Self-organized networks: Darwinian evolution of dynein rings, stalks, and stalk heads

Abstract

Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality (self-organized criticality). Dynein has three distinct titled subunits, but how these units connect to function as a molecular motor is mysterious. Dynein binds to tubulin through two coiled coil stalks and a stalk head. The energy used to alter the head binding and propel cargo along tubulin is supplied by ATP at a ring 1500 amino acids away. Here we show how many details of this extremely distant interaction are explained by water waves quantified by thermodynamic scaling.Water waves have shaped all proteins throughout positive Darwinian evolution, and many aspects of long-range water-protein interactions are universal (described by self-organized criticality). Dynein water waves resembling tsunami produce nearly optimal energy transport over 1500 amino acids along dynein's one-dimensional peptide backbone. More specifically, this paper identifies many similarities in the function and evolution of dynein compared to other cytoskeleton proteins such as actin, myosin, and tubulin. \body

Phase transitions may explain why SARS-CoV-2 spreads so fast and why new variants are spreading faster

“…This decrease occurs because edge 2 has shifted into better agreement with edges 4 and 6. Such long-range or allosteric interactions occur in motor proteins, where they were quantified by hydropathic scaling 17 . They are known to occur in principle 18 but when small but are detectable using the hydropathic scale with 20 exponents.…”

Synchronized attachment and the Darwinian evolution of coronaviruses CoV-1 and CoV-2

“…The present application uses a technique called hydropathic scaling, which has successfully explained small sequence differences in the evolutions of many protein families The thermodynamic principles of self-organized criticality [3] are universal, and have successfully produced strong signals from the evolution of many proteins [4] , [5] , [6] , [7] , [8] , [9] , [10] , [11] . The shape of a globular protein depends strongly on its ins and outs relative to its center.…”

No waves of intelligent design

“…In PNAS, Phillips ( 1 ) attempts to explore the evolution of dynein, a major motor protein of the eukaryotic cytoskeleton, using different hydropathy scales, and comes to several dramatic conclusions. The results of this analysis are taken to indicate that self-organized criticality (SOC) is integral to evolutionary optimization, that evolution of all proteins occurs, primarily, via positive selection, that this pervasive positive selection is shaped by “water waves” traveling along proteins, and even that the optimization in protein evolution stems from intelligent design.…”

“…The simplest argument against this interpretation is the conservation of the structures and, accordingly, the hydropathy patterns of numerous proteins across hundreds of millions and even billions of years of evolution. Dynein, in particular, is conserved in all eukaryotes and retains the key structural elements and underlying sequence motifs throughout 1.5 billion years or so since the last common eukaryotic ancestor ( 6 ); hence the conservation of the hydropathy patterns that is apparent, in particular, in plots shown by Phillips ( 1 ). There is no reason to believe that the patterns of hydropathy in protein sequences are maintained by positive selection for functionally important “water waves” as opposed to the well-characterized purifying selection eliminating mutations that perturb the protein fold and hence are deleterious.…”