Fig. 8

Hydrogen bonding patterns in molecular dynamics simulations. The number of H-bonds formed over each picosecond of the MD simulations (described in this Chapter) have been shown in this figure. Each of the six panels (systems) shows the H-bond traces from three replicates (represented in different colours). a Active RNase PH monomer. b Inactive RNase PH monomer. c Active RNase PH dimer. d Inactive RNase PH dimer. e PELOTA_1 domain from the ‘uncharacterised’ protein in complex with kink-turn RNA. f L7Ae K-turn binding domain from A. fulgidus in complex with kink-turn RNA from H. marismortui