rad. Bio. Med. 2020, 148, 162-169
  9. B. Zalewska-Piątek, M. Olszewski, T. Lipniacki, S. Błoński, M. Wieczór, P. Bruździak, A. Skwarska, B. Nowicki, S. Nowicki, R. Piątek. A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin. PLoS Path. 2020, 16, e1008247

2019

  1. M. Kogut, C. Kleist, J. Czub. Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail. PLoS Comput. Biol. 2019, 15, e1007383.
  2. W. Przychodzeń, J. Chojnacki, Ł. Nierzwicki. Medium-sized cyclic bis(anisylphosphonothioyl)disulfanes and their corresponding cyclic sulfane-structures and most characteristic reactions. New J. Chem. 2019, 43, 15413-15434.
  3. A. Hałuszczuk, N. Babul, Ł. Nierzwicki, W. Przychodzeń. General, Mild, and Metal‐Free Functionalization of Indole and Its Derivatives Through Direct C3‐Selenylation, Eur. J. Org. Chem. 2019, 10.1002/ejoc.201900632.
  4. O. K. Shrestha , R. Sharma, B. Tomiczek, W. Lee, M. Tonelli, G. Cornilescu, M. Stolarska, Ł. Nierzwicki, J. Czub, J. L. Markley, J. Marszalek, S. J. Ciesielski, E. A. Craig. Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70. PLoS ONE 2019, 14, e0217098.

2018

  1. K. E. Greber, J. Zielińska, Ł. Nierzwicki, K. Ciura, P. Kawczak, J. Nowakowska, T. Bączek, W. Sawicki. Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation. BBA-Biomembranes 2018, 1861, 93-99
  2. P. Rakowska, M. Kogut, J. Czub, J. Stangret. Effect of Osmolytes of Different Type on DNA Behaviour in Aqueous Solution. Experimental and Theoretical Studies. J. Mol. Liq. 2018, 271, 186-201
  3. E. Grela, M. Wieczór, R. Luchowski, J. Zielińska, A. Barzycka, W. Grudziński, K. Nowak, P. Tarkowski, J. Czub, W. Gruszecki. A Mechanism of Binding of an Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single Membrane Imaging, Micro-Spectroscopy, and Molecular Dynamics. Mol. Pharm. 2018, 15, 4202-4213
  4. B. Adamczak, M. Kogut, J. Czub. Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions. Phys. Chem. Chem. Phys. 2018, 20, 11174-11182
  5. B. Żołnowska, J. Sławiński, K. Szafrański, A. Angeli, C. T. Supuran, A. Kawiak, M. Wieczór, J. Zielińska, T. Bączek, S. Bartoszewska. Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies. Eur. J. Med. Chem. 2018, 143, 1931-1941

2017

  1. P. Wityk, M. Wieczór, S. Makurat, L. Chomicz-Mańka, J. Czub, J. Rak. Dominant pathways of adenosyl radical-induced DNA damage revealed by QM/MM metadynamics. J. Chem. Theory Comput. 2017, 13, 6415–6423
  2. W. Grudziński, Ł. Nierzwicki, R. Welc, E. Reszczynska, R. Luchowski, J. Czub, W. I. Gruszecki. Localization and Orientation of Xanthophylls in a Lipid Bilayer. Sci. Rep. 2017, 7, 9619
  3. J. Pilipczuk, B. Zalewska-Piątek, P. Bruździak, J. Czub, M. Wieczór, M. Olszewski, M. Wanarska, B. Nowicki, D. Augustin-Nowacka, R. Piątek. Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli. J. Biol. Chem. 2017, 292, 16136–16149
  4. M. Wieczór, J. Czub. How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1. Nucleic Acids Res. 2017, 45, 7643–7654.
  5. J. Czub, M. Wieczór, B. Prokopowicz, H. Grubmüller. Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase. J. Am. Chem. Soc. 2017, 139, 4025–4034.

2016

  1. M. Kogut, C. Kleist, J. Czub. Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad–a common structural unit of G-quadruplex DNA. Nucleic Acids Res. 2016, 44, 3020–3030.
  2. A. Neumann, M. Wieczor, J. Zielinska, M. Baginski, J. Czub. Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer. Langmuir 2016, 32, 3452–3461. 
  3. T. Laskowski, J. Czub, P. Sowiński, J. Mazerski. Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy. J. Biomol. Struct. Dyn. 2016, 34, 653–663.
  4. W. Delewski, B. Paterkiewicz, M. Manicki, B. Schilke, B. Tomiczek, S. J. Ciesielski, L. Nierzwicki, J. Czub, R. Dutkiewicz, E. A. Craig, J. Marszalek. Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction. Mol. Biol. Evol. 2016, 33, 643–656.
  5. J. Zielińska, M. Wieczór, T. Bączek, M. Gruszecki, J. Czub. Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail. Sci. Rep. 2016, 6, 19109.
  6. B. Adamczak, M. Wieczór, M. Kogut, J. Stangret, J. Czub. Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme. Biochem. J. 2016, 473, 3705–3724.
  7. K. Szwarc, M. Płosiński, K. Czerniejewska, T. Laskowski, A. Leniak, J. Czub, P. Kubica, P. Sowiński, J. Pawlak, E. Borowski. Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 – structural and molecular modeling studies. Magn. Reson. Chem. 2016, 54, 953–961.
  8. A. Nowak-Zaleska, M. Wieczór, J. Czub, Ł. Nierzwicki, R. Kotłowski, A. Mikucka, E. Gospodarek. Correlation between the number of Pro–Ala repeats in the EmrA homologue of Acinetobacter baumannii and resistance to netilmicin, tobramycin, imipenem and ceftazidime. J. Glob. Antimicrob. Resist. 2016, 7, 145–149. 

