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   Nerdy Jobs S1E1, Exploring the Magic of Protein Crystallization

   Nerdy Jobs season 1, episode 1, 11:53. Dr. Raven grows protein crystals with structural biologist Dr. Sarah Bowman at the Hauptman-Woodward Medical Research Institute. The video is unlisted on YouTube. The link works, but the video does not show up in YouTube search.

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   Transcript

   From the episode transcript. Times come from the matching YouTube captions.

   [0:00] (upbeat soul music)

   [0:14] They say that diamonds are a girl’s best friend, but crystals are everybody’s best friend today. Because today, we are at the Hauptman-Woodward Medical Research Institute working with Dr. Sarah Bowman and learning all about crystallography. And you know, we never do science alone and that’s why I found a perfect partner for today. Say hello to Sydney.

   [0:40] How... Where did you come from? How long have you been back there? Is it... Girl, is this Nerdy Jobs?

   [0:48] Yes, you’re on Nerdy Jobs!

   [0:50] Girl, I’m on Nerdy Jobs!

   [0:52] You’re on Nerdy Jobs. Girl, you wanna be my co-host?

   [0:54] Yes!

   [0:55] Let’s go!

   [0:56] (upbeat music)

   [1:01] Hi, Dr. Bowman.

   [1:02] Thank you so much for coming, Dr. Baxter. I’m thrilled to have you here and thrilled to have you as well, soon-to-be Dr. Sydney. My name’s Dr. Sarah Bowman. I work here at Hauptman-Woodward Medical Research Institute and I’m a structural biologist. I do macro-molecular X-ray crystallography. So we’re gonna talk about crystals.

   [1:21] [Raven] Okay, so Dr. Bowman is kind of a big deal. She’s the director of the National Crystallization Center that opened in 2000, and since then, they’ve set up over 25 million crystallization experiments on more than 18,000 biomolecules, advancing medical research to almost 2,000 labs around the world.

   [1:39] Why is it important that we learn about crystallography today and what is the bigger picture about all of this?

   [1:44] When we’re thinking about structural biology, what we’re really looking at is what do proteins look like? And so, proteins are the different molecular machines in our bodies that kind of make everything happen. So you can imagine that if we wanna figure out how to design a vaccine and how to design drugs to treat diseases, we need to know what these pieces and parts actually look like. So, structural biology is really the kind of way that we look at these three-dimensional structures to be able to understand what the three-dimensional shapes of these proteins look like. To do X-ray crystallography, what we have to do is take our protein sample, coax it into being in a crystal form, and then take that crystal and shoot X-rays at it to collect diffraction patterns, and then we use a bunch of math and computation to actually solve the structures to be able to look at what these things look like.

   [2:40] Okay, so we’re making non-edible crystals in the lab.

   [2:43] [Sarah] Non-edible crystals being made in the lab.

   [2:47] But safety first! We’ve got our close-toed shoes, our lab coats, our goggles, and of course I had to ice Sydney out (laughs). Who said scientists can’t have fun?

   [3:01] Great, so what we’re gonna do is crystallize some of this lysozyme protein that we’ve already got prep-prepared. So the first thing we need to do is put some into one of these little tubes. What we need is 150 microliters. Wanna do that, Raven?

   [3:13] Yeah, let’s do it!

   [3:14] Cool.

   [3:15] [Raven] What we’re doing is taking a small amount of lysozyme protein, putting it into a tube, putting that tube in a machine that’s then gonna put that small amount into a 96-well plate where we’ll grow crystals in.

   [3:26] So we’ve got everything already all set up here. So it’s gonna wash the syringes, it’s gonna wash the special syringe that the protein goes into, and then it’s gonna pull stuff out of here, deliver it into the 96-well tray, and then it’s gonna pull the protein out and deliver that in really tiny volumes, which is why we use robots. So, let’s go ahead and use that. So we’re just washing with water right now. So, and what this is doing is putting water up and pushing it back down just to make sure that it’s nice and clean for getting the protein in there.

   [4:00] Okay.

   [4:01] So. This is where the protein’s being dispensed, into each of those little drops.

   [4:07] [Raven] The drop is tiny.

   [4:13] [Sydney] My eyes can’t see that.

   [4:14] You may have to wait ’til we look at it under the microscope, or in the imager, to be able to really see it.

   [4:19] That is incredible.

   [4:21] But you’ll be able to see it’s really there. It’s really dispensing stuff out.

   [4:24] I didn’t really see. It looks like a tiny, little sneeze from this angle.

   [4:28] (laughs) Essentially, everything in these pipets is gonna come out with a lot of precision and every time you actually put your syringes down and dispense into something where you’re touching other things, you may kind of get contamination or interaction between things so that fact that we are able to kind of essentially dispense stuff down and then kind of shoot the protein out, it means that you’re never gonna have contamination.

   [4:56] Okay so robots.

   [4:57] Robots.

   [4:58] Not taking our jobs, but making our jobs easier.

   [5:00] Making our jobs better.

   [5:01] Better. A protein’s shape is important because its shape determines its function, but how do proteins get their shapes?

