Dynamic Protein Folding


A very exciting aspect of Dynamic Evolution is the subject of protein folding; a function that occurs all the time in almost every one of our body cells.

protein_folding_cube

There are more than 23,000,000 protein sequences that have been identified through genomic sequencing which aim to determine an organism’s entire DNA sequence. Current scientific methods take from a few months to many years to determine a single structure. Protein structure prediction requires extremely powerful computational resources to explore the huge number of possible structural conformations of proteins.

Each protein consists of a chain of amino acids. When two amino acids bond together, they can take on one of roughly ten different orientations. So a chain of 3 amino acids can be 10^3 different shapes.

The fastest folding protein discovered so far is a structure called a 3-stranded beta sheet. As its name suggests, it is a surface formed from three strands of protein that bind together. In total, these sheets contain up to 90 amino acids. Therefore, in theory they can take on any of 10^90 different shapes. If these shapes were tried at the rate of 100 billion a second, it would take longer than the age of the Universe to find the correct fold. And yet, more than 7 million of these 3-stranded beta sheets are folded in just one second!

proteinfolding-l

But there is a problem with our current understanding of how this works. Proteins ought to be more stable at lower temperatures. But they’re not. A well-known property of many proteins is that their structure collapses as the temperature drops. So any model of protein folding has to account for this too.

Protein folding does not occur in isolation but in solution. So the amino acid chain is surrounded by water molecules. At close range, these form a shell around the protein chain.

The water molecules form hydrogen bonds with the amino acids. As long as the temperature remains relatively high, the hydrogen bonds are constantly being broken and forming again and the folding proceeds in the usual rapid fashion. But if the temperature drops, the hydrogen bonds become permanent, allowing the protein to take on new low-energy configurations.

This suggests that a powerful new understanding of protein folding could come from a better understanding of the properties of water at these tiny scales.

The network of links between water molecules confined on this scale have a dramatic impact on the behavior of protein folding. There may even be a quantum coherence associated with these links, which suggests a new way to approach this problem — treating it as a kind of quantum computation.

For further details, see the book Dynamic Evolution, available in the Introduction section.

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