What do structural biologists do?

Structural biologists are best known for taking molecular “pictures” of proteins and other macromolecules (using methods like x-ray crystallography and cryo electron microscopy (cryoEM)). But that’s just one part of their work. The real fun in my opinion comes from using follow-up biochemistry experiments to study what those “pictures” reveal about how the molecules’ form (structure) relates to their functions. But to do all this cool stuff, you typically need a lot of really pure protein. So a huge part of most structural biology is expressing and purifying proteins! And lots of optimization and troubleshooting to try to get cooperative proteins! Although parts of the job require a lot of “dry,” computational work to generate and refine the atomic models of the proteins, etc. you want to look at, be prepared to spend a lot of time at the bench getting messy with “wet work!”
blog form: bit.ly/structural_biology_ove...
Note: some people in structural biology labs specialize more in specific aspects so they might only deal with the computational parts or the biochemistry parts, etc. but for lots of structural biologists, especially when training, they do it all. Or, in some cases one person will do the expression and purification and hand it off to another person, potentially in a different lab, who will do the actual structural determination part (collect and analyze data using crystallography, cryo-EM, etc.). Collaborating like this can be a huge win for both! And for the public at large because it allows us to capitalize on various labs’ diverse expertise and interests to get structures of a huge variety of molecules.
Note: I did my PhD in a structural biology lab (Dr. Leemor Joshua-Tor’s lab at Cold Spring Harbor Laboratories) and did some crystallography but mainly focused on the biochemistry side of things. But I like being structurally-adjacent! And have a deep appreciation for the structural parts of structural biology even though I prefer to leave the structure determination to others. So I deeply appreciate the people who prefer to do that side of things! But back to the story…
So, say you solve the structure (figure out the position of the atoms making up that protein, etc.) Now what?
You can learn a lot about how a protein works by seeing what it looks like (imagine seeing a picture of an open Swiss army knife). And you can also learn about how a protein might “not work” if you can tie up or hide certain parts with another molecule, like a pharmaceutical drug. There’s a lot you can learn from structures and a lot of hypotheses you can generate, but you also need some experimental proof to see whether your ideas pan out. So a big part of structural biology is doing biochemistry and biophysics-type experiments in the lab (as well as sometimes cell-based experiments, often in collaboration with other labs) to test them.
Thanks to molecular biology, we can use site-directed mutagenesis to introduce specific mutations to the genetic recipes for making the proteins, introducing changes to the resulting proteins. We can make changes parts of the protein that the structure suggests are important for something and then see whether doing so screws up that “something” (but make sure you don’t just screw up protein folding or something else in the process!)
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Going back to our Swiss army knife analogy, it’s like if you see a corkscrew and you want to prevent people from de-corking bottles you could file down the point of the screw so people couldn’t get it into the cork.
So these structure-directed mutations can help us work out how molecules work. And they also can help us see how we might be able to prevent them from working! We might want to do this to tamp down a hyperactive protein that’s causing a disease or to inactivate a viral protease (protein cutter) to prevent it from making more virus.
You’re not going to be able to mutate* a protein inside an actual person, but you can introduce pharmaceutical drugs that bind to the site! And knowing what that site looks like can help.
Similarly to how you could design a “cap” that covers up the pointy tip of the corkscrew, if you can see what a protein’s “active site” looks like, the part where the protein “does stuff” (e.g. the place in a viral protease where it grabs onto and cuts proteins), you can better design a drug that binds there and blocks it. Instead of designing from scratch, scientists often start by using crystallography to screen pre-existing drugs (some of which are already approved for treating other diseases) through a compound library screen, or screening pieces (a fragment screen). Once they get hits they can then look closely at how it interacts with the protein and how they might be able to alter the molecule to bind better. More here: bit.ly/mproinhibitors
Finished in comments

[@thebumblingbiochemist]

