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Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design

Nature Structural & Molecular Biology volume 22, pages 788794 (2015) | Download Citation


Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interactions and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. Here we devised a computational method to assess the relative stability of protein-protein interfaces and used it to design improved candidate vaccines for two poorly stable, but globally important, serotypes of FMDV: O and SAT2. We used a restrained molecular dynamics strategy to rank mutations predicted to strengthen the pentamer interfaces and applied the results to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralizing-antibody responses to stabilized particles compared to parental viruses and wild-type capsids.

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We thank the World Reference Laboratory for VNT determination; beamline staff at the Diamond Light Source for assistance; J. Dong and J. Diprose for computing support; P. Afonine and G. Murshudov for advice on Phenix and Refmac; K. Harlos and T. Walter for help with crystallography; D. Goovaerts and E. Rieder for helpful discussions; and B. Haas (Friedrich-Loeffler-Institut) for providing ZZ_R 127 cells. We are grateful to the Wellcome Trust (WT) for a Translation Award to fund this work (grant no. 089755 to B.C., E.E.F., T.J. and F.F.M.). T.J. and B.C. were funded by the Biotechnology and Biological Sciences Research Council Institute Strategic Programme on Livestock Viral Diseases at The Pirbright Institute. The Oxford Particle Imaging Centre electron microscopy facility was founded by a WT Joint Infrastructure Fund award (060208/Z/00/Z to D.I.S.) and is supported by a WT equipment grant (093305/Z/10/Z to K. Grünewald). The WT, UK Medical Research Council (MRC) and Biotechnology and Biology Research Council also support the National EM facility, which provided the K2 detector. B.C. and D.I.S. are supported as Jenner investigators, J.R. and A.K. are WT supported, and E.E.F. and D.I.S. are supported by the UK MRC (grant no. G100099 to D.I.S.). The work of the WT Centre in Oxford is supported by the WT core award 090532/Z/09/Z.

Author information

Author notes

    • Abhay Kotecha
    •  & Julian Seago

    These authors contributed equally to this work.


  1. Division of Structural Biology, University of Oxford, Oxford, UK.

    • Abhay Kotecha
    • , Jingshan Ren
    • , Claudine Porta
    • , Helen M Ginn
    • , C Alistair Siebert
    • , Juha T Huiskonen
    • , Robert M Esnouf
    • , Elizabeth E Fry
    •  & David I Stuart
  2. Pirbright Institute, Pirbright, UK.

    • Julian Seago
    • , Alison Burman
    • , Claudine Porta
    • , Terry Jackson
    • , Eva Perez-Martin
    •  & Bryan Charleston
  3. Transboundary Animal Disease Programme, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort, South Africa.

    • Katherine Scott
    •  & Francois F Maree
  4. Animal and Microbial Sciences, University of Reading, Reading, UK.

    • Silvia Loureiro
    •  & Ian M Jones
  5. Merck Sharp & Dohme Animal Health, Cologne, Germany.

    • Guntram Paul
  6. Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa.

    • Francois F Maree
  7. Diamond Light Source, Didcot, UK.

    • David I Stuart


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A.K., E.E.F., R.M.E. and D.I.S. developed MD-simulation protocols; A.K., J.S., K.S., A.B., S.L. and C.P. prepared samples; J.R., H.M.G., J.T.H., E.P.-M., G.P., C.A.S., F.F.M. and E.E.F. assisted in research; A.K., J.S., F.F.M., E.E.F., T.J., I.M.J., R.M.E., D.I.S. and B.C. designed the study; all authors analyzed data; and A.K., J.S., E.E.F., B.C. and D.I.S. wrote the manuscript.

Competing interests

A number of the stabilizing mutations are patented (patent no. WO 2014154655 A1, patent holders: R.M.E., E.E.F., A.K. and D.I.S.), and work on a VLP-based stabilized vaccine antigen is ongoing at Intervet (MSD Animal Health), in collaboration with the authors (except that F.F.M. and K.S. are not part of this ongoing work). This work was not funded by MSD Animal Health but by a Wellcome Trust Translation Award.

Corresponding authors

Correspondence to Francois F Maree or Bryan Charleston or David I Stuart.

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    Supplementary Text and Figures

    Supplementary Figures 1–7, Supplementary Tables 1–3 and Supplementary Note

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    Supplementary Data Set 1

    Full length SDS-PAGE gels from truncated panels of Figure 2c

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