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Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle

Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates o...

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Autores principales: Lee, Eunjeong, McLeod, Matthew J., Redzic, Jasmina S., Marcolin, Barbara, Thorne, Robert E., Agarwal, Pratul, Eisenmesser, Elan Zohar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10461185/
https://www.ncbi.nlm.nih.gov/pubmed/37645217
http://dx.doi.org/10.3389/fmolb.2023.1244587
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author Lee, Eunjeong
McLeod, Matthew J.
Redzic, Jasmina S.
Marcolin, Barbara
Thorne, Robert E.
Agarwal, Pratul
Eisenmesser, Elan Zohar
author_facet Lee, Eunjeong
McLeod, Matthew J.
Redzic, Jasmina S.
Marcolin, Barbara
Thorne, Robert E.
Agarwal, Pratul
Eisenmesser, Elan Zohar
author_sort Lee, Eunjeong
collection PubMed
description Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates of the catalytic cycle and whether these were relegated to just the active site or the entirety of the enzyme. Through X-ray crystallography, we determined the apo BLVRB structure for the first time, revealing subtle global changes compared to the holo structure and identifying the loss of a critical hydrogen bond that “clamps” the R78-loop over the coenzyme. Amide and Cα chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, with more distant global changes observed upon coenzyme binding compared to substrate interactions. NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB during the catalytic cycle. Specifically, the inherently dynamic R78-loop that becomes ordered upon coenzyme binding persists through the catalytic cycle while similar regions experience dynamic exchange. However, the dynamic exchange processes were found to differ through the catalytic cycle with several groups of residues exhibiting similar dynamic responses. Finally, both local and distal structural and dynamic changes occur within BLVRB that are dependent solely on the oxidative state of the coenzyme. Thus, through a comprehensive analysis here, this study revealed structural and dynamic alterations in BLVRB through its catalytic cycle that are not simply relegated to the active site, but instead, are allosterically coupled throughout the enzyme.
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spelling pubmed-104611852023-08-29 Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle Lee, Eunjeong McLeod, Matthew J. Redzic, Jasmina S. Marcolin, Barbara Thorne, Robert E. Agarwal, Pratul Eisenmesser, Elan Zohar Front Mol Biosci Molecular Biosciences Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates of the catalytic cycle and whether these were relegated to just the active site or the entirety of the enzyme. Through X-ray crystallography, we determined the apo BLVRB structure for the first time, revealing subtle global changes compared to the holo structure and identifying the loss of a critical hydrogen bond that “clamps” the R78-loop over the coenzyme. Amide and Cα chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, with more distant global changes observed upon coenzyme binding compared to substrate interactions. NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB during the catalytic cycle. Specifically, the inherently dynamic R78-loop that becomes ordered upon coenzyme binding persists through the catalytic cycle while similar regions experience dynamic exchange. However, the dynamic exchange processes were found to differ through the catalytic cycle with several groups of residues exhibiting similar dynamic responses. Finally, both local and distal structural and dynamic changes occur within BLVRB that are dependent solely on the oxidative state of the coenzyme. Thus, through a comprehensive analysis here, this study revealed structural and dynamic alterations in BLVRB through its catalytic cycle that are not simply relegated to the active site, but instead, are allosterically coupled throughout the enzyme. Frontiers Media S.A. 2023-08-14 /pmc/articles/PMC10461185/ /pubmed/37645217 http://dx.doi.org/10.3389/fmolb.2023.1244587 Text en Copyright © 2023 Lee, McLeod, Redzic, Marcolin, Thorne, Agarwal and Eisenmesser. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Lee, Eunjeong
McLeod, Matthew J.
Redzic, Jasmina S.
Marcolin, Barbara
Thorne, Robert E.
Agarwal, Pratul
Eisenmesser, Elan Zohar
Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle
title Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle
title_full Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle
title_fullStr Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle
title_full_unstemmed Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle
title_short Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle
title_sort identifying structural and dynamic changes during the biliverdin reductase b catalytic cycle
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10461185/
https://www.ncbi.nlm.nih.gov/pubmed/37645217
http://dx.doi.org/10.3389/fmolb.2023.1244587
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