Biophysical constraints on RNA synthesis (3)

By: James V. Kohl | Published on: March 26, 2019

Excerpt: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on DNA base pairs in solution and RNA-mediated amino acid substitutions to chromosomal rearrangements via pheromone-controlled changes in the microRNA / messenger RNA balance. 3/2/16
Update: pH-dependent gating mechanism of the Helicobacter pylori urea channel revealed by cryo-EM 3/20/19

Site-specific mutations in the periplasmic domain and urea pore identified key residues important for channel function.

In summary, we have determined the structures of the closed and open conformations of H. pylori UreI channel both at a resolution of 2.7 Å.

Reported as: Key details about bacterium that increases risk for stomach cancer (3/26/19)

Zhou, Munson and their colleagues also engineered variations of the urea channel, shuffling different amino acids into key spots. They tested those variations at different levels of acidity to see which substitutions interfered with the protein’s action. The experiments enabled the scientists to identify which parts of the urea channel are involved in sensing acidity and altering its shape to let in urea.

Naturally occurring energy-dependent variations link selection for codon optimality to biophysically constrained viral latency via RNA interference, which prevents the formation of toxic amino acids/toxic peptides/toxic residues.
The toxicity increases with acidity because viral replication occurs more rapidly with slight changes towards the lowered potential of hydrogen (pH). Typically, hydrogen-atom transfer in DNA base pairs in solution is linked from the creation of ATP and the creation of RNA to biophysically constrained healthy longevity.
But see:
Systemic effects of cancer: role of multiple proteases and their toxic peptide products (2005)
Bad taste protects fruit flies from eating a toxic amino acid in plants (2009)

An orphan G-protein-coupled gustatory receptor mediates detection of the plant poison L-canavanine in fruit flies.

Halo Assay for Toxic Peptides and Other Compounds in Microorganisms (2016)

Di-/tripeptides are one of the major sources of nitrogen, carbon, and amino acids for all organisms. Synthetic peptides containing a toxic amino acid residue provide an experimental approach to measure peptide transport and/or utilization in Saccharomyces cerevisiae.

Conditional potency is a hallmark of viral protein-derived toxic peptides (2017)

…conditional potency of viral protein-derived toxic peptides could at least in part explain cell senescence upon viral infections.

Conditional potency and toxicity of viruses can now be measured in the context of links from energy-dependent changes in angstroms to ecosystems in the context of what is known about ecological adaptations and pH-dependent changes in fluorescence.
See: Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems (2018)
In pH-dependent gating mechanism of the Helicobacter pylori urea channel revealed by cryo-EM, they linked hydrogen-atom transfer in DNA base pairs in solution from the light-activated assembly of the microRNA-RNA-peptide nanocomplex to protection from bacteriophages in H. pylori via pH-dependent fixation of RNA-mediated amino acid substitutions.
Who remembers when Barry Marshall predicted this in 1985?
See also: “Ronning’s team focused on H. pylori’s use of a unique biosynthetic pathway to synthesize vitamin K2, which aids in the electron transfer processes, or chemical reactions, of all organisms.
One of the things I like most about facts that come from years of test development for use in the medical laboratory is how the facts attest to the overwhelming ignorance of theorists who still tout their nonsense about mutation-driven evolution.  For example,  at a resolution of 2.7 Å, “…the cryo-EM structures… in closed and open conformations… define a gating mechanism that is pH dependent and requires cooperativity between protomers in the hexamer.” That links light-activated energy-dependent changes to supercoiled DNA.
The ability of different peptides to inhibit autophosphorylation of EGFR is presented by the decrease of the fluorescent signal (Y axis).
That claim was linked to the prevention and/or the effective treatment of all cancers.
Please place all similar claims about the links from angstroms to ecosystems and fluorescence into the context of this parody.

 “Every angstrom is dynamic from the 5 prime to the 3.”

Join the serious scientists who will continue to ridicule biologically uninformed theorists.
Link the virus-driven degradation of messenger RNA from the creation of toxic peptides to disease via the “Virus-mediated archaeal hecatomb in the deep seafloor” The light-activated assembly of the microRNA-RNA-peptide nanocomplex links the physiology of reproduction to all biodiversity in all living genera via the creation of anti-entropic virucidal sunlight and Eukaryotic plankton diversity in the sunlit ocean.
On 2/4/19, that fact led me to ask an antagonist if he knew how peptides are created. He wrote:

Do I know how peptides are created? Hmm, I wrote a PhD on protein biochemistry. So yeah, I’d say I have a fair idea champ.

Immediately, I realized that I should have asked if he knew where the energy to create the peptides and other building blocks came from.
Ages ages 10+ can learn what he hadn’t learned by playing Subatomic and Cytosis

For comparison, re: Dr Darren Saunders @whereisdaz

You are blocked from following @whereisdaz and viewing @whereisdaz‘s Tweets.

See also:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on DNA base pairs in solution and RNA-mediated amino acid substitutions to chromosomal rearrangements via pheromone-controlled changes in the microRNA / messenger RNA balance. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent & pH-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Critical limits for enhanced medical care already include what is known about the RNA-mediated physics and chemistry of biologically-based ecological, social, neurogenic and socio-cognitive niche construction. The epigenetic landscape is clearly linked to the physical landscape of supercoiled DNA and top-down causation is manifested in increasing organismal complexity in species from microbes to humans. In all vertebrates and invertebrates the reciprocal relationships of species-typical nutrient-dependent & pH-dependent morphological and behavioral diversity are enabled by microRNAs, adhesion proteins, and pheromone-controlled reproduction. Ecological variation and biophysically constrained natural selection of nutrients cause the RNA-mediated behaviors that enable ecological adaptations, which include development of the brain during life history transitions. Ideas from population genetics typically exclude ecological factors, which must be linked to cell type differentiation. Theories are integrated with an experimental evidence-based approach that establishes what is currently known in the context of this mammalian model.

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