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MetalPredator: a web server to predict iron–sulfur cluster binding proteomes

Yana Valasatava, Antonio Rosato, Lucia Banci, Claudia Andreini
2016 Bioinformatics  
Results: We developed a web server to predict iron-sulfur proteins from protein sequence(s).  ...  Motivation: The prediction of the iron-sulfur proteome is highly desirable for biomedical and biological research but a freely available tool to predict iron-sulfur proteins has not been developed yet.  ...  We propose a novel computational tool, called MetalPredator, to predict metal-binding sites in protein sequence(s) at the whole proteome scale.  ... 
doi:10.1093/bioinformatics/btw238 pmid:27273670 fatcat:vs3nwgjm4bc6rpjs56ygmwn7bu

Prediction of the Iron–Sulfur Binding Sites in Proteins Using the Highly Accurate Three-Dimensional Models Calculated by AlphaFold and RoseTTAFold

Béatrice Golinelli-Pimpaneau
2021 Inorganics  
In this article, I question the accuracy of these methods to predict ironsulfur binding sites.  ...  In all cases, the amino acids that presumably coordinate the cluster were gathered together and facing each other, which led to a quite accurate model of the Fe–S cluster binding site.  ...  Metalpredator is a web server that has been developed to predict Fe-S binding proteins from protein sequence(s) [9] (http://metalweb.cerm.unifi.it/tools/metalpredator/; 18 December 2021).  ... 
doi:10.3390/inorganics10010002 fatcat:wasfrwutyrbudfuggrskixfvsu

Differential contribution of two organelles of endosymbiotic origin to iron-sulfur cluster synthesis and overall fitness in Toxoplasma

Sarah Pamukcu, Aude Cerutti, Yann Bordat, Sonia Hem, Valérie Rofidal, Sébastien Besteiro, Dominique Soldati-Favre
2021 PLoS Pathogens  
Iron-sulfur (Fe-S) clusters are one of the most ancient and ubiquitous prosthetic groups, and they are required by a variety of proteins involved in important metabolic processes.  ...  Both Fe-S cluster synthesis pathways are necessary for optimal parasite growth in vitro, but their disruption leads to markedly different fates: impairment of the plastidic pathway leads to a loss of the  ...  We also thank the MRI imaging facility for providing access to their microscopes and flow cytometers, and the Mass Spectrometry Proteomics Platform (MSPP) of the BPMP laboratory. Thanks to F.  ... 
doi:10.1371/journal.ppat.1010096 pmid:34793583 pmcid:PMC8639094 fatcat:hi4zts7nkvgfzi6lxjplsgeidm

Bioinformatics of Metalloproteins and Metalloproteomes

Yan Zhang, Junge Zheng
2020 Molecules  
This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life  ...  We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases.  ...  MetalPredator [44] , another web-based tool to predict Fe-S proteins from protein sequences, was also developed to process complete proteomes with high-precision prediction, providing new resources for  ... 
doi:10.3390/molecules25153366 pmid:32722260 pmcid:PMC7435645 fatcat:m2y5sgbgzjc3li6ofkj34dqksy

Arabidopsis Iron Superoxide Dismutase FSD1 Protects Against Methyl Viologen-Induced Oxidative Stress in a Copper-Dependent Manner

Pavol Melicher, Petr Dvořák, Yuliya Krasylenko, Alexey Shapiguzov, Jaakko Kangasjärvi, Jozef Šamaj, Tomáš Takáč
2022 Frontiers in Plant Science  
Iron superoxide dismutase 1 (FSD1) was recently characterized as a plastidial, cytoplasmic, and nuclear enzyme with osmoprotective and antioxidant functions.  ...  Prolonged exposure to MV led to reduced ascorbate levels and higher protein carbonylation in fsd1 mutants and transgenic plants lacking a plastid FSD1 pool as compared to the wild type.  ...  The iron-sulfur cluster binding proteins from amino acid sequences of the differential proteomes of WT, fsd1-1, and fsd1-2 mutants were predicted using MetalPredator (Valasatava et al., 2016) .  ... 
doi:10.3389/fpls.2022.823561 pmid:35360337 pmcid:PMC8963501 fatcat:6v6wq5wrlrfz3bc5zuyylm725e