Simulations on BlueGene of a Fast Folding Mutant of Lambda(6-85)

Friday, January 18, 2008 - 9:35am - 10:05am
EE/CS 3-180
Using the BlueGene computer at IBM Research we have performed extensive simulations on a mutant construct of lambda repressor. The protein consists of 80 amino acids stuctured as a five helix bundle in the folded state. The mutant was designed in the Gruebele lab at UIUC to exhibit sub-10 microsecond folding times in laser temperature jump experiments. Our simulations employed replica exchange and traditional molecular dynamics at a number of different temperatures. Although it is very difficult to thoroughly equilibrate and sample molecular systems of this size and complexity, our simulations clearly reveal very complex folding behavior. In particular, different structural elements exhibit different degrees of thermodynamic stability and melt at different temperatures. Some of the structural transitions appear to be relatively cooperative, whereas others are quite diffuse.
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