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Figure S1

Posted by Bonnie_Real on 19 Jan 2007 at 01:18 GMT

(see Figure S1)

Due to a PLoS error, this figure is presented as the final figure in the paper (doi:10.1371/journal.pone.0000136.g008) rather than in Supporting Information. The legend was also omitted, it is as follows:

Dependence of the J factor and ΔGloop on the dihedral angle, τPP, between LacR dimers in the v-shaped tetramer conformation. All calculations were done for the case of a rigid LacR tetramer assembly. Loop topoisomers were labeled as (-) or (+) depending on whether the total loop twist was respectively less than or greater than that for a relaxed loop. (A) J factor and ΔGloop as functions of τPP for 163-bp (torsionally in-phase) and 179-bp (torsionally out-of-phase) loops in the LB conformation. In the case of the 179-bp LB loop, values for both (+) and (-) loop topoisomers as well as their sum are shown. The 163-bp LB loop is only very slightly underwound and therefore contributions from the (+) topoisomer are negligible. (B) J factor and ΔGloop as functions of τPP for 179-bp (torsionally in-phase) and 163-bp (torsionally out-of-phase) WA loops. Individual contributions from (+) and (-) loop topoisomers as well as totals are shown for the 163-bp loop. (C) J-factor and ΔGloop dependence on τPP for 179-bp (torsionally in-phase) and 165-bp (partially out-of-phase) WT loops. Solutions for mechanical-equilibrium conformations failed to converge near the expected J-factor minimum (163-bp), most likely because of high strain energy in strongly under- and overwound WT conformations. Interestingly, there is only slight asymmetry present in the nearly parabolic dependence on dihedral angle.