Transcription factor allosteric regulation through substrate coordination to zinc
Author(s)
Almeida, Beatriz C; Kaczmarek, Jennifer A; Figueiredo, Pedro R; Prather, Kristala LJ; Carvalho, Alexandra TP
DownloadPublished version (3.864Mb)
Publisher with Creative Commons License
Publisher with Creative Commons License
Creative Commons Attribution
Terms of use
Metadata
Show full item recordAbstract
<jats:title>Abstract</jats:title>
<jats:p>The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight into allosteric transcription factors (aTFs). Here we studied the aTF UxuR, a homodimer of two domains connected by a highly flexible linker region. To explore how ligand binding to UxuR affects protein dynamics we performed molecular dynamics simulations in the free protein, 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 Escherichia 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 can 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 harness these systems for biological systems engineering.</jats:p>
Date issued
2021Department
Massachusetts Institute of Technology. Department of Chemical EngineeringJournal
NAR Genomics and Bioinformatics
Publisher
Oxford University Press (OUP)