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

Wanling Song; Robin A. Corey; T. Bertie Ansell; C. Keith Cassidy; Michael R. Horrell; Anna L. Duncan; Phillip J. Stansfeld; Mark S.P. Sansom

doi:10.1021/acs.jctc.1c00708

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

Wanling Song^*, Robin A. Corey, T. Bertie Ansell, C. Keith Cassidy, Michael R. Horrell, Anna L. Duncan, Phillip J. Stansfeld, Mark S.P. Sansom^*

^*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

101 Citations (Scopus)

Abstract

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.

Original language	English
Journal	Journal of Chemical Theory and Computation
Volume	18
Issue	2
Pages (from-to)	1188-1201
Number of pages	14
ISSN	1549-9618
DOIs	https://doi.org/10.1021/acs.jctc.1c00708
Publication status	Published - Feb 2022
Externally published	Yes

Keywords

Binding Sites
Ligands
Lipid Bilayers/chemistry
Lipids
Membrane Proteins/chemistry
Molecular Dynamics Simulation

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title = "PyLipID: A Python Package for Analysis of Protein-Lipid Interactions from Molecular Dynamics Simulations",

abstract = "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.",

keywords = "Binding Sites, Ligands, Lipid Bilayers/chemistry, Lipids, Membrane Proteins/chemistry, Molecular Dynamics Simulation",

author = "Wanling Song and Corey, {Robin A.} and Ansell, {T. Bertie} and Cassidy, {C. Keith} and Horrell, {Michael R.} and Duncan, {Anna L.} and Stansfeld, {Phillip J.} and Sansom, {Mark S.P.}",

note = "Funding Information: We thank Yi Hao for designing the PyLipID logo. Research in the M.S.P.S. group is supported by Wellcome (Grant 208361/Z/17/Z), BBSRC (Grant BB/R00126X/1), and PRACE (Partnership for Advanced Computing in Europe; Grant 2016163984). Research in P.J.S.{\textquoteright}s laboratory is supported by Wellcome (Grant 208361/Z/17/Z), BBSRC (Grants BB/P01948X/1, BB/R002517/1, and BB/S003339/1), and MRC (Grant MR/S009213/1). W.S. acknowledges support from the Newton International Fellowship. T.B.A. is supported by a Wellcome studentship (Grant 102164/Z/13/Z). This project made use of time on ARCHER via the HECBioSim consortium, supported by EPSRC (Grant EP/L000253/1). This research was funded in whole, or in part, by the Wellcome Trust (208361/Z/17/Z). For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. Publisher Copyright: {\textcopyright} ",

year = "2022",

month = feb,

doi = "10.1021/acs.jctc.1c00708",

language = "English",

volume = "18",

pages = "1188--1201",

journal = "Journal of Chemical Theory and Computation",

issn = "1549-9618",

publisher = "American Chemical Society",

number = "2",

}

PyLipID: A Python Package for Analysis of Protein-Lipid Interactions from Molecular Dynamics Simulations. / Song, Wanling; Corey, Robin A.; Ansell, T. Bertie et al.
In: Journal of Chemical Theory and Computation, Vol. 18, No. 2, 02.2022, p. 1188-1201.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - PyLipID

T2 - A Python Package for Analysis of Protein-Lipid Interactions from Molecular Dynamics Simulations

AU - Song, Wanling

AU - Corey, Robin A.

AU - Ansell, T. Bertie

AU - Cassidy, C. Keith

AU - Horrell, Michael R.

AU - Duncan, Anna L.

AU - Stansfeld, Phillip J.

AU - Sansom, Mark S.P.

N1 - Funding Information: We thank Yi Hao for designing the PyLipID logo. Research in the M.S.P.S. group is supported by Wellcome (Grant 208361/Z/17/Z), BBSRC (Grant BB/R00126X/1), and PRACE (Partnership for Advanced Computing in Europe; Grant 2016163984). Research in P.J.S.’s laboratory is supported by Wellcome (Grant 208361/Z/17/Z), BBSRC (Grants BB/P01948X/1, BB/R002517/1, and BB/S003339/1), and MRC (Grant MR/S009213/1). W.S. acknowledges support from the Newton International Fellowship. T.B.A. is supported by a Wellcome studentship (Grant 102164/Z/13/Z). This project made use of time on ARCHER via the HECBioSim consortium, supported by EPSRC (Grant EP/L000253/1). This research was funded in whole, or in part, by the Wellcome Trust (208361/Z/17/Z). For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. Publisher Copyright: ©

PY - 2022/2

Y1 - 2022/2

N2 - 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.

AB - 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.

KW - Binding Sites

KW - Ligands

KW - Lipid Bilayers/chemistry

KW - Lipids

KW - Membrane Proteins/chemistry

KW - Molecular Dynamics Simulation

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U2 - 10.1021/acs.jctc.1c00708

DO - 10.1021/acs.jctc.1c00708

M3 - Journal article

C2 - 35020380

AN - SCOPUS:85123941747

SN - 1549-9618

VL - 18

SP - 1188

EP - 1201

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

IS - 2

ER -

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

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Keywords

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