Tuesday, August 11, 2015

Could protein dynamics be dictated by the magnetic body of the protein with the mediation of water?

Hans Frauenfelder et al propose a unified model of protein dynamics based on experimental findings. The key proposal is that protein dynamics is slaved by the hydration shell and by the bulk solvent. The dynamics of master should be slower than that of slave. The conformational motions of proteins have time scale in the range 1 ns-1 s. The frequencies corresponding to the splitting of hydrogen bonds are above 10 THz and hence splitting dynamics is faster than protein dynamics. Therefore the claimed master-slave relation looks strange at the first glance. One can however think that the cleaving of hydrogen bonds defines the control dynamics as dynamics of switching and is much faster process than processes occurring between switchings. Changing the position of switch would correspond to a catastrophe in catastrophe theoretic formulation. The dynamics at a given sheet of catastrophe is indeed slow except at the critical lines defining its boundaries.

This suggests that various phases of water define environments for water controlling the behavior of proteins. Quantum phase transitions would put switches on and off. If the phase is hydrogen bonded water clathrate, the protein finds itself inside "ice" layer and cannot move. Protein unfolding proceeding as quantum phase transition would represent a basic example of this situation. When the hydrogen bonds disappear due to the melting of the EZ around protein by the splitting of protein-water and water-water hydrogen bonds, protein becomes able to change its conformation and protein un-folding can occur. The "ice" layer around protein can melt by the feed of external energy at energies below metabolic energy quantum. This radiation could arrive as dark photons from dark magnetic body decaying into bunches of ordinary photons with same frequency and inducing fast melting of the entire layer. The bulk solvent could control large scale protein motions by changing the viscosity achieved by modifying the density of hydrogen bonds. Protein would move in the direction where the resistance is smallest.

In ZEO the reverse process would correspond to melting but in non-standard time direction. One can interpret the situation also in terms of consciousness theory. The period between folding and unfolding would define self and the control action would generate the time reversal of self.

But "who" is the master? In TGD framework it would be naturally the dark magnetic body containing at its flux tubes dark proton sequences associated with proteins. The motor actions of the magnetic body would induce those of proteins. The only condition is that the inherent protein dynamics is fast enough to follow the dynamics of the magnetic body. The fingerprints of biomolecules are in energy region .05-.25 eV (this is also the energy range for hydrogen bond energies) and the frequencies are above 10 THz. Therefore the time scales of protein dynamics would actually reflect those of dark magnetic body.

The modelling of protein folding as a random process in which system tries all options and ends up to the bottom of potential well representing the final configuration has problems: the basic paradox is that the folding should take extremely long time. If protein folding is macroscopic quantal self-organization process governed by NMP in present of large heff phases, these problems might be circumvented. Folding could to high extent reduce to the folding of the underlying magnetic flux tube structure: proteins would follow automatically if they are surrounded by the "ice" layer of ordered water.

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

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

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