   [5:10] If you think about it, a protein is a set of different amino acids that are all formed together, and if we just thought about it as one long, linear chain, they’d just be not shaped at all, but in reality, as the protein is actually coming off of the ribosome it is folding into a three-dimensional compact shape and so, how exactly the protein folding kind of occurs is a question that people still are researching, but the actual shape of proteins, that’s really what we do as structural biologists is try to understand how the different shapes come together for the different proteins and for the different biomolecules.

   [5:53] [Raven] And our protein crystals are already growing.

   [5:56] So we’re gonna just look really quickly, and in fact, you can see that in the one we just set up, we’ve got a couple.

   [6:03] Those are pretty!

   [6:05] Those are pretty, aren’t they?

   [6:06] I love the colors! I see pink, there’s blue.

   [6:08] [Sarah] There’s blue, there’s a little yellow.

   [6:10] [Sydney] There’s a little purple moment over there in the corner.

   [6:12] Yeah. So these are crystals that are forming off the protein that we literally just set up. This one’s a smaller drop, and maybe has some crystals that’ll show up like maybe tomorrow.

   [6:22] So what are those darker circles?

   [6:24] In here?

   [6:25] Yeah.

   [6:26] Those are precipitates. So this is the protein has precipitated out. Now here’s one of the really interesting things. It has precipitated out, but it is crystallizing out of the precipitate. This is an ugly crystal, okay? So this tray has been in since yesterday and so there’s some...

   [6:48] Wow!

   [6:49] That form really pretty crystals.

   [6:51] (Raven and Sydney exclaim)

   [6:52] But it took a while. What you’re seeing at the bottom here is actually a time course. So this is maybe after about four hours, you’ve got these little dots, and then you’re gonna watch those dots just kind of pop in.

   [7:04] [Sydney] Is there any information that you can get from these timelapse?

   [7:06] So in some experiments, you need super tiny crystals, and so for those, you could actually stop the crystallization process right here by kind of adding some additional stuff. There’s some that you need massive crystals for and so for those, you wanna just kind of keep letting them go, and so there’s just, it’s kind of dependent on what kind of experiment you’re doing and what you need to do, and sometimes you form crystals and then you go back and you’re like okay, these are pretty good, but I’m gonna optimize around them and stuff like that.

   [7:35] Why would we wanna know what the shape of those proteins inside the crystals are?

   [7:39] Okay, so one example that we can think about. Hemoglobin. Hemoglobin is what makes your blood red. It’s got a haem cofactor in it, which has iron, and that particular protein is what binds oxygen and it circulates through your body to kind of deliver oxygen to your muscles and you know, your brain and all the pieces that need oxygen. And it has a particular three-dimensional shape when oxygen’s bound, and a slightly different shape when oxygen isn’t bound. So understanding what those, what hemoglobin, the protein, looks like helps us to kind of better understand how that process is even happening. One of the cool things is to think about, for instance, when we’re looking at something like SARS-CoV-2, so the main protease is a major drug target for SARS-CoV-2, and we’re trying to kind of understand what this looks like in different kinds of conditions, as well as when we got different drugs bound. Because it actually looks different. That helps us to design better drugs to treat COVID-19. There’s all kinds of diseases like this that if we know what the proteins look like that are maybe different in the disease state relative to the kind of natural state, the healthy state, that would help us to better design drugs or treatments or things like that.

   [9:09] So for the folks at home who are not structural biologists, what is the main thing that you want them to know?

   [9:17] Well, that’s a great question (laughs). So, I think that... So, here’s some things to kind of know about structural biology. That the more we know about what things look like, the better we’re able to understand how they work. And so, if we know what the different pieces and parts say of the virus, of the SARS-CoV-2 virus, look like, we can better understand, for instance, why variants are causing changes to how infections are happening and transmission. So the pandemic in some ways have given us a lot of things to think about in terms of how we talk about science, in terms of how we communicate science, which of course you’re familiar with, and you know, how we talk about what we’re doing, because I think that, again, if we know what things look like we can make things to kind of treat diseases. But the other thing we’ve learned is, you know, how scientists can work together and how we can all really come together and talk about the really important things and share data and kind of communicate with just not each other, although that’s really important, but also with the public about, okay, here’s why all of these different pieces of science are really important, and here’s why we really need to kind of make these things happen.

   [10:44] I couldn’t agree more. It sounds like structural biology is a really important part of science and medicine. And you know what? I think that this Nerdy Job is done. Wow, that was fun. Thank you, Sydney. Thank you, Dr. Bowman, for having us at HWI. We’re already on to our next Nerdy Job. I’ll see you in the next episode.

   [11:08] Raven! Raven!

   [11:10] [Raven] It was so much fun having Sydney with me today to learn about structural biology and to make protein crystals. Be sure to share this episode and what you learned with everyone you know. Also, be sure to hit that Subscribe button on YouTube and follow me, @DrRaventheScienceMaven, on all socials so that you don’t miss a Nerdy Job. Can you tell what my next nerdy job is? Leave a comment and guess. Oh, here’s a hint. Look at what I’m wearing. And oh, one more thing (laughs). One more thing. This show was made possibly by generous donations from awesome supporters. Visit my website to learn more about the show and help us do these nerdy jobs.

   [11:50] (soul music)