GCN4 is a basic leucine zipper protein and is the main regulator of the transcriptional response to amino acid starvation in yeast. When bound to DNA, a �chopstick-shape� is formed and an antagonistic folding occurs. By performing computer simulations on the 100ns timescale, we are able to understand how GCN4 recognizes these DNA sequences. To understand the interactions responsible for sequence-specific binding, we are analyzing: hydrogen bonds, electrostatic interactions, RMSF, RMSD, and patterns in atomic fluctuations. Through running these specific analyses, we can conclude why these proteins bind the way they do. In the future, this will lead to continuing investigation in specific mutations and how they affect protein binding.

Sequence specific DNA binding behavior of GCN4

244th National Meeting (2012)

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