The Baker Lab tests Foldit player-designed proteins
The Baker Lab has recently ordered materials to construct a batch of Foldit protein designs in the lab! We will express and purify the proteins from bacteria culture. For those proteins that we can successfully produce and isolate, we will conduct experiments to measure stability and solubility. If a designed protein is exceptionally well-behaved, we may be able to determine its native structure at atomic resolution.
Our process for selecting Foldit designs was as follows:
First, Baker Lab scientists visually inspected top-scoring and "Scientist-Shared" player designs for their favorite folding candidates. For the most part, these are well-ordered, contain significant secondary structure, have a well-packed and hydrophobic core, and also include enough complexity to demonstrate significant design.
These designs were then queued for ab initio folding predictions with the Rosetta@home distributed computing project. Computer power from volunteers around the world was used to generate hundreds of thousands of fold predictions for each design sequence. These results were then compiled into an "energy landscape" for each design sequence. For symmetric multi-chain designs, additional docking simulations were executed to sample alternative inter-molecular interactions. Only designs which show strong preference for the intended fold and docking scheme are included below.
In some cases, the prediction results suggested that a design could be significantly improved with minimal modification. Some of the designs to be tested are slightly modified versions of the player designs shown below. Please note that many solutions from past Foldit puzzles are still being processed.bkoep 84 1240 | Fri, 11/01/2013 - 06:28 | 2 comments )