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. Author manuscript; available in PMC: 2011 May 21.
Published in final edited form as: J Mol Biol. 2010 Mar 25;398(5):672–689. doi: 10.1016/j.jmb.2010.03.032

Fig. 8. BLUE helices in an anti-parallel configuration.

Fig. 8

(A) Model of the first 280 residues of BLUE threaded onto α-actinin. Structure shown is before minimization and MD simulation. Residues that are close to anti-parallel and then cross are highlighted in color of the residue type. (B) Structure after minimization and 21 ns of MD simulation. (C) Structure of residues 7158–7183 KQEADAKLQKENDDKLKQEADAKLKK and 7217–7239 NDDKLKQEADAKLQKENDDKLKQ) from α-actinin threading after minimization and 21 ns of MD. MD greatly disrupted the anti-parallel bundle conformation of the actinin based structure and the two helices crossed as shown. The interacting hydrophobic residues are the leucines at opposite ends of two LQKENDDKL repeats with the asparagine residue between the leucines the center of the interaction (asterisked residues in sequences in D). The residues of the LNL interaction and the salt bridges are labeled on the structure and the the sequence in D. (D) Sequences of the peptides with the location of the 8-4-2-2 hydrophobic residues and octad repeat. (E) Helical net showing the interacting residues. Residues on the peptide from 7158 to 7183 are marked with a ×. Residues on the peptide from 7217 to 7239 are marked with a ‘+’. Helical net does not represent 7158 to 7239 only a schematic of the interacting residues on these two peptides.