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

doi:10.3389/fmolb.2021.710623

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

Journal Article · 14 September 2021 · Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2021.710623 · OSTI ID:1820812

Bux, Khair ^[1]; Shen, Xiayu ^[2]; Tariq, Muhammad ^[1];

^[3]; Moin, Syed Tarique ^[1];

^[3];

^[2]

Univ. of Karachi (Pakistan)
Univ. College London (United Kingdom)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1820812

Journal Information:: Frontiers in Molecular Biosciences, Journal Name: Frontiers in Molecular Biosciences Vol. 8; ISSN 2296-889X

Publisher:: Frontiers Media S.A.Copyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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Title: Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

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