A Molecular Dynamics Study On The Proton Conduciton Mechanism Of M2Channel From Influenza A Virus

Influenza virus can lead to acute respiratory infection. Its frequentbreakout will lead to numerous death all over the world, which has becomethe source of human being’s fear. Among all3types of influenza viruses,type A has drawn the most attentions, since it is not only a total disaster foravian and animal husbandry any more, but also an extreme threaten topublic health. Generally speaking, different influenza viruses can only liveon their own specific host cell, which means it is supposed to beimpossible for avian influenza virus to infect human beings. However,18patients in Hong Kong were reported to be infected by avian influenzavirus, which were believed to cross the species barrier immediatelywithout the mediate host in1997. As a result, the harm of influenza A hasattracted prevailing focus recently. What is the most horrible thing is thatInfluenza A virus replicates itself very quickly, and more and more newmutant type A viruses have obtained the ability of anti-drugs. Lacking ofefficient prevention and treatment makes people afraid that the miserableSpanish influenza epidemic in1918will occur once again.Matrix2Protein (M2), which is a highly conservative motif frominfluenza A, enjoys highly homology among different subtypes ofinfluenza viruses. As a result, it has been widely used in the diagnosis ofall kinds of influenza virus, which is considered as one of the mostsignificant sequence from influenza A virus. Its importance as a protonselective channel has been confirmed, which plays a key role in the virallife cycle by allowing proton flux into the virion. By selecting and directing protons passing uniaxially from the outside virus into the insidearea, it can help to modulate pH inside the virus, thus leading to theuncoating of the viral nuclei acid in endosomes. In addition, the protonpermeation currents observed in mouse erythroleukemia cells, as well asby measuring the intracellular pH variance of oocytes of Xenopus lavevisin low PH condition, all help to verify its characteristic as a protonselective channel.Molecular dynamic simulation is the most widely used computationmethod, mainly based on solving the classic Newton Equation of Motionof every particle within the complex. After obtained the information aboutlocation and velocity of every particle, statistical mechanics method isused to convert the information of micro particles to the structure andthermodynamic properties of the whole macro-system. Thebiomacromolecule system has become the dominant subject beinginvestigated by MD method.Herein, we adopted MD method to study two recently reported M2structures:2L0J and3LBW. To explore the structure property andproton-relay mechanism of AM2, we designed3different protonationstates for each structure, namely keeping on increasing the His-37sidechains to be protonated. For each system,50ns MD simulation hasconducted to analyze its conformation change, pore radius change, thedistribution of water molecules along the channel, as well as the freeenergy for water permeation through the channel.In order to investigate the structural properties and conductancemechanism of the M2proteins from inlfuenza A virus, molecular dynamicssimulations were carried out on different protonation states of two recentlyobtained structures,2L0J and3LBW. Compared with2L0J,3LBW lacksthe intracellular domain of M2proteins. As a result, models of3LBWshowed higher deviations during the simulations, suggesting theimportance of the intracellular domain on the stability of M2proteins.What’s more, with more His37sidechains being protonated, the models of 3LBW resulted in higher deviations in the intracellular end of the helicesand more constriction around the Val-27valve. Hence the more protonatedconfiguration may be not good for the stability of the helical bundle of theM2channel, which need to be fixed by the interactions of the intracellulardomain, as in the simulations of the models of2L0J. Although the modelsof the two structures resulted in different structural stabilities, neither ofthem suggests a possible "continuous water-wire" in the channel during the50ns simulations, based on the density of water molecules. The free energyprofiles for water permeation through the M2channels also refute thepossibility of the formation of a "water-wire" upon the protonation of moreHis37. The results of the simulations above provided a direct evidence toinvalidate the "water-wire" model for the first time, as we know.