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although during the hairpin the terminal loops tremendously facilitate enough structural oscillations, also the absolutely free DNA demonstrates adequate bending on making contact with the protein, in this case connected with its lengthy-wavelength fluctuations. a fascinating approach to prove experimentally this idea could possibly be to test to work with a hairpin construct but with much longer flanking sequences, so as to retain the closing loops as significantly as you can, remaining and suitable of the SSB hole, As a result approaching the no cost DNA condition.
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that's why, we selected the ideal docking configuration obtaining the proper orientation of Zn1-Zn2 with regard on the SSB finishes, whether or not this isn't the one giving the most beneficial HADDOCK score and RMSD worth. This configuration was then used since the commencing input construction for a long MD simulation of 0.six μs at T = 310 K. This starting off configuration has Zn2 interacting with nucleotides G1 (the \(5^ \key \)) and T23, the isolated nucleotide facing the SSB.
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