Paper Citing NAMD - Abstract
Hu, Guodong; Chen, Liao Y.; Wang, Jihua
Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z
JOURNAL OF MOLECULAR MODELING, 18:3731-3741, AUG 2012
Aquaporin Z (AQPZ) is a tetrameric protein that forms water channels in the cell membrane of Escherichia coli. The histidine residue (residue 174) in the selectivity filter (SF) region plays an important role in the transport of water across the membrane. In this work, we perform equilibrium molecular dynamics (MD) simulations to illustrate the gating mechanism of the SF and the influences of residue 174 in two different protonation states: Hsd174 with the proton at N delta, and Hse174 with the proton at N epsilon. We calculate the pore radii in the SF region versus the simulation time. We perform steered MD to compute the free-energy profile, i.e., the potential of mean force (PMF) of a water molecule through the SF region. We conduct a quantum mechanics calculation of the binding energy of one water molecule with the residues in the SF region. The hydrogen bonds formed between the side chain of Hsd174 and the side chain of residue 189 (Arg189) play important roles in the selectivity mechanism of AQPZ. The radii of the pores, the hydrogen-bond analysis, and the free energies show that it is easier for water molecules to permeate through the SF region of AQPZ with residue 174 in the Hse state than in the Hsd state.
