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Active site remodeling switches HIV specificity of antiretroviral TRIMCyp

Nature Structural & Molecular Biology volume 16, pages 1036–1042 (2009)Cite this article

Abstract

TRIMCyps are primate antiretroviral proteins that potently inhibit HIV replication. Here we describe how rhesus macaque TRIMCyp (RhTC) has evolved to target and restrict HIV-2. We show that the ancestral cyclophilin A (CypA) domain of RhTC targets HIV-2 capsid with weak affinity, which is strongly increased in RhTC by two mutations (D66N and R69H) at the expense of HIV-1 binding. These mutations disrupt a constraining intramolecular interaction in CypA, triggering the complete restructuring (>16 Å) of an active site loop. This new configuration discriminates between divergent HIV-1 and HIV-2 loop conformations mediated by capsid residue 88. Viral sensitivity to RhTC restriction can be conferred or abolished by mutating position 88. Furthermore, position 88 determines the susceptibility of naturally occurring HIV-1 sequences to restriction. Our results reveal the complex molecular, structural and thermodynamic changes that underlie the ongoing evolutionary race between virus and host.

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Figure 1: HIV-2 binds CypA with weak affinity.
Figure 2: Two CypA mutations dictate lentiviral binding and restriction sensitivity.
Figure 3: Structure of the N-terminal capsid domain of HIV-2.
Figure 4: RhTC CypA has been re-targeted from HIV-1 to HIV-2.
Figure 5: Capsid residue 88 is a key determinant of lentiviral sensitivity to RhTC.
Figure 6: CypA targets HIV-1 and HIV-2 using different mechanisms.

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Acknowledgements

This work was funded by the UK Medical Research Council and a Wellcome Trust fellowship (WT076608) to G.J.T. We would like to thank the European Synchrotron Radiation Facility (ESRF) staff at beamline ID14-1 and local contact E. Fioravanti. We also thank S. Hue, P. Bieniasz and J. Heeney for helpful discussion and A. Lever, D. Trono and A. Thrasher and L. Gurtler via the National Institute of Biological Standards and Controls (NIBSC) AIDS Reagents Programme, for reagents.

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Author notes

  1. Flavia Marzetta & Sam J Wilson

    Present address: Present addresses: Viral Pathogens and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy (F.M.); Aaron Diamond AIDS Research Center, Howard Hughes Medical Institute and the Rockefeller University, New York, New York, USA.,

  2. Amanda J Price and Flavia Marzetta: These authors contributed equally to this work.

Authors and Affiliations

  1. Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK

    Amanda J Price, Michael Lammers & Leo C James

  2. Division of Infection and Immunity, Medical Research Council Centre for Medical Molecular Virology, University College London, London, UK

    Flavia Marzetta, Laura M J Ylinen, Torsten Schaller, Sam J Wilson & Greg J Towers

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Contributions

A.J.P. and F.M. performed experiments and analyzed data; M.L., L.M.J.Y., T.S. & S.J.W. performed additional experiments; G.J.T. and L.C.J. analyzed data and wrote the manuscript.

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Correspondence to Greg J Towers or Leo C James.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 (PDF 269 kb)

Supplementary Movie 1

D66N and R69H trigger conformational rearrangement in CypA. Structural intermediates between the RhCyp structure and parental CypA structure (2CPL)2 were generated using the morph server (http://www.molmovdb.org/molmovdb/morph/) to illustrate the degree of rearrangement caused by the two mutations D66N and R69H. Structures were rendered in PyMOL1 coloring the secondary structure in grey and the side-chains of Loop64-74 in yellow. The initial frame depicts the CypA structure in which D66 constrains the loop through a bifurcated hydrogen bond with the main-chain. Mutation of this residue and R69 leads to complete loop rearrangement and the new conformation present in RhCyp. (MOV 3063 kb)

Supplementary Movie 2

Loss of interaction with rearranged Loop64-74 abrogates HIV-1 binding to RhCyp. The CypA structural intermediates generated in Movie 1 were superposed on a CypA domain from the HIV1:CypA complex (1AK4)3. CypA is shown as a semi-transparent grey molecular surface with the side-chains of Loop64-74 in yellow. The HIV-1 N-terminal capsid domain is shown in green together with the side-chains of the CypA-binding loop. The initial frame depicts the solved complex in which the capsid interacts with Loop64-74, in particular between CA A88 and G72 and CA H87 and N71. Rearrangement of Loop64-74 leads to loss of these interactions. (MOV 1714 kb)

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Price, A., Marzetta, F., Lammers, M. et al. Active site remodeling switches HIV specificity of antiretroviral TRIMCyp. Nat Struct Mol Biol 16, 1036–1042 (2009). https://doi.org/10.1038/nsmb.1667

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