Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations.

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.