β-Propeller blades as ancestral peptides in protein evolution.

Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. De...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Klaus O Kopec, Andrei N Lupas
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b9b82564f6c44fbdbcc1e75921bd994e
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:b9b82564f6c44fbdbcc1e75921bd994e
record_format	dspace
spelling	oai:doaj.org-article:b9b82564f6c44fbdbcc1e75921bd994e2021-11-18T08:51:00Zβ-Propeller blades as ancestral peptides in protein evolution.1932-620310.1371/journal.pone.0077074https://doaj.org/article/b9b82564f6c44fbdbcc1e75921bd994e2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24143202/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD), type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world.Klaus O KopecAndrei N LupasPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e77074 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Klaus O Kopec Andrei N Lupas β-Propeller blades as ancestral peptides in protein evolution.
description	Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD), type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world.
format	article
author	Klaus O Kopec Andrei N Lupas
author_facet	Klaus O Kopec Andrei N Lupas
author_sort	Klaus O Kopec
title	β-Propeller blades as ancestral peptides in protein evolution.
title_short	β-Propeller blades as ancestral peptides in protein evolution.
title_full	β-Propeller blades as ancestral peptides in protein evolution.
title_fullStr	β-Propeller blades as ancestral peptides in protein evolution.
title_full_unstemmed	β-Propeller blades as ancestral peptides in protein evolution.
title_sort	β-propeller blades as ancestral peptides in protein evolution.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/b9b82564f6c44fbdbcc1e75921bd994e
work_keys_str_mv	AT klausokopec bpropellerbladesasancestralpeptidesinproteinevolution AT andreinlupas bpropellerbladesasancestralpeptidesinproteinevolution
_version_	1718421284398825472

β-Propeller blades as ancestral peptides in protein evolution.

Ejemplares similares