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Rotational Diffusion of Proteins in Nanochannels
Navaneeth Haridasan,
Published in American Chemical Society
2019
PMID: 31117604
Volume: 123
   
Issue: 23
Pages: 4825 - 4832
Abstract
The rotational diffusion coefficient is an essential parameter in determining the mechanistic features of biomolecules in both crowded and confined environments. Understanding the influence of nanoconfinement on rotational diffusion is vital in conceptualizing dynamics of biomolecules (such as proteins) in nanopores. The control of the translational movement of biomolecules is practiced widely in nanopore experiments. However, the restrictions on the translational movement may affect other dynamic properties such as rotational diffusion. In this paper, we use a coarse-grained molecular dynamics approach to study the rotational dynamics of a sample protein under the influence of cylindrical nanopore confinement. Our simulation reveals a 2-fold reduction in magnitude from the bulk rotational diffusion coefficient value as the confinement radius reaches double the size of protein's hydrodynamic radius. However, the changes in the rotational diffusion coefficient are relatively small compared to the changes in the translational diffusion coefficient. Interestingly, the rotational anisotropy also varies considerably when pore radii approach protein dimensions. Our simulations point out that the confinement effects cause the breakdown of small angular displacement theory when the pore radius is close to the protein hydrodynamic radius. © 2019 American Chemical Society.
About the journal
JournalData powered by TypesetJournal of Physical Chemistry B
PublisherData powered by TypesetAmerican Chemical Society
ISSN15206106
Open AccessNo
Concepts (14)
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    Biomolecules
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    Hydrodynamics
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    Molecular dynamics
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    Nanopores
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    Proteins
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    ANGULAR DISPLACEMENT
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    COARSE-GRAINED MOLECULAR DYNAMICS
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    Confined environment
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    CYLINDRICAL NANOPORES
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    ROTATIONAL ANISOTROPY
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    Rotational diffusion
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    ROTATIONAL DIFFUSION COEFFICIENTS
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    TRANSLATIONAL DIFFUSION COEFFICIENT
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    Diffusion in solids