Zakład Fizyki Makromolekularnej
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od 2020-09-20

Dr Michał Taube  | 2006-10 - obecnie


   WF UAM pokój: 131      +48 61-829-5030

  0000-0002-8876-929X     35088864400  

Publikacje      Projekty           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)


Razew M., Warkocki Z., Taube M., Kolondra A., Czarnocki-Cieciura M., Nowak E., Łabędzka-Dmoch K., Kawińska A., Piątkowski J., Golik P., Kozak M., Dziembowski A., Nowotny M.

Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination. mtEXO is composed of Dss1 3'-to-5' exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast. Here, we present the structure of mtEXO and a description of its mechanism of action. The crystal structure of Dss1 reveals domains that are responsible for interactions with Suv3. Importantly, these interactions are compatible with the conformational changes of Suv3 domains during the helicase cycle. We demonstrate that mtEXO is an intimate complex which forms an RNA-binding channel spanning its entire structure, with Suv3 helicase feeding the 3' end of the RNA toward the active site of Dss1.

Nature Communications, 9, 97 (2018)

DOI: 10.1038/s41467-017-02570-5   (Pobrane:  2020-07-21)


Hołubowicz R., Wojtas M., Taube M., Kozak M., Ozyhar A., Dobryszycki P.

Effect of calcium ions on structure and stability of the C1q-like domain of otolin-1 from human and zebrafish Otolin-1 is a collagen-like protein expressed in the inner ear of vertebrates. It provides an organic scaffold for otoliths in fish and otoconia in land vertebrates. In this study, the expression and purification procedure of C1q-like domain of otolin-1 from human and zebrafish was developed. The structure and stability of the proteins were investigated. The results of sedimentation velocity analytical ultracentrifugation and small-angle X-ray scattering indicated that the C1q-like domain of otolin-1 forms stable trimers in solution in the presence of calcium ions. It was also observed that calcium ions influenced the secondary structure of the proteins. C1q-like domains were stabilized by the calcium ions. The human variant was especially affected by the calcium ions. The results indicate the importance of the C1q-like domain for the assembly of the organic matrix of otoliths and otoconia.

FEBS Journal, 284(24), 4278-4297 (2017)

DOI: 10.1111/febs.14308   (Pobrane:  2018-04-03)


Tarczewska A., Kozłowska M., Bystranowska D., Jakob M., Taube M., Kozak M., Czarnocki-Cieciura M., Ozyhar A.

European Biophysics Journal with Biophysics Letters, 46(S1), S177-S177 (2017)

   (Pobrane:  2018-04-03)


Stępień A., Knop K., Dolata J., Taube M., Bajczyk M., Barciszewska-Pacak M., Pacak A., Jarmołowski A., Szweykowska-Kulińska Z.

Posttranscriptional coordination of splicing and miRNA biogenesis in plants MicroRNAs (miRNAs) are short, single-stranded, noncoding RNAs that play a crucial role in basic physiological and morphological processes and in response to various stresses in eukaryotic organisms. However, the miRNA biogenesis, which is based on the action of complex protein machinery, varies between plants and animals, with the differences largely concerning the location of the process, the protein composition of the microprocessor, the mechanism of miRNA action on mRNA target, and the miRNA gene (MIR) structure. Roughly half of known Arabidopsis MIRs contain introns, and 29 miRNAs are encoded within the introns of host genes. Selection of alternative transcription start sites, alternative splice sites (SSs), and polyadenylation sites has been identified within miRNA primary transcripts (pri-miRNAs), and such variety is essential for the production and fine-tuning of miRNA levels. For example, the posttranscriptional processing of intron-containing pri-miRNAs involves the action of additional RNA metabolism machineries, such as the spliceosome and polyadenylation machinery, and to a large extent is based on direct communication between SERRATE (one of the core components of the plant microprocessor) and U1 snRNP auxiliary proteins. Moreover, the position of the miRNA stem-loop structure relative to the closest active 5′SS is essential for the miRNA production efficiency. Indeed, it is highly probable that this pre-miRNA location affects recruitment of the microprocessor to pri-miRNAs and therefore influences miRNA maturation and target mRNA regulation. Such complicated crosstalk between several machineries is important for a proper miRNA-connected response to biotic and abiotic stresses, ensuring plant survival in a changing environment.

WIREs (Wiley Interdisciplinary Reviews: RNA), 8(3), e1403 (2017)

DOI: 10.1002/wrna.1403


Knop K., Stępień A., Barciszewska-Pacak M., Taube M., Bielewicz D., Michalak M., Borst J.W., Jarmołowski A., Szweykowska-Kulińska Z.

