A new resolution limit for protein imaging with cryo-electron microscopy

"Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery"

Cell 165, 1–10, June 16, 2016

Single cells are tiny things. So tiny that 200 red blood cells could fit across the width of a single human hair. 

Yet a single cell is packed with thousands of even tinier proteins. Even though each protein molecule is so tiny that hundreds of them could fill a single cell, each of them is an incredibly complex, uniquely specific, dynamic thing. There are thousands of uniquely shaped proteins across the kingdoms of life. The diversity of forms is staggering in its scale.

Each of these proteins is a complex nanomachine - some act as motors, others as structural scaffolding. Many are enzymes - catalysts for the chemical reactions that give rise to life. And many are completely unkown and remain to be understood.

Some examples of protein structures 

Each protein is composed of distinct physical parts that have different functions. Some have little "battery packs" that power the activity of the protein. Many have moving parts - hinges that swing, pores that open and shut. 

Each protein has a physical form. You can think of it as a very small shape made of atoms, an incredibly intricate kind of molecular origami. Biologists call this shape a 'structure'. Biologists who study the structures of proteins are called 'structural biologists'.

Understanding the structures of proteins has enormous potential for drug discovery. Drugs like antibiotics target specific bacterial proteins and disable them, killing dangerous bacteria. Knowing the structure of target proteins in disease could guide the design of drugs to target them.

X-ray crystallography

Studying an object as small as a protein is very technically challenging. Historically, one of the main methods for doing this has been a technique called X-ray crystallography. In this method, scientists must first make large amounts of the protein they are studying, and then coax these fickle, fragile molecules into forming well-ordered solid crystals. This is very difficult, and can consume years of a scientist's life.

Once the crystals are made they are treated with chemicals and zapped with powerful X-rays inside giant particle accelerators, creating a pattern of dots that can be 'read' to determine the positions and orientations of the atoms in the protein molecule. This is the 'structure' - the location and orientation of all the individual atoms that make up a protein.

Although X-ray crystallography is an incredibly powerful technique that has lead to multiple Nobel Prizes, it has a very serious limitation - proteins can only be studied after being made into solid crystals, but proteins do not form these kinds of crystals inside the cells where they live and work. There is always a worry that the 'crystal' structure being studied is very different from the 'native' structure of the protein inside a living cell. 

Scanning EM image of a fly's head

A more recent method for studying protein structures that is gaining popularity is called cryo-electron microscopy. Electron microscopy (EM) is a form of microscopy that replaces a beam of photons with a beam of electrons, giving rise to much higher resolution magnification. Electron microscopes have been used to take stunningly detailed images of cells and insects, but until recently technical limitations have prevented it from being used to study structures as small as individual proteins.

Technical advancements in cryo-EM have the potential to bring in a new era of structural biology, allowing scientists to get atomic resolution structures of individual proteins in a more 'native' form, although it carries its own set of limitations.

Cryo-EM image of glutamate dehydrogenase,
taken from the paper

A recent paper from Sriram Subramaniam's lab at the NIH in Bethesda, Maryland has broken the previous resolution barriers to cryo-EM. Whereas previously cryo-EM was limited to studying very large protein complexes like entire virus particles or the ribosome, the authors in this study overcome these technical barriers to obtain atomic scale structures of two small protein enzymes (lactate dehydrogenase and glutamate dehydrogenase) that have been implicated in cancer. 

Excitingly, the authors were also able to image physical interactions of the proteins with drug molecules. This kind of analysis has the potential to guide the design of newer, more effective medicines targeting specific proteins implicated in human disease.