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Proteins have slip knots, like a shoelace bow?

In “A Knotty Puzzle” (Biologic Perspectives, June 6, 2012), Ann Gauger, senior scientist at the ID-friendly Biologic Institute, discusses the current conundrum around the way proteins fold:

Until fairly recently, scientists believed that folded proteins could be unfolded into a simple polypeptide chain by tugging on one end, unlike those ear buds you keep in your pocket. But it is now known that some proteins also fold themselves into knots of various kinds. This is a puzzle.

As a recent press release states,

“Relatively little is known about protein folding, the process by which a polypeptide chain with a specific sequence of amino acid chains forms the three-dimensional structures—their “native states”—required to become functional.

“How this process reproducibly achieves the required structure is the subject of intensive study. Even harder is understanding how this is accomplished for knotted proteins, where the chain loops around itself in entanglements of varying complexity—or the even rarer slipknotted proteins, where a loop is bound by another segment of the protein chain, similar to a shoelace bow.

Let me untangle the rhetoric. The reason why knots in folded proteins are unlikely is because they are hard to achieve, without resulting in misfolded proteins, aggregation, and possible disease states. Even though it’s unlikely they evolved—let’s make that highly unlikely—we know knotted proteins must have evolved somehow, simply because they exist.

Evolved somehow? When did “somehow” enter the lexicon of science?

At one time, science was about “exactly,” not “somehow.”

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