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A cellular cop that does its job too well
While most of us regard protein as something that ought to be in a fair amount of the food we eat, proteins spark even more interest among microbiologists than they do among nutritionists. That's because proteins are the major component of all cells and they play a leading role in, well, just about everything a living organism does.
PHOTO: Claudio Calligaris
As they go about performing their tasks, proteins are folded within the cells that house them. If proteins aren't folded correctly, calamity ensues, often in the form of different types of hereditary diseases, such as cystic fibrosis and hereditary emphysema.
The process surrounding protein folding has largely remained a mystery, but a team of McGill scientists believes it has solved a big part of the puzzle. Their discovery was published in a recent edition of the research journal, Molecular Cell.
The research was a joint effort between the Biotechnology Research Institute and McGill. The key players included the BRI's Joe Schrag and Mirek Cygler, Professor John Bergeron, chair of the Department of Anatomy and Cell Biology, and Professor David Thomas, chair of the Department of Biochemistry. Schrag is an adjunct professor in Bergeron's department, while Cygler is an adjunct professor in Thomas's department.
Bergeron says that the discovery is a first step in filling a large knowledge gap in the biochemistry field.
"Protein folding is one of the challenging problems in molecular biology; we really don't know much about the rules which proteins follow when they fold."
The late researcher Christian Anfinsen won a Nobel Prize for pointing out that there are thousands of ways proteins could fold; yet, in the cell, proteins fold only one way, and in a way that retains biological activity. That one precise way corresponds to the protein's lowest energy level.
"If the energy level is too high, the protein will not perform the way it is supposed to," notes Bergeron.
Researchers have traditionally studied ribonuclease when they investigate protein folding.
"Ribonuclease is a molecule which has at least 105 protein folding pathways which it can pursue, but it only selects one of them for productive folding and that's the only one which leads to biological activity."
While this process would take several hours to duplicate in a test tube, it takes less than five minutes to naturally occur in the cell.
"The cell has evolved what we call molecular chaperones to guide protein folding... When proteins fold, there are sticky parts which the protein tries to mask; the chaperones help them do that."
One of those chaperones is known as the calnexin cycle, which Bergeron and Thomas discovered 10 years ago. The team's more recent discovery provides insight into the mechanism by which it does its vital work.
"Calnexin enables productive protein folding by recruiting protein-folding enzymes and creating a micro-environment that enables the protein to select the correct folding pathways. This environment sequesters the proteins from each other; otherwise, it could not fold properly.
"When proteins fold, they expose sticky surfaces like fly paper," adds Bergeron. "The molecular chaperones provide a sequestered environment to try to ensure that they don't stick to each other. If they did stick, they would fail to fold properly."
Calnexin also acts as a "quality control" mechanism for detecting improperly folded proteins.
"Calnexin coordinates protein folding with changes in the sugar content of a protein -- this was totally unexpected. It recognizes a residue of glucose which, it turns out, is only present on incompletely folded proteins. Calnexin binds to these sugars and distinguishes, by an unexpected mechanism, an incompletely folded protein from one that's misfolded. As a consequence the misfolded protein is then destroyed."
This surprising feature of calnexin is essential because it destroys mutated proteins that can cause disease. Unfortunately, and ironically, that quality control process sometimes works too well. It can lead to disease by going too far and destroying valuable proteins containing only insignificant defects.
"Certain mutant proteins can never fold properly; the calnexin cycle recognizes these proteins as misfolded, through their glucose residues, and then presents them to a degradation machinery. The proteins are destroyed, and can never go to where they are supposed to in the cell."
The team now believes that the destruction of the proteins -- not the mutations that prompt their destruction -- is the cause of a number of diseases, including hereditary emphysema, cystic fibrosis and Charcot-Marie-Tooth syndrome, a hereditary neurological disorder.
"The cystic fibrosis protein, for example, is a fully functional protein; the mutation that is part of the protein is of no consequence. It would be like having a car with a broken tail light; you can still drive it, but the police stop you and decide to overreact and destroy the whole car. Calnexin is like the police, but it doesn't know if the mutation is a serious one or an unimportant one.
"So in the case of these diseases, it is as if the body does not produce proteins with an important function, because it destroys them to get rid of a minor mutation."
The next step will be to figure out how to promote proper protein folding.
"Instead of trying to go after these diseases with gene therapy, which a lot of people have tried, our focus will be on trying to affect the folding of these proteins, get them back on the correct folding track, and bypass the quality control machinery. Then they can access the normal compartment of the cell and fulfill their function."
Bergeron says that determining the structure of calnexin may help scientists understand the elusive code by which proteins fold.
"Since calnexin recognizes just the glucose part, the cell has evolved a mechanism to tag incompletely folded proteins with glucose. That tagging mechanism is where the protein-folding code is being deciphered.
"We are now starting to focus on the enzyme that puts the glucose on an incompletely folded or misfolded protein. We have no idea what the protein folding code is, but that enzyme 'knows' it. By studying this enzyme and other constituents of the calnexin cycle, the hope is that we will be able to break the code."
If the code can be deciphered, it could open the door to a vast array of medical applications.
"Once we've broken that code, we believe that we can use computer modelling to predict, just from the structure of amino acids in a protein, what the final three dimensional structure of the molecule will be [once it has folded].
"This is applicable not just to the hereditary diseases which are a consequence of calnexin's stringent quality control mechanism. It would be applicable to all of biology, because we would be able to predict the structures of all proteins, and be able to target drugs to any protein that we wanted."
Once the code is broken, it could pave the way for drugs that could conceivably attack any and all diseases.
"There are tens of thousands of proteins in each cell; solving the three-dimensional structure of just one of them experimentally, through trial and error, can take years. But if we knew the rules, and could calculate the structure of each through computer modelling, we could focus on those that cause disease, and target drugs to them."
The team has just received a grant from Genome Canada to extend its research.
"They are funding us to identify a large number of different molecules involved in basic functions of the cell."
This massive work will be conducted through a research network that Bergeron directs, the Montreal Proteomics Centre. The network will be based in the new Montreal Genome and Proteome Building, which is being built next to the Strathcona Anatomy and Dentistry Building.