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Every morning, many people drive to work, while others may bike, take the
bus or the metro.
Similarly, various biomolecules in the human body also reach their
destinations in diverse manners.
For example, to cross the cellular membrane, small hydrophobic gas molecules diffuse through the lipid
bilayer, while water molecules pass through specialized channel proteins named
aquaporins (AQPs).
Interestingly, just like one may get to work both by bus and by
driving, it has been found recently that some gas molecules may have more
than one way to cross the membrane, i.e., besides diffusion through
lipids, oxygen and carbon dioxide may also pass through AQPs.
However, the pathways that these gas molecules take remained elusive.
Using molecular dynamics performed with
NAMD, researchers have investigated the gas
permeability of AQP1 in a recent study with
two complementary methods (explicit gas diffusion simulation and implicit ligand
sampling). The simulation results suggest that while the four
monomeric pores of AQP1 function as water channels,
the central pore of AQP1 may serve as a pathway for gas molecules to
cross the membrane. More information on the simulations can be found on
the aquaporin web page.