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dc.contributor.author
Galaz Davison, Pablo
dc.contributor.author
Ferreiro, Diego
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dc.contributor.author
Ramírez Sarmiento, César A.
dc.date.available
2023-09-26T15:36:26Z
dc.date.issued
2022-06
dc.identifier.citation
Galaz Davison, Pablo; Ferreiro, Diego; Ramírez Sarmiento, César A.; Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors; John Wiley & Sons; Protein Science; 31; 6; 6-2022; 1-11
dc.identifier.issn
0961-8368
dc.identifier.uri
http://hdl.handle.net/11336/213078
dc.description.abstract
The NusG protein family is structurally and functionally conserved in all domains of life. Its members directly bind RNA polymerases and regulate transcription processivity and termination. RfaH, a divergent sub-family in its evolutionary history, is known for displaying distinct features than those in NusG proteins, which allows them to regulate the expression of virulence factors in enterobacteria in a DNA sequence-dependent manner. A striking feature is its structural interconversion between an active fold, which is the canonical NusG three-dimensional structure, and an autoinhibited fold, which is distinctively novel. How this novel fold is encoded within RfaH sequence to encode a metamorphic protein remains elusive. In this work, we used publicly available genomic RfaH protein sequences to construct a complete multiple sequence alignment, which was further augmented with metagenomic sequences and curated by predicting their secondary structure propensities using JPred. Coevolving pairs of residues were calculated from these sequences using plmDCA and GREMLIN, which allowed us to detect the enrichment of key metamorphic contacts after sequence filtering. Finally, we combined our coevolutionary predictions with molecular dynamics to demonstrate that these interactions are sufficient to predict the structures of both native folds, where coevolutionary-derived non-native contacts may play a key role in achieving the compact RfaH novel fold. All in all, emergent coevolutionary signals found within RfaH sequences encode the autoinhibited and active folds of this protein, shedding light on the key interactions responsible for the action of this metamorphic protein.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
John Wiley & Sons
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dc.rights
info:eu-repo/semantics/restrictedAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
DIRECT COUPLING ANALYSIS
dc.subject
EVOLUTION
dc.subject
FOLD-SWITCH
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METAMORPHIC PROTEINS
dc.subject
PROTEIN FOLDING
dc.subject
TRANSCRIPTION FACTOR
dc.subject.classification
Biofísica
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dc.subject.classification
Ciencias Biológicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2023-07-07T22:45:06Z
dc.journal.volume
31
dc.journal.number
6
dc.journal.pagination
1-11
dc.journal.pais
Estados Unidos
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dc.journal.ciudad
Nueva Jersey
dc.description.fil
Fil: Galaz Davison, Pablo. Millennium Institute for Integrative Biology; Chile. Pontificia Universidad Católica de Chile; Chile
dc.description.fil
Fil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
dc.description.fil
Fil: Ramírez Sarmiento, César A.. Millennium Institute for Integrative Biology; Chile. Pontificia Universidad Católica de Chile; Chile
dc.journal.title
Protein Science
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/pro.4337
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1002/pro.4337
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