We have recently developed the "FR method" for calculating simultaneously both the PMF and the diffusion coefficient of a molecule moving along the axis of a nanopore by employing a small number of fast non-equilibrium MD pullings in both forward and time reverse directions [1]. After demonstrating its viability in the case of single-file water transport in carbon nanotubes, the FR method is applied to water, glycerol and glucose transport through the aquaglyceroporin GlpF and maltoporin channel proteins.
As a biological application, we predict that, contrary to the general belief, in active cell membranes passive and spatially asymmetric channel proteins (e.g., GlpF) can act as active transporters by consuming energy from nonequilibrium fluctuations fueled by cell metabolism [2]. By calculating the glycerol flux through GlpF, it is found that, as a result of channel asymmetry, glycerol uptake driven by a concentration gradient is enhanced significantly in the presence of non-equilibrium fluctuations. Furthermore, the enhancement caused by a ratchet-like mechanism is larger for the outward, i.e., from the cytoplasm to the periplasm, flux than for the inward one, suggesting that the same non-equilibrium fluctuations also play an important role in protecting the interior of the cell against poisoning by excess uptake of glycerol.
Work supported in part by grants from the University of Missouri Research Board, the Institute for Theoretical Sciences, a joint institute of Notre Dame University and Argonne National Laboratory, the U.S. Department of Energy, Office of Science through contract No.~W-31-109-ENG-38, and NSF through FIBR-0526854.
[1] I. Kosztin, B. Barz and L. Janosi, J. Chem. Phys. 124, 064106 (2006).
[2] I. Kosztin and K. Schulten, Phys. Rev. Lett. 93, 238102 (2004).