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Researchers Find Way to “See” Water Molecules Hidden Inside Proteins

A team of researchers from Case Western Reserve University has discovered a way to look at water molecules hidden deep inside proteins, revealing a network through which information flows when proteins are switched “on.”

The team looked inside rhodopsin, the protein found in the retina at the back of the eye that is responsible for dim light perception. Rhodopsin is a member of a group of proteins called the G-protein coupled receptor (GPCR) superfamily, which physically change shape when turned “on,” leading to interactions with other proteins and sending information across cell membranes to regulate many important molecular pathways. Rhodopsin is switched on by light, causing it to change shape and start a series of molecular events that make night vision possible.

The research team combined two techniques to investigate water’s role in the protein’s shape shifting. With radiolytic protein footprinting at NSLS beamline X28C they created hydroxyl radicals from the water molecules, which then chemically modify nearby amino acids inside the protein.

The researchers detected the chemical modifications using mass spectrometry and created molecular maps showing where water molecules sit inside the protein when it was off and on. They found that the water molecules rearranged in response to the protein being turned on and interacted with key areas necessary for the protein’s function.

Specifically, water makes an electrostatic network within the proteins, which mediates the flow of information from one side of the protein to the other across the cell membrane.

Genetic mutations within the regions of the protein found to associate with water are known to cause diseases. For example, mutations in these areas of the rhodopsin protein cause a type of genetic night blindness that often leads to complete vision loss. GPCRs are also the gatekeepers that jumpstart many other biological responses, such as the flight or fight response, mood, and even heart function.

If scientists can learn how to turn these proteins and signaling pathways on and off, they can make a large-scale impact on biological response.

T.E. Angel, S. Gupta, B. Jastrzebska, K. Palczewski, M.R. Chance, “Structural Waters Define a Functional Channel Mediating Activation of the GPCR Rhodopsin,” PNAS, 106 (34), 14367-72 (2009).

Left: Radiolytic footprinting of the membrane bound G-protein coupled receptor rhodopsin demonstrates the structural activation of bound waters as a function of receptor signaling status. X-rays ionize water molecules inside and outside the membrane protein structure to radicals (•OH, glowing spheres) that react with adjacent amino acid side chains. As the protein changes its structure during signaling, the pattern of reactivity of water within the protein changes reflecting the transmission of the signal through the membrane.

Right: Sayan Gupta, co-author of the study.

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