Sequence structure mappings of proteins

In this section we do not aim at a presentation of the current state of the art in the design of proteins by variation and selection. This will be done in great detail in the other chapters of this volume. What we shall try to do instead is a comparison of results derived for proteins and RNA molecules to point out common features as well as differences. 

Protein sequence space was postulated as a useful tool for discussing protein evolution already in 1970 [54]. Later on most extensive model studies were more or less 

Neutral networks [41] represent more or less the basic and most important feature of genotype-phenotype mappings. Although protein structure and function has been discussed with respect to neutrality for a very long time, direct evidence for neutrality and neutral networks came only recently from empirical potentials and neural network studies [58, 59]. Other investigations on protein foldability landscapes are in general agreement with the existence of extended neutral networks too [60, 61], 

It is worth mentioning in this context that there seems to be a general difference between RNA and protein landscapes Certain amino acid composition ratios between hydrophobic and hydrophilic amino acids presumably give rise to insoluble aggregates and this may lead to holes in protein sequence space. Perhaps, the concept of holey adaptive landscapes as favored in a series of recent papers on models of evolution [62] might be useful in this context. 

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