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Tandemly repeated trinucleotides - comparative analysis

100%

Piwowar M., Meus J., Piwowar P., Wiśniowski Z., Stefaniak J., Roterman I.

2006

vol. 53

issue 2

279-287

Characteristics of 64 possible tandem trinucleotide repeats (TSSR) from Homo sapiens (hs), Mus musculus (mm) and Rattus norvegicus (rn) genomes are presented. Comparative analysis of TSSR frequency depending on their repetitiveness and similarity of the TSSR length distributions is shown. Comparative analysis of TSSR sequence motifs and association between type of motif and its length (n) using ρ-coefficient method (quantitatively measuring the association between variables in contingency tables) is presented. These analyses were carried out in the context of neurodegenerative diseases based on trinucleotide tandems. The length of these tandems and their relation to other TSSR is estimated. It was found that the higher repetitiveness (n) the lower frequency of trinucleotides tandems. Differences between genomes under consideration, especially in longer than n=9 TSSR were discussed. A significantly higher frequency off A- and T-rich tandems is observed in the human genome (as well as in human mRNA). This observation also applies to mm and rn, although lower abundant in proportion to human genomes was found. The origin of elongation (or shortening) of TSSR seems to be neither frequency nor length dependent. The results of TSSR analysis presented in this work suggest that neurodegenerative disease-related microsatellites do not differ versus the other except the lower frequency versus the other TSSR. CAG occurs with relatively high frequency in human mRNA, although there are other TSSR with higher frequency that do not cause comparable disease disorders. It suggests that the mechanism of TSSR instability is not the only origin of neurodegenerative diseases.

Silver ions as em marker of congo red ligation sites in amyloids and amyloid-like aggregates

84%

Rybarska J., Konieczny L., Jagusiak A., Chłopaś K., Zemanek G., Piekarska B., Stopa B., Piwowar P., Woźnicka O., Roterman I.

2017

vol. 64

issue 1

161-169

Congo red (CR) is a known selective amyloid ligand. The focus of our work is identification (by EM imaging) of dye binding sites and their distribution in amyloids and amyloid-like aggregates formed in vitro. In order to produce the required contrast, CR has been indirectly combined with metal via including Titan yellow (TY) by intercalation which exhibits a relatively strong affinity for silver ions. The resulting combined ligand retains its ability to bind to proteins (which it owes to CR) and can easily be detected in EM studies thanks to TY. We have found, however, that in protein aggregates where unfolding is stabilized by aggregation and therefore is irreversible, TY alone may serve as both, the ligand and the metal carrier. The formation of ordered structures in amyloids was studied using IgG light chains with amyloidogenic properties, converted into amyloids by shaking. The resulting EM images were subjected to interpretation on the basis of the authors' earlier research on the CR/light chain complexation process. Our results indicate that dimeric light chains, which are the subject of our study, produce amyloids or amyloid-like complexes with chain-like properties and strong helicalization tendencies. Cursory analysis suggests that the edge polypeptide loops belonging to unstable light chains form intermolecular bridges which promote creation of loose gel deposits, or are otherwise engaged in the swapping processes leading to higher structural ordering.

Formation of amyloid-like aggregates through the attachment of protein molecules to a Congo red scaffolding framework ordered under the influence of an electric field

68%

Stopa B., Piekarska B., Konieczny L., Król M., Rybarska J., Jagusiak A., Spólnik P., Roterman I., Urbanowicz B., Piwowar P., Lewiński K.

Open Chemistry

2010

vol. 8

issue 1

41-50

This study describes a technique which makes it possible to introduce the amyloid-like order to protein aggregates by using the scaffolding framework built from supramolecular, fibrillar Congo red structures arranged in an electric field. The electric field was used not only to obtain a uniform orientation of the charged dye fibrils, but also to make the fibrils long, compact and rigid due to the delocalization of pi electrons, which favors ring stacking and, as a consequence, results in an increased tendency to self-assemble. The protein molecules (immunoglobulin L chain lambda, ferritin) attached to this easily adsorbing dye framework assume its ordered structure. The complex precipitating as plate-like fragments shows birefringence in polarized light. The parallel organization of fibrils can be observed with an electron microscope. The dye framework may be removed via reduction with sodium dithionite, leaving the aggregated protein molecules in the ordered state, as confirmed by X-ray diffraction studies. [...]

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2 Acta Biochimica Polonica

1 Open Chemistry

1 2017

1 2010

1 2006

3 Piwowar P.

3 Roterman I.

2 Jagusiak A.

2 Konieczny L.

2 Piekarska B.

2 Rybarska J.

2 Stopa B.

1 Chłopaś K.

1 Król M.

1 Lewiński K.

1 Meus J.

1 Piwowar M.

1 Spólnik P.

1 Stefaniak J.

1 Urbanowicz B.

1 Wiśniowski Z.

1 Woźnicka O.

1 Zemanek G.

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Tandemly repeated trinucleotides - comparative analysis

Silver ions as em marker of congo red ligation sites in amyloids and amyloid-like aggregates

Formation of amyloid-like aggregates through the attachment of protein molecules to a Congo red scaffolding framework ordered under the influence of an electric field