In living organisms, hundreds of DNA-binding proteins carry out a plethora of roles in homeostasis, transcriptional regulation in response to stress, and in maintenance and transmission of genetic information. These DNA-binding proteins do so faithfully due to their distinct DNA-binding specificity towards their cognate DNA sites.
Yet it remains unclear how related proteins, sometimes with a very similar DNA-recognition motif, can recognize entirely different DNA sites. What were the changes at the molecular level that brought about the diversification in DNA-binding specificity? As proteins evolved, did their intermediates in this process drastically switch DNA-binding specificity or did they transit gradually through promiscuous states that recognized multiple DNA sequences?
To answer these questions, the PhD student will employ a pair of evolutionarily related DNA-binding proteins each with a different DNA preference as model systems. By combining systematic mutational scanning, X-ray crystallography, and biophysical techniques, the student will understand biophysical requirements and constraints to evolve a new protein-DNA interface. The methodologies and concepts that the student develops will be applicable to studying the biophysics and evolutions of other DNA-binding protein families, and to engineer novel protein-DNA complex for synthetic biology applications.