Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics

Abstract

Proteins are the main executors of complicated biological functions in nature. All the function-related structures and dynamics of proteins are encoded through the sequences with a 20-letter amino acid alphabet. Though the amino acid alphabets and the sequences are much more complex than that of the nucleic acids, the ubiquitous structural and functional homologs suggest there is much redundancy in the sequences and the alphabets. The discovery of the hidden simplicity of the amino acid alphabet could greatly help to disclose the regularities of protein systems and may stimulate some novel designs of protein, and has become one area in biological physics with continuous attentions. Physically, this kind of simplicity is a reflection and requirement of the folding landscape of proteins. In this review, we would like to describe the simplification problem of amino acid alphabet from physics aspect. The resultant extensions in bioinformatics and the relevant physical implications would also be discussed.