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Implementation of a cylindrical distribution function for the analysis of anisotropic molecular dynamics simulations.

ABSTRACT: The cylindrical distribution function (CDF) is a convenient anisotropic analogue of the radial distribution function, the difference being the use of cylindrical shells for binning. As such, CDF analysis can be a powerful tool for the analysis of positional correlations within anisotropic systems, such as liquid crystals. Here we describe a lightweight Python tool, cylindr, for the calculation of cylindrical distribution function, which is compatible with the output of a number of popular MD engines. We demonstrate the use of cylindr in computing the CDF of a number of exemplar materials: classical and ferroelectric nematics; lamellar and columnar liquid crystals.

SUBMITTER: Mandle RJ

PROVIDER: S-EPMC9803122 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Implementation of a cylindrical distribution function for the analysis of anisotropic molecular dynamics simulations.

Mandle Richard J RJ

PloS one 20221230 12

The cylindrical distribution function (CDF) is a convenient anisotropic analogue of the radial distribution function, the difference being the use of cylindrical shells for binning. As such, CDF analysis can be a powerful tool for the analysis of positional correlations within anisotropic systems, such as liquid crystals. Here we describe a lightweight Python tool, cylindr, for the calculation of cylindrical distribution function, which is compatible with the output of a number of popular MD eng ...[more]

PMID: 36584026

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Project description:Spin-labeled lipids are commonly used as fluorescence quenchers in studies of membrane penetration of dye-labeled proteins and peptides using depth-dependent quenching. Accurate calculations of depth of the fluorophore rely on the use of several spin labels placed in the membrane at various positions. The depth of the quenchers (spin probes) has to be determined independently; however, experimental determination of transverse distributions of spin probe depths is difficult. In this Article, we use molecular dynamics (MD) simulations to study the membrane behavior and depth distributions of spin-labeled phospholipids in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. To probe different depths within the bilayer, a series containing five Doxyl-labeled lipids (n-Doxyl PC) has been studied, in which a spin moiety was covalently attached to nth carbon atoms (where n = 5, 7, 10, 12, and 14) of the sn-2 stearoyl chain of the host phospholipid. Our results demonstrate that the chain-attached spin labels are broadly distributed across the model membrane and their environment is characterized by a high degree of mobility and structural heterogeneity. Despite the high thermal disorder, the depth distributions of the Doxyl labels were found to correlate well with their attachment positions, indicating that the distribution of the spin label within the model membrane is dictated by the depth of the nth lipid carbon atom and not by intrinsic properties of the label. In contrast, a much broader and heterogeneous distribution was observed for a headgroup-attached Tempo spin label of Tempo-PC lipids. MD simulations reveal that, due to the hydrophobic nature, a Tempo moiety favors partitioning from the headgroup region deeper into the membrane. Depending on the concentration of Tempo-PC lipids, the probable depth of the Tempo moiety could span a range from 14.4 to 18.2 Å from the membrane center. Comparison of the MD-estimated immersion depths of Tempo and n-Doxyl labels with their suggested experimental depth positions allows us to review critically the possible sources of error in depth-dependent fluorescence quenching studies.

Dataset Information

Implementation of a cylindrical distribution function for the analysis of anisotropic molecular dynamics simulations.

Publications

Implementation of a cylindrical distribution function for the analysis of anisotropic molecular dynamics simulations.

Similar Datasets

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