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1688: Cubane FeS Binder Design
Status: Closed


Name: 1688: Cubane FeS Binder Design
Status: Closed
Created: 06/19/2019
Points: 100
Expired: 06/26/2019 - 23:00
Difficulty: Intermediate
Description: Design a protein for electron transfer!

Metallo-proteins are an important class of proteins that bind metals like iron or magnesium, and are involved in myriad life-sustaining chemistry. A cubane type [4Fe-4S] iron-sulfur cluster is a "cube" made out of alternating iron and sulfur atoms, and is bound by carefully-placed cysteine residues in a protein. Iron-sulfur metallo-proteins are responsible for electron transfer in light-harvesting, cellular respiration, many other processes. We'd like to design an iron-sulfur protein so that we can better understand electron transfer in proteins. By changing the environment around the iron-sulfur cluster, we could tune the electron transfer properties of the protein, which could open the door to metabolic engineering and new chemistry!

We're asking Foldit players to design a protein that can bind a cubane type iron-sulfur cluster! In this puzzle, players start with a short loop that contains three cysteine residues bound to the iron-sulfur cluster. The loop and the cluster are frozen in place, but players may fold up the residues on either side of the loop. The final protein will need to include the frozen loop, but should still be well-folded with a large core. See the puzzle comments for Objective details. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall

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bkoep's picture
User offline. Last seen 5 hours 59 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

Residue IE Score (max +500)
Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence (max +1000)
Ensures that at least 25% of residues are buried in the core of the protein.

SS Design (max +500)
Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in helices.

Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 66, at a cost of 55 points per residue. Players may use up to 76 residues in total.

Joined: 01/19/2019
Groups: Go Science
PDB structures

The fixed 4Fe-4S loop CISCGAC matches PDB 1FDN, 1FCA, and 2FDN (RCSB PDB motif search). All of these structures show the protein uniprot:P00198. This protein binds two clusters, one with the CISCGAC loop and the other with a CIDCGAC loop. A fourth cystine residue comes from outside the loops to stablize the complex, but this is not scored for in this puzzle.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons