Cargando…

Energetic Selection of Topology in Ferredoxins

Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins, enclosing an Fe(4)S(4) metal center, is an attractive candidate for such a...

Descripción completa

Detalles Bibliográficos
Autores principales: Kim, J. Dongun, Rodriguez-Granillo, Agustina, Case, David A., Nanda, Vikas, Falkowski, Paul G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320576/
https://www.ncbi.nlm.nih.gov/pubmed/22496635
http://dx.doi.org/10.1371/journal.pcbi.1002463
_version_ 1782228861746937856
author Kim, J. Dongun
Rodriguez-Granillo, Agustina
Case, David A.
Nanda, Vikas
Falkowski, Paul G.
author_facet Kim, J. Dongun
Rodriguez-Granillo, Agustina
Case, David A.
Nanda, Vikas
Falkowski, Paul G.
author_sort Kim, J. Dongun
collection PubMed
description Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins, enclosing an Fe(4)S(4) metal center, is an attractive candidate for such an early peptide. Ferredoxins are ancient proteins and the simple α+β fold is found alone or as a domain in larger proteins throughout all three kingdoms of life. Previous analyses of the heptapeptide conformation in experimentally determined ferredoxin structures revealed a pervasive right-handed topology, despite the fact that the Fe(4)S(4) cluster is achiral. Conformational enumeration of a model CGGCGGC heptapeptide bound to a cubane iron-sulfur cluster indicates both left-handed and right-handed folds could exist and have comparable stabilities. However, only the natural ferredoxin topology provides a significant network of backbone-to-cluster hydrogen bonds that would stabilize the metal-peptide complex. The optimal peptide configuration (alternating α(L),α(R)) is that of an α-sheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster binding.
format Online
Article
Text
id pubmed-3320576
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-33205762012-04-11 Energetic Selection of Topology in Ferredoxins Kim, J. Dongun Rodriguez-Granillo, Agustina Case, David A. Nanda, Vikas Falkowski, Paul G. PLoS Comput Biol Research Article Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins, enclosing an Fe(4)S(4) metal center, is an attractive candidate for such an early peptide. Ferredoxins are ancient proteins and the simple α+β fold is found alone or as a domain in larger proteins throughout all three kingdoms of life. Previous analyses of the heptapeptide conformation in experimentally determined ferredoxin structures revealed a pervasive right-handed topology, despite the fact that the Fe(4)S(4) cluster is achiral. Conformational enumeration of a model CGGCGGC heptapeptide bound to a cubane iron-sulfur cluster indicates both left-handed and right-handed folds could exist and have comparable stabilities. However, only the natural ferredoxin topology provides a significant network of backbone-to-cluster hydrogen bonds that would stabilize the metal-peptide complex. The optimal peptide configuration (alternating α(L),α(R)) is that of an α-sheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster binding. Public Library of Science 2012-04-05 /pmc/articles/PMC3320576/ /pubmed/22496635 http://dx.doi.org/10.1371/journal.pcbi.1002463 Text en Kim et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Kim, J. Dongun
Rodriguez-Granillo, Agustina
Case, David A.
Nanda, Vikas
Falkowski, Paul G.
Energetic Selection of Topology in Ferredoxins
title Energetic Selection of Topology in Ferredoxins
title_full Energetic Selection of Topology in Ferredoxins
title_fullStr Energetic Selection of Topology in Ferredoxins
title_full_unstemmed Energetic Selection of Topology in Ferredoxins
title_short Energetic Selection of Topology in Ferredoxins
title_sort energetic selection of topology in ferredoxins
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320576/
https://www.ncbi.nlm.nih.gov/pubmed/22496635
http://dx.doi.org/10.1371/journal.pcbi.1002463
work_keys_str_mv AT kimjdongun energeticselectionoftopologyinferredoxins
AT rodriguezgranilloagustina energeticselectionoftopologyinferredoxins
AT casedavida energeticselectionoftopologyinferredoxins
AT nandavikas energeticselectionoftopologyinferredoxins
AT falkowskipaulg energeticselectionoftopologyinferredoxins