Molecular dynamics simulation of a hydrated diphytanol phosphatidylcholine lipid bilayer containing an alpha-helical bundle of four transmembrane domains of the influenza A virus M2 protein.
An alpha-helical bundle composed of four transmembrane portions of the M2 protein from the Influenza A virus has been studied in a hydrated diphytanol phosphatidylcholine bilayer using molecular dynamics (MD) calculations. Experimentally, the sequence utilized is known to aggregate as a four-helix bundle and act as a pH-gated proton-selective ion channel, which is blocked by the drug amantadine hydrochloride. In the presented simulation, the ion channel was initially set up as a parallel four-helix bundle. The all-atom simulation consisted of almost 16,000 atoms, described classically, using a forcefield from the CHARMM22 database. Bilayers with and without the bundle were shown to be stable throughout the nanosecond timescale of the MD simulation. Structural and dynamical properties of the bilayer both with and without the transmembrane protein are reported.
Husslein
T
T
Centre for Molecular Modelling, University of Pennsylvania, Philadelphia 19104-6323, USA.
Moore
P B
PB
Zhong
Q
Q
Newns
D M
DM
Pattnaik
P C
PC
Klein
M L
ML
D003198:Computer Simulation; D008051:Lipid Bilayers; D008958:Models, Molecular; D010713:Phosphatidylcholines / Q000737:chemistry*; D011485:Protein Binding; D017510:Protein Folding; D014763:Viral Matrix Proteins / Q000737:chemistry*; D000086082:Viroporin Proteins
D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D014763:Viral Matrix Proteins; C031540:M-protein, influenza virus; C488937:M2 protein, Influenza A virus; D000086082:Viroporin Proteins