Cargando…
Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers
Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexame...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479113/ https://www.ncbi.nlm.nih.gov/pubmed/34604302 http://dx.doi.org/10.3389/fmolb.2021.710623 |
_version_ | 1784576178656378880 |
---|---|
author | Bux, Khair Shen, Xiayu Tariq, Muhammad Yin, Junqi Moin, Syed Tarique Bhowmik, Debsindhu Haider, Shozeb |
author_facet | Bux, Khair Shen, Xiayu Tariq, Muhammad Yin, Junqi Moin, Syed Tarique Bhowmik, Debsindhu Haider, Shozeb |
author_sort | Bux, Khair |
collection | PubMed |
description | Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process. |
format | Online Article Text |
id | pubmed-8479113 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-84791132021-09-30 Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers Bux, Khair Shen, Xiayu Tariq, Muhammad Yin, Junqi Moin, Syed Tarique Bhowmik, Debsindhu Haider, Shozeb Front Mol Biosci Molecular Biosciences Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process. Frontiers Media S.A. 2021-09-15 /pmc/articles/PMC8479113/ /pubmed/34604302 http://dx.doi.org/10.3389/fmolb.2021.710623 Text en Copyright © 2021 Bux, Shen, Tariq, Yin, Moin, Bhowmik and Haider. 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 Bux, Khair Shen, Xiayu Tariq, Muhammad Yin, Junqi Moin, Syed Tarique Bhowmik, Debsindhu Haider, Shozeb Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers |
title | Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers |
title_full | Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers |
title_fullStr | Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers |
title_full_unstemmed | Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers |
title_short | Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers |
title_sort | inter-subunit dynamics controls tunnel formation during the oxygenation process in hemocyanin hexamers |
topic | Molecular Biosciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479113/ https://www.ncbi.nlm.nih.gov/pubmed/34604302 http://dx.doi.org/10.3389/fmolb.2021.710623 |
work_keys_str_mv | AT buxkhair intersubunitdynamicscontrolstunnelformationduringtheoxygenationprocessinhemocyaninhexamers AT shenxiayu intersubunitdynamicscontrolstunnelformationduringtheoxygenationprocessinhemocyaninhexamers AT tariqmuhammad intersubunitdynamicscontrolstunnelformationduringtheoxygenationprocessinhemocyaninhexamers AT yinjunqi intersubunitdynamicscontrolstunnelformationduringtheoxygenationprocessinhemocyaninhexamers AT moinsyedtarique intersubunitdynamicscontrolstunnelformationduringtheoxygenationprocessinhemocyaninhexamers AT bhowmikdebsindhu intersubunitdynamicscontrolstunnelformationduringtheoxygenationprocessinhemocyaninhexamers AT haidershozeb intersubunitdynamicscontrolstunnelformationduringtheoxygenationprocessinhemocyaninhexamers |