The near-symmetry of protein oligomers: NMR-derived structures

Maayan Bonjack,David Avnir

doi:10.1038/s41598-020-65097-8

Abstract

The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry. Despite the many advantages of symmetric packing, protein oligomers are only nearly symmetric, and the origin of this phenomenon is still in need to be fully explored. Here we apply near-symmetry analyses by the Continuous Symmetry Measures methodology of protein homomers to their natural state, namely their structures in solution. NMR-derived structural data serves us for that purpose. We find that symmetry deviations of proteins are by far higher in solution, compared to the crystalline state; that much of the symmetry distortion is due to amino acids along the interface between the subunits; that the distortions are mainly due to hydrophilic amino acids; and that distortive oligomerization processes such as the swap-domain mechanism can be identified by the symmetry analysis. Most of the analyses were carried out on distorted C2-symmetry dimers, but C3 and D2 cases were analyzed as well. Our NMR analysis supports the idea that the crystallographic B-factor represents non-classical crystals, in which different conformers pack in the crystal, perhaps from the conformers which the NMR analysis provides.

Highlights

The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry
A proposition which may emerge from our NMR data analysis is that the crystal of a protein is not the classical case of having the exact same conformer repeating itself in an ideal translational symmetry, but that instead, the translational movement may lead to different conformers along that path, perhaps from the family of the conformers which the NMR analysis identifies
We selected for that purpose the N-terminal domain dimer of HPV16 E6, a viral oncoprotein which is an essential factor for cervical cancers induced by “high-risk” mucosal HPV (PDB 2LJY40)

Summary

Introduction

The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry. Some of our main findings detailed below are that the symmetry deviations as evaluated by the CSM analysis for homomers in solution, are by far higher – that is, more distorted - in solution, compared to the CSM values obtained in the crystalline state; that, as in the crystalline state, much of the symmetry distortion is concentrated in amino acids along the near-symmetry axis; and, that despite the aqueous environment, this distortion is mainly due to interactions between hydrophilic amino acids along the border between the homomer units, resulting mainly in asymmetric hydrogen bonds which link the subunits; we show, using NMR data, the importance of domain swapping mechanism in inducing asymmetry in homomers; and we show that the higher symmetries - C3, D2 – require more case-focused analyses, which depend on the specific geometries that carry these symmetries. We are not the first to come up with the idea that protein crystals are non-classical from that point of view: For instance, Woldeyes et al.[20], proposed that many protein conformers are populated in a single crystal, and that this conformational heterogeneity is averaged in time and space in x-ray crystallography datasets; our study supports this notion

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Results

Conclusion