2015

  1. A. Panuszko, B. Adamczak, J. Czub, E. Gojło, J. Stangret. Hydration of amino acids: FTIR spectra and molecular dynamics studies. Amino Acids 2015, 47, 2265–2278.
  2. P. Bruździak, B. Adamczak, E. Kaczkowska, J. Czub, J. Stangret. Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies. Phys. Chem. Chem. Phys. 2015, 17, 23155–23164.
  3. Ł. Marcinkowski, A. Kloskowski, J. Czub, J. Namieśnik, D. Warmińska. Solvation of ionic liquids based on N-methyl-N-alkyl morpholinium cations in dimethylsulfoxide – volumetric and compressibility studies. J. Chem. Thermodyn. 2015, 88, 36–43.
  4. Ł. Nierzwicki, J. Czub. Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail. J. Phys. Chem. Lett. 2015, 6, 784–790.
  5. Ł. Nierzwicki, M. Wieczor, V. Censi, M. Baginski, L. Calucci, S. Samaritani, J. Czub, C. Forte. Interaction of cisplatin and two potential antitumoral platinum (II) complexes with a model lipid membrane: a combined NMR and MD study. Phys. Chem. Chem. Phys. 2015, 17, 1458–1468.

2014

  1. J. Starzyk, M. Gruszecki, K. Tutaj, R. Luchowski, R. Szlazak, P. Wasko, W. Grudzinski, J. Czub, W. I. Gruszecki. Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic. J. Phys. Chem. B 2014, 118, 13821–13832.
  2. J. Czub, H. Grubmüller. Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase. J. Am. Chem. Soc. 2014, 136, 6960–6968.
  3. M. Wieczór, P. Wityk, J. Czub, L. Chomicz, J. Rak. A first-principles study of electron attachment to the fully hydrated bromonucleobases. Chem. Phys. Lett. 2014, 595–596, 133–137.
  4. M. Wieczór, A. Tobiszewski, P. Wityk, B. Tomiczek, J. Czub. Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA. PLoS ONE 2014, 9, e89460.

2013

  1. A. Neumann, M. Bagiński, S. Winczewski, J. Czub. The effect of sterols on amphotericin B self-aggregation in a lipid bilayer as revealed by free energy simulations. Biophys. J. 2013, 104, 1485–1494.

2011

  1. J. Czub, H. Grubmüller. Torsional elasticity and energetics of F1-ATPase. Proc. Natl. Acad. Sci. USA 2011, 108:7408–7414.
  2. C. Kutzner, J. Czub, H. Grubmüller. Keep it flexible: driving macromolecular rotary motion in atomistic simulations with GROMACS. J. Chem. Theory Comput. 2011, 7:1381–1393.

2010

  1. A. Neumann, M. Baginski, J. Czub. How do sterols determine the antifungal activity of amphotericin B? Free energy of binding between the drug and its membrane targets. J. Am. Chem. Soc. 2010, 132:18266–18272.

2009

  1. A. Neumann, J. Czub, M. Baginski. On the possibility of the amphotericin B-sterol complex formation in cholesterol- and ergosterol containing lipid bilayers – a molecular dynamics study. J. Phys. Chem. B 2009, 113:15875–15885.
  2. M. Baginski, J. Czub. Amphotericin B and its new derivatives – mode of action. Curr. Drug Metabolism 2009, 10:459–469.
  3. J. Czub, A. Neumann, E. Borowski, M. Baginski. Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives – a molecular dynamics study. Biophys. Chem. 2009, 141:105–116.

2007

  1. M. Slisz, B. Cybulska, J. Grzybowska, J. Czub, R. Prasad, E. Borowski. The mechanism of overcoming multidrug resistance (MDR) of fungi by amphotericin B and its derivatives. J. Antib. 2007, 60:436–446.
  2. J. Czub, E. Borowski, M. Baginski. Interactions of amphotericin B derivatives with lipid membranes - a molecular dynamics study. BBA-Biomembranes 2007, 1768:2616–2626.

2006

  1. M. Baginski, J. Czub, K. Sternal. Interaction of Amphotericin B and its selective derivatives with membranes: molecular modeling studies. Chem. Rec. 2006, 6:320–332.
  2. J. Czub, M. Baginski. Modulation of amphotericin B membrane interaction by cholesterol and ergosterol - a molecular dynamics study. J. Phys. Chem. B 2006, 110:16743–16753.
  3. J. Czub, M. Baginski. Comparative molecular dynamics study of lipid membranes containing cholesterol and ergosterol. Biophys. J. 2006, 90:2368–2382.
  4. P. Seroka, M. Plosinski, J. Czub, P. Sowinski, J. Pawlak. Monosaccharides as internal probes for the determination of the absolute configuration of 2-butanol. Magn. Reson. Chem. 2006, 44:132–138.

2005

  1. M. Baginski, K. Sternal, J. Czub, E. Borowski. Molecular modelling of membrane activity of amphotericin B, a polyene macrolide antifungal antibiotic. Acta Biochim. Pol. 2005, 52:655–658.

2004

  1. K. Sternal, J. Czub, M. Baginski. Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies. J. Mol. Model. 2004, 10: 223-232.

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