ArticleThe journal of physical chemistry. B2019
Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations.
Article in The journal of physical chemistry. B, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- How soluble misfolded proteins bypass chaperones at the molecular level.Nature communications · 2023Pooled it
- Rotational dynamics of a disk in a thin film of weakly nematic fluid subject to linear friction.The European physical journal. E, Soft matter · 2024Article
- Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly.ACS applied bio materials · 2024Review
- Protein Crowding and Cholesterol Increase Cell Membrane Viscosity in a Temperature Dependent Manner.Journal of chemical theory and computation · 2023Article
- Article
- Fluorescence microscopy imaging of a neurotransmitter receptor and its cell membrane lipid milieu.Frontiers in molecular biosciences · 2022Review
- Article
- The current understanding of KRAS protein structure and dynamics.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
3 authors.
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Abstract
We investigate system-size effects on the rotational diffusion of membrane proteins and other membrane-embedded molecules in molecular dynamics simulations. We find that the rotational diffusion coefficient slows down relative to the infinite-system value by a factor of one minus the ratio of protein and box areas. This correction factor follows from the hydrodynamics of rotational flows under periodic boundary conditions and is rationalized in terms of Taylor-Couette flow. For membrane proteins like transporters, channels, or receptors in typical simulation setups, the protein-covered area tends to be relatively large, requiring a significant finite-size correction. Molecular dynamics simulations of the protein adenine nucleotide translocase (ANT1) and of a carbon nanotube porin in lipid membranes show that the hydrodynamic finite-size correction for rotational diffusion is accurate in standard-use cases. The dependence of the rotational diffusion on box size can be used to determine the membrane viscosity.
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