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PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations

[Image: see text] 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 object...

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Autores principales: Song, Wanling, Corey, Robin A., Ansell, T. Bertie, Cassidy, C. Keith, Horrell, Michael R., Duncan, Anna L., Stansfeld, Phillip J., Sansom, Mark S. P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2022
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830038/
https://www.ncbi.nlm.nih.gov/pubmed/35020380
http://dx.doi.org/10.1021/acs.jctc.1c00708
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author Song, Wanling
Corey, Robin A.
Ansell, T. Bertie
Cassidy, C. Keith
Horrell, Michael R.
Duncan, Anna L.
Stansfeld, Phillip J.
Sansom, Mark S. P.
author_facet Song, Wanling
Corey, Robin A.
Ansell, T. Bertie
Cassidy, C. Keith
Horrell, Michael R.
Duncan, Anna L.
Stansfeld, Phillip J.
Sansom, Mark S. P.
author_sort Song, Wanling
collection PubMed
description [Image: see text] 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 while 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 data sets of multiple species of membrane proteins.
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spelling pubmed-88300382022-02-11 PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations Song, Wanling Corey, Robin A. Ansell, T. Bertie Cassidy, C. Keith Horrell, Michael R. Duncan, Anna L. Stansfeld, Phillip J. Sansom, Mark S. P. J Chem Theory Comput [Image: see text] 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 while 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 data sets of multiple species of membrane proteins. American Chemical Society 2022-01-12 2022-02-08 /pmc/articles/PMC8830038/ /pubmed/35020380 http://dx.doi.org/10.1021/acs.jctc.1c00708 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Song, Wanling
Corey, Robin A.
Ansell, T. Bertie
Cassidy, C. Keith
Horrell, Michael R.
Duncan, Anna L.
Stansfeld, Phillip J.
Sansom, Mark S. P.
PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations
title PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations
title_full PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations
title_fullStr PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations
title_full_unstemmed PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations
title_short PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations
title_sort pylipid: a python package for analysis of protein–lipid interactions from molecular dynamics simulations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830038/
https://www.ncbi.nlm.nih.gov/pubmed/35020380
http://dx.doi.org/10.1021/acs.jctc.1c00708
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