PFRMAT TS 
TARGET T0052 
AUTHOR 7397-8542-2481 
METHOD MEDLINE SEARCH 
METHOD A medline search of cyanovirin yielded a few interesting papers detailing 
METHOD recent experimental work on this protein.  From these papers, we learned 
METHOD that cyanovirin has two disulfide bonds and is a repeat (Gustafson, Sowder, 
METHOD Henderson, et al., Biochemical and Biophysical Research Communications, 
METHOD 238, 223-228, 1997).   
METHOD  
METHOD PSI-BLAST  
METHOD The cyanovirin was the only "hit" identified with PSI-BLAST, although 
METHOD there appears to be a weak homology to penicillin binding protein PBP-2X. 
METHOD 
METHOD JPRED 
METHOD Predictions performed using JPRED (Cuff and Barton, unpublished) were  
METHOD used to derive several alternative patterns of secondary structure  
METHOD elements for the aligned cyanovirin repeats.   
METHOD  
METHOD THREADING 
METHOD These patterns, mostly beta with a few inconsistent alpha helices, and 
METHOD the constraint on the known disulfides were then used to search through 
METHOD representatives of the SCOP database (one structure from each species  
METHOD level) for possible matches using the MAP program (Russell, Copley, & 
METHOD Barton, J. Mol. Biol. 259, 349-365, 1996) and the LH program (Koretke, 
METHOD Luthey-Schulten, Wolynes, Protein Science, 5, 1043-1059, 1996).  A  
METHOD number of small proteins, including SH3 domains, OB folds and beta-grasps,  
METHOD and open faced beta sandwich domains were found, though the searches were 
METHOD inconsistent, and the similar scores for different folds (in many  
METHOD searches) suggested that none were good matches for the target. 
MODEL  1 
PARENT NONE 
TER 
END 
