scholarly journals New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins involved in Iron Sulfur Cluster Biogenesis

2017 ◽  
Author(s):  
Marco Fantini ◽  
Duccio Malinverni ◽  
Paolo De Los Rios ◽  
Annalisa Pastore
Keyword(s):  
Protein Interactions ◽  
Strong Support ◽  
Scaffold Protein ◽  
Direct Coupling ◽  
Protein Protein Interactions ◽  
Coupling Analysis ◽  
Iron Sulfur Cluster ◽  
Sulfur Cluster ◽  
Iron Sulfur ◽  
Direct Coupling Analysis

ABSTRACTDirect coupling analysis (DCA) is a powerful tool based on protein evolution and introduced to predict protein fold and protein-protein interactions which has been applied also to the prediction of entire interactomes. We have used DCA to analyse three proteins of the iron-sulfur biogenesis machine, an essential metabolic pathway conserved in all organisms. We show that, although based on a relatively small number of sequences due to its distribution in genomes, we can correctly recapitulate all the features of the fold of the CyaY/frataxin family, a protein involved in the human disease Friedreich’s ataxia. This result gave us confidence in the use of this tool. Application of DCA to the iron-sulfur cluster scaffold protein IscU, which has been suggested to function both as an ordered and a disordered form, allows us to clearly distinguish evolutionary traces of the structured species, suggesting that, if present in the cell, the disordered form has not left any evolutionary imprinting. We observe instead, for the first time, direct indications of how the protein can dimerize head-to-head and bind 4Fe4S clusters. Analysis of the alternative scaffold protein IscA provides strong support to a coordination of the cluster mediated by a dimeric rather than a tetrameric form as previously suggested. Our analysis also suggests the presence in solution of a mixture of monomeric and dimeric species and guide us to the prevalent one. Finally, we used DCA to analyse protein-protein interactions between some of these proteins and discuss the potentialities and the limitations of the method.

scholarly journals Structural basis of RICs iron donation for iron-sulfur cluster biogenesis

2021 ◽  
Author(s):  
Liliana S. O. Silva ◽  
Pedro M. Matias ◽  
Célia V. Romão ◽  
Lígia M. Saraiva
Keyword(s):  
Escherichia Coli ◽  
Protein Interactions ◽  
Structural Characteristics ◽  
Structural Basis ◽  
Single Mutation ◽  
Protein Protein Interactions ◽  
Iron Sulfur Cluster ◽  
Sulfur Cluster ◽  
Iron Sulfur ◽  
Iron Sulfur Proteins

AbstractEscherichia coli YtfE is a di-iron protein, of the widespread RIC family, with capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. Herein we identify in E. coli a previously unrecognized link between the YtfE protein and the major bacterial system for iron-sulfur cluster (ISC) assembly. We show that YtfE establishes protein-protein interactions with the scaffold IscU, where the transient cluster is formed, and the cysteine desulfurase IscS. Moreover, we found that promotion by YtfE of the formation of an Fe-S cluster in IscU requires two glutamates, E125 and E159 in YtfE. Both glutamates form part of the entrance of a protein channel in YtfE that links the di-iron centre to the surface. In particular, E125 is crucial for the exit of iron, as a single mutation to leucine closes the channel rendering YtfE inactive for the build-up of Fe-S clusters. Hence, we provide evidence for the key role of RICs as bacterial iron donor proteins involved in the biogenesis of Fe-S clusters.ImportanceThe ubiquitous iron-sulfur proteins require specialized cellular machineries to promote the assembly of the cofactor. These systems include proteins that provide sulfur and iron, and scaffold proteins where the cluster is formed. Although largely studied the nature of the iron donor remains to be fully clarified. In this work, we show that Escherichia coli YtfE, which belongs to the RIC protein family, establishes protein-protein interactions with two of the major proteins of the ISC system, and we reveal the structural characteristics necessary for the exit of iron ions from YtfE. Altogether our results prove that RICs can be considered a family of iron donor proteins involved in the biogenesis of iron-sulfur containing proteins.

scholarly journals Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Liliana S. O. Silva ◽  
Pedro M. Matias ◽  
Célia V. Romão ◽  
Lígia M. Saraiva
Keyword(s):  
Protein Interactions ◽  
Structural Basis ◽  
Single Mutation ◽  
Protein Protein Interactions ◽  
Cysteine Desulfurase ◽  
Iron Sulfur Cluster ◽  
Sulfur Cluster ◽  
E Coli ◽  
Iron Sulfur ◽  
Crucial Component

Escherichia coli YtfE is a di-iron protein of the widespread Repair of Iron Centers proteins (RIC) family that has the capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. In this work we identify in E. coli a previously unrecognized link between the YtfE protein and the major bacterial system for iron-sulfur cluster (ISC) assembly. We show that YtfE establishes protein-protein interactions with the scaffold IscU, where the transient cluster is formed, and the cysteine desulfurase IscS. Moreover, we found that promotion by YtfE of the formation of an Fe-S cluster in IscU requires two glutamates, E125 and E159 in YtfE. Both glutamates form part of the entrance of a protein channel in YtfE that links the di-iron center to the surface. In particular, E125 is crucial for the exit of iron, as a single mutation to leucine closes the channel rendering YtfE inactive for the build-up of Fe-S clusters. Hence, we provide evidence for the key role of RICs as bacterial iron donor proteins involved in the biogenesis of Fe-S clusters.

scholarly journals Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis

2016 ◽  
Vol 113 (43) ◽  
pp. 12186-12191 ◽  
Author(s):  
Thomas Gueudré ◽  
Carlo Baldassi ◽  
Marco Zamparo ◽  
Martin Weigt ◽  
Andrea Pagnani
Keyword(s):  
Protein Interactions ◽  
Multiple Scales ◽  
Sequence Data ◽  
Direct Coupling ◽  
Physical Contact ◽  
Protein Protein Interactions ◽  
Homologous Proteins ◽  
Coupling Analysis ◽  
Large Joint ◽  
Direct Coupling Analysis

Understanding protein−protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein−protein interactions are urgently needed. Such methods should connect multiple scales from evolutionary conserved interactions between families of homologous proteins, over the identification of specifically interacting proteins in the case of multiple paralogs inside a species, down to the prediction of residues being in physical contact across interaction interfaces. Statistical inference methods detecting residue−residue coevolution have recently triggered considerable progress in using sequence data for quaternary protein structure prediction; they require, however, large joint alignments of homologous protein pairs known to interact. The generation of such alignments is a complex computational task on its own; application of coevolutionary modeling has, in turn, been restricted to proteins without paralogs, or to bacterial systems with the corresponding coding genes being colocalized in operons. Here we show that the direct coupling analysis of residue coevolution can be extended to connect the different scales, and simultaneously to match interacting paralogs, to identify interprotein residue−residue contacts and to discriminate interacting from noninteracting families in a multiprotein system. Our results extend the potential applications of coevolutionary analysis far beyond cases treatable so far.

scholarly journals Anatomy of an iron-sulfur cluster scaffold protein: Understanding the determinants of [2Fe–2S] cluster stability on IscU

2015 ◽  
Vol 1853 (6) ◽  
pp. 1448-1456 ◽  
Author(s):  
Miquel Adrover ◽  
Barry D. Howes ◽  
Clara Iannuzzi ◽  
Giulietta Smulevich ◽  
Annalisa Pastore
Keyword(s):  
Scaffold Protein ◽  
Iron Sulfur Cluster ◽  
Sulfur Cluster ◽  
Cluster Stability ◽  
Iron Sulfur
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