FIGURE 4.

HNH domain activation observed through long time scale MD simulations. (a) The HNH domain (green) is shown to approach the catalytic site on the DNA target strand (TS), changing conformation from a preactive X-ray structure (PDB code: 5F9R) to the active state identified by MD (top panel). The time evolution of the distance between the catalytic H840 and the scissile phosphate (H840–P_DNA) is computed along ~400 ns Gaussian accelerated MD (GaMD, central panel) and along ~16 μs of a continuous MD simulation using Anton2 (bottom panel). A black dashed line indicates the preactive conformation (PDB code: 5F9R), which has been used as a starting point for MD simulations. (b) Conformational change of REC2 and REC3 during the HNH activation, identified by single molecule FRET (smFRET) experiments (top panel). The evolution along a ~16 μs MD run of the smFRET pairs D273–E60 (middle panel) and S701–S960 (bottom panel). Transparent bars (pink) indicate the experimental distribution of the smFRET distances in the activated conformation.¹⁷ Reprinted with permission from Reference 17 Copyright 2018 Cambridge University Press. https://doi.org/10.1017/S0033583518000070