Proteins folding in aqueous solution


DesCartes world as vortices
DesCartes' drawing of a world built of vortices


     For hundreds of millions of years before life appeared amino acids and protein chains mus
proteins folding in aqueous solutiont have been organizing themselves in water under the influence of sunlight. Moving through seawater, developing hydrophilic and hydrophobic sites, these molecules took on specific chemical bonding characteristics that influenced their folding patterns.
     Surely these rhythmic radiative and thermal sources must have created agitations and movements
folded protein among water molecules and solutes that influenced molecular combinations in the submicroscopic realms where life originated in the ambiance of these very small comings and goings. No wonder the most primitive organisms take on the oscillatory characteristics of water.

     It further follows that with life temperatures limited to a tiny slice of the temperature spectrum the frequencies of the biochemistry of life could not proceed at all possible reaction rates. In addition, on this small scale, the mass of molecules and the frequency characteristics of light would have distributed the rhythms of life into discrete spectra. All the more so when you consider that water as a basic ingredient of life itself can take only certain thermal agitations at normal atmospheric pressures before being bound in an ice lattice or boiling away into steam.

     In addition, wh
ile they were moving, joining, rejecting each other, evolving their autocatalytic properties, the solutes were swimming in water according to their own ionic attractions and repulsions and their stereochemical properties. Moreover, the wind, sun, the earth’s rotation and the moon’s pull drove them too, together imposing their frequencies, flow forms and agitations on the molecules of life.
     The thermal agitation that starts chemical reactions going in living protoplasm may have randomness in it, but the responses of the cytosol to those agitations must be limited by the nature of water and by the chemical constituents dissolved in it.
    Since the major biological energy transactions involve phosphorylation, the rhythmic characteristics of phosphorous in water probably helped shape the original frequencies of mitochondrial chemistry and they are still latent in it. In Investigations, Stuart Kauffman reasons that in this reaction a pyro-phosphate molecule carries the added energy. This PP molecule is cleaved to form P+P and the energy released pushes forward the auto-catalytic reactions permitting life. However, the energy dissipates quickly and Kauffman acknowledges that unless we “add energy to resynthesis PP from P+P” the reactions break down. “To do so,” he continues,

“I invoke an additional source of free energy in the form of an electron e, which absorbs a photon, hv [hv is the formula for Planck’s constant (h) times the frequency of the photon (v)]; is driven endergonically to an excited state e+, and falls back endergonically to its low energy state, e, in a reaction that is coupled to the synthesis of PP from P+P.” 24

     Here is Kauffman’s problem: where do the photons come from? They must exist in nature. If they find their way into life through sunlight on water, as we have argued, they will drive the autocatalytic reactions not randomly at odd moments but in wave fronts or packets with specific frequency and amplitude characteristics. These then find their way into life by generating resonances in the oscillatory media of the molecules.
     Water itself exists in various configurations in the presence of other elements, and bulk water takes on different characteristics according to the ions dissolved in it. Geometric shells of H2O form around solutes. hydration structureThis structured water remains distinguishable from the bulk water around it. So in principle we should be able to detect the rhythmic interplay between bulk water, the hydration structures it builds around other molecules in the water, the water mediated redox reactions and the molecular foldings flowing through it.

       soluteComplex water structure                                              
    Cell membranes themselves are organized by their responsiveness to water; the cell membranes from protozoa to man are constructed of a lipid bilayer with its hydrophobic areas sandwiched between two hydrophilic surfaces punctuated by numerous membrane proteins forming valves and channels, through which all nourishment and information must enter and leave the cell, usually borne by water. You can find a good description of these processes in Christian De Duve‘s marvelous study, A Guided Tour of the Living Cell. 25
     The hydrogen bonds in the water and the ions and charged particles of the matter dissolved in it in turn interact with photons from the sun—and these interactions when life was first forming on the surface of the waters must have influenced the folding of polypeptide chains. Proteins still show their watery influences. They form hydrophilic and hydrophobic regions and turn toward and away from water. They twist into helices that look like tiny whirlpools; they have chirality and turn clockwise or counterclockwise. Perhaps they reflect the Coriolis forces induced in them by the turning earth. The bonding characteristics of water shape its kinetics on small and large scales. Hydrogen bonds are continuously broken and reformed as water rolls and turns.
     In the rates of these tiny spinning vortices, we may find the evolutionary sources for ultradian rhythms that shape biological processes. Arthur Winfree found these whirlpools everywhere in living nature.

“We found it… in tissues made of clocks—and then found the clocks themselves indispensable: in excitable tissue the singularity became the rotating pivot of a spiral wave. We saw it not only in excitable tissue but in nonliving chemical media as well, no longer an abstraction about timing relations but now a visible rotating source of waves. And there we saw the first singularity in its fullest development, as a tornado-like filament arching through three dimensional space to close in a ring.

“Each kind of organizing center is woven in its own distinctive way from fibers of phase singularity, as though from the funnels of chemical tornadoes, organizing centers are little chemical engines made of rotating parts…except that the rotating parts are only patterns of chemical activity, like ghosts in the material substrate. "26     

    Carl Woese, the microbial geneticist who helped develop the paradigmatic theories of horizontal gene transfers between primitive cells, recently wrote “It is becoming increasingly clear that to understand living systems in any deep sense, we must come to see them not as machines, but as stable, complex dynamic organizations.” Freeman Dyson explained in a recent talk “Woese likens organisms to eddies in a turbulent stream that reappear no matter how often they are disturbed.” He invokes the image of the whirlpool. Its rhythmicity is basic to life, carrying and sustaining the information for origin, development and behavior in its spin.27    
     Ivanitsky, Krinsky and Mornev, Russian scientists writing near the end of the Soviet era, showed how oscillating systems generate vortices in all living tissue. Speaking of slime molds they state, “Here again revolving reverberator vortices are the fastest of all local sources of autowaves, because autowave sources have identical properties in all active media, and all other sources are, therefore, suppressed… This is an example of how nature uses reverberators for building up a structure in extreme conditions.”28