The N-terminal domain of RfaH plays an active role in protein fold-switching.

The bacterial elongation factor RfaH promotes the expression of virulence factors by specifically binding to RNA polymerases (RNAP) paused at a DNA signal. This behavior is unlike that of its paralog NusG, the major representative of the protein family to which RfaH belongs. Both proteins have an N-...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Pablo Galaz-Davison, Ernesto A Román, César A Ramírez-Sarmiento
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/1462933c4c2b499cbea461320e2947f8
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:1462933c4c2b499cbea461320e2947f8
record_format	dspace
spelling	oai:doaj.org-article:1462933c4c2b499cbea461320e2947f82021-12-02T19:57:51ZThe N-terminal domain of RfaH plays an active role in protein fold-switching.1553-734X1553-735810.1371/journal.pcbi.1008882https://doaj.org/article/1462933c4c2b499cbea461320e2947f82021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1008882https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The bacterial elongation factor RfaH promotes the expression of virulence factors by specifically binding to RNA polymerases (RNAP) paused at a DNA signal. This behavior is unlike that of its paralog NusG, the major representative of the protein family to which RfaH belongs. Both proteins have an N-terminal domain (NTD) bearing an RNAP binding site, yet NusG C-terminal domain (CTD) is folded as a β-barrel while RfaH CTD is forming an α-hairpin blocking such site. Upon recognition of the specific DNA exposed by RNAP, RfaH is activated via interdomain dissociation and complete CTD structural rearrangement into a β-barrel structurally identical to NusG CTD. Although RfaH transformation has been extensively characterized computationally, little attention has been given to the role of the NTD in the fold-switching process, as its structure remains unchanged. Here, we used Associative Water-mediated Structure and Energy Model (AWSEM) molecular dynamics to characterize the transformation of RfaH, spotlighting the sequence-dependent effects of NTD on CTD fold stabilization. Umbrella sampling simulations guided by native contacts recapitulate the thermodynamic equilibrium experimentally observed for RfaH and its isolated CTD. Temperature refolding simulations of full-length RfaH show a high success towards α-folded CTD, whereas the NTD interferes with βCTD folding, becoming trapped in a β-barrel intermediate. Meanwhile, NusG CTD refolding is unaffected by the presence of RfaH NTD, showing that these NTD-CTD interactions are encoded in RfaH sequence. Altogether, these results suggest that the NTD of RfaH favors the α-folded RfaH by specifically orienting the αCTD upon interdomain binding and by favoring β-barrel rupture into an intermediate from which fold-switching proceeds.Pablo Galaz-DavisonErnesto A RománCésar A Ramírez-SarmientoPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 9, p e1008882 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Pablo Galaz-Davison Ernesto A Román César A Ramírez-Sarmiento The N-terminal domain of RfaH plays an active role in protein fold-switching.
description	The bacterial elongation factor RfaH promotes the expression of virulence factors by specifically binding to RNA polymerases (RNAP) paused at a DNA signal. This behavior is unlike that of its paralog NusG, the major representative of the protein family to which RfaH belongs. Both proteins have an N-terminal domain (NTD) bearing an RNAP binding site, yet NusG C-terminal domain (CTD) is folded as a β-barrel while RfaH CTD is forming an α-hairpin blocking such site. Upon recognition of the specific DNA exposed by RNAP, RfaH is activated via interdomain dissociation and complete CTD structural rearrangement into a β-barrel structurally identical to NusG CTD. Although RfaH transformation has been extensively characterized computationally, little attention has been given to the role of the NTD in the fold-switching process, as its structure remains unchanged. Here, we used Associative Water-mediated Structure and Energy Model (AWSEM) molecular dynamics to characterize the transformation of RfaH, spotlighting the sequence-dependent effects of NTD on CTD fold stabilization. Umbrella sampling simulations guided by native contacts recapitulate the thermodynamic equilibrium experimentally observed for RfaH and its isolated CTD. Temperature refolding simulations of full-length RfaH show a high success towards α-folded CTD, whereas the NTD interferes with βCTD folding, becoming trapped in a β-barrel intermediate. Meanwhile, NusG CTD refolding is unaffected by the presence of RfaH NTD, showing that these NTD-CTD interactions are encoded in RfaH sequence. Altogether, these results suggest that the NTD of RfaH favors the α-folded RfaH by specifically orienting the αCTD upon interdomain binding and by favoring β-barrel rupture into an intermediate from which fold-switching proceeds.
format	article
author	Pablo Galaz-Davison Ernesto A Román César A Ramírez-Sarmiento
author_facet	Pablo Galaz-Davison Ernesto A Román César A Ramírez-Sarmiento
author_sort	Pablo Galaz-Davison
title	The N-terminal domain of RfaH plays an active role in protein fold-switching.
title_short	The N-terminal domain of RfaH plays an active role in protein fold-switching.
title_full	The N-terminal domain of RfaH plays an active role in protein fold-switching.
title_fullStr	The N-terminal domain of RfaH plays an active role in protein fold-switching.
title_full_unstemmed	The N-terminal domain of RfaH plays an active role in protein fold-switching.
title_sort	n-terminal domain of rfah plays an active role in protein fold-switching.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/1462933c4c2b499cbea461320e2947f8
work_keys_str_mv	AT pablogalazdavison thenterminaldomainofrfahplaysanactiveroleinproteinfoldswitching AT ernestoaroman thenterminaldomainofrfahplaysanactiveroleinproteinfoldswitching AT cesararamirezsarmiento thenterminaldomainofrfahplaysanactiveroleinproteinfoldswitching AT pablogalazdavison nterminaldomainofrfahplaysanactiveroleinproteinfoldswitching AT ernestoaroman nterminaldomainofrfahplaysanactiveroleinproteinfoldswitching AT cesararamirezsarmiento nterminaldomainofrfahplaysanactiveroleinproteinfoldswitching
_version_	1718375764632535040

The N-terminal domain of RfaH plays an active role in protein fold-switching.

Ejemplares similares