Extremely rapid water: Scientists decipher a protein-bound water chain

Jul 06, 2011

Researchers from the RUB-Department of Biophysics of Prof. Dr. Klaus Gerwert have succeeded in providing evidence that a protein is capable of creating a water molecule chain for a few milliseconds for the directed proton transfer. The combination of vibrational spectroscopy and biomolecular simulations enabled the elucidation of the proton pump mechanism of a cell-membrane protein in atomic detail. The researchers demonstrated that protein-bound water molecules play a decisive role in the function. Their results were selected for the Early Edition of PNAS.

Specific proteins can transport from one side (uptake side) of the to the other side (release side). This is a central process in biological energy conversion. In past editions of Nature and the researchers from the Department of had already published their observations that in the ground state the protein-bound at the release side are optimally arranged for the release of protons. "As with dominos, the protein initiates movement of the protons which finally leads to their release", explains Prof. Gerwert. Just how the protein re-attains its initial state in order to start another pumping cycle remained to be clarified. New protons must be acquired at the uptake side of the protein to substitute the released protons. The researchers in Bochum discovered that a chain of only three water molecules is formed for just a few thousandths of a second to transfer the protons into the interior of the protein.

The protein kills two birds with one stone. The water molecules are disordered during the release phase, which prevents the protons from being transported in the false direction. Only during the uptake phase, they are correctly aligned and can conduct protons. These results are the solution to the riddle as to why proton transfer only functions in one direction at the uptake side and why the protein is capable of effective and directional pumping. "This paper, together with the two preceding publications, now constitutes a trilogy which supplies a full explanation for the proton pumping cycle at an atomic level", summarizes Prof. Gerwert.

The researchers combined experimental physics with theoretical chemistry to be able to observe the processes with a high spatial and temporal resolution at a nano-level. Steffen Wolf simulated the structural changes within the protein using biomolecular computer simulations (molecular dynamics simulations). Erik Freier subsequently verified the effects experimentally using a special kind of vibrational spectroscopy developed by Prof. Gerwert (time-resolved step-scan FTIR spectroscopy). "This interdisciplinary interplay, which showed that the individual components of the protein are as precisely synchronized as the gears of a machine, was the key to success", says Prof. Gerwert.

The protein arranges the three water molecules so skillfully that they transport the protons using the physico-chemical Grotthuss mechanism. In the 1950s, the Nobel Prize winner Manfred Eigen elucidated this mechanism to explain extremely rapid, non-directional proton transport in water. Surprisingly enough, the publications of the RUB researchers now reveal that amino acids coupled with protein-bound can give this extremely rapid transportation a direction of movement. Prof. Gerwert's team was thus able to augment Manfred Eigen's results and apply them to protein research.

The group of research scientists in Bochum primarily works with the membrane bacteriorhodopsin, which is used by certain bacteria to carry out an archaic form of photosynthesis. Bacteriorhodopsin creates a proton concentration gradient by transporting protons from the interior to the exterior of a cell. Other proteins use this gradient to produce ATP, the universal cellular fuel. It is important that the proton transport has a specific direction and that spontaneous backflow of protons is prevented to ensure that light energy can be effectively used.

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More information: References:

Freier, E., Wolf, S., Gerwert, K. Proton transfer via a transient linear water-molecule chain in a membrane protein. PNAS, early edition, doi: 10.1073/pnas.1104735108 (2011)

Wolf, S., Freier, E., Potschies, M., Hofmann, E., Gerwert, K. Directional Proton Transfer in Membrane Proteins Achieved through Protonated Protein-Bound Water Molecules: A Proton Diode. Angew. Chem. Int. Ed., 49, 6889-6893 (2010)

Garczarek, F., Gerwert, K.: „Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy". Nature, 439, 109-112 (2006)

Provided by Ruhr-University Bochum

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