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Interaction between Transcription Factors of E2F family and DNA Studied with Infrared Spectroscopy
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
(English)Manuscript (preprint) (Other academic)
Abstract [en]

The E2F transcription factors are crucial for the regulation of genes required for proper progression through the cell cycle. Since E2Fs can initiate both cell proliferation and cell death, it is not surprising that these proteins are the subjects of extensive studies. In this work we characterize the formation of E2F1- and E2F8-DNA complexes with Fourier transform infrared spectroscopy. We demonstrate the changes in the secondary structure of the E2F1 and E2F8, in particular the disappearance of regular α-helices. We also show the perturbation to the DNA double helix and characterize the interactions between the amino acids in the proteins and the bases in the DNA.

National Category
URN: urn:nbn:se:su:diva-101086OAI: diva2:698803
Available from: 2014-02-25 Created: 2014-02-25 Last updated: 2014-02-25
In thesis
1. Infrared spectroscopic studies: from small molecules to large
Open this publication in new window or tab >>Infrared spectroscopic studies: from small molecules to large
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Infrared light (IR) was first discovered by Friedrich Wilhelm Herschel in 1800. However, until 1940’s, molecular IR studies involved only water and small organic molecules, because of the long measurement times. Development Fourier transform infrared spectroscopy (FTIR) has minimized the time required to obtain data, making it possible to investigate bigger biological systems, e.g. proteins and nucleic acids.This thesis concentrates on the applications of different IR spectroscopic techniques to a variety of biological systems and development of new approaches to study complicated biological events.

The first paper in this work concerns using so-called caged compounds to study the aggregation of Alzheimer’s Aβ-peptide which is linked to the formation of neurotoxic fibrils in the brain. By adding caged-sulfate to the Aβ samples we were able to change the pH of the sample, while recording IR data and study fibril formation in a time-resolved manner. Then we used caged–ADP to study the production of ATP and creatine, mediated by creatine kinase (CK). Using CK as a helper enzyme we studied the effects of the phosphate binding on the secondary structure of SR Ca2+ATPse and determined the structural differences between two similar states Ca2E1ADP and Ca2E1ATP.

In the second part of the thesis we used ATR-FTIR spectroscopy and a specially designed dialysis setup, to develop a general method to detect ligand binding events by observing the IR absorbance changes in the water hydration shell around the molecules. The same method was used to determine the binding of DNA to the transcription factors of the E2F family. E2F proteins play main part in the gene regulatory networks that control cell development. However how they recognize their DNA-binding sites and the mechanism of binding is not well understood. By using ATR-FTIR, we observed the changes in the secondary structure of the proteins, as well as the distortions to the DNA upon E2F-DNA complex formation.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2014. 59 p.
Infrared spectroscopy, transcription factors, DNA, creatine kinase, CaATPase, water, ligand binding
National Category
Research subject
urn:nbn:se:su:diva-101077 (URN)978-91-7447-876-1 (ISBN)
Public defence
2014-03-28, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

Available from: 2014-03-06 Created: 2014-02-24 Last updated: 2014-02-26Bibliographically approved

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Eremina, Nadejda
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