A Human Transcription Factor in Search Mode

Abstract

Transcription factors (TF) change shape to search and recognize DNA, shifting the energy landscape from a weak binding mode to a tight binding mode. But the mechanism of TF conformational change, which deforms DNA during recognition, remains unresolved. Superhelical TFs have a modular helical topology that track along the DNA helical groove. Thus, TF and DNA helical pitch match. Our goal is to develop a mechanism of TF-DNA search and recognition using a superhelical TF as a model. Human MTERF1 is a superhelical TF that terminates transcription by unwinding mitochondrial DNA. The structure of apoMTERF1 is likely flexible: few packing interactions between modules and we are unable to crystallize it. We hypothesize that apoMTERF1 can have low strain conformations with low helical pitch that can track a B-DNA major groove. To characterize apoMTERF1, we used a coarse grained simulation to model intrinsic motions and atomistic MD to obtain a diverse structural ensemble. The coarse grained simulation showed the largest mode of apoMTERF1 is a pitching motion. The MD showed apoMTERF1 is flexible, and unstrained in a conformation with low pitch that matches B-DNA. To show that low pitch apoMTERF1 structures were stable in search mode, we docked these structures to B-DNA and equilibrated the complexes using atomistic MD. The search mode complexes were stable: decreasing in energy and increasing in structural complementarity. Surprisingly, the helical motion from the coarse grained and atomistic simulations was also present in the search mode. The helical motion permits the individual motifs to shift along the sequence in a stepping translocation process and might also be involved in unwinding DNA during recognition. We are currently modeling the transition to recognition mode to test if the mechanism can be explained by MTERF1 natural helical motions.