by Mitchell Zimmer
Mass spectrometry has been used to analyse amino acids and proteins since 1958. While many advances over this past half century have added more techniques to use with this method, it wasn’t until recently that Lars Konermann found a way to see how proteins change through time into their active conformations. Konermann’s advance has now been recognized by two awards from different organizations, the Ken Standing Award from Enabling Technologies Symposium (ETP) Inc., and the Fred P. Lossing Award from the Canadian Society for Mass Spectrometry.
The Fred P. Lossing Award is given annually to a distinguished Canadian mass spectrometrist.The Ken Standing Award honors a scientist who has made a significant contribution to technology development in support of the life sciences.
The Standing award recognizes tools that enable biologists to address certain problems. “In my case we did some work to figure out how we can monitor how proteins fold,” says Konermann. “This is a very important biological process and so this is something that we worked on a lot. We also applied some of the methods that we developed to look at proteins in aggregates that are implicated in Alzheimer’s disease.” One of the other problems that Konermann pursues is how proteins with many individual subunits, such as microtubules and flagella, come together. “We can see how this works and what the intermediates are along the way.”
Protein systems like these spontaneously self assemble, and Konermann monitors these processes by analyzing samples taken at many different time points, ranging from milliseconds to hours. He then sprays each sample into the mass spectrometer. “In the simplest case, just by doing a mass measurement, we can see how many things are assembled,” he says. “You can see when the mass has doubled, the next thing we have four mass units and so now it’s four, it goes from there.” In the case of heme groups found in the protein hemoglobin that contain iron or other proteins that contain metals, he factors those elements in. “Everything contributes a little bit to the mass, you can just work out what the composition is if you know what the mass is.”
The more recent work in Konermann’s lab involves monitoring how proteins fold. “We developed techniques that allow us to monitor these conformational changes almost at the atomic level. We do that by either using hydrogen–deuterium exchange or covalent labeling techniques. The basic idea behind these measurements is that protein regions that are unfolded and exposed to the solvent react very rapidly with chemical labels that you put into the protein’s environment. Each of these attached labelsresults in a mass shift that we can measure.” If the protein being studied is folded up, then there are fewer places exposed to the solvent. “Once they are buried inside they wouldn’t react because they are no longer accessible. We can then, after the fact, take the protein and chop it into little pieces and just weigh the individual pieces.” In this way Konermann can tell how much of the label is attached to these little pieces, and based on that information his group can then build models of what they think might the intermediates of these structures might look like in solution.
The method to determine the folding of proteins pioneered by Konermann has advantages over other procedures such as X-ray techniques which reveal the structure of a protein in a crystal “which is not necessarily the same as the structure of a protein in solution,” says Konermann. “Using mass spectrometry and those labeling techniques, we can probe the solution based structure directly.” The same can’t always be said for X-ray crystallography. Konermann says that proteins “can sometimes modify their shape so that they fit better together in the crystal, but if they were separate they would have different structures.” Konermann adds, “Right now, with one of my students, we just worked on a bacterial protein that has a very interesting function. When antibiotics bind to this protein it changes its conformation, but we don’t know exactly how this happens because the protein structures are strongly distorted in the exing crystallography data.”
The hydrogen-deuterium exchange labeling and covalent labeling had been partially developed in Konermann’s lab while the application of those techniques to look at things as a function of time in rapid timescales down to milliseconds was the novel element. “We look at very, very fast processes and we developed several rapid mixing techniques which we then couple with mass spectrometry. This allows us to look at these processes in a time-resolved fashion.”
Now that Konermann has established this technique, he would like to extend its range. “Currently our technology brings us down to say, maybe ten milliseconds. That is a speed barrier for us, but there are a lot of things that happen on much shorter time scales so currently we’re trying to push into the microsecond range. There are so many questions out there such as: How are the conformational dynamics of a protein linked to function? How is it that misfolded proteins aggregate and cause disease? How is it that a certain protein sequences results in a certain folded structure and when you change one amino acid, it doesn’t fold properly and does other weird things instead? Those are some of the big questions that we try to answer. It’s fundamental research, but at the same time it’s very much tied into medical aspects such as disease mechanisms. There is always the need for new technologies that allow us to address the next level of bioanalytical and biophysical questions.”