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Plos Computational Biology : Energetic Selection of Topology in Ferredoxins, Volume 8

By Kim, J. Dongun

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Book Id: WPLBN0003941178
Format Type: PDF eBook :
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Reproduction Date: 2015

Title: Plos Computational Biology : Energetic Selection of Topology in Ferredoxins, Volume 8  
Author: Kim, J. Dongun
Volume: Volume 8
Language: English
Subject: Journals, Science, Computational Biology
Collections: Periodicals: Journal and Magazine Collection (Contemporary), PLoS Computational Biology
Publication Date:
Publisher: Plos


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Kim, J. D. (n.d.). Plos Computational Biology : Energetic Selection of Topology in Ferredoxins, Volume 8. Retrieved from

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 Fe4S4 metal center, is an attractive candidate for such an early peptide. Ferredoxins are ancient proteins and the simple a+b 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 Fe4S4 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 aL,aR) is that of an asheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster Binding.


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