Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Khair Bux; Xiayu Shen; Muhammad Tariq; Junqi Yin; Syed Tarique Moin; Debsindhu Bhowmik; Shozeb Haider

doi:10.3389/fmolb.2021.710623

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Khair Bux, Xiayu Shen, Muhammad Tariq, Junqi Yin, Syed Tarique Moin, Debsindhu Bhowmik, Shozeb Haider

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

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.

Original language	English
Article number	710623
Journal	Frontiers in Molecular Biosciences
Volume	8
DOIs	https://doi.org/10.3389/fmolb.2021.710623
State	Published - Sep 15 2021

Funding

This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research, under contract number DEAC05-00OR22725. This research is sponsored in part by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U.S. Department of Energy. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract no. DE-AC05-00OR22725.

Funders	Funder number
U.S. Department of Energy
Office of Science
Advanced Scientific Computing Research	DEAC05-00OR22725
Advanced Scientific Computing Research
Oak Ridge National Laboratory	DE-AC05-00OR22725
Oak Ridge National Laboratory

Keywords

copper
deep learning
hemocyanin
metalloprotein
molecular dynamics

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10.3389/fmolb.2021.710623

Cite this

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title = "Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers",

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.",

keywords = "copper, deep learning, hemocyanin, metalloprotein, molecular dynamics",

author = "Khair Bux and Xiayu Shen and Muhammad Tariq and Junqi Yin and Moin, {Syed Tarique} and Debsindhu Bhowmik and Shozeb Haider",

note = "Publisher Copyright: {\textcopyright} Copyright {\textcopyright} 2021 Bux, Shen, Tariq, Yin, Moin, Bhowmik and Haider.",

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doi = "10.3389/fmolb.2021.710623",

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TY - JOUR

T1 - Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

AU - Bux, Khair

AU - Shen, Xiayu

AU - Tariq, Muhammad

AU - Yin, Junqi

AU - Moin, Syed Tarique

AU - Bhowmik, Debsindhu

AU - Haider, Shozeb

PY - 2021/9/15

Y1 - 2021/9/15

N2 - 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.

AB - 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.

KW - copper

KW - deep learning

KW - hemocyanin

KW - metalloprotein

KW - molecular dynamics

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U2 - 10.3389/fmolb.2021.710623

DO - 10.3389/fmolb.2021.710623

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VL - 8

JO - Frontiers in Molecular Biosciences

JF - Frontiers in Molecular Biosciences

M1 - 710623

ER -

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

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