Cryo-Talk featuring Rob Kirchdoerfer (University of Wisconsin-Madison)

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Eva Amsen: hi! And welcome to cryo-talk. I'm ava Amson, and i'm here today, with Robert Curse, dorifer, our first guest of season. 2

Eva Amsen: Rob, is assistant professor in the department of Biochemistry and the Institute for Molecular Virology at the University of wisconsin- Madison.

Eva Amsen: His research group has been using cryo em to study viral protein. So we'll hear a bit more about that today.

Eva Amsen: Rob. How are you?

Eva Amsen: I'm great. How are you this afternoon?

ROBERT N KIRCHDOERFER: Yeah. So I did my bachelor's degree here at the University of Wisconsin, Madison. I got a major in genetics in biochemistry, and I was doing undergraduate research studying protein folding

ROBERT N KIRCHDOERFER: And for graduate school, I decided I really wanted a higher resolution view of how the world worked. I really wanted to see how proteins interacted with one another. And so I decided that I was going to do structural biology for graduate school. So I went to the Scripts Research Institute in the Hoya, California, and I did my Phd. With Ian Wilson with the goal of looking at an influenza polymerase complex with crystallography.

ROBERT N KIRCHDOERFER: We never did solve a structure of an influenza polymerase with crystallography. But we did learn a lot about other interesting pathogenic systems, and we actually wound up collaborating with some really great electron microscopes at Scripts to do electron microscopy of the influenza polymerase. From there I actually stated scripts for my postdoc for for both of my postdocs. I did my first postdoc with Erica Olmann Sapphire doing crystallography of Ebola virus proteins.

ROBERT N KIRCHDOERFER: And then, you know, we we came across a problem in Ebola virus that we couldn't solve with crystallography. And so I started collaborating with Andrew Ward, who worked across the street also at Scripts to learn cryoelectron microscopy to study these Ebola virus proteins, and then kind of transition from there into studying Coronavirus protein. So I've been at Uw now for about 3 and a half years, starting up my own lab, and we've got a a pretty great group growing up

Eva Amsen: great.

Eva Amsen: So yeah, you you. You mentioned Coronavirus, and I think you started in Madison in 2,019. Is that right? So so where you You were looking at Coronavirus? And suddenly they became very irrelevant. Is that what happened?

ROBERT N KIRCHDOERFER: I have. I have noticed a reoccurring theme in my career that I tend to work on viruses that after I start working on them seem to cause pandemics. So I was working on influenza in 2,009 before swine flu

ROBERT N KIRCHDOERFER: hit, and I was working on Ebola virus in 2,014 when we had the West African Boulevard outbreak, so

ROBERT N KIRCHDOERFER: I I I tend to pick viruses that are very medically relevant. And have that impact. I don't ever look for pandemic. Maybe if you change your topic, let everyone know well ahead of time. I've been asked by family members to let them know if I ever start working on a new virus for that, for that very reason.

Eva Amsen: So so how have the last few years been for you working on Coronavirus structures?

ROBERT N KIRCHDOERFER: It's Really, it's been really busy. So it's been really great for the field in terms of the things that we learned, the advances that get made. We have a lot more technologies that are being used to address these problems from from with lots of different approaches. In terms of my lab this is presented a lot of challenges, because my lab is very young and very small, and with lots of international attention on Coronaviruses we have had to pivot

ROBERT N KIRCHDOERFER: repeatedly to find areas that we can contribute to the field where I don't have to worry about. You know, a young student being scooped 6 months into their project. So we have been kind of adapting that way, but it's it's exciting times, and I think that we're really drawing on a lot of the the international research that has come out of a research on COVID-19.

Eva Amsen: Hmm. Yeah, that's I guess it has. Its throwbacks to have everyone else in the world working on the same topic at the same time.

