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We produced two different PDB structures by isolating the protein and the DNA hairpin in the RCSB PDB entry 2N8A, which had been then reassembled by docking with HADDOCK. The Lively residues to bootstrap the docking had been: the residues Phe-44 and Leu-151 on the protein (belonging to Zn1 and Zn2 respectively), and the nucleotides G1 (\(five^ \primary \) finish of the hairpin), G45 (\(3^ \key \) stop), moreover the T23 (unpaired base dealing with the SSB hole) from the DNA. This resulted in docked clusters acquiring some of the interactions which were now check here established during the experimental NMR construction. Then, we picked the best docking pose according to the RMSD benefit as initial configuration, and carried out a 200-ns MD simulation at T = 310 K (Fig.
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in regards to the t = four hundred ns docking, the Original arrangement of Zn1 and Zn2 appears to stay little altered for The full 50 0ns MD; due to their mutual interaction, each zinc fingers seem to have a reduced conversation Using the SSB gap. nonetheless, an interesting information attained from your plots of this simulation in Fig. 6c contains the DNA bending angle speedily evolving toward very lesser angles, about \(one hundred twenty^ \circ \) in the second Portion of the trajectory, though simultaneously the SSB hole stays quite shut at twelve-thirteen nm.
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