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The role of DNA minor groove deformation in specific recognition of DNA by proteins
 Faltejsková, Kateřina ; Vondrášek, Jiří (advisor) ; Lepšík, Martin (referee)
The specific recognition of the DNA is crucial for the correct functioning of the cell. Although its mechanisms are extensively studied, the actual process is not yet fully understood, partly due to the variance observed in readout mechanisms so far. In this work, a particular type of specific recognition is examined: the shape readout in the DNA minor groove. Based on a sta- tistical analysis of three-dimensional structures of protein-DNA complexes acquired from the Protein Data Bank, I propose a previously unrecorded readout mechanism of widened minor grooves by hydrophobic amino acids. In addition, the effect of DNA sequence on the topography of the contacted locus, the preferred secondary structures and the interaction between the protein and DNA are explored, as well as the relative information amount of examined features concerning the DNA deformation. 1
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