Proton migration through a Grotthuss-like mechanism.

<p>The hydration promoted by the ion located in the five-fold cavity allows proton migration through the cavity. Protein atoms are indicated by a stick model with red and blue segments. Oxygens from water (H₂O) are denoted by small red spheres, and oxygen from hydroxyl ions (OH^-) are large red spheres. Solvent protons are small white spheres, and protein protons are white sticks. The Mg²⁺ is highlighted as a green sphere. Panels A-G show the sequence of events used for the QM calculations for proton transport induced by a pH gradient. Four OH^- located in the outer solvent region represent a high pH relative to the capsid inner solvent region. Red arrows point to the position of OH^- at each step of the simulation, and these points correspond to the H⁺ hole jumping stepwise from the top to the bottom. The yellow arrow indicates the water coordinated to the metal ion that participates in the inner part of the water wire. Panel E corresponds to the transition state (TS) between configurations D and F, in which the H⁺ hole overcomes a low energy barrier towards the capsid interior. Lower panels show the distances (in Å) at each step between the atoms participating in the proton transfer. For clarity, only a subset of the 536 atoms involved in the calculation was included in these panels.