Abstract
A theoretical framework is developed for modelling conformational adaptation processes that can occur in proteins that are processing flows of low-mass particles (ions, protons, electrons). The model takes into account the interplay between the substrate flow, which sends the protein through repeated cycles, and slow conformational degrees of freedom of the protein, which give the protein memory that extends beyond the timescale of a single cycle. The flow of particles imposes nonequilibrium conditions on the protein, which introduces a nonlinearity (feedback) in the functioning of the protein, and can lead to self-organized operational regimes with properties different from those of the relaxed `resting' state. With the example of a model charge-transfer system, we develop a stochastic theory of nonequilibrium charge–conformation interactions with allowance for nonmarkovian properties of both the structural modes and the flow of transferred particles. Possible applications to biological electron and ion transfer processes are discussed.
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