Solving structure
Membrane protein structures could lead to the development of improved drugs
Story by Tara Narwani/Illustration by Blair Kelly
If you suffer from excess stomach acid production, you may have taken a drug known as a proton-pump inhibitor, such as Prilosec or Prevacid. Similarly, if you’ve ever suffered from depression, you were likely prescribed a selective serotonin reuptake inhibitor (SSRI), such as Prozac or Zoloft. All of these drugs—in fact, 60% to 70% of all drugs currently on the market—work by targeting the activity of a type of protein called a membrane protein.
Each cell in our body, as well as various compartments within each cell, is surrounded by a membrane, which acts as a barrier between external and internal environments of the cell or compartment. Proteins embedded in these membranes, the membrane proteins, are known as “gatekeepers” because they play a critical role in controlling the movement of various molecules in and out of the cell. Membrane proteins are also involved in cellular communication by relaying signals across membranes. If a particular membrane protein doesn’t work properly, it can impair how a cell functions and can even lead to cell death.
Despite the importance of membrane proteins in physiology and drug development, “there is a lack of knowledge of membrane protein structures,” says Dr. M. Joanne Lemieux, an assistant professor in the Department of Biochemistry at the University of Alberta. Currently, the structures of only 302 membrane proteins have been identified; in contrast, researchers have identified the structures of tens of thousands of other types of proteins.
This lack of knowledge explains why researchers sometimes don’t have a complete understanding of how a particular drug works in the body. In other words, researchers don’t know exactly how the drug and membrane proteins interact. Furthermore, they can’t accurately determine the best way to enhance this interaction to improve the drug.
“With anti-depressants, for example: if the structure of the transporter (a type of membrane protein that carries the drug into the cell) was known, you could develop drugs that would bind to the protein with a higher binding affinity. That way you could possibly lower the dose patients take as well as reduce the side effects of the drug. In other words, you could possibly develop a more effective drug,” says Dr. Lemieux.
In her lab, Dr. Lemieux studies the structure and function of a recently discovered group of membrane proteins called rhomboids. These proteins may play a role in a number of human diseases because they function in cellular communication. Rhomboids are proteases—they break the structure of other proteins down into smaller parts. These parts can then act like chemical messengers in the cell, and activate other processes by triggering changes in the structure or function of the cell.
Before tackling the more difficult task of solving the structure of a rhomboid found in humans, Dr. Lemieux began with a rhomboid from a bacterium called Hemophilus influenza (not to be confused with the flu virus). The bacterium can cause pneumonia in infants and young children as well as other respiratory conditions.
The process of determining the structure of a protein is extremely challenging. It is a multistep process, requiring extreme attention to detail at each stage. Dr. Lemieux identified her first membrane protein structure (not a rhomboid) while finishing her Ph.D.—an achievement that took seven years from start to finish. However, the speed of discovery in the field is now growing exponentially.
The first hurdle that needs to be overcome in solving protein structures is the difficulty in obtaining a sufficient amount of protein. The current approach is to genetically engineer bacteria to produce large quantities of the protein. Next, the researchers need to purify the protein without disrupting its three-dimensional form and then force the proteins to pack together into crystal-like shapes.
“We then take these crystals to a synchrotron facility (a particle accelerator) where we shoot the protein crystals with x-rays and collect a bunch of images that represent the protein,” describes Dr. Lemieux. Finally, based on this data, her team builds a model of the protein’s atomic structure using computational software.
Once the initial rhomboid protein structure was identified, Dr. Lemieux and her team began testing the mechanism by which the rhomboid acts as protease. To do this, they mutated regions of the rhomboid to see how it would affect its structure and function. These experiments helped eliminate some ambiguity about how rhomboids break down other proteins.
Dr. Lemieux has already eagerly begun work on human rhomboids. Recent data from the scientific community suggest that certain rhomboids are activated in aggressive forms of breast cancer. Always with an eye on opportunities for drug development, Dr. Lemieux says, “Rhomboids could be a potential target in the fight against breast cancer if we knew their structure in humans.”
Membrane Protein Research Group
The Membrane Protein Research Group at the University of Alberta studies the expression, assembly, structure, and function of membrane proteins. Disruptions in membrane structure and function have been implicated in diseases such as Alzheimer's disease, cystic fibrosis, cancer, muscular dystrophy, and cardiovascular diseases. The group’s research will be used to develop novel approaches to therapies for membrane-associated disorders.
Source: Membrane Protein Research Group