Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 from Acidithiobacillus ferrooxidans

View ORCID ProfileVirginia Jiang, View ORCID ProfileSagar D. Khare, View ORCID ProfileScott Banta
doi: https://doi.org/10.1101/2021.03.22.436458
Virginia Jiang
1Department of Chemical Engineering, Columbia University in the City of New York, New York, NY 10027, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Virginia Jiang
Sagar D. Khare
2Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sagar D. Khare
Scott Banta
1Department of Chemical Engineering, Columbia University in the City of New York, New York, NY 10027, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Scott Banta
  • For correspondence: sbanta@columbia.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

Cyc2 is the key protein in the outer membrane of Acidithiobacillus ferrooxidans that mediates electron transfer between extracellular inorganic iron and the intracellular central metabolism. This cytochrome c is specific for iron and interacts with periplasmic proteins to complete a reversible electron transport chain. A structure of Cyc2 has not yet been characterized experimentally. Here we describe a structural model of Cyc2, and associated proteins, to highlight a plausible mechanism for the ferrous iron electron transfer chain. A comparative modeling protocol specific for trans membrane beta barrel (TMBB) proteins in acidophilic conditions (pH ~2) was applied to the primary sequence of Cyc2. The proposed structure has three main regimes: extracellular loops exposed to low-pH conditions, a TMBB, and a N-terminal cytochrome-like region within the periplasmic space. The Cyc2 model was further refined by identifying likely iron and heme docking sites. This represents the first computational model of Cyc2 that accounts for the membrane microenvironment and the acidity in the extracellular matrix. This approach can be used to model other TMBBs which can be critical for chemolithotrophic microbial growth.

Importance of work Acidithiobacillus ferrooxidans can oxidize both iron and reduced sulfur compounds and plays a key role in metal sulfide ore bioleaching used for the industrial recovery of metals. A. ferrooxidans has also been explored as a potential organism for emerging technologies such as e-waste recycling and biofuel production. Synthetic biology efforts are hampered by lack of knowledge about the mechanisms of iron oxidation and reduction, which is mediated by the Cyc2 transmembrane beta barrel (TMBB) protein.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Description of supplementary information - A “Supplementary information” file has been uploaded which contains primary sequence information, topology files, multiple sequence alignments, additional structural figures, and additional score vs RMSD plots.

  • https://www.modelarchive.org/doi/10.5452/ma-ln7x4

  • Abbreviations

    REU
    Rosetta Energy Unit
    TMBB
    trans-membrane beta barrel protein
    Cyc2
    gene name for outer membrane cytochrome c protein of A. ferrooxidans
    Cyc1
    gene name for cytochrome c552 protein of A. ferrooxidans
    Rcy
    rusticyanin protein of A. ferrooxidans
    RMSD
    root mean square deviation of atomic positions, given in angstroms (Å)
    OPM
    Orientations of Proteins in Membranes database (58)
    MIB
    Metal Ion-Binding Site Prediction and Docking Server (53)
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
    Back to top
    PreviousNext
    Posted March 22, 2021.
    Download PDF

    Supplementary Material

    Data/Code
    Email

    Thank you for your interest in spreading the word about bioRxiv.

    NOTE: Your email address is requested solely to identify you as the sender of this article.

    Enter multiple addresses on separate lines or separate them with commas.
    Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 from Acidithiobacillus ferrooxidans
    (Your Name) has forwarded a page to you from bioRxiv
    (Your Name) thought you would like to see this page from the bioRxiv website.
    CAPTCHA
    This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
    Share
    Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 from Acidithiobacillus ferrooxidans
    Virginia Jiang, Sagar D. Khare, Scott Banta
    bioRxiv 2021.03.22.436458; doi: https://doi.org/10.1101/2021.03.22.436458
    Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
    Citation Tools
    Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 from Acidithiobacillus ferrooxidans
    Virginia Jiang, Sagar D. Khare, Scott Banta
    bioRxiv 2021.03.22.436458; doi: https://doi.org/10.1101/2021.03.22.436458

    Citation Manager Formats

    • BibTeX
    • Bookends
    • EasyBib
    • EndNote (tagged)
    • EndNote 8 (xml)
    • Medlars
    • Mendeley
    • Papers
    • RefWorks Tagged
    • Ref Manager
    • RIS
    • Zotero
    • Tweet Widget
    • Facebook Like
    • Google Plus One

    Subject Area

    • Bioinformatics
    Subject Areas
    All Articles
    • Animal Behavior and Cognition (3479)
    • Biochemistry (7318)
    • Bioengineering (5296)
    • Bioinformatics (20196)
    • Biophysics (9976)
    • Cancer Biology (7701)
    • Cell Biology (11249)
    • Clinical Trials (138)
    • Developmental Biology (6417)
    • Ecology (9915)
    • Epidemiology (2065)
    • Evolutionary Biology (13276)
    • Genetics (9352)
    • Genomics (12551)
    • Immunology (7673)
    • Microbiology (18937)
    • Molecular Biology (7417)
    • Neuroscience (40887)
    • Paleontology (298)
    • Pathology (1226)
    • Pharmacology and Toxicology (2125)
    • Physiology (3140)
    • Plant Biology (6837)
    • Scientific Communication and Education (1270)
    • Synthetic Biology (1891)
    • Systems Biology (5296)
    • Zoology (1084)