Bux, K;
Shen, X;
Tariq, M;
Yin, J;
Moin, ST;
Bhowmik, D;
Haider, S;
(2021)
Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers.
Frontiers in Molecular Biosciences
, 8
, Article ARTN 710. 10.3389/fmolb.2021.710623.
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Abstract
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.
| Type: | Article |
|---|---|
| Title: | Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.3389/fmolb.2021.710623 |
| Publisher version: | https://doi.org/10.3389/fmolb.2021.710623 |
| Language: | English |
| Additional information: | © 2021 Bux, Shen, Tariq, Yin, Moin, Bhowmik and Haider. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). |
| Keywords: | hemocyanin, molecular dynamics, deep learning, metalloprotein, copper |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > UCL School of Pharmacy UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > UCL School of Pharmacy > Pharma and Bio Chemistry |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10136051 |
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