A Comparative Dynamics Framework for Isolating Embedded Bacterial Ferredoxin Domains within Larger Redox Enzymes

A Comparative Dynamics Framework for Isolating Embedded Bacterial Ferredoxin Domains within Larger Redox Enzymes | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL PROTEINS: Structure, Function, and Bioinformatics This is a preprint and has not been peer reviewed. Data may be preliminary. 17 January 2025 V1 Latest version Share on A Comparative Dynamics Framework for Isolating Embedded Bacterial Ferredoxin Domains within Larger Redox Enzymes Authors : Jan A. Siess 0000-0002-2352-7636 and Vikas Nanda [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.173713573.36044616/v1 301 views 147 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Bacterial ferredoxins are small iron-sulfur binding proteins that function as soluble electron shuttles between redox enzymes in the cell. Their simple 2x(β-α-β) fold, central metabolic function, and ubiquity across all kingdoms of life have led to the proposal that ferredoxins were likely among the earliest proteins. Today, ferredoxin-like folds are embedded in large, multidomain enzymes, suggesting ancient gene duplication and fusion events. In some cases, these embedded domains may have scant sequence or even structural homology to soluble counterparts, challenging the use of traditional phylogenetic tools to establish evolutionary relationships. In this study, we identify fragments of bacterial ferredoxins within larger oxidoreductases by integrating comparative sequence, structure, and dynamical attributes. Dynamics are computed using an elastic network model and analyzed for similarity of major normal modes. Using comparative dynamics, fragments of ferredoxin domains are found within larger proteins, even in cases of limited structural homology. This study also reveals a non-linear relationship between dynamical and structural similarities, suggesting that protein dynamics are more constrained than structure through evolutionary time. We propose that dynamical similarity is indicative of functional similarity. And, since nature selects for function, that the inclusion of dynamical similarity, in addition to sequence and structure similarities, provides a more robust framework for inferring homology. Inclusion of dynamical attributes in comparative analysis will lead to a greater understanding of the deep-time evolution of modern protein nanomachines. Supplementary Material File (wileyproteins_mainmanuscript_jansiess_viknanda.docx) Download 17.63 MB Information & Authors Information Version history V1 Version 1 17 January 2025 Copyright This work is licensed under a Non Exclusive No Reuse License. Collection PROTEINS: Structure, Function, and Bioinformatics Keywords anisotropic network model (anm) comparative dynamics ferredoxin domains protein evolution protein structure dynamics Authors Affiliations Jan A. Siess 0000-0002-2352-7636 Rutgers Robert Wood Johnson Medical School Department of Biochemistry and Molecular Biology View all articles by this author Vikas Nanda [email protected] Rutgers Robert Wood Johnson Medical School Department of Biochemistry and Molecular Biology View all articles by this author Metrics & Citations Metrics Article Usage 301 views 147 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Jan A. Siess, Vikas Nanda. A Comparative Dynamics Framework for Isolating Embedded Bacterial Ferredoxin Domains within Larger Redox Enzymes. Authorea . 17 January 2025. DOI: https://doi.org/10.22541/au.173713573.36044616/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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