  Molecular motion through pores plays a crucial role in various natural and
industrial processes. One of the most fascinating features of biological
channel-facilitated transport is a stochastic gating process, when the channels
dynamically fluctuate between several conformations during the translocation.
Although this phenomenon has been intensively investigated, many properties of
translocation in dynamically changing environment remain not well understood
microscopically. We developed a discrete-state stochastic framework to analyze
the molecular mechanisms of transport processes with stochastic gating by
explicitly calculating molecular fluxes through the pores. Two scenarios are
specifically investigated: 1) symmetry preserving stochastic gating with
free-energy changes, and 2) stochastic gating with symmetry changes but without
modifications in the overall particle-pore interactions. It is found that
stochastic gating can both accelerate or slow down the molecular translocation
depending on the specific parameters of the system. We argue that biological
systems might optimize their performance by utilizing conformational
fluctuations of channels. Our theoretical analysis clarifies physical-chemical
aspects of the molecular mechanisms of transport with stochastic gating.
