Transcription Factor Allosteric Regulation Through Substrate Coordination to Zinc

The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight on allosteric transcription factors (aTFs). Here we studied the aTF UxuR, which is a dimer, with each monomer consisting of two structured domains connected by a highly flexible linker region. In order to explore how ligand binding to UxuR affects protein dynamics we performed molecular dynamics simulations in the free protein and the aTF bound to the inducer D-fructuronate or the structural isomer D-glucuronate. We then validated our results by constructing a sensor plasmid for D-fructuronate in E. coli and performed site-directed mutagenesis. Our results show that zinc coordination is necessary for UxuR function, since mutation to alanines prevents expression de-repression by D-fructuronate. Analyzing the different complexes, we found that the disordered linker regions allow the N-terminal domains to display fast and large movements. When the inducer is bound, UxuR is able to sample an open conformation with a more pronounced negative charge at the surface of the N-terminal DNA binding domains. In opposition, in the free and D-glucuronate bond forms the protein samples closed conformations, with a more positive character at the surface of the DNA binding regions. These molecular insights provide a new basis to better harness these systems for biological systems engineering.