We will discuss how a protein's diffusion is affected by 1) its heterogeneous environment in living cells and, in the case of an enzyme, 2) catalytic reactions it performs from in vitro single molecule studies.
1) In the heterogeneous environment characteristic of living cells, proteins can exhibit apparent anomalous diffusion. We present an inverse modeling method to extract a microscopic model for this emergent anomalous behavior. In this collaborative work with Rich Day's lab at IU, we show that a distribution of protein binding affinities to DNA can give rise to apparent anomalous diffusion.
2) In collaboration with the labs of Carlos Bustamante and Susan Marqusee at UC Berkeley, we have investigated how single enzymes which perform highly exothermic reactions rapidly dissipate the catalytic reaction heat in order to sustain their high turnover efficiency. The reaction heats evolved in just one reaction often exceed the amount of energy required to unfold a small protein. We will discuss our jointly developed model suggesting that enzymes dissipate heat by transiently accelerating their center of mass (COM) immediately following an enzymatic turnover event. According to our model, COM acceleration happens because the enzymatic turnover event causes a quick asymmetric deformation of the protein which rapidly compresses the solvent closest to the catalytic site. We will discuss how the solvent's immediate response to this compression is two-fold: i) it dissipates part of the energy - transiently stored as a compression - as an outgoing acoustic wave in the solvent (a new 'chemoacoustic effect') and ii) by Newton's third law, the solvent also pushes back on the enzyme causing a COM displacement.