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This merged Zn1-Zn2-DNA configuration is consequently our best applicant for further equilibration at finite temperature and stress. immediately after one μs of MD simulation, the trajectory is clustered and consultant configurations were extracted.

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from the kinetics point of view, it seems that the DNA hairpin bending is usually as a result of spontaneous, cost-free thermal fluctuations till, at some later instant, the side protein loops Make contact with a DNA groove, and “lock-in” the conformation, whether it is a straight or even a bent hairpin. Conversely, the SSB gap opening is originally correlated with the DNA bending and twisting, however it is ultimately determined by the arrangement on the Zn fingers, primarily Zn2 that has the tendency to penetrate deep in the gap, and interacts Along with the nucleotides opposite to the SSB.

consequently, we chosen the most beneficial docking configuration owning the right orientation of Zn1-Zn2 with regard into the SSB finishes, although this is not the a single supplying the top HADDOCK rating and RMSD worth. This configuration was then used given that website the commencing enter framework for a protracted MD simulation of 0.6 μs at T = 310 K. This starting up configuration has Zn2 interacting with nucleotides G1 (the \(5^ \prime \)) and T23, the isolated nucleotide facing the SSB.

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