Diving with the Proteins
– a shrink ray adventure –
If you were granted one wish, what would it be (after infinite wealth)? Actually, don’t tell me, it’s gonna be dirty stuff anyway. Instead, let me tell you what I would wish for. I would like to do a proper shrink ray adventure, Rick and Morty style. I would like to go inside the human body (or any other organism) and see molecules at work.
Let’s assume I could see through water in there, like I could see through air right now. Let’s also assume, I could actually see every atom, maybe even electrons in reactions, and it would make sense to me, and not only be a blurry picture of waves, uncertainties and other quantum quirks. Let’s say, the smallest structures in our body would be as intuitive to look at as a bicycle, or a pair of scissors. What would I see inside a cell?
I want to take you to a fictitious journey, based on facts that we know from my favorite field in life sciences: Structural biology. And at the same time, I want to tell you a bit about how we know these things, and what we can learn from them.
A wild enzyme appears!
Alright, tiny Hannes is floating through a cell now, two nanometers large, independent of air (a O2 molecule would be the size of my fist, after all), and I could see through water, while still clearly seeing all other molecules.
The first thing I’d see are a loooot of molecules, from the size of a football, to the size of a yacht. The intracellular environment is more crowded than a System of a Down concert in 2005. Most of them are proteins, but there are also RNA (DNA’s amazing cousin), some metal ions and a lot of all kinds of smaller molecules. Depending on where you are, you might see walls made of lipids (we call them membranes), or maybe even some DNA.
Proteins, RNA and DNA are macromolecules. They are made of large chain of building blocks (amino acids for proteins, and nucleobases for DNA and RNA) that folds into a specific shape. This shape, we call it the structure, is crucial for its function. Actually, for DNA and some RNA the shape isn’t so important. They fulfil their function just fine by exposing the sequence of nucleobases. This is the genetic code which can be read by some proteins and other RNA molecules. All proteins, and some specific RNA molecules however, need to fold their specific structure. This is a bit like a thread of wool. Dangling around it’s no good, but knitted into the right shape, it can be a hat, a sweater, an egg warmer or a spaceship. Okay, maybe I got a bit too excited here, but you get the point. And so can amino acid chains folded into the right structure be an enzyme that breaks down small molecules, a membrane channel that selectively transports ions or just a green-glowing rave light (keyword for the curious: green fluorescent protein, check it out).
It used catalysis. It is very effective.
Let’s say we have an enzyme that consists of a chain of 250 amino acids. This chain folds into different substructures, like helices, flat sheets and parts that seem kind of random. All of them come together to give the protein one specific structure. Somewhere in that structure is a small pocket where a molecule can enter, and some amino acids in there are oriented in just the right way, so they can perform a chemical reaction with that molecule (we say, the enzyme acts as a catalyst for the reaction). For example, cleaving it in two pieces. On the other side of the protein might be a another pocket where a molecule can enter, but not react with anything. Merely by sitting there, it pushes away some amino acids, leading to a rearrangement of the entire protein that closes the catalytic pocket on the other side. We would call that molecule an inhibitor.
These structures large biomolecules are of high interest to us scientists. They can tell us how molecules work, what regulates their function and what went wrong then they stop working. Ultimately, it teaches us how life itself works. In the end, isn’t life but a complex network of chemical reactions happening in a confined space? Understanding how the molecules that make these reactions can tell us what drives the mere foundation of life.
How to get a closer look at the 3D structure of a protein
Unfortunately, no one ever made that shrink ray trip into a cell, and no one ever saw the actual structure of a protein at work with their own eyes. So we need to bring some new players into the field. Methods that can make the protein’s structure accessible for us, so we can study it and learn how they function.
Here is a quick guide to protein structure determination:
- Grow them in a crystal and shoot them with x-rays. I explained the basic principle in a previous post already. Basically, we use the the fact that x-ray diffraction of all atoms in the periodic crystal pattern lead to wave interference. The repetitive pattern leads to constructive interference here, and to destructive interference there. After a lot of complicated math, we can calculate the actual density of the electrons in the crystal unit which gives us the molecular structure.
- Use the magnetic properties of a nuclear spin to probe its chemical environment. Repetitive bond types and spin systems allow us to get specific information about intramolecular distances and bond angles that we can feed as restraints into a molecular dynamics simulation (say whaaaaat). Scientific jibber-jabber aside: NMR spectroscopy is a really complicated method, and since I work with it, I would love to explain it, but it will need at least one post for itself, so hang it there just a bit more!
- Take many, very blurry images of molecular complexes and put them together to a 3D picture. This works, because we use electrons instead of light which allows us to get a better resolution. Adding up thousands of these blurry images from all different angles, we can reconstruct a 3D picture at amazing detail thanks to modern computing software. This method has actually been around for quite a while, but only recent breakthroughs in image detection and data processing algorithms made it really huge in the last 10 years or so. It is called Cryo-Electron Microscopy and has been awarded the Nobel Prize in chemistry 2017.
These three methods can give us the complete structure of a biomolecule (of almost any molecule, really). Each has its advantages and limitations, but they have all in common that we can not use them in actual living organisms (in fact, it is possible somehow, and part of my PhD studies is doing exactly this). Most of the time, we have these molecules isolated in very unnatural conditions which can change their shape or some behaviour and properties. It is a bit like studying a dolphin in a swimming pool. Sure, it is the same animal like in the ocean, but it might behave very differently. Unlike marine biologists, we can’t just jump into a cell like they can dive in the ocean to study dolphins. We need to isolate our molecules and bring them in conditions that allow us to study them with a specific method.
The workhorses in life are too small to be seen
The problem here is just a very general one in (bio)chemistry. The things that we try to study here are so tiny that it is just very hard to get any information about them at all. This doesn’t apply only to proteins. From single molecules to entire subcellular structures, we have issues knowing what they look like and how they are doing their magic. Sure, we can study their functions, reactions, even size… but really knowing their 3D structure isn’t easy. With these methods up there, we can tackle these issues and in the last 60 years, we have been getting really good at it.
I devoted my PhD studies to solving the 3D structure of biomolecules (in my case RNA) and understanding how they work. Apart from doing it for medicine and understanding life, I do it because… I find them beautiful. And even more beautiful are all the methods that we developed to unravel these structures.
Outro
If you are ready now to take a simulated shrink ray adventure into the cell, then check out this YouTube video: There are many similar ones out there, and most are pretty amazing. Keep in mind, these are animations based on science. These images are not actual scientific data. I would like to point out one thing that is quite inaccurate (for a good reason): The cell interior seems quite empty here, everything is floating around with a lot of space. In reality, it is super crowded and you wouldn’t even see what they want to show.
Musical inspiration: Remarkably Human and Get Schwifty
