Interplay of Hydration and Protonation Dynamics in the K-Channel of Cytochrome c Oxidase

Abstract

Cytochrome c oxidase is a membrane protein of the respiratory chain that consumes protons and molecular oxygen to produce water and uses the resulting energy to pump protons across the membrane. Our molecular dynamics simulations with an excess proton located at different positions in one of the proton-conducting channels, the K-channel, show a clear dependence of the number of water molecules inside the channel on the proton position. A higher hydration level facilitates the formation of hydrogen-bonded chains along which proton transfer can occur. However, a sufficiently high hydration level for such proton transport is observed only when the excess proton is located above S365, i.e., the lower third of the channel. From the channel entrance up to this point, proton transport is via water molecules as proton carriers. These hydronium ions move with their surrounding water molecules, up to K362, filling and widening the channel. The conformation of K362 depends on its own protonation state and on the hydration level, suggesting its role to be proton transport from a hydronium ion at the height of K362 to the upper part of the channel via a conformational change. The protonation-dependent conformational dynamics of E101 at the bottom of the channel renders proton transfer via E101 unlikely. Instead, its role is rather that of an amplifier of H96’s proton affinity, suggesting H96 as the initial proton acceptor.

Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase

“…Similarly, the hydration of the K-channel is mainly affected by its own protonation state and the position of the ion, if present (see Table 2 and Table S7 ). As also previously observed [ 6 ], the protonation of K362 is associated with a high hydration level, but only when E101 is not simultaneously protonated (models *01 but not models *11). The protonation of E101 alone, or a K-channel without any excess proton (models *01 or *00), and models with a ion located in the lower part of the K-channel (*00a and *00b) show the lowest hydration level of the K-channel, with six–seven water molecules ( Table 2 ), which is the number of water molecules observed in the crystal structure [ 14 ].…”

“…The K-channel assumes its proton conductivity via the excess proton moving with its own hydration shell (see also [ 6 ]). With the excess proton located below S365, the hydration level of the K-channel is too low to render proton transport likely.…”

“…It hinders, however, back transfer to the lower part of the K-channel due to low hydration and consequently low hydrogen-bond connectivity in the lower part of the K-channel. Furthermore, our previous work [ 6 ] has shown that hydrogen-bond connectivity and the associated proton transfer probability in the K-channel favour proton transfer “upwards” as soon as K362 is protonated and in an “up” conformation [ 18 ].…”

“…The model setup was the same as that previously used for our molecular dynamics simulations of the Pr→ F redox state [ 24 ] and of the O→E state [ 6 , 18 ] and is repeated here for convenience. The redox state was modelled as described in ref.…”

“…The hydration level, in turn, depends on the location of the excess proton. Our previous simulation study of CcO in the O→E redox state showed the transfer of a proton past S365 (at about the lower third of the K-channel) to be determinant for an increase in channel hydration that allows proton transport further up the K-channel [ 6 ].…”