Atomic Physics Seminars

I use single-molecule optical microscopy to address a fundamental question in molecular biology: how does protein’s sequence encode its conformational dynamics and function? The model system that we study is the enzyme adenylate kinase (AK) from Escherichia coli. AK’s lid domain undergoes a large conformational change at the catalytic, millisecond timescale, which leads to a reasonable assumption that this lid dynamics is involved in AK’s enzymatic function; yet, its mechanistic roles and energetics remain elusive. Using the high-resolution time-dependent single-molecule FRET (Förster Resonance Energy Transfer) developed in our group, we have measured AK's lid movements on the millisecond scale and map out its entire conformational distribution along the FRET coordinate without a presumed model. Using these new pieces of information, we have quantitatively recovered AK's energetic landscape and related its stochastic lid dynamics to its catalytic function. Finally, the relationship between AK’s genetic coding and its catalytic function is experimentally established by introducing targeted mutation on specific AK sites. This study provides new perspectives on protein engineering.