Lipid Protein Interactions Of G Protein Coupled Receptors

Sejdiu, Besian I.; DeGagne, Christine; Corradi, Valentina; Tieleman, Peter

doi:10.1016/j.bpj.2015.11.2285

Cited by 2 publications

(2 citation statements)

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“…There is a considerable literature on identifying and characterizing GPCR/cholesterol interactions by MD simulations (e.g. [61][62][63] and it is not our aim to review these here (for recent reviews see e.g. 12,64 ).…”

Section: What Can Pylipid Teach Us About Protein Lipid Interactions?mentioning

confidence: 99%

PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations

Song¹,

Corey²,

Tb³

et al. 2021

Preprint

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Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations are frequently used to provide insights into the nature of these protein-lipid interactions. Systematic comparative analysis requires tools that provide algorithms for objective assessment of such interactions. We introduce PyLipID, a python package for the identification and characterization of specific lipid interactions and binding sites on membrane proteins from molecular dynamics simulations. PyLipID uses a community analysis approach for binding site detection, calculating lipid residence times for both the individual protein residues and the detected binding sites. To assist structural analysis, PyLipID produces representative bound lipid poses from simulation data, using a density-based scoring function. To estimate residue contacts robustly, PyLipID uses a dual-cutoff scheme to differentiate between lipid conformational rearrangements whilst bound from full dissociation events. In addition to the characterization of protein-lipid interactions, PyLipID is applicable to analysis of the interactions of membrane proteins with other ligands. By combining automated analysis, efficient algorithms, and open-source distribution, PyLipID facilitates the systematic analysis of lipid interactions from large simulation datasets of multiple species of membrane proteins.

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Section: What Can Pylipid Teach Us About Protein Lipid Interactions?mentioning

confidence: 99%

PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations

Song¹,

Corey²,

Tb³

et al. 2021

Preprint

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show abstract

“…FATSLiM 1 and MemSurfer, 2 for example, both specialise in the analysis of non-planar membranes such as buckled bilayers or vesicles. PyLipID 3 and ProLint 4 are designed for the easy and efficient analysis of lipid-protein interactions. ML-LPA is a recently developed Python package that employs various machine learning algorithms to identify the phase — L o or L d — of lipids in a bilayer.…”

Section: Introductionmentioning

confidence: 99%

LiPyphilic: A Python toolkit for the analysis of lipid membrane simulations

Smith

Lorenz

2021

Preprint

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Molecular dynamics simulations are now widely used to study emergent phenomena in lipid membranes with complex compositions. Here, we present LiPyphilic - a fast, fully tested, and easy to install Python package for analysing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flip-flop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field and resolution agnostic, and thanks to the powerful atom selection language of MDAnalysis it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to i) fix membranes split across periodic boundaries and ii) perform nojump coordinate unwrapping. Our implementation of nojump unwrapping accounts for fluctuations in box volume under the NPT ensemble — an issue that most current implementations have overlooked. The full documentation of LiPyphilic, including installation instructions, is available at https://lipyphilic.readthedocs.io/en/latest.Graphical TOC Entry

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Lipid Protein Interactions Of G Protein Coupled Receptors

Cited by 2 publications

References 0 publications

PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations

PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations

LiPyphilic: A Python toolkit for the analysis of lipid membrane simulations

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