Membrane proteins are responsible for transporting chemicals and messages between a cell and its environment. But determining their structure has proved challenging for scientists. A study by UC Santa Barbara's Han Research Group demonstrates a new tool to resolve the structure of membrane-embedded and membrane-associating proteins using the water dynamics gradient they found across and above the lipid bilayer as a unique ruler.
More than 25 percent of all human proteins are membrane proteins, which perform other essential functions, such as sensing and signaling. They also constitute approximately 50 percent of current drug targets, but the structure of only a small percentage has been resolved.
The UCSB study came about when researchers discovered that water on the membrane surface has a very distinct movement pattern: It is slowed down because the water is attracted to the membrane surface across several water layers. The scientists then wondered whether they could use this as an intrinsic ruler to determine how the associating protein is anchored into the membrane.
"It's very difficult to determine at what depth and in what conformation the protein is associating with the membrane, especially if you're talking about the interface or even the surface," said UCSB chemistry professor Song-I Han, the corresponding author of the study. "We found a contrast mechanism -- water dynamics -- which is distinctly different even above the membrane surface where there is no lipid density. The membrane surface distinctly changes the property of the water layers above it."
Postdoctoral scholar Chi-Yuan Cheng, the lead author of the study, and his colleagues used their unique spectroscopic tool to measure the water diffusivity at various positions of two membrane-associated proteins. These were carefully prepared by the Ralf Langen group at the University of Southern California, an expert team in the structure studies of membrane-associating proteins. The UCSB researchers then used the water dynamics gradient along the bilayer as an intrinsic ruler to determine structural information, such as topology, immersion depth and the location of the proteins, including the protein segments residing well away from the membrane surface -- information that was previously unresolved.
"Membrane proteins can sit deep inside the membrane but also associate at the periphery of the membrane," explained Cheng. "This can play a very important role in function, especially for peripheral and interfacial proteins."
"We are not suggesting our study can resolve the structure entirely, but it offers an important and missing puzzle piece to this problem," said Han. "While we may not be able to determine the entire structure, knowing the location and structure of a protein segment at the surface of membranes is very important."