Biochemical controls: evolution of protein folding (Introduction)

by David Turell , Tuesday, March 07, 2023, 19:27 (805 days ago) @ David Turell

A new investigation:

https://phys.org/news/2023-03-creative-destruction-probing-evolution-proteins.html

"Proteins have been around a lot longer than we have—as building blocks of biological evolution, our existence depends on them. And now, researchers at the Georgia Institute of Technology are applying a 20th-century theoretical concept to study how proteins evolve, and it might lead to the answer of one of humanity's oldest questions: How did we become us?

"Inside a typical human cell are tens of thousands of proteins. We need so many because proteins are the skilled laborers of the cell with each one performing a specific job. Some lend firmness to muscle cells or neurons. Others bind to specific, targeted molecules, ferrying them to new locations. And there are others that activate the process of cell division and growth.

"A protein's specific function depends on its shape, and to achieve its functional shape—it's native state—a protein folds. A protein begins its life as a long chain of amino acids, called a polypeptide. The sequence of amino acids determines how the protein chain will fold and form a complex, 3D structure that allow the protein to perform an intended task.

***

"'"They discovered that once a protein can fold and achieve its 3D structure, when it is combined with another protein which has folded into a different 3D structure, that combination can easily become a new structure. "So maybe it's not as difficult as we thought to go from one structure to another," said Williams, professor in the School of Chemistry and Biochemistry. "And maybe this can explain the diversity of protein structures that we see today."

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"Ever since the simplest and most ancient protein folds emerged on Earth billions of years ago, the number of folds has expanded to form the universe of protein function we see in modern biology.

"But the origins of protein folds and the evolutionary mechanisms at play pose central questions in biology that Williams and his team considered. For instance, how did protein folds arise, and what led to the diverse set of protein folds in contemporary biological systems, and why did nearly four billion years of fold evolution produce fewer than 2,000 distinct folds?

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"In creative destruction, they explain, one open reading frame—the span of DNA sequence that encodes a protein —merges with another to produce a fused polypeptide. The merger forces these two ancestors into a new structure. The resulting polypeptide can achieve a form that was inaccessible to either of the independent ancestors, before the merger. But these new folds are not totally independent of the old. That is, a daughter fold inherits some things from the ancestral fold."

Comment: Some folding is automatic based on ion charges, but the overall controls are still a mystery. Design is required.