In her new Nature Methods paper, 'Combining Native and ‘omics’ mass spectrometry to identify endogenous ligands bound to membrane proteins'
Carol Robinson and her team present a new way to perform mass spectrometry experiments. It's a way to capture all the associates of protein assemblies, all in one experiment. She calls her new method 'nativeomics,' which pulls together 'omics such as proteomics, lipidomics and metabolomics, with native mass spectrometry.
Here is the May Author File, which is a profile of her, and here is my podcast with and about her. A transcript of the podcast can be found below.
Note: These podcasts are produced to be heard. If you can, please tune in. Transcripts are generated using speech recognition software and there’s a human editor. But a transcript may contain errors. Please check the corresponding audio before quoting.
Transcript of podcast : Conversations with scientists: Carol Robinson
Hi. This is ‘conversations with scientists,’ I’m Vivien Marx.
I trained as a chemist. I love biology and I'm passionate about mass spec.
Vivien: That’s Professor Dame Carol Robinson of the University of Oxford.
Carol Robinson 0:19
We always think everything that we've discovered is just this small moment of time but it's been here a long time, mass spectrometry. It's just changed unbelievably. My supervisor always used to say, well, you know, you should leave mass spec, there'll be no new discoveries. Of course, you never know what's around the corner, because after he said that, we had to electrospray, whole proteins. He was trying to persuade me to go to NMR at the time. Oh, no, I really like mass spec, why would I do that.
Vivien: Carol Robinson, like many scientists these days, is now working from home. For now, due to COVID-19, she has had to shutter her lab.
Carol Robinson 1:00
To me, it's sort of heartbreaking, it's my passion, and my joy. But I do understand that there are people who are really seriously ill. And I don't want to put my people or anybody I know into a similar situation. I wouldn't feel happy about doing that. Yeah, we closed the lab and we have our virtual meetings. And it's a bit frustrating tho, because really would like to work on the virus. With everything we have at our disposal to try to find and repurpose some drugs that are already out there. But to do that puts people at risk so we can’t do that at the moment.
Vivien: Beside her position in Oxford’s chemistry department as Doctor Lee’s Professor of Chemistry, Carol Robinson is president of the Royal Society of Chemistry. She was the first female chemistry professor at Oxford. She was previously the first female professor of chemistry at the University of Cambridge. And she was appointed Dame Commander of the Order of the British Empire. Her work, as she says, is her joy.
Lately she has donated some of her equipment to local medical facilities. Some members of her lab are volunteering to help out in the battle against COVID-19.
In the now darkened Robinson lab at the University of Oxford sits a prototype of the new Tribrid mass spectrometer, with lots of bells and whistles. The team worked with Thermo Fisher to develop the instrument, that is called the Orbitrap Eclipse Tribrid Mass Spectrometer. Right up until the last moment before the lab closed in March of 2020, her team was getting all the data they could off of this and the other instruments.
The new instrument, and what it can do, is what she and her team present in a paper in Nature Methods. The instrument offers a way to do a different kind of experiment. It’s one that addresses the fact that in the cell proteins tend to not practice social distancing. Protein complexes have a whole host of associates.
Carol Robinson 3:01
I guess the way I look at it is that a lot of big proteins in assemblies -- Stop me if it doesn't make sense--Proteins and assembly sort of join together and we can capture that joining together in that communication. But it was always hard to simultaneously find out what small molecule is kind of regulating them or changing them in some way. So now we can do the same in one experiment rather than saying, OK, we have this complex. Now we need to extract the small molecules and do them on a different platform and separately, because that's the way we've always done it to take them off and do HPLC or something like that. But now we can say, well, let's keep it all together and let's dissociate it, or break it up inside this mass spectrometer. This method you take the assembly and you see the assembly and then you see what small things are actually attached to it. By releasing them in the gas phase.
Vivien: The instrument makes it possible for labs to determine, all at once, which small molecule associates shape an assembly’s behavior. To help hone the instrument, which has been three years in the making, two people from the Robinson lab decamped to Thermo Fisher’s lab. The two people are Joseph Gault and Idlir Liko.
Carol Robinson 4:21
They’ve were both were in the lab for a long time. They're stunningly capable. And actually one of the things was that they changed the focus to be not just focusing on the complex as a whole, but also to turn the attention towards the ligands, the small mass end at the same time. And that was the kind of transformational step.
