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Figure 6
Zipper-type target 2E42 with modified models as input to ARCIMBOLDO: (a) using only the helices (both) from the models leads to solutions for just two (1gtw and 1h8a ) of the five fragments; (b) using as search fragments just one long helix (30 amino acids) and the DNA fragment leads to solutions in only two of the five models (1gtw and 1h8a ); (c) the same two fragments (1gtw and 1h8a ) also lead to a solution if the DNA plus shorter helices (12 amino acids each) are used as search fragments; (d) using only the DNA of the models as a search fragment leads to a solution in only one case (1gtw ); (e) using the DNA-distant helices taken from the target structure 2E42 as search fragments leads to a clear solution; (f) cutting down this fragment even more to just one helix without the DNA leads to a solution for all five of the models (1gtw , 1h8a , 1jnm , 2c9l and 2h7h ); (g) even searching for two copies of a model helix of 30 amino acids leads to a solution as the DNA-binding part of the zipper helix is quite straight and does not deviate much from an ideal straight model helix. The smallest solving fragment represents 8.13% of the mass of the asymmetric unit.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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