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Proton wires play key role in the mechanism of proton transporters

Researchers at IRIG revealed true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a prototype model system to study proton transport. They show how hydrogen bonds not only serve as proton pathways, but are also indispensable for long-range communication, signaling and proton storage in proteins.

Published on 20 December 2022

​Hydrogen bonds are fundamental to the structure and function of biological macromolecules. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. 

Different research groups have determined bacteriorhodopsin structures at the ground and at functionally important intermediate states. Although this improved the understanding of bacteriorhodopsin, a light-driven proton pump, and provided some insight into proton transport, the resolution of these structures (at best 2 Å) did not allow to decipher the detailed molecular mechanism of proton transport.

For more than 20 years, solving crystallographic problems step by step, researchers at IRIG revealed the true-atomic-resolution structure of bacteriorhodopsin (about 1 Å). An amazing picture of the proton storage and release mechanism presented experimentally shows for the first time that linear chains of hydrogen bonds (often called proton wires) and low barrier hydrogen bonds described in terms of quantum mechanics and symmetry considerations are at the core of the mechanisms.

The complete picture of hydrogen bonds, CHBs and LBHBs, discloses their multifunctional roles in proton transport. The discoveries demonstrated how hydrogen bonds, CHBs and LBHBs, not only serve as proton pathways, but are also indispensable for long-range communication, signaling and proton storage in proteins.  This consistent picture of proton transport and storage is finally resolving long-standing debates and controversies.

This work does not only relate to a great problem of the mechanisms of proton transfer but also to a significant biological role of one-dimensional chains of hydrogen bonds and their symmetry described in terms of physics. The corresponding current studies aim to clarify the universality of the discovered mechanism (proton transfer reactions comprise more than 50% of all biochemical reactions) and their possible applications in nanomaterials.
It was 1971 when Dieter Oesterhelt and Walther Stoeckenius discovered bacteriorhodopsin, the first microbial rhodopsin. In 2021, Dieter Oesterhelt receiving the Lasker Prize mentioned: “I was met with everything from disinterest to complete disbelief from colleagues. The situation changed rapidly after 1972, when I collected the first data on the function of this molecule and showed that it was a pump that converts light energy into chemical energy for the cell – essentially a new form of photosynthesis.”

One of the reasons for high scientific interest was that the results obtained by D. Oesterhelt and W. Stockenius indicated that the proton gradient created by bacteriorhodopsin in H. salinarum plays the central role in energy coupling attributed to such electrochemical gradients by Mitchell's chemiosmotic theory, published in 1966 was first received with skepticism.  The eventual acceptance by scientific community came with the demonstration of coupled ATP synthesis in the bacteriorhodopsin-ATPsynthase lipid vesicles (Nobel prize, 1978).

However, elucidation of the molecular mechanism requires knowledge of high-resolution structures of bacteriorhodopsin.   It turned out to be a great challenge. Moreover, at that time it was considered to be impossible to crystallize a membrane protein. Hartmut Michel, wrote in his Nobel Prize (1988) autobiography: “Frustrated from the lack of the final success with bacteriorhodopsin, I tried to crystallize several other membrane proteins, mainly photosynthetic ones.

Richard Henderson initially developed cryoEM crystallography working with bacteriorhodopsin and in 1990 obtained an unprecedented for that time 3 Å resolution (Nobel Prize, 2017).   
One more breakthrough happened in 1996-97 when E. Landau and J. Rosenbush crystallized bacteriorhodopsin in an “exotic” lipidic cubic phase and Eva Pebay-Peyroula from IBS Grenoble solved bacteriorhodopsin structure at 2.7 Å (Science, 1997).

Interestingly, developing cubic phase crystallization with bacteriorhodopsin was instrumental for the downstream development of the structural studies of GPCR receptors, the largest family of human receptors which are also critical for the development of 30-40% of the existing drugs (Nobel Prize, 2012).
Bacteriorhodopsin is a protein used by Archaea, most notably by haloarchaea, a class of the Euryarchaeota. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell. The resulting proton gradient is subsequently converted into chemical energy.

G protein-coupled receptors (GPCRs) also known as seven-(pass)-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors, and G protein-linked receptors (GPLR), form a large group of evolutionarily-related proteins that are cell surface receptors that detect molecules outside the cell and activate cellular responses. Coupling with G proteins, they are called seven-transmembrane receptors because they pass through the cell membrane seven times.

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