Abstract
AbstractA spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein 'molten globule'. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty's (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Highlights
The symmetries of folded proteins remain something of a scientific mystery, in spite of decades of concerted attention
But less overtly ‘symmetric’, conformations, involve finite tilings of helices, sheets, and attachment loops that would seem better described using groupoid methods, following the arguments of Weinstein (1996): As Wolynes (1996) put the matter, “It is the inexact symmetries of biological molecules that are most striking”
The argument, an extension of Tlusty’s (2007) insights regarding the role of rate distortion constraints in evolutionary process, seems fairly direct, based on standard material from statistical physics and information theory
Summary
The symmetries of folded proteins remain something of a scientific mystery, in spite of decades of concerted attention. We will attempt to finesse this perspective by invoking, first, a rate distortion argument applied to the transmitted signal represented by the translation of the genome into the final condensation of the molten globule of the resulting amino acid string. The second stage is to examine the likely effect of limited availability of metabolic free energy, or processing time, on the fidelity of this transmission. The observation of a possible ‘metabolic singularity’ limiting that fidelity suggests, in turn, that possible protein symmetries were, in some measure, limited by energy availability in prebiotic circumstances, leading to early evolutionary lock-in by path dependence. The argument, an extension of Tlusty’s (2007) insights regarding the role of rate distortion constraints in evolutionary process, seems fairly direct, based on standard material from statistical physics and information theory
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