While we may be in the midst of the genomic era, being able to sequence genomes at speeds only rivaled by the molecular machinery used to create the genetic information, understanding the actions of protein molecules that execute the tasks encoded by our DNA blueprint is paramount to unlocking how cells behave—and often at times malfunction.
Now, researchers from the Salk Institute have developed a new set of tools that should afford scientists a better understanding of elusive steps involved in the biochemistry behind protein formation. The scientists created a pair of monoclonal antibodies that allowed them to map critical chemical tags, called phosphates, that bond to amino acids in the final stages of creating a protein.
“We know that 9 out of the 20 amino acids can be phosphorylated, but we know very little about most of them because they're so hard to study,” explained senior author Tony Hunter, Ph.D., professor in the Molecular and Cell Biology Laboratory and director of the Salk Institute Cancer Center.
The findings from this study were published recently in Cell through an article entitled “Monoclonal 1- and 3-Phosphohistidine Antibodies: New Tools to Study Histidine Phosphorylation.”
In the process of protein formation, the cell’s molecular machinery first hooks amino acids together in tandem, creating a long strand that bends and folds as it lengths. During the protein production process enzymes swarm the newly synthesized protein strand in order to make the much needed final tweaks to the protein structure by either trimming the structure or adding chemical tags, such as phosphates, to specific amino acids. The phosphorylation of individual amino acids helps shape the final function for the protein and until now, pinpointing exactly where (and why) all the phosphates were added has been difficult.
Typically, when a phosphate group is added to serine, threonine, or tyrosine it forms a strong chemical and is fairly easy to locate within the cell. However, with the remaining 6 amino acids that are able to be phosphorylated, weak and transient bonds loosely attach the phosphate group to the amino acids, making detection very problematic. In particular, phosphorylation of the amino acid histidine has been notoriously difficult to detect.
“With those strong phosphorylation events, you can label cells, isolate proteins, and analyze the proteins in various ways to find out where the phosphates are,” said Dr. Hunter. “You can't do that with phosphohistidine because it's so unstable it falls apart as you're trying to isolate the proteins.”
Dr. Hunter and his team used a chemical derivative of phosphate, called phosphonate, which allowed them to engineer a much tighter bond on the two spots of the histidine amino acid that can be phosphorylated. Then the researchers developed antibodies that specifically recognized these stable phosphohistidine analogs, but also detect authentic phosphohistidine in proteins.
To test these new tools, the team added their phosphohistidine antibodies to a collection of different mammalian cells grown on slides and observed where in the cell the antibodies bound, indicative of the areas within cells that have high levels of proteins with phosphohistidines.
“The thing that surprised us most is that when we stained the cells with the new antibodies, we saw discrete areas within the cells that had high levels of histidine phosphorylation, particularly when they were undergoing mitosis, the stage at which cells divide into two daughter cells,” Dr. Hunter stated.”
The Salk investigators were excited by the findings from their new antibodies and are continuing to test their reagents with the hope of revealing new hotspots of protein phosphorylation within the cell. Moreover, Dr. Hunter believes the antibodies will be useful for many researchers and explained that new method is “fairly easy for any lab to use, as it doesn't require a special instrument or anything, so I think it may be fairly quickly adopted.”