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1

Studying protein-DNA binding by dynamic light scattering

100%
Zhelev N. Z., Buckle R. S., Snyder D., Marsh P. J.
Cellular and Molecular Biology Letters
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1996
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tom 01
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nr 2
Light scattering experiments were undertaken to study binding of the Max transcription factor to its E-box DNA recognition sequence. Translational diffusion coefficients were measured and the average hydrodynamic radii (Rh) of complexes calculated using the Stokes-Einstein equation. We detected both dimerization of Max and the formation of a stable complex with its E-box DNA target. These results demonstrate the applicability of Dynamic Light Scattering for measuring protein-DNA interactions.
2
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WRKY transcription factors in response to ROS

86%
Vaahtera L., Koskela M., Jolma A., Nurkkala H., Varjosalo M., Brosche M.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
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2013
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tom 94
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nr 2
3

The nuclear protein p30 specifically interacts with a nuclear matrix attachment region from the rat genome

86%
Fedorov A., Lukyanov D., Rogolinski J., Widlak P., Podgornaya O., Rzeszowska-Wolny J.
Cellular and Molecular Biology Letters
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2004
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tom 09
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nr 1
In our previous study, a 454 bp DNA fragment was isolated from rat genomic DNA as an element which interacts with nuclear matrix proteins, i.e. a Matrix Associated Region (MAR). Computer analyses revealed that the right half of this fragment, named RME (Rat MAR Element), possesses a high matrix association potential and is likely to be responsible for the matrix association of the whole sequence. RME was used as a probe in an electrophoretic mobility shift assay (EMSA), and with the use of Southwestern blotting, a rat liver nuclear protein which binds specifically to it was identified. Its molecular mass was estimated by SDS-PAGE as 30 kDa (p30). Polyclonal antibodies raised against protein-RME complexes caused a super-shift of specific complexes in EMSA, and bound to p30 in nuclear extracts of rat liver in Western blotting. The immunofluorescence labelling of a rat embryonic fibroblast cell monolayer with anti-p30 antibody revealed a mainly intranuclear pattern of staining.
4

Functionality versus strength - has functional selection taken place in the case of the ecdysteroid receptor response element?

72%
Grad I., Kochman M., Ozyhar A.
Acta Biochimica Polonica
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2002
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tom 49
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nr 3
Nuclear receptors are ligand-dependent transcription factors responsible for con­trolling differentiation, growth and development of higher eukaryotes. Three amino acids within the recognition a-helix of the DNA-binding domain of the nuclear recep­tors constitute the so-called "P-box" which determines response element specificity. In the ultraspiracle (Usp) protein, which together with EcR forms the heterodimeric ecdysone receptor, the P-box residues are E19, G20 and G23. Substitution of E19, the most characteristic amino acid for estrogen receptor-like P-boxes, with alanine showed that the mutation did not appreciably alter the affinity of the wild-type Usp DNA-binding domain (UspDBDwT for a probe containing natural ecdysone response element (hsp27wt). Since in many cases E19 contacts a G/C base pair in position -4, which is absent in hsp27wt, we analysed the interaction of UspDBDwT, E19A and other P-box region mutants with the hsp27wt derivative which contains a G/C instead of an T/A base pair in position -4. UspDBDwT exhibited higher affinity for this ele­ment than for hsp27wt. Moreover, a different interaction pattern of P-box region mutants was also observed. Thus we conclude that the E19 residue of UspDBD is not involved in any hsp27wt sequence-discerning contacts. However, substitution of the hsp27wt T/A base pair in position –4 with G/C generates target sequence with distinct functional characteristics and possibly with a new specificity. These results could serve as a basis for understanding the role of the presence of a T/A or G/C base-pair in the position –4 in the two types of ecdysone response elements found in nature.
5

Phage display of proteins

72%
Koscielska K., Kiczak L., Kasztura M., Wesolowska O., Otlewski J.
Acta Biochimica Polonica
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1998
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tom 45
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nr 3
In recent years the phage display approach has become an increasingly popular method in protein research. This method enables the presentation of large peptide and protein libraries on the surface of phage particles from which molecules of desired functional property(ies) can be rapidly selected. The great advantage of this method is a direct linkage between an observed phenotype and encapsulated genotype, which allows fast determination of selected sequences. The phage display approach is a powerful tool in generating highly potent biomolecules, including: search for specific antibodies, determining enzyme specificity, exploring protein-protein and protein-DNA interactions, minimizing proteins, introducing new functions into different protein scaffolds, and searching sequence space of protein folding. In this article many examples are given to illustrate that this technique can be used in different fields of protein science. The phage display has a potential of the natural evolution and its possibilities are far beyond rational prediction. Assuming that we can design the selection agents and conditions we should be able to engineer any desired protein function or feature.
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