Allosteric
autoinhibition exists in many transcription factors. The ERG proteins
exhibit autoinhibition on DNA binding by the C-terminal and N-terminal
inhibitory domains (CID and NID). However, the autoinhibition mechanism
and allosteric pathway of ERG are unknown. In this study we intend
to elucidate the residue-level allosteric mechanism and pathway via
a combined approach of computational and experimental analyses. Specifically
computational residue-level fluctuation correlation data was analyzed
to reveal detailed dynamics signatures in the allosteric autoinhibition
process. A hypothesis of “NID/CID binding induced allostery”
is proposed to link similar structures and different protein functions,
which is subsequently validated by perturbation and mutation analyses
in both computation and experiment. Two possible allosteric autoinhibition
pathways of L286-L382-A379-G377-I360-Y355-R353 and L286-L382-A379-G377-I360-Y355-
A351-K347-R350 were identified computationally and were confirmed
by the computational and experimental mutations. Specifically we identified
two mutation sites on the allosteric inhibition pathways, L286P/Q383P
(NID/CID binding site) and I360G (pathway junction), which completely
restore the wild type DNA binding affinity. These results suggest
that the putative protein structure–function relationship may
be augmented with a general relationship of protein “structure/fluctuation–correlation/function”
for more thorough analyses of protein functions
