Paper Citing NAMD - Abstract
Pantano, Diego A.; Klein, Michael L.
Characterization of Membrane-Protein Interactions for the Leucine Transporter from Aquifex aeolicus by Molecular Dynamics Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13715-13722, OCT 22 2009
Multinanosecond molecular dynamics (MD) simulations have been employed to characterize the interaction of an integral membrane protein (IMP), the leucine transmitter front Aquifex aeolicus (Yamashita et al.. Nature 2005, 437, 215-223), with hydrated lipid bilayer membranes in their physiologically relevant liquid crystalline phases. Analysis of the MD trajectories for dimyristoyl phosphatidylcholine (DMPQ, 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC), and 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE) focused (in the contacts between aromatic and basic side chains of the IMP with the lipid head groups and water. Structural fluctuations of the IMP were investigated as well as the contact dynamics of neighboring lipids. In characterizing the IMP-membrane systems, the behaviors of the protein's cytoplasmic and periplasmic parts are considered separately. All three lipid membranes show a rather similar overall level of association with the IMP. However, for DMPC there is a better matching of the membrane core to the hydrophobic transmembrane portion of the IMP. The closed cytoplasmic end of the IMP exhibits a higher degree of association with lipids than the more open periplasmic end, an, observation which correlates with the more compact structure and a slower dynamics of surrounding lipids.
