Proteomics: It’s all about the structures

How do we determine the structure of a protein?

Proteomics: It’s all about the structures
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‘Structure Equals Function.’

It’s basically the secret password at the molecular biology club.

And if you’re ever looking to get knowing nods from your favorite molecularly aligned friends, this phrase kills.

That’s because most everything in molecular biology is centered on how molecules interact with one another.

This includes how two strands of DNA coil into a right-handed helix, how proteins bind to one another to create functional complexes, or how enzymes grab on to their co-factors and substrates to catalyze life-sustaining chemistry.

All of these things are essentially determined by their molecular structures!

These structures are pretty easy to determine for run of the mill chemical compounds, but proteins are macromolecules.

This just means they’re composed of thousands of atoms and can have highly complex structures!

But the complexity for proteins doesn’t end there, because they can also be modified after they are made.

These ‘post-translational modifications,’ or PTMs for short, can be as simple as the addition of a phosphate to a specific part of a protein all of the way to the addition of large chains of sugar molecules.

And you guessed it, the addition of these PTMs changes the structure of the protein which in turn changes its function!

Many PTMs are critical for proteins to operate correctly and they routinely serve as ‘on’ and ‘off’ switches.

They’re also important for determining which partners a protein can interact with and when!

So, a protein’s structure is REALLY freakin’ important for understanding what it does.

'But how do we determine the structure of a protein?'

I'm glad you asked!

X-ray Crystallography - The OG of structure determination involves creating pure extracts of the protein you want to look at and finding the perfect conditions (salt concentration, humidity, drying time) to create a pristine crystal. Those crystals are then bombarded with X-rays. And the structure of the underlying protein can be inferred based on how those X-rays bounced off of it! But one major drawback of crystallography is that crystals don’t have water! So they may not necessarily represent the ACTUAL structure we’d see inside of a wet environment.

Nuclear Magnetic Resonance Spectroscopy (NMR) - Best used on small proteins and peptides. Purified protein is exposed to radio waves and its structure can be determined by looking at resonance signals and calculating which atoms within a protein are near one another.

Cryogenic Electron Microscopy (CryoEM) - Purified proteins or large protein complexes are cryogenically frozen and then imaged with an electron microscope. The images of thousands of molecules are then combined to stitch together a 3D structure of the protein!