Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations.

One of the key steps in the infection of the cell by dengue virus is a pH-induced conformational change of the viral envelope proteins. These envelope proteins undergo a rearrangement from a dimer to a trimer, with large conformational changes in the monomeric unit. In this article, metadynamics simulations were used to enable us to understand the mechanism of these large-scale changes in the monomer. By using all-atom, explicit solvent simulations of the monomers, the stability of the protein structure is studied under low and high pH conditions. Free energy profiles obtained along appropriate collective coordinates demonstrate that pH affects the domain interface in both the conformations of E monomer, stabilizing one and destabilizing the other. These simulations suggest a mechanism with an intermediate detached state between the two monomeric structures. Using further analysis, we comment on the key residue interactions responsible for the instability and the pH-sensing role of a histidine that could not otherwise be studied experimentally. The insights gained from this study and methodology can be extended for studying similar mechanisms in the E proteins of the other members of class II flavivirus family.

[1]  Y. Modis,et al.  A ligand-binding pocket in the dengue virus envelope glycoprotein , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Werner Braun,et al.  Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules , 1998 .

[3]  Wei Zhang,et al.  Structure of the Immature Dengue Virus at Low pH Primes Proteolytic Maturation , 2008, Science.

[4]  Massimiliano Bonomi,et al.  PLUMED: A portable plugin for free-energy calculations with molecular dynamics , 2009, Comput. Phys. Commun..

[5]  K. Stiasny,et al.  Identification of specific histidines as pH sensors in flavivirus membrane fusion , 2008, The Journal of cell biology.

[6]  Bostjan Kobe,et al.  Histidine protonation and the activation of viral fusion proteins. , 2008, Biochemical Society transactions.

[7]  Richard J Kuhn,et al.  Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins , 2008, Nature Structural &Molecular Biology.

[8]  Francesco L Gervasio,et al.  Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding. , 2006, Journal of the American Chemical Society.

[9]  M. Rossmann,et al.  A structural perspective of the flavivirus life cycle , 2005, Nature Reviews Microbiology.

[10]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[11]  A. Laio,et al.  Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science , 2008 .

[12]  Bostjan Kobe,et al.  The Role of histidine residues in low-pH-mediated viral membrane fusion. , 2006, Structure.

[13]  A. Laio,et al.  Equilibrium free energies from nonequilibrium metadynamics. , 2006, Physical Review Letters.

[14]  Eric Darve,et al.  Assessing the efficiency of free energy calculation methods. , 2004, The Journal of chemical physics.

[15]  S. Harrison.  Mechanism of Membrane Fusion by Viral Envelope Proteins , 2005, Advances in Virus Research.

[16]  Jun Zhai,et al.  ArchPRED: a template based loop structure prediction server , 2006, Nucleic Acids Res..

[17]  C. Mandl,et al.  Role of Metastability and Acidic pH in Membrane Fusion by Tick-Borne Encephalitis Virus , 2001, Journal of Virology.

[18]  Eric F Darve,et al.  Calculating free energies using average force , 2001 .

[19]  Paul R. Young,et al.  Identification of novel target sites and an inhibitor of the dengue virus E protein , 2009, J. Comput. Aided Mol. Des..

[20]  David Chandler,et al.  Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.

[21]  Paul Schanda,et al.  Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy , 2007, Proceedings of the National Academy of Sciences.

[22]  K. Stiasny,et al.  Structure of a flavivirus envelope glycoprotein in its low‐pH‐induced membrane fusion conformation , 2004, The EMBO journal.

[23]  R. Kuhn,et al.  Closing the door on flaviviruses: entry as a target for antiviral drug design. , 2008, Antiviral research.

[24]  Jim Pfaendtner,et al.  Nucleotide-dependent conformational states of actin , 2009, Proceedings of the National Academy of Sciences.

[25]  Y. Modis,et al.  Structure of the dengue virus envelope protein after membrane fusion , 2004, Nature.

[26]  A. Laio,et al.  Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Jack Snoeyink,et al.  Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .

[28]  S. Harrison.  The pH sensor for flavivirus membrane fusion , 2008, The Journal of cell biology.

[29]  Francesco Luigi Gervasio,et al.  From A to B in free energy space. , 2007, The Journal of chemical physics.

[30]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[31]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

[32]  J. Lepault,et al.  Characterization of a Structural Intermediate of Flavivirus Membrane Fusion , 2007, PLoS pathogens.

[33]  A Marchler-Bauer,et al.  Structural requirements for low-pH-induced rearrangements in the envelope glycoprotein of tick-borne encephalitis virus , 1996, Journal of virology.

[34]  A. Cavalli,et al.  Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations. , 2009, Journal of the American Chemical Society.