Thermophilus and its proton pump

Membrane proteins are notoriously difficult to crystallise, so it’s not surprising that only few of them have had their structures fully described. In July, a team of international researchers added another integral membrane protein to the list, this time a polysulfide reductase found in the extremophile Thermus thermophilus.

Besides adding to our basic knowledge, what is interesting about the research, published in Nature Structural & Molecular Biology, is that a potentially new kind of proton pump mechanism has been suggested, adding to the known mechanisms of proton translocation. And in the world of structural biology, this is quite a big deal.

The great British biochemist Peter Mitchell first came up with his chemiosmotic theory in the early 1960s. That theory, scorned at first but which later won him the Nobel Prize for Chemistry, holds that the synthesis of the energy source of the cell, ATP, is generated by the movement of protons across a membrane during cellular respiration.

This proton-motive force, as it is known, is generated in many organisms by redox loops – where two enzyme complexes work together to pick up protons from one side of the membrane to release them on the other. Another is through a direct conformational proton pump mechanism.

The new research suggests that a different kind of proton pump can be found in thermophiles, in which the binding of a molecule called quinone causes conformational changes in the membrane protein and works as an additional proton pump.

The research was led by Dr Mika Jormakka, a Swedish native who now heads up the structural biology laboratory at the Centenary Institute of Cancer Medicine and Cell Biology in Sydney, and his mentor, the renowned structural biologist Professor So Iwata, from Imperial College London. Jormakka first met Iwata in Sweden, where the former was working at Stockholm University and the latter had set up a very active structural biology group at the University of Uppsala.

When Iwata decamped to Imperial College in 2000, Jormakka followed, and over the next several years the Iwata team determined the structure of two other membrane proteins, formate dehydrogenase-N (Fdn-N) and respiratory nitrate reductase (Nar), both important in the generation of the proton motive force in E. coli nitrate respiration through redox loops.

The enzyme the team has looked at in T. thermophilus is a polysulfide reductase (Psr), which they believe is a key energy-conserving enzyme in the bacteria’s respiratory chain. The reduction and oxidisation of polysulfides are vital to many bacteria, particularly the thermophiles that live near deep-sea vents and hot springs. According to the researchers, the reduction of polysulfide to hydrogen sulfide in these environments is linked to energy-generating respiratory processes and supports the growth of many microorganisms.

“[Polysulfide reductase] is found in Thermus thermophilus but is also found in many other types of bacteria,” Jormakka says. “But what was particularly interesting with this enzyme is that it describes a potentially new mechanism by which the proton motive force can be generated.

“We think that this polysulfide reductase is generating a proton gradient through a conformational proton pump driven by quinone binding. We don’t really know the details of it but we have some idea.”

Normally, respiratory complexes work by using redox loops, in which enzyme complexes work together, he says. “One enzyme, a lipophilic molecule such as quinone gets electrons from active sites of the first membrane protein, and then picks up protons from the inside of the membrane.

“This quinone is then released into the membrane and is transferred to the second complex. At the second complex it releases the protons on the other side of the membrane. It is through this sort of shuffling that the protons go from one side to the other.

“But in our case we think that the quinone binds to the outside of the membrane, releases protons and electrons that end up on the outside, and on top of that the binding of the quinone causes some sort of conformational change, so there is an additional proton pump from the inside to the outside.

“This is important for cell respiration in this organism but it could be important for many other organisms as well.”

One area that structural biology has great potential in is the development of new therapeutic drugs through structure based drug design. Jormakka, who also has a co-appointment in the Faculty of Medicine at the University of Sydney, is starting work on the structural biology of different types of transporters with medical relevance.

“One of particular interest is a multi-drug transporter which confers antibiotic resistance to bacteria,” he says. “We are hoping to solve that one and we are freezing some crystals in our cold room right now.”