The structure of proteins is not static

Over the past century, scientists have developed and deployed 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 you're walking outside and you see someone walking a dog, and if you've never seen a dog before and then you see a dachshund, you think, 'Well, that's what all dogs look like

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 these structural data with their respective protein-coding gene sequences allowed the team to perform ancestral sequence reconstruction— a computer-based molecular evolutionary method 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, who is also an assistant professor at the University of California, Berkeley, said: "The big finding of this paper is that it has a lot of structural plasticity

After completing the ancestral sequence reconstruction, the team conducted mutation experiments to see how altering rubisco assembly (in this case, breaking down hexamers into dimers) affected the enzyme's 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, that regions of the enzyme actually interact with carbon dioxide," said lead author Albert Liu, a graduate student

Co-author Paul Adams, Vice President, added: "The mix of technologies employed and the interdisciplinary nature of the team are the real keys

The structural biology experiment was conducted at Berkeley Lab's Advanced Light Source (ALS), a user facility

Albert K.