Biological complexity: enzyme control of protein shapes (Introduction)

by David Turell , Saturday, August 27, 2022, 19:03 (819 days ago) @ David Turell

In a plant study:

https://phys.org/news/2022-08-enzyme-proteins-ease.html

"A group of researchers from Lawrence Berkeley National Laboratory (Berkeley Lab) studying the world's most abundant protein, an enzyme involved in photosynthesis called rubisco, showed how evolution can lead to a surprising diversity of molecular assemblies that all accomplish the same task. The findings, published today in Science Advances, reveal the possibility that many of the proteins we thought we knew actually exist in other, unknown shapes.

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"The reconstruction suggests that the gene for form II rubisco has changed over its evolutionary history to produce proteins with a range of structures that transform into new shapes or revert back to older structures quite easily....According to the authors, it was assumed that most protein assemblies were entrenched over time by selective pressure to refine their function, like we see with form I rubisco. But this research suggests that evolution can also favor flexible proteins.

"'The big finding from this paper is that there's a lot of structural plasticity," said Shih, who is also an assistant professor at UC Berkeley. "Proteins may be much more flexible, across the field, than we've believed."

"After completing the ancestral sequence reconstruction, the team conducted mutational experiments to see how altering the rubisco assembly, in this case breaking a hexamer into a dimer, affected the enzyme's activity. Unexpectedly, this induced mutation produced a form of rubisco that is 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 is a great deal of interest in genetically modifying the rubisco in agricultural plant species to increase the protein's affinity for CO2, in order to produce more productive and resource-efficient crops. However, there has been a lot of focus on the protein's active site—the region of the protein where CO2 or O2 bind."

Comment: rubisco, as an enzyme, is a giant molecule of thousands of amino acids, which must be in a special arrangement to allow rubisco to do its work. How did natual selection find it? There are enormous odds against a natural discovery. It reeks of design.