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Study on plant enzyme demonstrates proteins can transform their structural arrangement with surprising ease

Protein structures aren't set in stone
An assessment of rubisco assemblies from different species, illustrating an array of structures including a dimer, tetramer, hexamer, octamer, and hexadecamer (16 unit protein). Credit: Shih Lab/Berkeley Lab

Once you think about proteinsthe enzymes, signaling molecules, and structural components atlanta divorce attorneys living thingyou might think about single strands of proteins, organized like beads on a string. But almost all proteins contain multiple strands folded up and bound one to the other, forming complicated 3D superstructures called molecular assemblies. Among the key steps to understanding biology is discovering what sort of protein does its job, which requires understanding of its structures right down to the atomic level.

In the last century, scientists are suffering from and deployed amazing technologies such as for example X-ray crystallography and cryo-electron microscopy to find out structure, and thereby answered countless important questions. But new work demonstrates understanding can often be more difficult than we think.

Several researchers from Lawrence Berkeley National Laboratory (Berkeley Lab) studying the world’s most abundant protein, an enzyme involved with photosynthesis called rubisco, showed how evolution can result in a surprising diversity of molecular assemblies that accomplish exactly the same task. The findings, published today in Science Advances, reveal the chance that most of the proteins we thought we knew actually exist in other, unknown shapes.

Historically, if scientists solved a structure and determined a protein was dimeric (made up of two units), for instance, they could assume that similar proteins also existed in a dimeric form. But and sampling biasunavoidable factors considering that it is rather difficult to convert naturally liquid proteins into solid, crystallized forms which can be examined via X-ray crystallography were obscuring reality.

Protein structures aren't set in stone
Albert Lui (left) and Patrick Shih demonstrate how they studied the structure and evolution of rubisco, the enzyme that plants use to harness CO2 to generate sugars, in Koshland Hall at UC Berkeley. Credit: Marilyn Sargent/Berkeley Lab

“It’s like in the event that you walked outside and saw someone walking their dog, in the event that you had never seen your dog before then saw a wiener dog, you’d think, ‘OK, this is exactly what all dogs appear to be.’ But what you must do is visit the dog park and see all of the dog diversity that’s there,” said lead author Patrick Shih, a faculty scientist in the Biosciences Area and Director of Plant Biosystems Design at the Joint BioEnergy Institute (JBEI). “One takeaway out of this paper that goes beyond rubisco, to all or any proteins, may be the question of if we have been seeing the real selection of structures in nature, or are these biases rendering it look like everything appears like a wiener dog.”

Hoping to explore all of the different rubisco arrangements at the metaphorical dog park, and learn where they originated from, Shih’s lab collaborated with Bioscience Area structural biology experts using Berkeley Lab’s Advanced SOURCE OF LIGHT. Together, the team studied a kind of rubisco (form II) within bacteria and a subset of photosynthetic microbes using traditional crystallographya technique with the capacity of atomic-level resolutioncombined with another structure-solving technique, small-angle X-ray scattering (SAXS), which has lower resolution but may take snapshots of proteins within their native form if they come in liquid mixtures. SAXS gets the additional benefit of high-throughput capability, and therefore it could process a large number of individual protein assemblies in quick succession.

Previous work had shown that the higher studied kind of rubisco within plants (form I) always takes an “octameric core” assembly of eight large protein units arranged with eight small units, whereas form II was thought to exist mostly as a dimer with several rare types of six-unit hexamers. After using these complementary ways to examine examples of rubisco from the diverse selection of microbe species, the authors observed that a lot of form II rubisco proteins are in fact hexamers, with the casual dimer, plus they discovered a never-before-seen tetrameric (four unit) assembly.

Combining this structural data with the respective protein-coding gene sequences allowed the team to execute ancestral sequence reconstructiona computer-based molecular evolution method that may estimate what ancestral proteins appeared as if in line with the sequence and appearance of modern proteins that evolved from their website.

Protein structures aren't set in stone
Albert Liu checking some culture plates of E. coli with the genes to create form II rubisco. Credit: Albert Liu

The reconstruction shows that the gene for form II rubisco has changed over its evolutionary history to create proteins with a variety of structures that transform into new shapes or revert back again to older structures without difficulty. In contrast, during evolution, selective pressures resulted in a number of changes that locked form I rubisco in placea process called structural entrenchmentwhich is excatly why the octameric assembly may be the only arrangement we see now. Based on the authors, it had been assumed that a lot of protein assemblies were entrenched as time passes by selective pressure to refine their function, like we see with form I rubisco. But this research shows that evolution may also favor flexible proteins.

“The big finding out of this paper is that there surely is plenty of structural plasticity,” said Shih, who’s also an assistant professor at UC Berkeley. “Proteins could be a lot more flexible, over the field, than we’ve believed.”

After completing the ancestral sequence reconstruction, the team conducted mutational experiments to observe how altering the rubisco assembly, in this instance breaking a hexamer right into a dimer, affected the enzyme’s activity. Unexpectedly, this induced mutation produced a kind of rubisco that’s better at utilizing its target molecule, CO2. All naturally occurring rubisco frequently binds the similarly sized O2 molecule on accident, lowering the enzyme’s productivity. There exists a lot of fascination with genetically modifying the rubisco in agricultural plant species to improve the protein’s affinity for CO2, to be able to produce more productive and resource-efficient crops. However, there’s been lots of concentrate on the protein’s active sitethe region of the protein where CO2 or O2 bind.

“That is a fascinating insight to us since it suggests that to be able to have significantly more fruitful results engineering , we can not just consider the simplest answer, the spot of the enzyme that truly interacts with CO2,” said first author Albert Liu, a graduate student in Shih’s lab. “Maybe you can find mutations beyond that that truly take part in this activity and may potentially change function in a manner that we wish. So that’s a thing that really opens doors to future avenues of research.”

Co-author Paul Adams, Associate Laboratory Director for Biosciences and Vice President for Technology at JBEI added, “The mixture of techniques employed and the interdisciplinary nature of the team was a genuine key to success. The task highlights the energy of combining genomic data and structural biology solutions to study probably the most important problems in biology, and reach some unexpected conclusions.”

More info: Albert Liu et al, Structural plasticity enables evolution and innovation of RuBisCO assemblies, Science Advances (2022). DOI: 10.1126/sciadv.adc9440.

Citation: Study on plant enzyme demonstrates proteins can transform their structural arrangement with surprising ease (2022, August 26) retrieved 27 August 2022 from

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