Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity

Enzymes exist as
ensembles of conformations that are important
for function. Tuning these populations of conformational states through
mutation enables evolution toward additional activities. Here we computationally
evaluate the population shifts induced by distal and active site mutations
in a family of computationally designed and experimentally optimized
retro-aldolases. The conformational landscape of these enzymes was
significantly altered during evolution, as pre-existing catalytically
active conformational substates became major states in the most evolved
variants. We further demonstrate that key residues responsible for
these substate conversions can be predicted computationally. Significantly,
the identified residues coincide with those positions mutated in the
laboratory evolution experiments. This study establishes that distal
mutations that affect enzyme catalytic activity can be predicted computationally
and thus provides the enzyme (re)­design field with a rational strategy
to determine promising sites for enhancing activity through mutation.