Douglas Axe - J.Mol.Biol.(2000) 301, 585-595
Previous blog post here.
This paper examines the idea that there are many amino acid residues in an enzyme which almost act as non-specific spacer residues and the nature of their side groups is almost completely irrelevant to the enzyme function. The only requirement is that the external residues be polar and the internal ones be hydrophobic (the binary code hypothesis). The paper argues that this idea is erroneous. Axe’s arguments rely on data from two different, unrelated enzymes.
Firstly, several amino acids are exchanged with several other very similar amino acids on the surface of the molecule and away from the active site and the effects measured. When roughly 1 in 5 of these residues is changed this results in complete loss of function in both enzymes examined.
Secondly, hybrids are constructed between two different versions of B-lactamase enzymes using various combinations of their surface sections. All of these hybrids are inactive.
Axe concludes that homologues that share less than 2/3 sequence identity should be considered as distinct designs with their own set of optimising features.
These results were surprising as they followed similar experiments where the hydrophobic core or an enzyme was systematically replaced and the conclusion was that general hydrophobicity was the only requirement for these core residues.
It was expected that the surface residues distant from the active site would show an even greater degree of tolerance to change than the hydrophobic core residues.
Axe compares the two hybrid situations with two functionally equivalent linguistic messages where exchanges between the non-conserved letters is functionally disastrous.