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

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 a...

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Autores principales:	Maayan Bonjack, David Avnir
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/20ec46fe47f54c7abe9e85ff57cbcd7b
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spelling	oai:doaj.org-article:20ec46fe47f54c7abe9e85ff57cbcd7b2021-12-02T14:58:38ZThe near-symmetry of protein oligomers: NMR-derived structures10.1038/s41598-020-65097-82045-2322https://doaj.org/article/20ec46fe47f54c7abe9e85ff57cbcd7b2020-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-65097-8https://doaj.org/toc/2045-2322Abstract 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 C 2 -symmetry dimers, but C 3 and D 2 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.Maayan BonjackDavid AvnirNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-14 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maayan Bonjack David Avnir The near-symmetry of protein oligomers: NMR-derived structures
description	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 C 2 -symmetry dimers, but C 3 and D 2 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.
format	article
author	Maayan Bonjack David Avnir
author_facet	Maayan Bonjack David Avnir
author_sort	Maayan Bonjack
title	The near-symmetry of protein oligomers: NMR-derived structures
title_short	The near-symmetry of protein oligomers: NMR-derived structures
title_full	The near-symmetry of protein oligomers: NMR-derived structures
title_fullStr	The near-symmetry of protein oligomers: NMR-derived structures
title_full_unstemmed	The near-symmetry of protein oligomers: NMR-derived structures
title_sort	near-symmetry of protein oligomers: nmr-derived structures
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/20ec46fe47f54c7abe9e85ff57cbcd7b
work_keys_str_mv	AT maayanbonjack thenearsymmetryofproteinoligomersnmrderivedstructures AT davidavnir thenearsymmetryofproteinoligomersnmrderivedstructures AT maayanbonjack nearsymmetryofproteinoligomersnmrderivedstructures AT davidavnir nearsymmetryofproteinoligomersnmrderivedstructures
_version_	1718389251504078848

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

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