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Membranes
Volume 12
Issue 1
10.3390/membranes12010017
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Article

Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric

by
Julian C. Shillcock
1,*,
David B. Thomas
2,
Jonathan R. Beaumont
3,
Graeme M. Bragg
2,
Mark L. Vousden
2 and
Andrew D. Brown
2
1
Blue Brain Project and Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
2
Department of Electronics and Computer Science, University of Southampton, Highfield, Southampton SO17 1BJ, UK
3
Department of Electronic Engineering, Imperial College London, London SW7 2AZ, UK
*
Author to whom correspondence should be addressed.
Membranes 2022, 12(1), 17; https://doi.org/10.3390/membranes12010017
Submission received: 26 November 2021 / Revised: 17 December 2021 / Accepted: 21 December 2021 / Published: 23 December 2021
(This article belongs to the Special Issue Membrane Biological Function in Health and Disease)
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Abstract

Phospholipid membranes surround the cell and its internal organelles, and their multicomponent nature allows the formation of domains that are important in cellular signalling, the immune system, and bacterial infection. Cytoplasmic compartments are also created by the phase separation of intrinsically disordered proteins into biomolecular condensates. The ubiquity of lipid membranes and protein condensates raises the question of how three-dimensional droplets might interact with two-dimensional domains, and whether this coupling has physiological or pathological importance. Here, we explore the equilibrium morphologies of a dilute phase of a model disordered protein interacting with an ideal-mixing, two-component lipid membrane using coarse-grained molecular simulations. We find that the proteins can wet the membrane with and without domain formation, and form phase separated droplets bound to membrane domains. Results from much larger simulations performed on a novel non-von-Neumann compute architecture called POETS, which greatly accelerates their execution compared to conventional hardware, confirm the observations. Reducing the wall clock time for such simulations requires new architectures and computational techniques. We demonstrate here an inter-disciplinary approach that uses real-world biophysical questions to drive the development of new computing hardware and simulation algorithms.
Keywords: membrane domains; intrinsically-disordered protein; phase separation; biomolecular condensate; coarse-grained simulation; event-based computing; hardware-accelerated simulation; application-specific hardware membrane domains; intrinsically-disordered protein; phase separation; biomolecular condensate; coarse-grained simulation; event-based computing; hardware-accelerated simulation; application-specific hardware
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MDPI and ACS Style

Shillcock, J.C.; Thomas, D.B.; Beaumont, J.R.; Bragg, G.M.; Vousden, M.L.; Brown, A.D. Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric. Membranes 2022, 12, 17. https://doi.org/10.3390/membranes12010017

AMA Style

Shillcock JC, Thomas DB, Beaumont JR, Bragg GM, Vousden ML, Brown AD. Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric. Membranes. 2022; 12(1):17. https://doi.org/10.3390/membranes12010017

Chicago/Turabian Style

Shillcock, Julian C., David B. Thomas, Jonathan R. Beaumont, Graeme M. Bragg, Mark L. Vousden, and Andrew D. Brown. 2022. "Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric" Membranes 12, no. 1: 17. https://doi.org/10.3390/membranes12010017

APA Style

Shillcock, J. C., Thomas, D. B., Beaumont, J. R., Bragg, G. M., Vousden, M. L., & Brown, A. D. (2022). Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric. Membranes, 12(1), 17. https://doi.org/10.3390/membranes12010017

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