Eva Amsen: Yeah, you you mentioned when you started using, and how are you using it at the moment? Is there any specific application that you like you're focusing on. Yeah, we really do single particle cryoelectron microscopy. So one of the things that my lab specializes in is is preparing

ROBERT N KIRCHDOERFER: really highly purified protein samples, and we reconstitute our complexes in vitro, and then really trying to get at

ROBERT N KIRCHDOERFER: how those complexes interact with one another. Right? So how does this protein talk to that one? And cryoem has been really great for that? Because not only can we get the structural information, but we also get.

ROBERT N KIRCHDOERFER: or rather get around some of these issues of heterogeneity. And so with crystallography, you want that that rock solid sample that's going to crystallize. But in cryoem. You can look at flexible things. You can look at sub stoichiometric complexes, and on slightly unassembled complexes.

ROBERT N KIRCHDOERFER: And so it's really amenable for us looking at some of these more dynamic machines.

Eva Amsen: Great: yeah. And and what makes it so useful for viable proteins? I know you mentioned earlier that it's kind of like the resolution and the detail.

ROBERT N KIRCHDOERFER: Yeah. So what I love about any structural biology is really being able to see one protein interact with another. And for for me. The the best part of structural biology is when you get that first map, and you can now see your protein in the map. You can actually see. Oh, this amino acid context, that amino acid.

ROBERT N KIRCHDOERFER: you know I I love looking at Rna in electron density. I think that it's beautiful.

ROBERT N KIRCHDOERFER: So so yes, I I think that we can. We can use cryoelectron microscope, for you know, a really a a lot of things with with viral proteins. But I think it's a much broader technique for really looking at any sort of purified biological sample that we we want to look at. And of course the the field is expanding, so maybe we don't always need to purify as well as we used to.

Eva Amsen: And you were working on on Ebola before. Is there? Are you planning on going back to that like. Has it all just been Coronavirus these last few years? Because that's what everyone needed to know about at the moment. Or

ROBERT N KIRCHDOERFER: this is the plan for this change. When I, when I started up my lab, was to go Coronas and stick with Coronavirus to to kind of maintain a lab focus.

ROBERT N KIRCHDOERFER: We do look to kind of expand to some other viruses, but I think we will probably stay in the the positive sense Rna viruses. So this is going to be other other viruses that have similar genome architectures to Coronas.

ROBERT N KIRCHDOERFER: and part of that is is just to make sure that we, you know, keep some common themes in lab and and kind of have a more cohesive scientific environment.

Eva Amsen: So so, what are some other viruses that would fall in that category.

ROBERT N KIRCHDOERFER: Well, so we usually think of coronaviruses, As you know, we talk about the Coronavirus, but Coronaviruses are actually a very large family of viruses. And so one of the themes in our lab is to really look more broadly across the Coronavirus family at different species of Coronavirus.

ROBERT N KIRCHDOERFER: to kind of get a sense of what is conserved. What are the general themes that evolution has maintained across this this broader family?

ROBERT N KIRCHDOERFER: We're also working with a a number of groups. We're we're part of a a consortium. This has been funded by Nih to identify antiviral drugs, and so this is a consortium being run out of U. N. C. Chapel Hill, with Ralph Eric to look at a number of positive and negative sense, Rna viruses.

ROBERT N KIRCHDOERFER: and in particular trying to figure out how particular small molecule drugs can can impact the activity of a viral polymerases. And so that's another way that we've kind of expanded our our repertoire of viruses.

Eva Amsen: Yeah. And I guess anything you learn about one virus that also tells you a bit more about a related virus as well it does. I I think that that's a major power of structural biology and biochemistry is being able to draw parallels and and even contrasts one for solving problems. You know I I have this

ROBERT N KIRCHDOERFER: trick that worked for this protein. I can probably apply it again for this other protein. But then also for biological themes, as well in terms of mechanism and interaction.

Eva Amsen: and just going back quickly to to cry, Oem! Is there anything? What? Where do you see? Cryo am going in the future? What do you hope it will be able to do?

