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Title: Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways

Abstract

The ferredoxin (Fd) protein family is a structurally diverse group of iron–sulfur proteins that function as electron carriers, linking biochemical pathways important for energy transduction, nutrient assimilation, and primary metabolism. While considerable biochemical information about individual Fd protein electron carriers and their reactions has been acquired, we cannot yet anticipate the proportion of electrons shuttled between different Fd-partner proteins within cells using biochemical parameters that govern electron flow, such as holo-Fd concentration, midpoint potential (driving force), molecular interactions (affinity and kinetics), conformational changes (allostery), and off-pathway electron leakage (chemical oxidation). In this paper, we describe functional and structural gaps in our Fd knowledge within the context of a sequence similarity network and phylogenetic tree, and we propose a strategy for improving our understanding of Fd sequence–function relationships. We suggest comparing the functions of divergent Fds within cells whose growth, or other measurable output, requires electron transfer between defined electron donor and acceptor proteins. By comparing Fd-mediated electron transfer with biochemical parameters that govern electron flow, we posit that models that anticipate energy flow across Fd interactomes can be built. This approach is expected to transform our ability to anticipate Fd control over electron flow in cellular settings, an obstacle tomore » the construction of synthetic electron transfer pathways and rational optimization of existing energy-conserving pathways.« less

Authors:
 [1];  [1];  [1]; ORCiD logo [1]
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  1. Rice Univ., Houston, TX (United States)
Publication Date:
Research Org.:
Rice Univ., Houston, TX (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF)
OSTI Identifier:
1534417
Grant/Contract Number:  
SC0014462; R3E821
Resource Type:
Accepted Manuscript
Journal Name:
Biochemistry
Additional Journal Information:
Journal Volume: 55; Journal Issue: 51; Journal ID: ISSN 0006-2960
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Redox reactions; Charge transfer; Peptides and proteins; Assays; Cluster chemistry

Citation Formats

Atkinson, Joshua T., Campbell, Ian, Bennett, George N., and Silberg, Jonathan J. Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways. United States: N. p., 2016. Web. doi:10.1021/acs.biochem.6b00831.
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Atkinson, Joshua T., Campbell, Ian, Bennett, George N., & Silberg, Jonathan J. Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways. United States. https://doi.org/10.1021/acs.biochem.6b00831
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Atkinson, Joshua T., Campbell, Ian, Bennett, George N., and Silberg, Jonathan J. Mon . "Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways". United States. https://doi.org/10.1021/acs.biochem.6b00831. https://www.osti.gov/servlets/purl/1534417.
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@article{osti_1534417,
title = {Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways},
author = {Atkinson, Joshua T. and Campbell, Ian and Bennett, George N. and Silberg, Jonathan J.},
abstractNote = {The ferredoxin (Fd) protein family is a structurally diverse group of iron–sulfur proteins that function as electron carriers, linking biochemical pathways important for energy transduction, nutrient assimilation, and primary metabolism. While considerable biochemical information about individual Fd protein electron carriers and their reactions has been acquired, we cannot yet anticipate the proportion of electrons shuttled between different Fd-partner proteins within cells using biochemical parameters that govern electron flow, such as holo-Fd concentration, midpoint potential (driving force), molecular interactions (affinity and kinetics), conformational changes (allostery), and off-pathway electron leakage (chemical oxidation). In this paper, we describe functional and structural gaps in our Fd knowledge within the context of a sequence similarity network and phylogenetic tree, and we propose a strategy for improving our understanding of Fd sequence–function relationships. We suggest comparing the functions of divergent Fds within cells whose growth, or other measurable output, requires electron transfer between defined electron donor and acceptor proteins. By comparing Fd-mediated electron transfer with biochemical parameters that govern electron flow, we posit that models that anticipate energy flow across Fd interactomes can be built. This approach is expected to transform our ability to anticipate Fd control over electron flow in cellular settings, an obstacle to the construction of synthetic electron transfer pathways and rational optimization of existing energy-conserving pathways.},
doi = {10.1021/acs.biochem.6b00831},
journal = {Biochemistry},
number = 51,
volume = 55,
place = {United States},
year = {Mon Nov 21 00:00:00 EST 2016},
month = {Mon Nov 21 00:00:00 EST 2016}
}
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https://doi.org/10.1021/acs.biochem.6b00831
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Figures / Tables:

Table 1 Table 1: List of Fd-partner proteins organized by metabolic pathway. For each partner protein, we indicate whether the partner is found in Archaea (A), Bacteria (B) Eukaryotes (E), and Viruses (V). Source annotations were based on the MetaCyc database.
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    • Trindade, Inês B.; Silva, José M.; Fonseca, Bruno M.
    • Journal of Biological Chemistry, Vol. 294, Issue 1
    • DOI: 10.1074/jbc.ra118.005041

    Solution structure for an Encephalitozoon cuniculi adrenodoxin‐like protein in the oxidized state
    journal, January 2020

    • Shaheen, Shareef; Barrett, Kayleigh F.; Subramanian, Sandhya
    • Protein Science, Vol. 29, Issue 3
    • DOI: 10.1002/pro.3818
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