Paper Citing NAMD - Abstract
Baylon, Javier L.; Tajkhorshid, Emad
Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7882-7893, JUN 25 2015
Hemagglutinin (HA) is a protein located on the surface of the influenza virus that mediates viral fusion to the host cellular membrane. During the fusion process the HA fusion peptide (HAfp), formed by the first 23 N-terminal residues of HA and structurally characterized by two alpha helices (Helix A and Helix B) tightly packed in a hairpin-like arrangement, is the only part of the virus in direct contact with the host membrane. After encountering the host cell, HAfp is believed to insert into the membrane, thereby initiating the fusion of the viral and host membranes. Detailed characterization of the interactions between the HAfp and cellular membrane is therefore of high relevance to the mechanism of viral entry into the host cell. Employing HMMM membrane representation with enhanced lipid mobility, we have performed a large set of independent simulations of unbiased membrane binding of HAfp. We have been able to capture spontaneous binding and insertion of HAfp consistently in nearly all the simulations: A reproducible membrane-bound configuration emerges from these simulations, despite employing a diverse set of initial configurations. Extension of several of the simulations into full Membrane systems confirms the stability of the membrane bound form obtained from HMMM binding simulations. The resulting model allows for the characterization of important interactions between the peptide and the membrane and the details of the bin:ding process of the peptide for the first time. Upon membrane binding, Helix A inserts much deeper into the membrane than Helix B, suggesting that the former is responsible for hydrophobic anchoring of the peptide into the membrane. Helix 13, in contrast, is found to establish major amphipathic interactions at the interfacial region thereby contributing to binding strength of HAfp.
