Jamie Duke


The EGR family of transcription factors is known to be activated in cells exposed to growth factors in a variety of tissues. The overall structure of the family is highly conserved while the amino acid sequence can be quite diverse allowing for a wide array of DNA recognition sequences. Through homology modeling it is possible to reproduce the structure of the DNA binding domain of EGR proteins, which consists of three zinc fingers. It has also been determined through molecular dynamic simulations that most side chains within the domain reach an equilibrium state. However, residues that are essential for DNA binding are seen throughout the simulation as not reaching an equilibrium state, but constantly sampling available conformational space. Furthermore, through cluster analysis the three recognition residues in each zinc finger are found to have side chain conformations that are optimal for DNA recognition. These studies help to show a possible mechanism for zinc finger recognition of DNA and create homology modeled proteins that are able to be used in protein – DNA interaction prediction.

Library of Congress Subject Headings

DNA-protein interactions; Transcription factors--Analysis; Zinc-finger proteins; Cluster analysis; Amino acid sequence; Biochemical templates

Publication Date


Document Type


Department, Program, or Center

Biomedical Sciences (CHST)


Skuse, Gary - Chair


Note: imported from RIT’s Digital Media Library running on DSpace to RIT Scholar Works. Physical copy available through RIT's The Wallace Library at: QP624.75.P74 D84 2006


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