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Figure 3
Time evolution of the centre-of-mass distance between the T2Cu and the Asp98 residue in its protonated and unprotonated states. (a) The MD trajectories for the Asp98p (blue) and Asp98 (green) states are shown for the three monomers of the AcNiR trimer. The separation between centres of mass for Asp98 and the type 2 Cu atom remains constant at ∼3.8 Å throughout the simulation. In Asp98p the separation increases in all three monomers to ∼6–7 Å within 7–9 ns in chains A and B and by 31 ns in chain C. This increased distance is associated with a switch of the Asp98p residue between its proximal and gatekeeper orientations, a motion that is not observed in the Asp98 protein over the same timescale. Asp98p shows three distinct positions in the MD trajectories, one short-lived and only observed in the initial part of the simulation, which corresponds to the proximal position of Asp98, a second gatekeeper configuration, as observed in cryogenic structures, and a third at intermediate positions (Int-1 and Int-2) to the gatekeeper position, as shown by MD snapshots after ∼20 ns in (b). The MD simulation is shown in ball-and-stick representation and the crystal structure by thin lines. The two conformations of AspCAT in the proximal and gatekeeper positions are shown in thicker green and blue lines, respectively. HisCAT is displaced from its crystallographic position in the MD when Asp98 is not protonated (`prox'), but it remains hydrogen-bonded to the bridging water. In the Int-1, Int-2 and gate positions, HisCAT has rotated away from the crystallographic position and no longer forms the bridging hydrogen bond.

IUCrJ
Volume 4| Part 4| July 2017| Pages 495-505
ISSN: 2052-2525
https://doi.org/10.1107/S2052252517007527