Active 5' splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes Arabidopsis, miR402 that is encoded within the first intron of a protein-coding gene At1g77230, is induced by heat stress. Its upregulation correlates with splicing inhibition and intronic proximal polyA site selection. It suggests that miR402 is not processed from an intron, but rather from a shorter transcript after selection of the proximal polyA site within this intron. Recently, introns and active 5΄ splice sites (5΄ss’) have been shown to stimulate the accumulation of miRNAs encoded within the first exons of intron-containing MIR genes. In contrast, we have observed the opposite effect of splicing inhibition on intronic miR402 production. Transient expression experiments performed in tobacco leaves revealed a significant accumulation of the intronic mature miR402 when the 5΄ss of the miR402-hosting intron was inactivated. In contrast, when the miR402 stem-loop structure was moved into the first exon, mutation of the first-intron 5΄ss resulted in a decrease in the miRNA level. Thus, the 5΄ss controls the efficiency of miRNA biogenesis. We also show that the SERRATE protein (a key component of the plant microprocessor) colocalizes and interacts with several U1 snRNP auxiliary proteins. We postulate that SERRATE-spliceosome connections have a direct effect on miRNA maturation.

Nucleic Acids Research, 45(5), 2757-2775 (2017)

DOI: 10.1093/nar/gkw895


Kozak M., Gielnik M., Taube M., Zhukov I.

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

Spectroscopic and SAXS studies of human prion protein variants complexed with divalent cations Neurodegenerative diseases are probably the most difficult diseases to find for them a successful treatment strategy. The discovery of new potential drugs, which can be useful in the treatment of neurodegenerative diseases, require full structural characterization of all proteins involved in development of these diseases. One of the human neurodegenerative disorders is Creutzfeldt-Jakob disease (CJD). This disease is caused by misfolded (pathogenic) form of prion protein (PrP), which is a membrane protein exposed into synaptic cleft [1]. So far, the structures of several variants of prion proteins from various organisms (hamster, bovine or human) have been solved by protein crystallography and NMR. The molecule of cellular form of human PrP protein is composed of two domains: unstructured and flexible N-terminal domain containing four tandem octarepeats and structured C-terminal domain [2]. The aim of our study was to obtain the structural information for several complexes of the human prion protein. As an object of the study presented here we have chosen the cellular form of human prion protein PrPC (23-231) and its mutant form (H61A). The low resolution structures of both forms complexed with divalent cations were characterized by SAXS technique. The conformational changes of proteins studied were also detected by spectrofluorimetry, circular dichroism and NMR. This work was supported by the funds from the National Science Centre (Poland) granted on the basis of decision no. No. 2014/15/B/ST4/04839

Biophysical Journal, 112(3) S1, 190A (2017)

DOI: 10.1016/j.bpj.2016.11.1053   (Pobrane:  2020-11-05)


Kozłowska M., Tarczewska A., Jakób M., Bystranowska D., Taube M., Kozak K., Czarnocki-Cieciura M., Dziembowski A., Orłowski M., Tkocz K., Ożyhar A.

Nucleoplasmin-like domain of FKBP39 from Drosophila melanogaster forms a tetramer with partly disordered tentacle-like C-terminal segments Nucleoplasmins are a nuclear chaperone family defined by the presence of a highly conserved N-terminal core domain. X-ray crystallographic studies of isolated nucleoplasmin core domains revealed a β-propeller structure consisting of a set of five monomers that together form a stable pentamer. Recent studies on isolated N-terminal domains from Drosophila 39-kDa FK506-binding protein (FKBP39) and from other chromatin-associated proteins showed analogous, nucleoplasmin-like (NPL) pentameric structures. Here, we report that the NPL domain of the full-length FKBP39 does not form pentameric complexes. Multi-angle light scattering (MALS) and sedimentation equilibrium ultracentrifugation (SE AUC) analyses of the molecular mass of the full-length protein indicated that FKBP39 forms homotetrameric complexes. Molecular models reconstructed from small-angle X-ray scattering (SAXS) revealed that the NPL domain forms a stable, tetrameric core and that FK506-binding domains are linked to it by intrinsically disordered, flexible chains that form tentacle-like segments. Analyses of full-length FKBP39 and its isolated NPL domain suggested that the distal regions of the polypeptide chain influence and determine the quaternary conformation of the nucleoplasmin-like protein. These results provide new insights regarding the conserved structure of nucleoplasmin core domains and provide a potential explanation for the importance of the tetrameric structural organization of full-length nucleoplasmins.

