Please Help: Tertiary Protein Structure Prediction

Please Help: Tertiary Protein Structure Prediction

Postby Proteinglow on Wed Oct 14, 2009 12:43 pm

I am using Swiss-PdbViewer to determine the
structure of a fluorescent protein with a sequence homology to know
fluorescent proteins, such as GFP and DsRed. The protein of interest
has four domains due to gene duplication. Based on this information I
am using DsRed as a model, since the structure of DsRed has been
solved and it is tetrameric. I would like to know if there is a way
for me to add a linker to connect each of the DsRed in the tetrameric
structure. I have added some hypothetical linker amino acids to the C-
termial of one of the DsRed in the tetrameric structure; however, I am
unable to connect the linker to the N-terminal of 2nd DsRed in the
structure. I have also utilized sequence based homology modeling, but
that only predicts structure for one of the domain relative to the
know fluorescent proteins. I have also used PredictProtein to
determine the structure of my protein, but I have been unable to
determine whether or not predicted linkers are long enough to give my
protein a classical tetrameric structure of a fluorescent protein. I
would greatly appreciate any and all suggestions and advise regarding
this problem. Please let me know if this is not the correct place for
this sort of email and if that is the case, then please feel free to
direct my email to an appropriate location.

Posts: 1
Joined: Wed Oct 14, 2009 8:59 am

Re: Please Help: Tertiary Protein Structure Prediction

Postby AlexanderSimmons on Thu Sep 16, 2010 12:12 am

In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The evolutions in motif identification and side chain modeling present the prospect of nearly automatic model building for a large fraction of newly determined protein sequences. Anyway nice post..
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Joined: Wed Sep 15, 2010 10:26 pm

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