*mutation technically refers to changes at the gene level, but we commonly refer to the resultant changes in the protein as mutations as well. But some people might get irritated if you do so be forewarned!
Although you can’t “mutate” proteins inside a person, you can give a person mutated proteins! Don’t worry - mutations can be good! Based on structures of insulin, for example, scientists have been able to make modified versions that are longer-lasting or faster-acting. Much more on how here: blog form: bit.ly/insulin_diabetes_biochem ; CZcams: czcams.com/video/Mp8jUqfjMBs/video.html
Those are a couple examples of “translational” research, what we call research that has a direct applicational benefit. But structural biology is also crucial to “basic” research, where we focus primarily on trying to figure out how things work (and this can lead to important applications, etc. down the line).
Structures can guide crucial experiments and what’s especially awesome about them is that they are freely accessible through the PDB (Protein DataBank) for anyone to use to inform their own experiments - or just to peruse!
If you want to learn more about how: intro to PDB, crystal structure entries, crystal contents, resolution: bit.ly/pdbstructures & czcams.com/video/Re2gwi-_OEw/video.html & czcams.com/video/IZtHsUFbyes/video.html      
But before I make this all seem too simple… getting a structure usually involves a LOT of hard work. Sometimes by multiple people. Because (assuming you are trying to solve the structure of a protein or proteins that you express recombinantly, not ones you purify in their “native” state from cells) you have to…
- clone the protein(s) (stick their genetic recipes into a form you can work with, usually a circular piece of DNA that you can stick into cells)
- Express LOTS of the protein(s) (stick that cloned DNA into cells like bacteria, insect, yeast, or mammalian cells and get them to make it)
- [Figure out why the cells don’t want to express your protein… maybe change the construct (version of the recipe)… use a different cell type…]
- Purify the protein(s) SUPER well (typically using multiple column chromatography steps)
- [Figure out why it isn’t getting very pure despite your attempts at it…]
- Prepare complexes if applicable (mix proteins together, etc.)
- Prepare the samples for data collection (vitrify grids for cryo or crystallize the protein for crystallography)
- [Do TONS of screening of different conditions to try to get the protein to crystallize… go back to the start and try altering the construct, maybe removing regions predicted to be disordered]
- For cryo-EM you often start by screening things with a low-resolution technique like negative staining or a screening microscope, then optimize conditions before going for the big time collection
- Collect LOTS of HIGH QUALITY data
- [start over to get better data…]
- Process all that data
- Generate a model based on that data
- Refine the model
- [these last couple parts involve a lot of time at a computer]
And that’s “just” to get the structure! Then comes the analysis, functional follow-up studies etc.
Note: the workflow will differ depending on the project and the experimental systems you use - more on experimental systems here: bit.ly/experimentalsystems & czcams.com/video/fewMfNw9Je0/video.html
Hope that helped give you a flavor of structural biology - I know it can seem really obscure, but it’s super useful. And super cool. And involves more than “just” solving structures (which IS a super important - and hard - part of it).
To review:
* The what: Structural biology is a scientific discipline that looks at the molecular structure of biological macromolecules and how that STRUCTURE relates to its FUNCTION
* The why: To answer questions like:
* Why do molecules work the way they do?
* What specifically makes one (or a group of them) well-suited for a particular task?
* Can we manipulate them to work even better or do other things?
* The how:
* incorporates principles and techniques of: biochemistry, biophysics, molecular biology
Bottom line: Structure & function are intimately connected. We can exploit this relationship to learn about function from structure and structure from function. It’s hard, but fun and often rewarding, work.
For more structural-biology content, I created a page on my blog with links to my past posts on it: bit.ly/structural_biology  
 
and here's a link to my CZcams structural biology playlist: czcams.com/play/PLUWsCDtjESrGhwVxsRbTJdL-BEsN60RCs.html  
 
and here's a link to my CZcams structural biology playlist: czcams.com/play/PLUWsCDtjESrGhwVxsRbTJdL-BEsN60RCs.html  
 
Also, for all that protein expression and purification: 
- blog page: bit.ly/proteinpurificationtech
- CZcams playlists 
- recombinant protein expression & purification: czcams.com/play/PLUWsCDtjESrHrxSeKsNxMlooYe0NwEQbV.html
- protein chromatography: czcams.com/play/PLUWsCDtjESrEtqQkEXsQpTyRfMhywBVQ7.html
more on site-directed mutagenesis: bit.ly/mutagenesisconstructs & czcams.com/video/vm6p5Nq2sTg/video.html
more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbiochemist.com

[@sohinisaha4069]

I have recently gotten interested in structural biology and various techniques used in studying proteins. Your channel is wonderful. I love every video you post

[@thebumblingbiochemist]

Thank you so much! Best of luck! There's definitely a bit of a steep learning curve for structural biology but it's a lot of fun once it clicks!

[@oromhal]

Thank you so so much! Such a helpful video for understanding what is Structural Biology!

[@thebumblingbiochemist]

I'm so glad it was helpful! I never knew before grad school what it was!