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Kim JD, Rodriguez-Granillo A, Case DA, Nanda V, Falkowski PG. Energetic selection of topology in ferredoxins. PLoS Comput Biol 2012; 8:e1002463. [PMID: 22496635 PMCID: PMC3320576 DOI: 10.1371/journal.pcbi.1002463] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 02/22/2012] [Indexed: 11/18/2022] Open
Abstract
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 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 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 αL,αR) is that of an α-sheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster binding. The ferredoxin fold is one of the oldest structures capable of catalyzing electron transfer reactions. In nature, only a right-handed topology exists in the ferredoxin fold. To understand how a specific fold-handedness was selected, we analyzed the structural motif using the tools of de novo protein design, searching in an unbiased fashion for backbone geometries that can favorably interact with the tetrahedral iron-sulfur cluster. In silico, we found both left-handed and right-handed folds can be formed, however the right-handed folds provide up to six hydrogen bonds that can stabilize the reduced iron-sulfur cluster, whereas left-handed folds at most form three hydrogen bonds. The difference in electrostatic conformational energy may have influenced selection of topology early in the evolution of iron-sulfur cluster containing proteins. This observation led us to establish a fundamental protein design principle that only right-handed peptide folds can properly interact while maintain redox function. Our results provide guidance in the creation of artificial proteins capable of carrying out redox reactions.
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Affiliation(s)
- J. Dongun Kim
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Agustina Rodriguez-Granillo
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey, United States of America
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Vikas Nanda
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey, United States of America
| | - Paul G. Falkowski
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
- Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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Balueva KE, Malygin AA, Karpova GG, Nevinsky GA, Zharkov DO. Interactions of human ribosomal protein S3 with intact and damaged DNA. Mol Biol 2008. [DOI: 10.1134/s0026893308020143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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