Yu Zhou1,2, Chao Wu2,3, Lifeng Zhao2 and Niu Huang1,2,*

Article first published online: 9 JUN 2014

DOI: 10.1002/prot.24606

Author Information

  1. College of Life Sciences, Beijing Normal University, Beijing, China
  2. National Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park, Beijing, China
  3. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri

*Correspondence to: Niu Huang, National Institute of Biological Sciences, Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China. E-mail: huangniu@nibs.ac.cn


Hemagglutinin (HA) mediates the membrane fusion process of influenza virus through its pH-induced conformational change. However, it remains challenging to study its structure reorganization pathways in atomic details. Here, we first applied continuous constant pH molecular dynamics approach to predict the pKa values of titratable residues in H2 subtype HA. The calculated net-charges in HA1 globular heads increase from 0e (pH 7.5) to +14e (pH 4.5), indicating that the charge repulsion drives the detrimerization of HA globular domains. In HA2 stem regions, critical pH sensors, such as Glu1032, His181, and Glu891, are identified to facilitate the essential structural reorganizations in the fusing pathways, including fusion peptide release and interhelical loop transition. To probe the contribution of identified pH sensors and unveil the early steps of pH-induced conformational change, we carried out conventional molecular dynamics simulations in explicit water with determined protonation state for each titratable residue in different environmental pH conditions. Particularly, energy barriers involving previously uncharacterized hydrogen bonds and hydrophobic interactions are identified in the fusion peptide release pathway. Nevertheless, comprehensive comparisons across HA family members indicate that different HA subtypes might employ diverse pH sensor groups along with different fusion pathways. Finally, we explored the fusion inhibition mechanism of antibody CR6261 and small molecular inhibitor TBHQ, and discovered a novel druggable pocket in H2 and H5 subtypes. Our results provide the underlying mechanism for the pH-driven conformational changes and also novel insight for anti-flu drug development. Proteins 2014;. © 2014 Wiley Periodicals, Inc.