(57f) Force Fluctuations Play a Key Role in Biomolecular Kinetics

A wide array of biological processes occur at rates that vary significantly with force. Instantaneous molecular forces fluctuate due to thermal noise and active processes, leading to concomitant fluctuations in biomolecular rate constants. While such fluctuations are generally ignored in the current prevailing view of force-dependent enzyme kinetics, we employ a widely-applicable analytic method to demonstrate that force fluctuations can have a dramatic impact on effective rates.

A critical question in cellular biology is how the proteins responsible for reading and replicating the genome process packaged DNA. We address one aspect of this problem by considering the kinetics of RNA polymerase as it transcribes through DNA wrapped around nucleosomes, the lowest level of the chromatin packing hierarchy.  We develop a simple mechanical model for the forces experienced by RNAP as it approaches the nucleosome and consider the pausing behavior of the polymerase under these fluctuating forces. Incorporating fluctuations in the amount of downstream DNA unwrapped from the nucleosome yields  predictions for the pausing timescales that differ by an order of magnitude from those under the average force alone.

We use our model to illustrate the broad range of behaviors that can arise in biomolecular processes that are susceptible to force fluctuations. The fluctuation time scale, which varies significantly for in vivo biomolecular processes, yields qualitatively different results for overall rates and dramatically alters the force regime of relevance to the transition. For our example system, polymerase pausing rates are dominated by transient excursions to high forces. These calculations thus motivate the need for single-molecule measurements of enzymatic rates under forces far above the in vivo average.  Our results demonstrate that accounting for force fluctuations is essential to  developing a quantitative understanding of enzyme kinetics in the dynamic environment of a living cell.