ROBERT N KIRCHDOERFER: Well, you know, I think Cryoem is well on its way to really looking at more biological structures in situ, you know, really looking at more cellular structures, at higher resolution, with with better annotation, with higher, with

ROBERT N KIRCHDOERFER: more sorting of of the available heterogeneity. You know right now. I think this is mostly limited to relatively large complexes, like ribosomes. But I would love to see that applied to smaller and smaller protein complexes

ROBERT N KIRCHDOERFER: There, there's gonna be need to be some technical advancements for that. But I I really think that we're we're on on our way to to getting there.

Eva Amsen: Yeah, yeah, that would be interesting to see see everything you see to.

Eva Amsen: So the changing tactics a little bit. Let's talk about, not work. What do you do when you're not in the lab and not looking at protein structures.

ROBERT N KIRCHDOERFER: Oh, I I I i'm a gym rat. I go to the gym. I like to swim is is one of my sports. Otherwise I really just like to spend time outdoors, and that could be walking through the woods or sitting on a boat.

ROBERT N KIRCHDOERFER: Just that kind of quiet outdoor time is really what I I look forward to

Eva Amsen: have You Have you had a chance to go outdoors a lot lately

ROBERT N KIRCHDOERFER: in Wisconsin, and it's really cold. Winter Winter is not my season. I I look forward to spring, spring, and fall, so I still go on walks pretty regularly. But you you kind of bundled up, and there's not a lot of you know, wildlife to look at this time of year.

Eva Amsen: Yeah, I just went on a very cold walls myself this morning, and it's not even that cold in London, but it was just just about freezing, and it's the faster you walk, the warmer you get, but still

Eva Amsen: so I've got a a a few quickfire questions so you could just answer them really quickly. The first one. Do you enjoy traveling?

Eva Amsen: I am. I am not a a big traveler. I am a bit of a home body. Traveling kind of stresses me out. But I love being other places, so I guess I I have a mixed feelings about traveling. The process and the destination are not the same. Yeah, do you have any favorite places where you've been?

ROBERT N KIRCHDOERFER: I I I love San Diego, which is where I did my my Phd. Work. I've not been back since I left when I was doing my postdoc because of of Covid, and i'd love to go back and hang out. I think that San Diego has some of the nice micro breweries in the country.

Eva Amsen: That's a reason to go back.

Eva Amsen: Do you enjoy cooking?

ROBERT N KIRCHDOERFER: I do. I don't get to cook every night, so. Most of my cooking projects are kind of weekend cooking projects, and they tend to be a bit bigger, so it's. It's like food prep for the week. But recently I've been making my own pasta, and I also make my own yogurt

Eva Amsen: nice. Yeah, I was gonna ask if you had any recommendations with past the self-interesting.

Eva Amsen: What about reading? Do you like to read?

ROBERT N KIRCHDOERFER: I do like to read, so I obviously read a lot at work

ROBERT N KIRCHDOERFER: which is all non-fiction. But when I get home I really like to read fiction, and especially fantasy. And so one book that I read this past year is, it's called a Wizards Guide to defensive baking, which is a slightly humorous touch of magic kind of kind of story, and I it's it's lighter reading, but I really enjoyed it.

Eva Amsen: It sounds fun from the title. I might read that, too. And what about the the big and small screen? Do you like film or TV?

ROBERT N KIRCHDOERFER: I generally do. I've not been to a lot of movies in the last couple of years, and I all of my TV is now switched to streaming services. So you know I I kind of cruise, Netflix, to see what's new and what's interesting right now. I'm working my way through Netflix Wednesday, which is kind of dark and fun, but also kind of creepy. So

Eva Amsen: yeah, I finished watching that not too long ago. That was fun.

And do you listen to music?

ROBERT N KIRCHDOERFER: I do. I like a lot of different types of music. I i'm a big fan of kind of the Indie Rock, the modest mouse cage, the elephant sort of things. But then I mix in like dance music from Lady Gaga and cash

ROBERT N KIRCHDOERFER: things like that never. And then i'll turn it around, and i'll put on some instrumental folk music for for a change. So I it all kind of depends on on what moved by net.

