Editorial: hypotheses about protein folding - the proteomic code and wonderfolds

Abstract

Theoretical biology journals can contribute in many ways to the progress of knowledge. They are particularly well-placed to encourage dialogue and debate about hypotheses addressing problematical areas of research. An online journal provides an especially useful forum for such debate because of the option of posting comments within days of the publication of a contentious article.

Internal conformation of the 'protein folding code' inferred from empirical tertiary structural classifications using Tlusty's topological approach

“…But the genetic code is only the first of a large nested set of biological information processes, characterized, in its second step, by protein production also constrained by rate distortion dynamics and metabolic free energy [8]. Here we make an application of the topological argument in [1][2][3][4][5][6] to the 'protein folding code' [9]: As Kamtekar et al [10] point out, experimental studies of natural proteins show how their structures are remarkably tolerant to amino acid substitution, but that tolerance is limited by a need to maintain the hydrophobicity of interior side chains. Thus, 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.…”