Cellular respiration, a process of oxidizing nutrient molecules to carbon dioxide and water, involves the transfer of election through a series of membrane protein complexes. This process is coupled with generation of an electrochemical gradient across the membrane, which can be used to drive the synthesis of ATP. Cytochrome c Oxidase (CcO), the terminal enzyme of the respiratory chain, catalyzes the reduction of dioxygen to water as follows 02+4H++4e-⇒ 2H20. The transfer of four electrons from cytochrome c to dioxygen is accompanied by the translocation of eight protons, four being consumed internally in the reduction of oxygen and the other four being pumped across the membrane.
Seven out of the eight protons taken up from the cytoplasmic side of the membrane are transferred into the enzyme by the so-called D-pathway that leads approximately halfway into the membrane and ends at the wall conserved Glu-242. Although the proton translocation in this pathway have been investigated extensively by using standard molecular dynamics, the molecular properties and detailed mechanisms governing the explicit proton translocation in this channel have remained elusive.
Therefore, the aim of this project is to study the proton transport (PT) in the D-pathway and its extended path by means of classical MD simulations using the MS-EVB2 model. The mechanism of proton translocation along the D-pathway was characterized by a potential of mean force calculation, and our data support a two-step mechanism of PT to Glu-242. The proton moves quickly along a proton wire at the beginning of the channel, stalls at the wide pore region, and then moves along the second part of the channel via another independently formed water chain.
The D-pathway is used both for protons to be consumed in formation of water and protons to be translocated. Although water molecules form an efficient pathway for protons up to Glu-242, there is no obvious continuation of the pathway from there. The questions have been raised as to how protons are transferred further from Glu-242 and what strictly controls the switch between directing the protons to either the oxygen reduction site or to the exit channel. Our future research will be concerned with he aspects of PT beyond the Glu-242, as well as the role of the reduction of the heme groups in the proton translocation process.
