Principal component analysis of alpha-helix deformations in transmembrane proteins.

α-helices are deformable secondary structural components regularly observed in protein folds. The overall flexibility of an α-helix can be resolved into constituent physical deformations such as bending in two orthogonal planes and twisting along the principal axis. We used Principal Component Analy...

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Autores principales:	Alexander Bevacqua, Sachit Bakshi, Yu Xia
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/75872cd3ffb7421492670feeca4d7639
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spelling	oai:doaj.org-article:75872cd3ffb7421492670feeca4d76392021-12-02T20:06:16ZPrincipal component analysis of alpha-helix deformations in transmembrane proteins.1932-620310.1371/journal.pone.0257318https://doaj.org/article/75872cd3ffb7421492670feeca4d76392021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0257318https://doaj.org/toc/1932-6203α-helices are deformable secondary structural components regularly observed in protein folds. The overall flexibility of an α-helix can be resolved into constituent physical deformations such as bending in two orthogonal planes and twisting along the principal axis. We used Principal Component Analysis to identify and quantify the contribution of each of these dominant deformation modes in transmembrane α-helices, extramembrane α-helices, and α-helices in soluble proteins. Using three α-helical samples from Protein Data Bank entries spanning these three cellular contexts, we determined that the relative contributions of these modes towards total deformation are independent of the α-helix's surroundings. This conclusion is supported by the observation that the identities of the top three deformation modes, the scaling behaviours of mode eigenvalues as a function of α-helix length, and the percentage contribution of individual modes on total variance were comparable across all three α-helical samples. These findings highlight that α-helical deformations are independent of cellular location and will prove to be valuable in furthering the development of flexible templates in de novo protein design.Alexander BevacquaSachit BakshiYu XiaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 9, p e0257318 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Alexander Bevacqua Sachit Bakshi Yu Xia Principal component analysis of alpha-helix deformations in transmembrane proteins.
description	α-helices are deformable secondary structural components regularly observed in protein folds. The overall flexibility of an α-helix can be resolved into constituent physical deformations such as bending in two orthogonal planes and twisting along the principal axis. We used Principal Component Analysis to identify and quantify the contribution of each of these dominant deformation modes in transmembrane α-helices, extramembrane α-helices, and α-helices in soluble proteins. Using three α-helical samples from Protein Data Bank entries spanning these three cellular contexts, we determined that the relative contributions of these modes towards total deformation are independent of the α-helix's surroundings. This conclusion is supported by the observation that the identities of the top three deformation modes, the scaling behaviours of mode eigenvalues as a function of α-helix length, and the percentage contribution of individual modes on total variance were comparable across all three α-helical samples. These findings highlight that α-helical deformations are independent of cellular location and will prove to be valuable in furthering the development of flexible templates in de novo protein design.
format	article
author	Alexander Bevacqua Sachit Bakshi Yu Xia
author_facet	Alexander Bevacqua Sachit Bakshi Yu Xia
author_sort	Alexander Bevacqua
title	Principal component analysis of alpha-helix deformations in transmembrane proteins.
title_short	Principal component analysis of alpha-helix deformations in transmembrane proteins.
title_full	Principal component analysis of alpha-helix deformations in transmembrane proteins.
title_fullStr	Principal component analysis of alpha-helix deformations in transmembrane proteins.
title_full_unstemmed	Principal component analysis of alpha-helix deformations in transmembrane proteins.
title_sort	principal component analysis of alpha-helix deformations in transmembrane proteins.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/75872cd3ffb7421492670feeca4d7639
work_keys_str_mv	AT alexanderbevacqua principalcomponentanalysisofalphahelixdeformationsintransmembraneproteins AT sachitbakshi principalcomponentanalysisofalphahelixdeformationsintransmembraneproteins AT yuxia principalcomponentanalysisofalphahelixdeformationsintransmembraneproteins
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Principal component analysis of alpha-helix deformations in transmembrane proteins.

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