Sep. 2, 2014: Single Molecule Time Series Analysis of Supermolecular Motor Proteins, Prof. Chun-Biu Li

 


Single Molecule Time Series Analysis of Supermolecular Motor Proteins


Tuesday, Sep. 2, 2014, 15:15, ML E 12, ETH Zurich

Prof. Chun-Biu Li
Assistant Professor, Research Institute for Electronic Science, and Department of Mathematics, Hokkaido University, Japan
 
Abstract
How enzymes achieve extraordinary reaction rate acceleration and specificity has long been one of most important keys in understanding the algorithm of living systems. Among them is the significant and ubiquitous super-molecular motor, Adenosine Triphosphate Synthase (F0F1-ATP synthase), which uses its rotation for catalysis and synthesis of ATP effectively to power many biological machines. Recent advances in single molecule (SM) experiments enable us to unravel the detailed complex kinetics of these super-molecules on the SM level. In this talk, I will summarize our recent progress in unveiling the kinetics of chemo-mechanical couplings of the F1-ATPase in terms of nonlinear time series analysis. F1-ATPase is the water-soluble component of the F0F1-ATP synthase that rotates upon ATP hydrolysis.
In particular, we have developed a generic but simple trend/change-point detection scheme to objectively identify the catalytic dwells in the staircase-like protein motor time series. By applying to the recent dark-field imaging data with nanometer and microsecond spatio-temporal revolutions, we are able to build up statistics of the F1 catalytic states directly from the time series, and to study in detail the kinetics of different components in the catalytic cycle of F1-ATPase, namely, ATP binding, ADP release, ATP hydrolysis and Phosphate release. By using a simple reaction-diffusion model similar to the Sumi-Marcus model for electron transfer kinetic, we propose that a possible role of the ATP hydrolysis reaction step is to accelerate the completion of the catalytic cycle, despite the fact that the free energy given out by hydrolyzing a bounded ATP in the enzyme is relatively small in compared to the ATP binding and Phosphate release reaction steps. I will also discuss how the catalytic rates can be modulated by thermal fluctuations based on the same theoretical framework.
 
Keywords: Single molecule experiment, molecular motor, F1-ATPase, time series analysis, nonequilibrium thermodynamics.