Amino acid coevolution induces an evolutionary Stokes shift

Proceedings of the National Academy of Sciences of the United States of America
David D PollockRichard A Goldstein

Abstract

The process of amino acid replacement in proteins is context-dependent, with substitution rates influenced by local structure, functional role, and amino acids at other locations. Predicting how these differences affect replacement processes is difficult. To make such inference easier, it is often assumed that the acceptabilities of different amino acids at a position are constant. However, evolutionary interactions among residue positions will tend to invalidate this assumption. Here, we use simulations of purple acid phosphatase evolution to show that amino acid propensities at a position undergo predictable change after an amino acid replacement at that position. After a replacement, the new amino acid and similar amino acids tend to become gradually more acceptable over time at that position. In other words, proteins tend to equilibrate to the presence of an amino acid at a position through replacements at other positions. Such a shift is reminiscent of the spectroscopy effect known as the Stokes shift, where molecules receiving a quantum of energy and moving to a higher electronic state will adjust to the new state and emit a smaller quantum of energy whenever they shift back down to the original ground state. Predictions ...Continue Reading

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Related Concepts

Purple acid phosphatase 26, Arabidopsis
Acid Phosphatase
Neoglycoproteins
Phylogeny
Plant Proteins
Fluorescence Spectroscopy
Thermodynamics
Protein Folding, Globular
Evolution, Molecular
Amino Acid Substitution

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