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Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA

Figure 6

MPT and the conformational dynamics of DPO4 change with the flexibility of the linker.

is the parameter which controls the flexibility of the linker. There are two groups of shown. The filled symbols correspond to the linker biased to the B-state while the empty symbols correspond to the linker biased to the A-state. (A) MPT as a function of . (B) The conformational population distribution of the A-, I- and B-state of DPO4 in the US, EC, IS and BS with different . Notice that when equals 10.0 and 100.0, the BS cannot be observed in the simulations when the linker is biased to the A-state. MPT is calculated as the largest observation time. The error bar represents the standard error of the corresponding MPT.

doi: https://doi.org/10.1371/journal.pcbi.1003804.g006