Abstract
AbstractTlusty's topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. The underlying 'protein folding code network' is found to have one major, highly dominant 'spherical' component, a minor attachment handle in the Morse Theory sense, and as many as two or three additional subminor handles.
Highlights
Tlusty’s application of rate distortion and topological approach to the genetic code [1,2,3,4,5,6] is significant for insights regarding the code itself, and for possible applications to a broad class of biological phenomena associated with information transmission
The rate distortion argument in [1,2,3,4,5,6] can be rigorously restated in more traditional information theory terms and generalized to nonequilibrium dynamics constrained by the availability of environmental metabolic free energy [7]
The genetic code is only the first of a large nested set of biological information processes, characterized, in its second step, by protein production constrained by rate distortion dynamics and metabolic free energy [8]
Summary
Tlusty’s application of rate distortion and topological approach to the genetic code [1,2,3,4,5,6] is significant for insights regarding the code itself, and for possible applications to a broad class of biological phenomena associated with information transmission. While the information needed to encode a particular protein fold is highly degenerate, this degeneracy is constrained by a requirement to control the locations of polar and nonpolar residues. This is the precise protein folding analog to Tlusty’s error network analysis of [1,2,3,4,5,6], and his graph coloring arguments should apply, in some measure, to protein folding as well, allowing inference on the underlying structure of the ‘protein folding code’
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