Vivien: The team picked some particular proteins to show the types of experiments labs can do with this new instrument. For example they chose the E.coli outer membrane porin F, which controls access to bacterial cells.
Carol Robinson 5:00
The outer membrane protein F: we chose that because it does three different things that binds to an antibiotic, a lipid and a drug. And we wanted to show that this particular platform could do all three of those without us having to tell it what to do. It would discover the lipid, it would discover the drug, and it would discover in a sort of semi-automated way with databases.
Vivien: Looking at multiple things at the same time can be valuable in many experiments. When it comes to the virus SARS-CoV-2 that causes COVID-19 for example,
many groups are using electron microscopy and cryo-electron microscopy.
Carol Robinson 5:45
You could see the virus spike by EM. So you always have to be a bit mindful that you don't want to do something less well than something that can do that. You couldn't necessarily see the lipids that are binding to the receptor or any other small molecules that might be changing the conformation of the receptor, for example. So we don't want to compete with EM for sure because we can't but we do want to see small molecules involved in these assemblies that are sometimes invisible. Often in cryo-EM, cryo-EM is amazing. In cryo-EM you see beautiful structures, but sometimes the small molecules, it's sometimes hard to pick out exactly what they are because the resolution of the small molecule is often not quite good enough, for it's not pure enough, there might be multiple small molecules binding, so it's hard to see exactly what's there.
Vivien: Often enough it’s not known which associates a protein complex has.
Carol Robinson 6:47
Here, we’re saying maybe this assembly binds to a particular regulator, a co-factor, but we don’t know what it is. We haven’t added anything, we’re going to find it de novo if you like. We didn’t add it, it comes along with the complex and then we find out what it is and then it helps us to work out what it might be doing. So, for example, many complexes, we don't really know what their role is in the body, but if we find a small molecule, for example, an amino acid or a peptide or some sort of like dopamine or something like that, then we would say, oh, but that could be the dopamine transporter, for example, or some other such activity.
Vivien: With this mass spec approach, what was once a task that required multiple experiments is now one. And it brings together a number of aspects that have driven Carol Robinson’s work. She began her career, as she says, working on small things and moved on to protein complexes. Now she can look at both simultaneously. At age 16, she tested out of school, joined Pfizer as a lab technician and felt immediately at home with a mass spectrometer. She studied chemistry part time, left Pfizer and obtained her master’s degree, and continued at Cambridge, where she completed her PhD in the lab of Dudley Williams. She took an eight-year child-rearing break and returned to science as a postdoctoral fellow at Oxford, followed by her appointment at Cambridge and then returned to Oxford. In science, she believes it’s important to stay imaginative.
Carol Robinson 8:35
One thing I think is important in science is imagination. I think we all get a bit kind of constrained. And somebody once said to me, oh, you know, if you hadn't had a career break, you would never have tried those experiments because we'd all worked out what the limits would be. And I just thought, well actually I'm glad I didn't know that, because if you knew limits, then you kind of work to that, whereas if you don’t know anything and you just kind of use your imagination, you can go beyond what people think are the limits. I think it's not to be too constrained, really?
Vivien When she mentors people, she encourages them to keep going even when it doesn’t seem like things will work.
Carol Robinson 9:22
Sometimes they come to me and say you know that experiment, it won't work. You know. And I just think. You haven't actually tried it, have you, and you've already decided it won't work. So probably it won't work. But if you go in thinking it might work, then there's often a chance. And some of my favorite, we don't have favorites, but some of the best postdocs and students, the ones who said it's not working yet. Because the yet word is so important. I think that there'll be a way we'll get it to work.
Vivien: In the Age of COVID-19, meetings and social gatherings have to happen online for the most part. But one could also have imaginary meetings. I asked Carol Robinson whom she might invite for an imaginary online tea and an imaginary virtual tour of the lab. One guest she mentioned is Marie Curie.
Carol Robinson 10:12
I kind of like her because I think, you know, she was ahead of her time in terms of women in science. So that's why I like her. But I guess I'd invite J.J. Thompson because he separated isotopes. And now I'd like to say, look what you started.
Vivien That was Conversations with Scientists, today with Dr Carol Robinson, Dame Commander of the Order of the British Empire and professor at the University of Oxford. I’m Vivien Marx, thanks for listening.