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The hematopoietic transcription factor RUNX1 : a structural view

by Bäckström, Stefan

Abstract (Summary)
The malfunction of the transcriptional regulator RUNX1 is the major cause of several variants of acute human leukemias and its normal function is to regulate the development of the blood system in concert with other transcriptional co-regulators. RUNX1 belongs to a conserved family of heterodimeric transcription factors that share a conserved DNA binding domain, the Runt domain (RD), named after the first member of this group – Runt - found in Drosophila melanogaster. The binding partner CBF? serves as a regulator of RUNX by enhancing its DNA binding affinity through an allosteric mechanism.The main focus ofo my thesis work has been the crystallization and structural analysis of the RUNX1 RD and involved also more technical methodological aspects that can be applied to X-ray crystallography in general.The high resolution crystal structure of the free RD shows that this immunoglobulin-like molecule undergoes significant structural changes upon binding to both CBF? and DNA. This involves a large flip of the L11 loop from a closed conformation in the free protein to an open conformation when CBF? and/or DNA are bound. We refer to this transition as the “S-switch”. Smaller but significant conformational changes in other parts of the RD accompany the “S-switch”. We suggest that CBF? triggers and stabilizes the “S-switch” which leads to the conversion of the RD into a conformation enhanced for DNA binding.During the structural analysis of the RD we identified two chloride ions that are coordinated by residues otherwise involved in DNA binding. In electrophoretic mobility-shift analyses (EMSA) we demonstrated a chloride ion concentration dependent stimulation of the DNA binding affinity of RUNX1. We further showed by NMR line width broadening experiments that the chloride binding occurred within the physiological range. A comparable DNA binding stimulation of RUNX1 was seen in the presence of negative amino acids. This suggests a regulation of the DNA binding activity of RUNX1 proteins through acidic amino acid residues possibly provided by activation domains of transcriptional co-regulators that interact with RUNX1.The use of the anomalous signal from halide ions has become a powerful technique for obtaining phase information. By replacing the sodium chloride with potassium bromide in the crystallisation conditions of the RD, we could demonstrate in a single wavelength anomalous diffraction (SAD) experiment that the anomalous signal from 2 bromide ions were sufficient to phase a 16 kDa protein. Due to lack of completeness in the low-resolution shells caused by overloaded intensities, density modification schemes failed and the resulting electron density maps were not interpretable. By combining the highresolutionsynchrotron data with low-resolution data from a native data set collected on a home X-ray source, the density modified bromide phases gave easily traceable maps.
Bibliographical Information:

Advisor:

School:Umeå universitet

School Location:Sweden

Source Type:Doctoral Dissertation

Keywords:MEDICINE; Dermatology and venerology,clinical genetics, internal medicine; Internal medicine; Molecular medicine (genetics and pathology); Molecular medicine; RUNX1; Runt domain; CBF?; transcription factor; leukaemia; protein crystallography; anomalous diffraction; Molekylärmedicin; molekylärbiologi; Molecular Biology

ISBN:91-7305-476-3

Date of Publication:01/01/2004

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