The M2 protein of influenza A viruses forms a proton channel involved in modifying virion and trans Golgi pH during infection. Previous studies of the proton current using whole-cell patch clamp of mouse erythroleukaemia (MEL) cells expressing the M2 protein of the "Weybridge" strain provided evidence for two protonation sites, one involved in permeation, the other in activation by acid pH. The present report compares the M2 channels of two different strains of influenza virus, "Weybridge" (WM2) and "Rostock" (RM2). Whereas with external acid pH the current-voltage relations showed similar small degrees of inward rectification, a similar apparent K(d) of approximately 10 microM for proton permeation and a high selectivity for protons over Na(+), the two M2 proteins differed in whole-cell conductance at low and high pH. The proton conductance of unit membrane area was on average 7-fold greater in RM2- than WM2-expressing MEL cells. At high external pH WM2 was shown previously to have small conductance for outward current at positive driving potential. In contrast, RM2 shows high conductance for outward current with high external pH, but shows small conductance for inward current with high internal pH, conditions in which WM2 shows high conductance for inward current. The different properties of the conductances due to the two channels at high pH were determined by three amino acids in their transmembrane domains. All intermediate mutants possessed one or other property and transformation of the WM2 phenotype into that of RM2 required substitution in all three residues V27I, F38L and D44N; single substitutions in RM2 effected the opposite phenotypic change. The significance of this difference for virus replication is not clear and it may be that the higher proton flux associated with RM2 is the main factor determining its increased ability to dissipate pH gradients. It is apparent, however, from the specific differences in the sidedness of the pH-induced changes in voltage dependence of the whole-cell current that this is an intrinsic property of the virus proton channel which may have parallels with regulation of other proton channels.