Antithetical conclusions (6)

By: James V. Kohl | Published on: August 20, 2016

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Biochemical and Structural Insights into Doublecortin-like Kinase Domain 1 (Subscription required)

Abstract excerpt:

This structure also allowed for the mapping of cancer-causing mutations within the kinase domain, suggesting that a loss of kinase function may contribute to tumorigenesis.

Continued

See: Antithetical conclusions (5, 4, 3, 2)

In the same issue of this journal, see: A Second RNA-Binding Site in the NS1 Protein of Influenza B Virus (Subscription required)

Abstract excerpt:

We demonstrate that single-site alanine replacements of basic residues in this site lead to reduced RNA-binding activity, and that recombinant influenza B viruses expressing these mutant NS1B proteins are severely attenuated in replication. This novel RNA-binding site of NS1B is required for optimal influenza B virus replication. Most importantly, this study reveals an unexpected RNA-binding function in the C-terminal domain of NS1B, a novel function that distinguishes influenza B viruses from influenza A viruses.

They linked virus-driven energy theft from hydrogen-atom transfer in base pairs in solution to the RNA-mediated amino acid substitution “…that distinguishes influenza B viruses from influenza A viruses.” They report the substitution in the context of “single-site alanine replacements of basic residues.” Energy-dependent fixation of the basic residues links hydrogen-atom transfer in base pairs in solution to healthy longevity.

If I had access to the publication or to the one that links angstroms to ecosystems in all living genera in the context of the Structural diversity of supercoiled DNA, I might be able to link virus-driven energy theft to all pathology in the context of what is already known about the links from angstroms to ecosystems in all living genera. For example: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

See how I forced the authors of Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution to admit that viruses do not evolve. They adapt to their host cell or host organism via energy theft. The authors wrote: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

The Quest to End the Flu (my comment)

Note: SARCASM ALERT: When I wrote “I’m not sure that the laws of physics apply to viruses and their replication.” — I should have warned readers that I was using sarcasm to force their response. Of course the laws of physics apply to viruses. Their claims indicated the laws of physics might not apply.

jvkohl • 3 years ago

See also: “Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution”
The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.
The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.
If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).
If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.
Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?