Scientific Reports, , 40405 (2017)

DOI: 10.1038/srep40405


Kolonko M., Ożga K., Hołubowicz R., Taube M., Kozak M., Ożyhar A., Greb-Markiewicz B.

Intrinsic disorder of the C-terminal domain of drosophila methoprene-tolerant protein Methoprene tolerant protein (Met) has recently been confirmed as the long-sought juvenile hormone (JH) receptor. This protein plays a significant role in the cross-talk of the 20-hydroxyecdysone (20E) and JH signalling pathways, which are important for control of insect development and maturation. Met belongs to the basic helix-loop-helix/Per-Arnt-Sim (bHLH-PAS) family of transcription factors. In these proteins, bHLH domains are typically responsible for DNA binding and dimerization, whereas the PAS domains are crucial for the choice of dimerization partner and the specificity of target gene activation. The C-terminal region is usually responsible for the regulation of protein complex activity. The sequence of the Met C-terminal region (MetC) is not homologous to any sequence deposited in the Protein Data Bank (PDB) and has not been structurally characterized to date. In this study, we show that the MetC exhibits properties typical for an intrinsically disordered protein (IDP). The final averaged structure obtained with small angle X-ray scattering (SAXS) experiments indicates that intrinsically disordered MetC exists in an extended conformation. This extended shape and the long unfolded regions characterise proteins with high flexibility and dynamics. Therefore, we suggest that the multiplicity of conformations adopted by the disordered MetC is crucial for its activity as a biological switch modulating the cross-talk of different signalling pathways in insects.

PloS ONE, 11(9), 598-606 (2016)

DOI: 10.1371/journal.pone.0162950


Kozak M., Pietralik Z., Szymańska A., Taube M.

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

Spectroscopic and SAXS studies of human cystatin c mutants - early stages of amyloid formation process Human cystatin C (HCC) is a cysteine protease inhibitor. This protein in pathological conditions, forms dimers via a “domain swapping” mechanism. HCC is also associated with two types of amyloid deposition diseases - hereditary amyloid angiopathy (related to the Leu68Gln mutation) and wild-type cystatin C co-precipitation.

The aim of our studies was the characterisation of the self-assembling properties of native and mutated (at positions 57 or 68) forms of human cystatin C in solution. The structure, overall conformation and secondary structure changes in solution were studied by Fourier transformed infrared spectroscopy (FTIR), circular dichroism spectroscopy (CD), dynamic light scattering (DLS) and time resolved small angle scattering of synchrotron radiation (TR-SAXS).

SAXS data for native and mutated HCC were subjected to analysis by using SVD and MCR-ALS methods as well as the low resolution structure determination. Besides the monomeric forms of human cystatin C, also dimers and higher oligomers were formed even after short (50-ms) exposure on synchrotron radiation. In addition we observed for first time, formation of domain swapped dimers of human cystatin C induced by irradiation. The spectroscopic studies confirmed conformational changes.

Authors acknowledge also the partial support by HARMONIA3 grant (Project No. 2012/06/M/ST4/00036) from National Science Centre (Poland).

Biophysical Journal, 108(2) S1, 516A (2015)

DOI: 10.1016/j.bpj.2014.11.2827   (Pobrane:  2020-11-05)


Andrzejewska W., Pietralik Z., Taube M., Skrzypczak A., Kozak M.

Structural and spectroscopic studies on the formation of lipoplexes between DNA and cationic gemini surfactants The process of complex formation between cationic gemini surfactants, 3,3'-[α,ω-(dioxaalkane)]bis(1-dodecylimidazolium) dichloride, with deoxyribonucleic acid (DNA) was studied. The study was performed for ten surfactants having spacer groups of different lengths used in 6 concentrations (5 mM, 2 mM, 1 mM, 0.5 mM, 0.2 mM, 0.1 mM) and a 6.5 μM DNA solution. The complex formation was verified by circular dichroism spectroscopy and gel electrophoresis. The complexes were found to be stable and the process of complex formation was reproducible, efficient and immediate.

Polimery/Polymers, 59(7-8), 569-574 (2014)

DOI: 10.14314/polimery.2014.569
WWW:   (Pobrane:  2021-01-10)


Taube M., Pieńkowska J.R., Jarmołowski A., Kozak M.

