Zakład Fizyki Makromolekularnej
Strona główna


od 2020-09-20

Dr Magdalena Murawska  | 2009-10 <> 2015-07


Publikacje                Magistrowie           Seminaria


Chrabąszczewska M., Maszota-Zieleniak M., Pietralik Z., Taube M., Rodziewicz-Motowidło S., Szymańska A., Szutkowski K., Clemens D., Grubb A., Kozak M.

Cyclic trimer of human cystatin C, an amyloidogenic protein - molecular dynamics and experimental studies Human cystatin C (HCC) is a cysteine protease inhibitor that takes a series of oligomeric forms in solution (e.g., dimers, trimers, tetramers, decamers, dodecamers, and other higher oligomers). The best-known form of cystatin C is the dimer, which arises as a result of a domain swapping mechanism. The formation of the HCC oligomeric forms, which is most likely due to this domain swapping mechanism, is associated with the aggregation of HCC into amyloid fibrils and deposits. To investigate the structure of a specific HCC oligomer, we developed a covalently stabilized trimer of HCC. An atomic model of this HCC trimer was proposed on the basis of molecular docking and molecular dynamics simulations. The most stable model of the HCC trimer obtained from the molecular dynamics simulations is characterized by a well-preserved secondary structure. The molecular size and structural parameters of the HCC trimer in solution were also confirmed by Small Angle Neutron Scattering and Nuclear Magnetic Resonance Diffusometry. Published by AIP Publishing.

Journal of Applied Physics, 123(17), Article Number: 174701 (2018)

DOI: 10.1063/1.5023807   (Pobrane:  2019-03-21)


Murawska M., Szymańska A., Grubb A., Kozak M.

Overall conformation of covalently stabilized domain-swapped dimer of human cystatin C in solution Human cystatin C (HCC), a small protein, plays a crucial role in inhibition of cysteine proteases. The most common structural form of human cystatin C in crystals is a dimer, which has been evidenced both for the native protein and its mutants. In these structures, HCC dimers were formed through the mechanism of domain swapping. The structure of the monomeric form of human cystatin C was determined for V57N mutant and the mutant with the engineered disulfide bond (L47C)–(G69C) (known as stab1-HCC). On the basis of stab1-HCC, a number of covalently stabilized oligomers, including also dimers have been obtained. The aim of this study was to analyze the structure of the covalently stabilized dimer HCC in solution by the small angle X-ray scattering (SAXS) technique and synchrotron radiation. Experimental data confirmed that in solution this protein forms a dimer, which is characterized by the radius of gyration RG = 3.1 nm and maximum intramolecular distance Dmax = 10.3 nm. Using the ab initio method and program DAMMIN, we propose a low resolution structure of stabilized covalently cystatin C in solution. Stab-HCC dimer adopts in solution an elongated conformation, which is well reconstructed by the ab initio model.

Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 411, 136-140 (2017)

DOI: 10.1016/j.nimb.2017.02.090   (Pobrane:  2017-12-13)


Andrzejewska W., Wilkowska M., Chrabąszczewska M., Kozak M.

The study of complexation between dicationic surfactants and the DNA duplex using structural and spectroscopic methods Dicationic (also known as gemini or dimeric) bis-alkylimidazolium surfactants belong to a group of non-viral transfection systems proposed for the successful introduction of different types of nucleic acids (i.e., siRNA, DNA oligomers, and plasmid DNA) into living cells. Our studies reveal the formation of complexes composed of dicationic (gemini) surfactants, 3,3′-[α,ω-(dioxaalkane)]bis(1-dodecylimidazolium)chlorides, and 21 base pair deoxyribonucleic acid duplexes (dsDNA). The studied dsDNA and its complex formation process was analysed by small-angle X-ray scattering (SAXS), molecular modelling (dsDNA), agarose gel electrophoresis (AGE) and circular dichroism spectroscopy (CD). We observed the formation of stable complexes for charge ratio values of p/n > 2. Moreover, we noted conformational changes similar to those observed during the transition of B-DNA to C-DNA, X-DNA, and Z-DNA in several spatial structures (i.e., micellar, hexagonal and cubic) formed in mixtures. The surfactants used in this study were investigated for the influence of dioxaalkane spacer length and the presence of an imidazolium moiety on the complexation process. The complexes formed were stable, and the complexation process was reproducible and efficient. Toxicity tests done on HeLa cells allowed for the determination of non-toxic concentrations of studied surfactants. Transfection tests have confirmed that the studied surfactant systems are effective DNA carriers.

RSC Advances, 7(42), 26006-26018 (2017)

DOI: 10.1039/c6ra24978g   (Pobrane:  2020-10-23)


Pietralik Z., Murawska M., Szymańska A., Kumita J.R., Dobson C.M., Kozak M.

Abstrakt lub materiały konferencyjne, albo abstrakt publikacji
z dodatkowymi numerami DOI

Structural studies of the oligomerization process of human cystatin C variants Human cystatin C (HCC), an inhibitor of cysteine proteases, is also involved in amyloidogenic processes within the human body. In the crystal structure, as in solution, wild-type (WT) cystatin C dimerizes via a domain swapping mechanism. The same process has also been shown to be important for protein oligomerization. Aggregation of HCC results in a heterogeneous mixture of species, both oligomeric and fibrillar, with varying shapes, sizes and molecular weights.
The goal of our study was to characterize the assembly process of potentially neurotoxic oligomers of WT and variant HCC in solution. The oligomerization processes of several point mutation variants of HCC (V57N, V57P, V57D, V57G and L68V), with specific dimerization properties [3], were compared to the WT protein. Prepared oligomers were purified by size-exclusion chromatography and using TEM and AFM studies, we observed characteristic donutlike structures along with fibrils and we determined the size distribution of cystatin C oligomers obtained from the WT and variant forms. Independently, the oligomerization process was analyzed by fluorescence spectroscopy and visualized by native electrophoresis. Additionally, induced secondary structure changes were characterised by circular dichroism (CD) and infrared (FTIR) spectroscopies. Finally, the structural studies were supplemented with the modelling of the larger HCC oligomers using molecular dynamics simulations, allowing the identification of the most stable oligomeric forms of HCC to be determined.

Biophysical Journal, 110(3) S1, 26A (2016)

DOI: 10.1016/j.bpj.2015.11.205   (Pobrane:  2017-12-08)


Andrzejewska W.J., Skupin M., Murawska M., Skrzypczak A., Kozak M.

Abstrakt lub materiały konferencyjne, albo abstrakt publikacji
z dodatkowymi numerami DOI

The study of complexation process between cationic gemini surfactants and dna using structural and spectroscopic methods Dicationic (gemini) surfactants are intensively studied group of chemical compounds, because of the broad range of applications in medicine, chemical technology or pharmaceutical industry. In solution they can form with nucleic acids the complex structures (lipoplexes), which can be used as drug delivery systems in nonviral transfection. Lipoplexes in gene therapy offer efficient introduction of a therapeutic material to the living cells. Gemini surfactants also allow introduction of a transgene without inducing natural immunological response and release it inside the cell. In our study, we analyzed the process of complexation of cationic gemini surfactants (3.3'- [1,6- (2,n-dioxyalcane)] bis(1-dodecyloxyimidazolium dichlorides)) with DNA, using small angle X-ray scattering, circular dichroism spectroscopy and gel electrophoresis. Surfactants which have been used had of variable length of the spacer group. We observed the formation of stable complexes in these systems and the process of complex formation was reproducible, efficient and immediate.

Biophysical Journal, 108(2) S1, 392A (2015)

DOI: 10.1016/j.bpj.2014.11.2152   (Pobrane:  2020-11-05)


Murawska M., Wiatr M., Nowakowski P., Szutkowski K., Skrzypczak A., Kozak M.

The structure and morphology of gold nanoparticles produced in cationic gemini surfactant systems Potential applications of gold nanoparticles (GNP) are strictly connected with their size and shape. The influence of different dicationic (gemini) surfactants, alkyloxymethylimidazolium derivatives derivatives, on the structure and morphology of GNP was studied. The synthesis of nanoparticles was performed in the presence of various gemini surfactants-dodecyloxymethylimidazolium nitrate (IMI_NO3_C4_C12), propionate (IMI_PROP_C4_C12) and 3,3'-[1,9-(2,8-dioxanonane)]bis-(1-nonyloxymethylimidazolium) chloride (IMI_Cl_oxyC7_C9), used as stabilizers and templates for obtaining different size and shape of gold nanoparticles. The samples obtained were examined using transmission electron microscopy (TEM), small angle scattering of synchrotron radiation (SAXS), UV-vis spectroscopy and NMR PFG spectroscopy. For the obtained solutions of nanoparticles the plasmon resonance was observed at the wavelengths corresponding to the presence of gold nanoparticles of sizes ranging from 5-100 nm, with a significant shift towards higher wavelength for the samples prepared with addition of dicationic surfactants. TEM images evidence the presence of gold nanoparticles with tetrahedral and spherical morphology in solutions prepared with the surfactants IMI_PROP_C4_C12, IMI_NO3_C4_C12, and those of spherical morphology, but strongly aggregated, in the solution with the cationic surfactant IMI_Cl_oxyC7_C9.
(C) 2013 Elsevier Ltd. All rights reserved.

Radiation Physics and Chemistry, 93, 160-167 (2013)

DOI: 10.1016/j.radphyschem.2013.05.024


Murawska M., Skrzypczak A., Kozak M.

Structure and morphology of gold nanoparticles in solution studied by TEM, SAXS and UV-VIS Gold nanoparticles have a great number of applications, among others in material sciences, biology and medicine. A method for the synthesis of gold nanoparticles in solution with the use of gemini surfactant was proposed and the nanoparticles obtained were subjected to thorough characterisation. The method proposed is a modification of the Turkevich method, based on reduction of tetrachloroauric acid in the presence of trisodium citrate and a dicationic (gemini) surfactant - 1,1'-(1,4-butan)bis(3-dodecyloxymethylimidazolium) di-propionate. Morphology and size distribution of gold nanoparticles obtained were examined by the transmission electron microscopy (TEM), UV-Vis spectroscopy and small angle scattering of synchrotron radiation (SAXS). The plasmon resonance of the nanoparticles obtained was observed in the wavelength range corresponding to the presence of gold nanoparticles with sizes ranging from 5 to 100 nm. TEM images confirmed that the spherical shape of nanoparticles was dominated in reference solutions prepared of sodium citrate and tetrachloroauric acid. In the solutions prepared with addition of gemini surfactant, the gold nanoparticles of triangular morphology were observed.

Acta Physica Polonica A, 121(4), 888-892 (2012)

DOI: 10.12693/APhysPolA.121.888
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