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Title: Mechanical coupling in the nitrogenase complex

Abstract

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, itmore » is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4];  [1];  [5]; ORCiD logo [6]; ORCiD logo [2];  [1]
+ Show Author Affiliations
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  2. Montana State Univ., Bozeman, MT (United States)
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Univ. of Washington, Seattle, WA (United States)
  4. Utah State Univ., Logan, UT (United States)
  5. Washington State Univ., Pullman, WA (United States)
  6. Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Utah State Univ., Logan, UT (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division
OSTI Identifier:
1784748
Report Number(s):
PNNL-SA-154305
Journal ID: ISSN 1553-7358
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
PLoS Computational Biology (Online)
Additional Journal Information:
Journal Name: PLoS Computational Biology (Online); Journal Volume: 17; Journal Issue: 3; Journal ID: ISSN 1553-7358
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; crystal structure; covariance; electron transfer; deuterium; ATP hydrolysis; geodesics; nucleotides; allosteric regulation

Citation Formats

Huang, Qi, Tokmina-Lukaszewska, Monika, Johnson, Lewis E., Kallas, Hayden, Ginovska, Bojana, Peters, John W., Seefeldt, Lance C., Bothner, Brian, and Raugei, Simone. Mechanical coupling in the nitrogenase complex. United States: N. p., 2021. Web. doi:10.1371/journal.pcbi.1008719.
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Huang, Qi, Tokmina-Lukaszewska, Monika, Johnson, Lewis E., Kallas, Hayden, Ginovska, Bojana, Peters, John W., Seefeldt, Lance C., Bothner, Brian, & Raugei, Simone. Mechanical coupling in the nitrogenase complex. United States. https://doi.org/10.1371/journal.pcbi.1008719
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Huang, Qi, Tokmina-Lukaszewska, Monika, Johnson, Lewis E., Kallas, Hayden, Ginovska, Bojana, Peters, John W., Seefeldt, Lance C., Bothner, Brian, and Raugei, Simone. Thu . "Mechanical coupling in the nitrogenase complex". United States. https://doi.org/10.1371/journal.pcbi.1008719. https://www.osti.gov/servlets/purl/1784748.
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@article{osti_1784748,
title = {Mechanical coupling in the nitrogenase complex},
author = {Huang, Qi and Tokmina-Lukaszewska, Monika and Johnson, Lewis E. and Kallas, Hayden and Ginovska, Bojana and Peters, John W. and Seefeldt, Lance C. and Bothner, Brian and Raugei, Simone},
abstractNote = {The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.},
doi = {10.1371/journal.pcbi.1008719},
journal = {PLoS Computational Biology (Online)},
number = 3,
volume = 17,
place = {United States},
year = {Thu Mar 04 00:00:00 EST 2021},
month = {Thu Mar 04 00:00:00 EST 2021}
}
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