Proteases, which play an essential role in many of our physiological systems, are enzymes that cleave other proteins. Until recently, it was thought that they recognize certain amino acid sequences to know when to cleave other proteins.
However, through extensive studies on rhomboid proteases, Syed Moin and Sinisa Urban from Hopkins School of Medicine recently proposed a novel mechanism by which proteins in the cell membrane recognize their targets. Proteases cleave proteins into smaller functional and non-functional segments, ultimately allowing mechanisms such as digestion, blood clotting, and apoptosis to occur. They are also known to recognize very specific targets.
These enzymes can be categorized into two distinct groups: soluble and intermembrane proteases. Soluble proteases diffuse within the cell’s aqueous cytoplasm, while the intermembrane proteases have evolved in the membrane. While soluble proteases have been well characterized in the past, understanding intermembrane proteases have been much more difficult.
Intermembrane proteins, however, are very interesting to study. Only a small number of protein families have evolved to rule the border between the inside and outside worlds of the cell. These proteins have been widely conserved in nature, suggesting that they are crucial for the cell’s survival.
An important question arises: how does the membrane environment affect the function of a protein? Moin and Urban tackled this question by investigating rhomboid proteases, a type of intermembrane protein.
“Is the membrane just an environment in which enzymes reside?” Urban asked.
“When I jump into water, my physiology doesn’t change — just my environment does,” Urban said. He later explained that this is not the case for enzymes. The cell membrane is not a mere medium in which enzymes can reside. In fact, it can actively alter the properties of enzymes. His investigations on rhomboid proteases led him to this novel conclusion.
Previous studies have shown that soluble proteases detect specific amino acid sequences to determine when to begin breaking the peptide bonds that make up the target proteins’ structure. This has been the canonical view of proteolysis, or protein cleavage.
Through numerous biophysical and biochemical methods, however, Moin and Urban found that rhomboid proteases can sense the structural stability of other membrane proteins. When these membrane proteins lose their stable helical structure in the binding region, the rhomboid proteases will cleave them.
Moin and Urban noticed that rhomboid proteases could not function well once they were taken out of the native membrane environment. The membrane facilitates the recognition of its targets. Since different environments confer different properties to enzymes, these proteases may have evolved within the membrane to effectively patrol for unwanted structures.
Through alterations of membrane components, Urban also discovered that the specificity of the target was was derived from properties of the membrane, which somehow directs the position of cleavage.
When rhomboid proteases were expressed in vitro in detergent micelles, they allowed more proteins to enter their gates and cut them. This led Moin and Urban to believe that the artificial environment was hampering the enzyme’s ability to recognize its specific targets. They postulated that the rigid cell membrane may be limiting protein dynamics, while micelles, which are much more fluid, allow the protein gates to flexibly welcome other targets.
“Our next step would be to look into the biological and evolutionary implications,” Urban said.