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Structural basis for the function and inhibition of an influenza virus proton channel

Nature volume 451, pages 596–599 (2008)Cite this article

A Corrigendum to this article was published on 20 March 2008

Abstract

The M2 protein from influenza A virus is a pH-activated proton channel that mediates acidification of the interior of viral particles entrapped in endosomes. M2 is the target of the anti-influenza drugs amantadine and rimantadine; recently, resistance to these drugs in humans, birds and pigs has reached more than 90% (ref. 1). Here we describe the crystal structure of the transmembrane-spanning region of the homotetrameric protein in the presence and absence of the channel-blocking drug amantadine. pH-dependent structural changes occur near a set of conserved His and Trp residues that are involved in proton gating2. The drug-binding site is lined by residues that are mutated in amantadine-resistant viruses3,4. Binding of amantadine physically occludes the pore, and might also perturb the pKa of the critical His residue. The structure provides a starting point for solving the problem of resistance to M2-channel blockers.

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Figure 1: Crystal structure of the M2 proton channel from the influenza A virus.
Figure 2: Asymmetric structure of the C-terminal His/Trp gate of M2TM.
Figure 3: Superpositions of the crystallographic tetramer demonstrate conformational differences in the C-terminal gating region of the channel.
Figure 4: Minimal mechanism of activation and conductance through the channel.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates for the apo form of M2TM have been deposited in the Protein Data Bank under the accession code 3BKD; coordinates for additional models are available from R.A.

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Acknowledgements

This work was primarily supported by a grant from the National Institute of General Medical Studies of the National Institutes of Health. We also acknowledge support from the Kimberly DeLape and Margaret DeLape Fellowship, the University of Pennsylvania’s MRSEC program, and the Nano/Bio Interface Center funded through the National Science Foundation. D.S. was a recipient of a postdoctoral fellowship from the Ministerio de Educación y Cultura (Spain). We thank J. Lear, L. Pinto, R. Lamb, L. Cristian, A. Polischuk, T. Kossiakoff, D. Christianson, M. Lewis and J. Chou for stimulating discussions. We also thank E. Jeavons, L.-H. (P.) Huang and K. Ellis for technical assistance.

Author Contributions D.S. grew the first high-resolution crystals of variants of M2TM, including the drug-free form reported here. A.L.S. selected additional variants and crystallized many other forms including the amantadine complex reported here. R.A. solved and refined both structures, and L.D.C. solved a monomeric form of M2TM used in molecular replacement. Data for the drug-free and amantadine-containing crystals were collected by S.S. and A.L.S., respectively. A.S.L. and V.T. also contributed to crystallization and data collection for crystal forms that were critical to obtaining and interpreting the crystal forms reported here. A.L.S., R.A., L.D.C., V.T. and S.S. processed and interpreted diffraction data. W.F.D., A.L.S., A.S.L., R.A., C.S.S. and V.N. each contributed to the analysis and understanding of the implications of the structure. C.S.S. and V.N. performed molecular modelling. W.F.D., A.S.L., A.L.S., R.A. and C.S.S. wrote the manuscript in consultation with the remaining authors. W.F.D. grew the first low-resolution crystals and supervised the project.

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Author notes

  1. Amanda L. Stouffer, David Salom, Anna S. Levine & Vikas Nanda

    Present address: Present addresses: Laboratory of Organic Chemistry, ETH Hönggerberg, 8093 Zurich, Switzerland (A.L.S.); Polgenix, Inc., Cleveland, Ohio 44106, USA (D.S); Box 2525, Brown University, Providence, Rhode Island 02912, USA (A.S.L.); Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA (V.N.).,

  2. Amanda L. Stouffer, Rudresh Acharya and David Salom: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Biophysics, School of Medicine,

    Amanda L. Stouffer, Rudresh Acharya, David Salom, Anna S. Levine, Cinque S. Soto, Vikas Nanda, Steven Stayrook & William F. DeGrado

  2. Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA,

    Amanda L. Stouffer, Luigi Di Costanzo & William F. DeGrado

  3. Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA,

    Valentina Tereshko

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Correspondence to William F. DeGrado.

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Competing interests

W.F.D. chairs the scientific advisory board of InfluMedix, a company that is working on the pharmaceutical intervention of influenza virus infections.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1–2 with Legends, which show the electron density of the interhelical salt bridge, the ordered detergent of the crystal lattice, heavy atom locations, and a structure based model of the S31N mutation. The file also includes crystallographic statistics (Supplementary Table 1). (PDF 234 kb)

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Stouffer, A., Acharya, R., Salom, D. et al. Structural basis for the function and inhibition of an influenza virus proton channel. Nature 451, 596–599 (2008). https://doi.org/10.1038/nature06528

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