Fig. 5: NBS formation during Molecular Dynamics simulations.
From: Rhodamine6G and Hœchst33342 narrow BmrA conformational spectrum for a more efficient use of ATP
A measure of the distance between the Nucleotide Binding Sites (NBS) during MD simulations for E504Aapo. The distances are measured between the Walker A motif of one monomer (G377) and the signature C motif of the other monomer (G472’), represented as solid line for 1 NBS and as dotted line for the other NBS. Replicate 1 is shown in blue (solid and dotted lines), replicate 2 in magenta and replicate 3 in black. B Representation of the NBDs seen from the trans-membrane domains of E504Aapo for the cryoEM structure (initial structure), shown in pink cartoon with the ATP as sticks. C The last frame of the MD simulation is shown in blue for monomer A and gray for the other monomer. The distances measured in (A) are shown as solid and dotted lines to match (A) with the same colors per replicate. D same as (A) for E504AR6G colored in red for replicate 1, orange for replicate 2 and black for replicate 3. E E504AR6G cryoEM structure (initial starting structure) and distances shown in pink as in (B). F same representation as (C) with monomer A colored in red. The NBS between G377 and G472 shown towards the top of the structures displayed is closing more than the one towards the bottom.
