Physical Chemistry Seminar: Dr. John King, Institute for Basic Science, Center for Soft and Living Matter, Ulsan, South Korea
About the Seminar
Insights into Biochemical Processes with Single-Molecule Spectroscopy and Super-Resolution Microscopy
Much of our understanding of protein function and mechanism of action is deduced from a static 3D structure of a native conformational state of the protein. However, proteins are soft, dynamic molecules that constantly move along complex free-energy landscapes, either through equilibrium fluctuations or through the input and dissipation of energy. Furthermore, kinetics of diffusion–limited reactions are dictated by transport mechanism, which can deviate significantly from simple behavior in complex environments. Characterizing the free-energy landscapes and the mechanism of sampling alternative states, as well as resolving the connection between transport and reaction kinetics, remain outstanding challenges in biophysics.
In the first part of the talk, I will discuss our studies of protein operating under nonequilibrium conditions. Despite the importance of motor and pump proteins, we have a limited understanding of how they achieve high efficiency directional action against randomizing thermal noise. Using novel implementations of single–molecule techniques, we have quantified key thermodynamic parameters including entropy production rate and heat dissipation, for the reaction cycle of an unmodified pump protein during its operation. This work highlights the connection between the thermodynamics of reaction cycles and the efficiency of protein function.
Secondly, I will discuss our studies on the transport properties of small molecules in biological condensates. Transport within protein–nucleic acid droplets formed through liquid–liquid phase separation (LLPS) is critical for the maintenance of biochemical reactivity. Though LLPS droplets are typically modelled as simple liquids, their structure is reminiscent of complex fluids, with complex physical and chemical interactions expected on the nanoscopic length scale. Leveraging super–resolution microscopy, deviations from Fickian diffusion is shown to be a general feature of transport within LLPS droplets. This work establishes a foundation for future studies connecting the unique transport within droplets to their function of enhancing the kinetics of biochemical reactions.