Eva Amsen: So there is there music playing in your lab, or does everyone just have their own headphones on? They all wear headphones? Because I I don't let them play music in lab. Yeah, I think, when when back in the day when I was in the lab, we used to have the radio on this

Eva Amsen: and this kind of discuss what we were listening to while working with. It was a bit distracting sometimes.

Eva Amsen: And this is a question I love to ask people If you weren't a scientist, what would you be?

ROBERT N KIRCHDOERFER: Oh, you know I've wanted to be a scientist for such a long time that i'm i'm gonna struggle to answer that.

ROBERT N KIRCHDOERFER: I I think I would. I would need to be in a career that I would be helping people, and so that that could be something like a teacher. But it also could be something like a doctor, just because that's that's where I get my My fulfillment from work

ROBERT N KIRCHDOERFER: is that even you know, as a researcher, i'm doing it making incremental advances that could someday help someone. But I still feel like I need need to contribute like that. Yeah, I feel like teacher and doctor, I kind of like science adjacent.

ROBERT N KIRCHDOERFER: So that's fun. So you you knew, even when you were a kid, that you wanted to be something related to science. One day, yeah, I I went through a number of different scientific paths as like a fourth grader.

ROBERT N KIRCHDOERFER: So yeah, it was gonna be. I was gonna be a marine biologist. And and I decided I was gonna do genetics because I watched Jurassic Park and darn it, let's let's you know. Bring back dinosaurs.

ROBERT N KIRCHDOERFER: and then I went to college, and I fell in love with biochemistry. So it's it's kind of

Eva Amsen: wandered a bit. But it's it's always kind of been figuring out how the natural world works and what we can, what we can really do with it.

Eva Amsen: Yeah. I also ended up in biochemistry eventually with I. I didn't really know that it existed until I started an undergrad, because you don't really in in high school. It's just this is chemistry. This is biology. Nobody tells you that there's an in between it's like, oh, I can do both. It's

Eva Amsen: Yeah. So

Eva Amsen: the and the other question I really love to hear. The answer to is, if you have any advice for researchers who are just starting out their career.

ROBERT N KIRCHDOERFER: I have tons of advice. So the thing, yeah. So. So the thing I always try to tell students when they are making choices about what lab they're going to join, and and how they're going to do their Phds is to find something that they're really passionate about. And just be really bold.

ROBERT N KIRCHDOERFER: So you know there's a lot of apprehension like, oh, can I make it in this field, Can I? Can I get that next big experiment to work?

ROBERT N KIRCHDOERFER: And I I think that if you really just have something you're excited about, and that you can bring your passion, your resilience to that

ROBERT N KIRCHDOERFER: as as long as you are willing to take that step and actually try that the rest all kind of fall into place. And so, you know, everybody wants a a 5 year plan and a 10 Year Plan about what they're gonna do with their lives, and inevitably all of those plans change. But I think that as long as you're pursuing something you're excited about, and you are willing to take those leaps and really chase those dreams that even if you don't wind up with the dream, you thought you were gonna have. You're still gonna wind up pretty happy. So

Eva Amsen: that's good advice. Yeah, yeah, I think students are also a little bit scared about, you know, if they take a big risk. What if it doesn't work? And I don't get results, and I can't write my thesis. But

ROBERT N KIRCHDOERFER: you can graduate with negative results. Things People just don't quite realize that you absolutely can. And I mean, if if you're doing science, if you're if you're testing hypotheses, then it's it's

ROBERT N KIRCHDOERFER: quite possible. Your hypothesis was wrong, but that's data, too. So so I mean, I wouldn't discard negative data because it's negative. You know you. You showed something. You prove something

Eva Amsen: absolutely

Eva Amsen: well. I think that brings us to the end of the episode. So thank you very much, Rob, and thanks everyone else for listening to or watching cryo talk today.

Creators and Guests

Robert Kirchdoerfer
Robert Kirchdoerfer
Kirchdoerfer Laboratory at University of Wisconsin-Madison, Department of Biochemistry
Cryo-Talk featuring Rob Kirchdoerfer (University of Wisconsin-Madison)