Abstract
Living systems display a variety of situations in which non-equilibrium fluctuations couple to certain protein functions yielding astonishing results. Here we study the bacterial channel OmpF under conditions similar to those met in vivo, where acidic resistance mechanisms are known to yield oscillations in the electric potential across the cell membrane. We use a three-dimensional structure-based theoretical approach to assess the possibility of obtaining fluctuation-driven transport. Our calculations show that remarkably high voltages would be necessary to observe the actual transport of ions against their concentration gradient. The reasons behind this are the mild selectivity of this bacterial pore and the relatively low efficiencies of the oscillating signals characteristic of membrane cells (random telegraph noise and thermal noise).
Highlights
Energy-transduction processes occurring in biosystems display astonishing high efficiencies that could be partially explained considering the contribution of non-equilibrium fluctuations [1]
We showed that OmpF porin, a non-specific channel located in the outer membrane of Escherichia coli (E. coli) [8,9], may perform as a molecular ratchet in conditions designed to mimic acidic stress on bacteria [7]
The channel fixed charge is obtained by using the University of Houston Brownian Dynamics (UHBD) code [16,17] to calculate the apparent pKa of the channel residues at the particular pH configuration of our study, using the three-dimensional structure of the OmpF channel (Protein Data Bank code: 2OMF) as obtained from X-ray analysis [18]
Summary
Energy-transduction processes occurring in biosystems display astonishing high efficiencies that could be partially explained considering the contribution of non-equilibrium fluctuations [1]. E. coli [10] may yield electrical pumping of ions against an external concentration gradient This uphill transport obtained in the OmpF channel is directional: depending on the orientation of the concentration gradient, the system can pump either cations or anions from the diluted solution to the concentrated one [7]. Entropy 2017, 19, 116 the relative contribution of each ion to the total current (the channel selectivity) cannot be anticipated because of the coupling between electrostatic and diffusional effects arising from the different diffusivities of ions [11]. We address this question using the three-dimensional (3D). We underscore the idea that due to the multiionic character of the channel, the actual uphill transport requires considerably larger potentials than those needed to just reverse the direction of the current
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