Science Advances: Protein structure is not static

When you think of proteins (including enzymes, signaling molecules, and the structural components of all living things), you might think of single-stranded amino acids, arranged like beads on a single line

Over the past century, scientists have developed amazing techniques such as X-ray crystallography and cryo-electron microscopy to determine the structure of proteins, thus answering countless important questions

A team of researchers from The Lawrence Berkeley Lab studied the world's richest protein: rubisco, an enzyme involved in photosynthesis, showing how evolution has led to an astonishing diversity of molecular assemblies that accomplish the same task

Historically, if scientists had solved a structure and determined that a protein was dimerized (consisting of two units), they might have hypothesized that similar proteins also existed

"It's like if you walk outside and see someone walking a dog, if you've never seen a dog before and then you see a dachshund, you think, 'Well, that's what all dogs look like

"One conclusion of this paper goes beyond rubisco and covers all proteins, which is whether we see the true range of structures in nature, or whether these biases make everything look like a dachshund

Shih's lab, using Berkeley Lab's advanced light source, in collaboration with structural biology experts in the Biosciences District, hopes to explore the different rubisco arrangements in the dog park and understand where they come from

Previous studies have shown that rubisco (Form I) found in plants typically employs a "octamer core" combination of 8 large protein units and 8 small protein units arranged, while Form II is thought to exist primarily in dimer form, with few examples

Combining this structural data with the sequences of their respective protein-coding genes allowed the team to perform ancestral sequence reconstruction — a computer-based approach to molecular evolution that estimates what ancestral proteins look like

The reconstruction showed that the type II rubisco gene had changed over its evolutionary history, producing a series of proteins of structure that could be transformed into new shapes or easily restored to old structures

Shih said: "The big finding of this paper is that proteins have a lot of structural plasticity

After completing the ancestral sequence reconstruction, the team conducted mutation experiments to see how altered rubisco assembly (in this case, the breakdown of hexamers into dimers) affected the activity

"This is an interesting insight for us because it shows that in order to get more productive rubisco engineering results, we can't just look at the simplest answer, the enzyme's region actually interacts with carbon dioxide," said lead author Albert Liu, "maybe there are mutations outside of this active site, they actually participate in this activity and may alter protein function

Co-author Paul Adams added: "The mix of technologies we employ and the interdisciplinary nature of the team are the real keys

Article title

Structural plasticity enables evolution and innovation of RuBisCO assemblies