Utilizing the information content in two-state trajectories

Abstract

The signal from many single molecule experiments monitoring molecular processes, such as enzyme turnover via fluorescence and opening and closing of ion channel via the flux of ions, consists of a time series of stochastic on and off (or open and closed) periods, termed a two-state trajectory. This signal reflects the dynamics in the underlying multi-substate on-off kinetic scheme (KS) of the process. The determination of the underlying KS is difficult and sometimes even impossible due to the loss of information in the mapping of the mutli dimensional KS onto two dimensions. Here we introduce a new procedure that efficiently and optimally relates the signal to all equivalent underlying KSs. This procedure partitions the space of KSs into canonical (unique) forms that can handle any KS, and obtains the topology and other details of the canonical form from the data without the need for fitting. Also established are relationships between the data and the topology of the canonical form to the on-off connectivity of a KS. The suggested canonical forms constitute a powerful tool in discriminating between KSs. Based on our approach, the upper bound on the information content in two state trajectories is determined.

The file contains: main text (+4 figures), supporting information (+9 figures), poster (1 page)

References in corpus (9)

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• Can one identify non-equilibrium in a three-state system by analyzing two-state trajectories?
• Manipulating single enzymes by an external harmonic force
• Toolbox for analyzing finite two-state trajectories
• Path probability density functions for semi-Markovian random walks
• Correctly validating results from single molecule data: the case of stretched exponential decay in the catalytic activity of single lipase B molecules
• Output-input coupling in thermally fluctuating biomolecular machines
• A three-state kinetic mechanism for scaffold mediated signal transduction