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Published on: March 24, 2017
The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope
Omry Morag1, Nikolaos G Sgourakis2, David Baker2
1School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel; and.
Abstract:
Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16.6-16.7 Å and a tilt of 36.1-36.6° between consecutive pentamers. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides, to our knowledge, the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study noncrystalline, high-molecular-weight molecular assemblies.
Insights
Researchers developed a structural model for intact M13 bacteriophage, a filamentous virus. This study showcases magic-angle spinning NMR for analyzing large, noncrystalline biological assemblies like virus capsids.
Area of Science:
- Structural biology
- Virology
- Biophysics
Background:
- Filamentous phages are elongated, semiflexible single-stranded DNA viruses infecting bacteria.
- The M13 phage, a member of the Inoviridae family, measures approximately 1 μm in length and 7 nm in diameter.
Purpose of the Study:
- To present a detailed structural model of the intact M13 bacteriophage capsid.
- To demonstrate the utility of magic-angle spinning solid-state NMR for studying complex viral structures.
Main Methods:
- Rosetta model building was employed, guided by structural restraints from magic-angle spinning solid-state NMR data.
- C5 subunit symmetry, consistent with fiber diffraction studies, was enforced during the model construction process.
Main Results:
- A structural model revealed stacked pentamers forming the capsid, with alpha-helical subunits featuring an N-terminal type II β-turn.
- Consecutive pentamers exhibited a rise of 16.6–16.7 Å and a tilt of 36.1–36.6°.
- Subunit packing is stabilized by hydrophobic stacking pockets, involving contributions from residues spread across the subunit sequence.
Conclusions:
- This study provides the first reported magic-angle spinning NMR structure of an intact filamentous virus capsid.
- The findings highlight the effectiveness of magic-angle spinning NMR for analyzing noncrystalline, high-molecular-weight molecular assemblies.
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