Biological complexity: protein folding creates life (Introduction)

by David Turell , Saturday, January 30, 2021, 19:37 (1393 days ago) @ David Turell

Without the ability of proteins to fold and create different functions life could not exist:

http://backreaction.blogspot.com/2021/01/has-protein-folding-been-solved.html

"Understanding how proteins fold is important because the function of a protein depends on its shape. Some mutations can lead to a change in the amino acid sequence of a protein which causes the protein to fold the wrong way. It can then no longer fulfil its function and the result can be severe illness. There are many diseases which are caused by improperly folded proteins, for example, type two diabetes, Alzheimer’s, Parkinson’s, and also ALS, that’s the disease that Stephen Hawking had. (my bold)

"So, understanding how proteins fold is essential to figuring out how these diseases come about, and how to maybe cure them. But the benefit of understanding protein folding goes beyond that. If we knew how proteins fold, it would generally be much easier to synthetically produce proteins with a desired function.

"But protein folding is a hideously difficult problem. What makes it so difficult is that there’s a huge number of ways proteins can fold. The amino acid chains are long and they can fold in many different directions, so the possibilities increase exponentially with the length of the chain.

"Cyrus Levinthal estimated in the nineteen-sixties that a typical protein could fold in more than ten to the one-hundred-forty ways. Don’t take this number too seriously though. The number of possible foldings actually depends on the size of the protein. Small proteins may have as “few” as ten to the fifty, while some large ones can have and a mind-blowing ten to the three-hundred possible foldings. That’s almost as many vacua as there are in string theory!

"So, just trying out all possible foldings is clearly not feasible. We’d never figure out which one is the most stable one.

"The problem is so difficult, you may think it’s unsolvable. But not all is bad. Scientists found out in the nineteen-fifties that when proteins fold under controlled conditions, for example in a test tube, then the shape into which they fold is pretty much determined by the sequence of amino acids. And even in a natural environment, rather than a test tube, this is usually still the case.

"Indeed, the Nobel Prize for Chemistry was awarded for this in 1972. Before that, one could have been worried that proteins have a large numbers of stable shapes, but that doesn’t seem to be the case. This is probably because natural selection preferentially made use of large molecules which reliably fold the same way.

"There are some exceptions to this. For example prions, like the ones that are responsible for mad cow disease, have several stable shapes. And proteins can change shape if their environment changes, for instance when they encounter certain substances inside a cell. But mostly, the amino acid sequence determines the shape of the protein.

Comment: this article goes own to explain how we are learning about the folding process and predicting how a protein might fold. The point I'm raising is that without this folding process life cannot exist, based on the biochemistry we know. God had to create this roulette game of chance knowing that molecules must be allowed to fold on their own to achieve the speed needed. He was able to create a great many good editing systems, but those systems rely on the same protein folding process, so errors are at times maintained but somehow the errors are insignificant enough that we humans were successfully evolved from bacteria. dhw ignores all of this. Perhaps it is from the lack of understanding the biochemistry of life.