Oxygen channels and fractal wave–particle duality in the evolution of myoglobin and neuroglobin

Abstract

The evolution of terrestrial and aquatic wild type (WT) globins is dominated by changes in two proximate -distal Histidine ligand exit channels, here monitored quantitatively by hydropathic waves. These waves reveal allometric functional features inaccessible to single amino acid stereochemical contact models, and even very large all-atom Newtonian simulations. The evolutionary differences between these features between myoglobin and neuroglobin are related to the two oxidation channels through hydropathic wave analysis, which identifies subtle interspecies functional differences inaccessible to traditional size and metabolic scaling studies. Our analysis involves dynamic synchronization of allometric interactions across entire globins.

Evolution of the ubiquitin-activating enzyme Uba1 (E1)

“…The hydrophobic extrema of neuroglobin form sophisticated patterns that are closely related to the evolution of specific species. For example, mouse and rabbit escape predators in different ways, and these differences are recognizable in their Ψ(aa,W*) profiles [9].…”

Giant hub Src and Syk tyrosine kinase thermodynamic profiles recapitulate evolution

“…1 the hydroprofiles Ψ(aa,21) of human Syk using both the first-order KD scale, and the second-order MZ scale. Careful study of these profiles, especially the hydrophobic peaks (spines) [7], and hydrophilic minima which function as elastic hinges [2], shows good correspondence with the Uniprot indicated Euclidean domain and region edges, determined entirely from static structural data. As expected, the differences between the two profiles are small, and appear to be too small to be quantified by evolution.…”

Thermodynamic Scaling of Interfering Hemoglobin Strain Field Waves

“…Hemoglobin (Hgb) transports small gas molecules (O 2 , CO) to and from tissues, while myoglobin (Mgb) stores these molecules in tissues, and neuroglobin (Ngb) also stores them, but specifically in the central nervous system and retina. In an earlier paper we showed that the evolutionary development of many subtle features of Mgb and Ngb could be monitored quantitatively by using hydropathic bioinformatic scaling. The main features of our recently developed bioinformatic scaling method were described there: amino acid (aa) specific hydropathic scales Ψ­(aa), and their intrachain averages over sliding windows of wavelength W , Ψ­(aa, W ).…”

“…Our hydropathic analysis shows that small-gas ligand entry and exit globin allometric dynamics can be dominated by longitudinal hydropathic strain at a single chain length, the spacing between proximate receptor–distal gate His. The importance of these gates has been demonstrated in many elegant experiments . Compared to enriched multidimensional Newtonian all-atom simulation models, our hypermodern approach based only on one-dimensional optimized hydropathic amino acid square wave profiles may appear simplistic.…”