Molecular dynamics simulations of growth factor independence 1 (GFI1)

Abstract

Growth factor independence 1 (GFI1) is a DNA-binding transcription factor and a key regulator of hematopoiesis. GFI1 is comprised of three distinct sections: (i) the C-terminal region containing six zinc-finger domains, (ii) an N-terminal region of 20 amino acids termed SNAG, and (iii) a central region connecting the other two. As large parts of the GFI1 protein seem to be intrinsically disordered, the present study tries to explore its configurational variety by employing molecular dynamics (MD) simulations. From the obtained MD trajectories the most significant configurations are extracted using a cluster algorithm and the Bayesian information criterion (BIC). It turns out that no dominant structure could be identified, which emphasizes the expected intrinsic structural disorder of the protein. During the four microsecond simulation no significant difference was found between two different variants of GFI1.