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Multiscale Molecular Dynamics Simulations of Ice-Binding Proteins

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Ice Binding Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2730))

Abstract

Ice-binding proteins (IBPs) are a diverse class of proteins that are essential for the survival of organisms in cold conditions. IBPs are diverse in their function and can prevent or promote ice growth and selectively bind to specific crystallographic planes of the growing ice lattice. Moreover, IBPs are widely utilized to modulate ice crystal growth and recrystallization in the food industry and as cryoprotectants to preserve biological matter. A key unresolved aspect of the mode of action is how the ice-binding sites of these proteins distinguish between ice and water and interact with multiple crystal facets of the ice. The use of molecular dynamics (MD) simulation allows us to thoroughly investigate the binding mechanism and energetics of ice-binding proteins, to complement and expand on the mechanistic understandings gained from experiments. In this chapter, we describe a series of molecular dynamics simulation methodologies to investigate the mechanism of action of ice-binding proteins. Specifically, we provide detailed instructions to set up MD simulations to study the binding and interaction of ice-binding proteins using atomistic and coarse-grained simulations.

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Acknowledgments

The author gratefully acknowledges discussions with Prof. Valeria Molinero, Dr. Yuqing Qiu, Prof. Francesco Paesani, and Dr. Daniel Moberg. The simulation trajectories were generated using the supercomputing resources and computer time provided by the Center for High Performance at the University of Utah.

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Authors and Affiliations

  1. Department of Chemistry, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL, USA

    Arpa Hudait

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  1. Arpa Hudait
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Correspondence to Arpa Hudait .

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Editors and Affiliations

  1. Dept. of Chemistry and Biochemistry, Yeshiva University, New York, NY, USA

    Ran Drori

  2. Matériaux, Laboratoire Polymères, École Polytechnique Fédérale de Lausa, Lausanne, Switzerland

    Corey Stevens

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Hudait, A. (2024). Multiscale Molecular Dynamics Simulations of Ice-Binding Proteins. In: Drori, R., Stevens, C. (eds) Ice Binding Proteins. Methods in Molecular Biology, vol 2730. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3503-2_13

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  • DOI: https://doi.org/10.1007/978-1-0716-3503-2_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3502-5

  • Online ISBN: 978-1-0716-3503-2

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