Membrane curvature sensing and symmetry breaking of the M2 proton channel from Influenza A

Abstract
Data availability
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Abstract

The M2 proton channel aids in the exit of mature influenza viral particles from the host plasma membrane through its ability to stabilize regions of high negative gaussian curvature (NGC) that occur at the neck of budding virions. The channels are homo-tetramers that contain a cytoplasm-facing amphipathic helix (AH) that is necessary and sufficient for NGC generation; however, constructs containing the transmembrane spanning helix, which facilitates tetramerization, exhibit enhanced curvature generation. Here we used all-atom molecular dynamics (MD) simulations to explore the conformational dynamics of M2 channels in lipid bilayers revealing that the AH is dynamic, quickly breaking the 4-fold symmetry observed in most structures. Next, we carried out MD simulations with the protein restrained in 4-fold and 2-fold symmetric conformations to determine the impact on the membrane shape. While each pattern was distinct, all configurations induced pronounced curvature in the outer leaflet, while conversely, the inner leaflets showed minimal curvature and significant lipid tilt around the AHs. The MD-generated profiles at the protein-membrane interface were then extracted and used as boundary conditions in a continuum elastic membrane model to calculate the membrane bending energy of each conformation embedded in different membrane surfaces characteristic of a budding virus. The calculations show that all three M2 conformations are stabilized in inward-budding, concave spherical caps and destabilized in outward-budding, convex spherical caps, the latter reminiscent of a budding virus. One of the C2-broken symmetry conformations is stabilized by 4 kT in NGC surfaces with the minimum energy conformation occurring at a curvature corresponding to 33 nm radii. In total, our work provides atomistic insight into the curvature sensing capabilities of M2 channels and how enrichment in the nascent viral particle depends on protein shape and membrane geometry.

Data availability

The original DEER data reported in Figure 7 of Kim et al. 2015 appears in panel B of Figure 2 (green curves). The raw data is included as Source data file 1 for Figure 2. This study used two previously published structures of M2 (PDBIDs 2L0J and 2N70) as well as a custom-built parallel AH domain construct based off of 2N70. The parallel AH domain construct structure is included as Source data file 2 for Figure 3.

The following data sets were generated

(2022) Parallel AH domain model
Zenodo, doi:10.5281/zenodo.6846507.

https://zenodo.org/record/6846507#.YtMQny-B0xM

The following previously published data sets were used

1. Kim SS
2. Upshur MA
3. Saotome K
4. Sahu ID
5. McCarrick RM
6. Feix JB
7. Lorigan GA
8. Howard KP
(2015) Data from: Cholesterol-Dependent Conformational Exchange of the C‐Terminal Domain of the Influenza A M2 Protein
Zenodo, doi:10.5281/zenodo.6846507.

https://zenodo.org/record/6846507#.YtMQny-B0xM
1. Sharma M
2. Yi M
3. Dong H
4. Qin H
5. Peterson E
6. Busath DD
7. Zhou HX
8. Cross TA
(2010) Data from: Insight into the mechanism of the influenza a proton channel from a structure in a lipid bilayer
RCSB Protein Data Bank, 2L0J.

https://www.rcsb.org/structure/2L0J
1. Andreas LB
2. Reese M
3. Eddy MT
4. Gelev V
5. Ni QZ
6. Miller EA
7. Emsley L
8. Pintacuda G
9. Chou JJ
10. Griffin RG
(2015) Data from: Structure and Mechanism of the Influenza A M218-60 Dimer of Dimers
RCSB Protein Data Bank, 2N70.

https://www.rcsb.org/structure/2N70

Article and author information

Author details

James Lincoff

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3090-1240
Cole VM Helsell

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States

Competing interests
The authors declare that no competing interests exist.
Frank V Marcoline

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States

Competing interests
The authors declare that no competing interests exist.
Andrew M Natale

Biophysics PhD program, University of California, San Francisco, San Francisco, United States

Competing interests
The authors declare that no competing interests exist.
Michael Grabe

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States

For correspondence
michael.grabe@ucsf.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3509-5997

Funding

National Institutes of Health (4T32HL007731-28)

James Lincoff

National Science Foundation (P0558710)

Michael Grabe

National Institutes of Health (R01GM117593)

Michael Grabe

National Institutes of Health (R01GM137109)

Michael Grabe

National Institutes of Health (R01GM089740)

Michael Grabe

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.