Gaining More Understanding of Membrane Protein Organization

One-third of our proteins are associated with a cellular membrane. And when membrane proteins are misdirected, it can impair our immune system’s ability to fight disease or lead to significant diseases such as cystic fibrosis and anomalies in embryonal development. 

 Understanding the best ways to get a membrane protein to its destination in a cell is crucial. There are some well-known methods to do this, like signaling transporter-like proteins to move the membrane protein. However, increasing evidence indicates that proteins also get sorted based on how they physically look.

Recent work from Northwestern Engineering’s Neha Kamat focused on how proteins are organized within cell membranes. Kamat and her team looked at hydrophobic mismatch, where a size difference between the protein and the membrane it's in makes it harder for the new protein to be made and inserted properly into the membrane. They also confirmed an idea that proteins might gather in specific areas within a membrane depending on this mismatch, which hadn't been proven experimentally before.

“Our study should be useful for any technology that uses membrane proteins, including biosensors that use membrane proteins as recognition elements or drug delivery vehicles or vaccine nanoparticles that use membrane proteins to target and bind specific cells or train the immune system,” said Kamat, associate professor of biomedical engineering at the McCormick School of Engineering and member of the Center for Synthetic Biology. “In all of these applications, the traditional route of membrane protein incorporation is expensive and time-intensive, requiring cell culture and protein purification all before integrating the protein into membrane scaffolds. Cell-free synthesis of membrane proteins circumvents many of these issues by allowing specific proteins to be synthesized and integrated into user-designed membranes all in one pot.”

“Learning rules that allow us to better control both the synthesis and sorting steps of membrane proteins will greatly reduce costs associated with manufacturing these types of systems.”

Kamat is the corresponding author of a paper about the work, titled “Hydrophobic Mismatch Drives Self-Organization of Designer Proteins into Synthetic Membranes,” published last month in the journal Nature Communications. Justin Peruzzi, a former member of Kamat’s lab, was the study’s first author.

The results support a long-held idea that differences in size between certain proteins and the fats in cell membranes can cause these fats and proteins to move around within the membrane. The researchers used a mix of experiments outside of cells, computer simulations, and newly created proteins in their work. This method could be used to dig deeper into other big questions in biology that regular methods can't reach. In the world of biotechnology, the findings could lead to better ways to make treatments that mimic cells and sensors that can use these proteins more efficiently. 

“We’ve shown that we can bias which nanoparticle membrane proteins integrate into when there is a mixed population of membrane-based nanoparticles present; and we’ve shown that within a single membrane we can use hydrophobic mismatch to control interactions between membrane proteins,” Peruzzi said. “This latter result will be useful in the design of membrane-based sensors that rely on two or more proteins coming together in a membrane to initiate a response.”

Two important advances made the study possible.

One was the use of cell-free systems, allowing the researchers to synthesize membrane proteins outside of the cell and in controlled environments where they could add lipid membranes of a specific length. Another advance was the design of more complex membrane proteins from David Baker’s lab at the University of Washington, which allowed Kamat’s team to adjust the length of a membrane protein without significantly changing its composition. The result was a platform where they could study how proteins of different lengths fold and sort in membranes after synthesis. 

The team’s work highlights lipids’ important role in the cell, not only as a scaffold that houses membrane proteins, but also as a complex transportation network that influences where membrane proteins go, ultimately leading them to sites where they will be transported to distant locations or conversely, remain close by.

“It’s amazing that there isn’t a master coordinator of protein trafficking,” Kamat said. “Rather, we are increasingly learning about the very subtle physical principles, like hydrophobic mismatch, that can push both lipids and proteins to reorganize themselves. It’s like a group of preschoolers standing in line and switching places with one another until they were organized by height, and doing so without an outside person telling them what to do.”