pH, water, amino acids and protein folding

Solubilities of amino acids in water at various pH values under 298.15 K and Translational tuning optimizes nascent protein folding in cells link what is currently known about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding to cell type differentiation in all genera via conserved molecular mechanisms.  Mutations are linked from perturbed protein folding to pathology. See for example:

From “Science Mission
5/2/15 at 12 pm Water diffusion and neurodegenerative disease linked to Hydration water mobility is enhanced around tau amyloid fibers

The human protein tau helps stabilize microtubules, which form a part of the cellular backbone. However, in pathological conditions marked by neurodegeneration, such as Alzheimer’s disease (AD), the tau protein can aggregate into fibers, which are broadly organized into a rigid core and a flexible coat.
The authors report inn PNAS that the fraction of water molecules undergoing diffusion around the fibers was 25% greater than that around the monomers, suggesting increased water entropy, which favors fiber formation. Further, the authors report that the increased movement of water around the fibers likely occurs around the coat rather than around the core of the fibers.
Increases in water diffusion in the hippocampus in the brain of AD patients have been previously proposed as a potential early biomarker of AD that is detectable through diffusion MRI. According to the authors, the reported increases in water diffusion may be partly attributable to enhanced water mobility around tau fibers, thus providing a potential basis for the clinical utility of the biomarker.

From “Science Mission

5/3/15  at ~10 am Dismantling the vibrational theory of smell linked to Implausibility of the vibrational theory of olfaction

The molecular mechanisms that allow humans and other animals to smell remain unclear. Researchers have proposed various theories of olfaction, the most controversial of which—known as the vibrational theory of olfaction (VTO)—posits that odorants are detected via their vibrational frequencies rather than through hand-in-glove-like substrate–receptor interactions.
According to the VTO, electron transfer should occur across odorants at the active sites of odorant receptors, and different electron transfer rates should be observed for isotopomers, which differ in their vibrational frequencies. Studies by VTO proponents showed that humans can distinguish among the smells of various isotopomers. However, the authors found no differences in receptor response to the odorants tested.
Furthermore, the current study demonstrates that the proposed electron transfer mechanism can be suppressed by quantum effects of nonodorant molecular vibrational modes. The authors suggest that the ability of humans to distinguish isotopomers reflects impurities or isotope effects occurring in the nasal mucus surrounding the receptor, rather than receptor-level vibrational effects.
According to the authors, the study provides experimental and theoretical evidence to contradict the VTO at the receptor level, and suggests that the theory is implausible.

My comment: The attempt to dismantle the vibrational theory of smell was introduced after I commented on the obvious link from soluabilities of amino acids in water to cell type differentiation linked from the epigenetic effects of food odors and pheromones to the physiology of reproduction in species from microbes to man. See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
No attempt has been made to address the facts that link the light-induced de novo creation of amino acids to nutrient-dependent amino acid substitutions that link metabolic networks to genetic networks via cell type differentiation in all genera. Instead, it sometimes appears that “Science Mission” would rather introduce obfuscation based on claims about theories. In this case, however, what they did obfuscates fact that link quantum physics, quantum smell, quantum biology, and quantum consciousness via Luca Turin’s theory. See: A Spectroscopic Mechanism for Primary Olfactory Reception; Molecular Vibration-Sensing Component in Human Olfaction; Electron spin changes during general anesthesia in Drosophila, and Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare.
Others have become aware of links that extend across species via what is currently known about physics, chemistry, and conserved molecular mechanisms of cell type differentiation. See also: Role of olfaction in Octopus vulgaris reproduction.

The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

My comment: Until there is another model of cell type differentiation in all genera that does not include Turin’s molecular vibration theory, dismissing it seems as inappropriate now as it did when he first proposed an alternative to the pseudoscientific nonsense about evolution that has been touted by evolutionary theorists.  They have not addressed what must be included, and it appears that they would rather the links were not considered by others. Unfortunately, the links from the biophysically constrained chemistry of nutrient-dependent RNA-mediated amino acid substitutions and protein folding must be considered. If they are not, the mission of “Science Mission” will fail.
See also from “Science Mission
Phytoplankton and Arctic warming feedback linked to Amplified Arctic warming by phytoplankton under greenhouse warming

One of the important impacts of marine phytoplankton on climate systems is the geophysical feedback by which chlorophyll and the related pigments in phytoplankton absorb solar radiation and then change sea surface temperature.

Yet such biogeophysical impact is still not considered in many climate projections by state-of-the-art climate models, nor is its impact on the future climate quantified.

A study published in the journal PNAS shows that, by conducting global warming simulations with and without an active marine ecosystem model, the biogeophysical effect of future phytoplankton changes amplifies Arctic warming by 20%.

Given the close linkage between the Arctic and global climate, the biologically enhanced Arctic warming can significantly modify future estimates of global climate change, and therefore it needs to be considered as a possible future scenario.”

My comment: Thermodynamic cycles of protein biosynthesis and degradation link every article cited above to the conserved molecular mechanisms of health and pathology via links from the epigenetic landscape to the physical landscape of DNA in the organized genomes of all genera. The links extend what is currently known about the de novo creation of amino acids to cell type differentiation in the context of the nutrient dependent physiology of reproduction that is linked to the biodiversity of species from microbes to man via RNA-mediated amino acid substitutions.

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