prof. dr hab. inż. Jacek Czub
Employment
- Professor at Department of Physical Chemistry
- Head of Department at Department of Physical Chemistry
Publications
Filters
total: 65
Catalog Publications
Year 2006
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Interaction of amphotericin B and its selected derivatives with membranes: molecular modeling studies
PublicationJest to praca przeglądowa obejmująca krytyczną analizę danych dotyczących oddziaływania amfoterycyny B (AmB) i jej wybranych, mniej toksycznych pochodnych, z błonami lipidowymi. Amfoterycyna B jest antybiotykiem przeciwgrzybowym ale ze względu na jej toksyczność trwają prace nad modyfikacjami chemicznymi tego związku. Celem molekularnym dla tego antybiotyku jest błona lipidowa i dlatego różnicowe powinowactwo AmB i jej pochodnych...
Year 2004
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Interaction of amphotericin B with phospholipids in the model membrane - molecular dynamics study.
PublicationAmfoterycyna B jest antybiotykiem używanym w leczeniu układowych infekcji grzybowych. Jej mechanizm działania polega na tworzeniu kanałów wewnątrz błon lipidowych. W przedstawianej pracy publikowane są wyniki symulacji przeprowadzonej dynamiką molekularną monomerycznej i dimerycznej formy antybiotyku wewnątrz błony lipidowej zbudowanej z cząsteczek DMPC. Wyniki te wskazują, że powinowactwo cząsteczek amfoterycyny wewnątrz dimeru...
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Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies.
PublicationAmfoterycyna B jest antybiotykiem z grupy polienów makrolidowych. Stosowany jest on w leczeniu układowych infekcji grzybowych. Wiadomo że związek ten oddziałuje ze składnikami błon lipidowych i tworzy kanały. W przedstawianej pracy prezentowane są wyniki symulacji przeprowadzonej dynamiką molekularną układu składającego się z 200 cząsteczek lipidów DMPC i jednej cząsteczki amfoterycyny ułożonej na powierzchni błony. Z przeprowadzonej...
Year 2015
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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublicationIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
Year 2007
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Interactions of amphotericin B derivatives with lipid membranes - a molecular dynamics study
PublicationW pracy analizowano oddziaływanie dwóch nisko-toksycznych pochodnych amfoterycyny B (związki SAmE i PAmE) z modelami błon lipidowych. Badania wykonane zostały za pomocą dynamiki molekularnej. Modele błon oprócz fosfolipidów DMPC zawierały odpowiednio cholesterol (model błony zwierzęcej) lub ertosterol (model błony grzybowej). Analiza wyników wykazała, że obie pochodne amfoterycyny B zachowują się inaczej w błonie cholesterolowej...
Year 2016
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Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.
PublicationImidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311...
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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublicationBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublicationMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublicationOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
Year 2011
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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublicationWe describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the...
Year 2021
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Light-Modulated Sunscreen Mechanism in the Retina of the Human Eye
PublicationThe functioning of the human eye in the extreme range of light intensity requires a combination of the high sensitivity of photoreceptors with their photostability. Here, we identify a regulatory mechanism based on dynamic modulation of light absorption by xanthophylls in the retina, realized by reorientation of pigment molecules induced by trans–cis photoisomerization. We explore this photochemically switchable system using chromatographic...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublicationThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
Year 2017
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Localization and Orientation of Xanthophylls in a Lipid Bilayer
PublicationXanthophylls (polar carotenoids) play diverse biological roles, among which are modulation of the physical properties of lipid membranes and protection of biomembranes against oxidative damage. Molecular mechanisms underlying these functions are intimately related to the localization and orientation of xanthophyll molecules in lipid membranes. In the present work, we address the problem of localization and orientation of two xanthophylls...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
Year 2024
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Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline
PublicationThe role of short strong hydrogen bonds (SSHB) in ligand-target binding remains largely unexplored, thereby hin- dering a potentially important avenue in the rational drug de- sign. Here, we investigate the interaction between bedaquiline (Bq), a potent anti-tuberculosis drug, and the mycobacterial ATP synthase, to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity....
Year 2018
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
Year 2023
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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