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New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins

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Abstract

Diseases caused by flaviviruses, such as dengue and zika, are globally recognized as major threats. During infection, a critical point in their replicative cycle is the maturation step, which occurs throughout the cellular exocytic pathway. This step is a pH-dependent process that involves the modification of the viral envelope by converting prM (pre-membrane) into M (membrane) proteins with the release of a “pr peptide”. After this reaction, the pr peptides remain bound to the viral envelope while the virions cross the acidic trans-Golgi network, and are released only at neutral pH after secretion of the virus particles. Despite this current knowledge, the molecular basis of the flavivirus maturation step is largely unknown. Here, based on the crystal structure of the dengue pr–E complex (“pr peptide” bound to virus envelope protein) and using molecular dynamics simulations, we found that the pH shift from acidic to neutral yields considerable structural changes in the system. Dynamic cross correlation maps and root mean square deviation analyses revealed that the pr–E junction is clearly unstable under neutral pH. Secondary structure analysis also revealed that the fusion loop region, present in the E protein, is sensitive to pH and tends to unstructure at a neutral environment. Moreover, we found that five residues present in the E protein, Gly102, His244, Thr70, Thr68 and Asn67 are critical to confer stability to the pr–E complex while inside the Golgi apparatus. This work brings details about the dynamical behavior of the pr–E system, helps to better understand the flavivirus biology and may also be of use in the development of novel antiviral strategies.

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Acknowledgements

This work was developed with the assistance of Núcleo Avançado de Computação de Alto Desempenho (NACAD) localized at Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia (COPPE), Universidade Federal do Rio de Janeiro (UFRJ). Edson Oliveira thanks Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for his post-doctoral fellowship. We also acknowledge the Brazilian foundations Fundação Carlos Chagas de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) (Grant Numbers: E-26/203.198/2016, E-26/010.002420/2016, E-26/201.258/2015) for the financial support.

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Authors and Affiliations

  1. Instituto de Química - Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149 Centro de Tecnologia, Bloco A, Sala 609, Cidade Universitária, Rio de Janeiro, RJ, CEP: 21941-909, Brazil

    Edson R. A. Oliveira, Ricardo B. de Alencastro & Bruno A. C. Horta

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  1. Edson R. A. Oliveira
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  2. Ricardo B. de Alencastro
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  3. Bruno A. C. Horta
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Correspondence to Bruno A. C. Horta.

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Oliveira, E.R.A., de Alencastro, R.B. & Horta, B.A.C. New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins. J Comput Aided Mol Des 31, 1009–1019 (2017). https://doi.org/10.1007/s10822-017-0076-8

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  • DOI: https://doi.org/10.1007/s10822-017-0076-8

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