Saturday, October 17, 2015

Quantum criticality and protein folding

In Thinking Allowed Original there was a link to a new observation about protein folding process. During folding some proteins hold single building blocks in shapes that were thought to be impossible to find in stable form. Stable shapes contained some parts, which were trapped like mosquitos in amber.

A concrete TGD based model relies on the general ideas of TGD inspired quantum biology.

  1. Biomolecules containing aromatic rings play a fundamental role. All DNA nucleotides contain them and there are 4 proteins, which also have them. trp and phe are of special importance and form a pair structurally analogous to a base pair in DNA strand. The rings are assumed to carry the analog of supra current and be in or at least be able to make transition to a state with large heff. The delocalization of electron pairs in aromatic ring could be a signature of heff/h>1.

  2. trp-phe pairing would be responsible for information molecule-receptor pairing. Information molecule and receptor would be at the ends of flux tubes serving as communication lines, and the attachment of info molecule to receptor would fuse the two flux tubes to longer one. After that communication would become possible as dark photon signals and dark supra currents. Formation of info molecule-receptor complex would be like clicking icon generating a connection between computers in net. Info molecules would generate the communication channels - they would not be the signals. This is the distinction from standard neuroscience.

  3. All quantum critical phenomena involve generation of large heff phases. Folding emerges or disappears at quantum criticality (QC) possible in certain temperature range of width about 40 K and depending on pH. The flux tubes associated with phe and trp containing aromatic rings carrying "supra current" would become dark (either h→ heff or heff> h increases) and thus much longer and reconnect temporarily and force phe and trp in a close contact after the reverse transition inducing shortening. This is a general mechanism making biomolecules able to find each other in what looks like molecular soup in the eyes of standard biochemist. The contacts between amino-acids phe and trp formed in this manner are structurally identical with the hydrogen bonding between members of DNA base pairs and they would fix the final folding pattern to high degree.
There was also a link to very interesting article about possible topological phenomena related to protein folding. Authors are Henrik and Jakob Bohr (akin to the Great Niels Bohr?) and Sören Brunak.

The article is very easy to read and explains the basic topological concepts like winding in a simple manner. The proposal is that the excitation of so called wringing modes of proteins are involved in the generation and disappearance of the protein folding. Excitation of wringing modes twisting the protein (think about how one wrings water from a wetted cloth) would make the protein folding state cold denatured unstable and transform in to stable folded (F) state. In the same manner their excitation would transform hot denatured (HD) stable state to folded state. Wringing modes could be excited by radiation.

In TGD framework the folding phase diagram CD-F-HD could be understood also in terms of quantum criticality (QC). Perhaps the simplest option is that the transitions CD-F and HD-F involve a generation of critical states leading to a generation of long range correlations (large heff) inducing the folding pattern. Absorption of photons to wringing modes would induce the criticality and the folding would proceed by the mechanism discussed above.

For background see the chapter More Precise TGD Based View about Quantum Biology and Prebiotic Evolution or article with the same title.

For a summary of earlier postings see Links to the latest progress in TGD.

3 Comments:

At 12:47 AM, Blogger Leo Vuyk said...

About the folding aspects of the micro world, I would suggest to assume that we have to do with the rotation with staps of 90 degrees internal quantum structure. see: https://www.flickr.com/photos/93308747@N05/albums/72157633110734398

 
At 12:31 PM, Blogger Ulla said...

https://www.newton.ac.uk/files/seminar/20120905115012101-153268.pdf

 
At 1:29 AM, Anonymous Matpitka6@gmail.com said...

DNA folding mechanism looks very interesting since it also distinguishes between prokaryotes and eukaryotes with much larger genome. Histones are proposed to contain kind of figure eights giving rise of 10 nm sized very loopy but un-knotted balls if I understood correctly. Does the reconnection of closed circular protein loop through which DNA goes and returns back give rise to these figure eights? Does re-connection giving rise to figure eight involve hydrogen bonding between aromatic rings of trp and phe so that it would be analogous to base pairing in DNA?

 

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