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585: CASP10 Target T0722
Status: Closed

Summary

Name: 585: CASP10 Target T0722
Status: Closed
Created: 06/25/2012
Points: 100
Expired: 07/04/2012 - 22:00
Difficulty: Advanced
Description: The eleventh CASP10 target is not an easy one. It's 152 residues and none of the alignment programs were able to find good templates for this target. It might be the case that this protein has no homologs. We are giving you 6 templates (in hope that one of them is correct) for now, and will provide you with some server predictions once they are released. More details about this CASP target are in the puzzle comments.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 1 day 2 hours ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this CASP target

Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casp10/target.cgi?id=137
____________________________________________________

Here is the sequence logo predicted by the SAM server.

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Leucines at residues 27, 31, 34, 60-61, 73, 82-84, 91-95, 101, 105, 116, 123, 130 & 140 are highly predicted to be in a helix. However, the Leucines at residues 14, 22-23, 150 & 152 are predicted to be anything.
____________________________________________________

Link to template PDBs:

http://www.pdb.org/pdb/explore/explore.do?structureId=1gqe
http://www.pdb.org/pdb/explore/explore.do?structureId=1ls4
http://www.pdb.org/pdb/explore/explore.do?structureId=3tul
http://www.pdb.org/pdb/explore/explore.do?structureId=3k29
http://www.pdb.org/pdb/explore/explore.do?structureId=1ya9
http://www.pdb.org/pdb/explore/explore.do?structureId=3lg7

infjamc's picture
User offline. Last seen 2 years 15 weeks ago. Offline
Joined: 02/20/2009
Groups: Contenders
Just out of curiosity...

What's going on with the sequence at the N-terminus? (Is it an added polyhistidine tag, or was it a part of the "natural" sequence?)

beta_helix's picture
User offline. Last seen 1 day 2 hours ago. Offline
Joined: 05/09/2008
Groups: None
Exactly, it's most likely a his tag

In fact, the RosettaServer only modeled this sequence:
SSGRENLYFQGAGPLLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLL
EKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDV
LSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSL

Although we can't be 100% sure since the CASP10 organizers did not give us any additional information about it. We'll have to see what all the servers did with the first 7 residues.

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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, RosettaCommons