Low-resolution structure of the full-length barley (Hordeum Vulgare) SGT1 protein in solution, obtained using small-angle X-ray scattering SGT1 is an evolutionarily conserved eukaryotic protein involved in many important cellular processes. In plants, SGT1 is involved in resistance to disease. In a low ionic strength environment, the SGT1 protein tends to form dimers. The protein consists of three structurally independent domains (the tetratricopeptide repeats domain (TPR), the CHORD-and SGT1-containing domain (CS), and the SGT1-specific domain (SGS)), and two less conserved variable regions (VR1 and VR2). In the present study, we provide the low-resolution structure of the barley (Hordeum vulgare) SGT1 protein in solution and its dimer/monomer equilibrium using small-angle scattering of synchrotron radiation, ab-initio modeling and circular dichroism spectroscopy. The multivariate curve resolution least-square method (MCR-ALS) was applied to separate the scattering data of the monomeric and dimeric species from a complex mixture. The models of the barley SGT1 dimer and monomer were formulated using rigid body modeling with ab-initio structure prediction. Both oligomeric forms of barley SGT1 have elongated shapes with unfolded inter-domain regions. Circular dichroism spectroscopy confirmed that the barley SGT1 protein had a modular architecture, with an alpha-helical TPR domain, a beta-sheet sandwich CS domain, and a disordered SGS domain separated by VR1 and VR2 regions. Using molecular docking and ab-initio protein structure prediction, a model of dimerization of the TPR domains was proposed.

PLoS ONE, 9(4), e93313 (2014)

DOI: 10.1371/journal.pone.0093313


Pietralik Z., Taube M., Balcerzak M., Skrzypczak A., Kozak M.

MAX-Lab Activity Report 2010, , 284-285 (2011)

WWW:   (Pobrane:  2011-09-22)


Pietralik Z., Taube M., Kozak A., Wieczorek D., Zielinski R., Kozak M.

MAX-Lab Activity Report 2010, , 286-288 (2011)

WWW:   (Pobrane:  2011-10-18)


Taube M., Jarmołowski A., Kozak M.

Low resolution structure of RAR1-GST-Tag fusion protein in solution RAR1 is a protein required for resistance mediated by many R genes and function upstream of signaling pathways leading to H(2)O(2) accumulation. The structure and conformation of RAR1-GST-Tag fusion protein from barley (Hordeum vulgare) in solution was studied by the small angle scattering of synchrotron radiation. It was found that the dimer of RAR1-GST-Tag protein is characterized in solution by radius of gyration R(G) = 6.19 nm and maximal intramolecular vector D(max) = 23 nm. On the basis of the small angle scattering of synchrotron radiation SAXS data two bead models obtained by ab initio modeling are proposed. Both models show elongated conformations. We also concluded that molecules of fusion protein form dimers in solution via interaction of GST domains.

Acta Physica Polonica A, 117(2), 307-310 (2010)



Pietralik Z., Taube M., Skrzypczak A., Kozak M.

SAXS study of influence of gemini surfactant, 1,1'-(1,4-butanediyl)bis 3-cyclododecyloxymethylimidazolium di-chloride, on the fully hydrated DMPC The study has been performed on model systems of biological membranes obtained on the basis of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and cationic gemini surfactant derivative of 1,1'-(1,4-butane)bis 3-alkyloxymethylimidazolium chlorides with cyclic chains. The small angle X-ray scattering SAXS results implied a gradual disappearance (as a function of surfactant concentration) of the lamellar phase typical of DMPC and formation of unilamellar phase - probably a bicellar phase.

Acta Physica Polonica A, 117(2), 311-314 (2010)

DOI: 10.12693/APhysPolA.117.311
WWW:   (Pobrane:  2021-01-10)


Kozak M., Taube M.

SAXS-WAXS studies of the low-resolution structure in solution of xylose/glucose isomerase from Streptomyces Rubiginosus The structure and conformation of molecule of xylose/glucose isomerase from Streptomyces rubiginosus in solution (at pH 6 and 7.6; with and without the substrate) has been studied by small- and wide-angle scattering of synchrotron radiation (SAXS-WAXS). On the basis of the SAXS-WAXS data, the low-resolution structure in solution has been reconstructed using ab inito methods. A comparison of the models of glucose isomerase shows only small differences between the model in solution and the crystal structure.
(C) 2009 Elsevier Ltd. All rights reserved.

Radiation Physics and Chemistry , 78(10), 125-128 (2009)

DOI: 10.1016/j.radphyschem.2009.03.085

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