AID/APOBEC3 Dynamic Catalytic Pockets and AID-α7 Regulation Mechanisms

Abstract

AID/APOBEC3s mutate dC to dU in ssDNA in the restriction of viruses, creation of anti-bodies, and when off-target affecting cancers. Little was known of the catalytic pocket dynamics of these enzymes in real time. As such, we utilised molecular dynamics analyses to determine catalytic pocket volumes and states. We found that most AID/APO-BECs remain predominantly in either a closed or indeterminate state to varying degrees while A3G-CD2 is predominantly open. This occurs chiefly from the catalytic residues themselves and the loop 1 serine/threonine in the "floor" of the catalytic pocket while other residues of the secondary catalytic loops 1, 3, 5, and 7 aid in these states. Surprisingly, we found that the presupposed stable position of AIDs unique 7 ({beta}-state) in contact with the {beta}-sheet and 6 was unstable while the -state in contact with 6 and loop7 was stable and caused pocket closure. Mutations could cause the destabilisation of the -state (R171Y and R178D) or stabilisation of the {beta}-state (R190D and R194A). Thus, pocket states are relatively similar in overall cause; however, multiple residues from secondary catalytic loops as well as AID-7 determine the rates at which these states occur, potentially affecting the chances any AID/APOBEC is able to have catalysis.