Molecular Dynamics Simulations on the Mechanism of Transporting Methylamine and Ammonia by Ammonium Transporter AmtB.

Jinan Wang,Huaiyu Yang,Zhili Zuo,Xiuhua Yan,Yong Wang,Xiaomin Luo,Hualiang Jiang,Kaixian Chen, and Weiliang Zhu

AmtB is one of the ammonium transporter proteins facilitating the ammonium transport across the cellular
membranes. Experimentally, the substrate used in in vitro studies is the radio labeled [14C]methylammonium,
rather than ammonium itself. To explore the similarity and difference of the conduction mechanism of
methylamine and ammonia molecules through AmtB, molecular dynamics simulations on 22 carefully designed
systems were performed, which demonstrated that methylamine could be automatically transported in a very
similar way to ammonia. The driving force for the conduction is mainly the hydrogen bond network comprising
His168, His318, and Tyr32, working in coordination with NH-π interaction with residue Trp212. Then,
Ser263 translocated the substrates from the exit gate into the cytoplasm by hydrogen bond interaction. The
aromatic ring of Trp212 acted like a springboard to facilitate the translocation of the substrates from site
Am2 to Am4 via NH-π interaction. Without the mediation of Trp212, further movement of substrate in the
channel would be hampered by the strong hydrogen bonding from His168. In agreement with experimental
results, the substrates could be transported by W212F mutant but not by W212A within the simulation time
as long as 20 ns. In addition, we predicted that the mutants S263D and S263C remain the function of the
transporter but S263A does not. The difference of transporting the two substrates is that methylamine involves
more hydrophobic interactions than ammonia. In conclusion, methylamine molecule is a good mimic for
investigating the translocation mechanism of ammonium transporter AmtB.