General Protocol for Constructing Molecular Models of Nanodiscs

Lisbeth R. Kjølbye; Leonardo De Maria; Tsjerk A. Wassenaar; Haleh Abdizadeh; Siewert J. Marrink; Jesper Ferkinghoff-Borg; Birgit Schiøtt

doi:10.1021/acs.jcim.1c00157

General Protocol for Constructing Molecular Models of Nanodiscs

Lisbeth R. Kjølbye, Leonardo De Maria, Tsjerk A. Wassenaar, Haleh Abdizadeh, Siewert J. Marrink, Jesper Ferkinghoff-Borg^*, Birgit Schiøtt^*

^*Corresponding author for this work

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

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Abstract

Nanodisc technology is increasingly being applied for structural and biophysical studies of membrane proteins. In this work, we present a general protocol for constructing molecular models of nanodiscs for molecular dynamics simulations. The protocol is written in python and based on geometric equations, making it fast and easy to modify, enabling automation and customization of nanodiscs in silico. The novelty being the ability to construct any membrane scaffold protein (MSP) variant fast and easy given only an input sequence. We validated and tested the protocol by simulating seven different nanodiscs of various sizes and with different membrane scaffold proteins, both circularized and noncircularized. The structural and biophysical properties were analyzed and shown to be in good agreement with previously reported experimental data and simulation studies.

Original language	English
Journal	Journal of Chemical Information and Modeling
Volume	61
Issue	6
Pages (from-to)	2869-2883
Number of pages	15
ISSN	1549-9596
DOIs	https://doi.org/10.1021/acs.jcim.1c00157
Publication status	Published - Jun 2021

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title = "General Protocol for Constructing Molecular Models of Nanodiscs",

abstract = "Nanodisc technology is increasingly being applied for structural and biophysical studies of membrane proteins. In this work, we present a general protocol for constructing molecular models of nanodiscs for molecular dynamics simulations. The protocol is written in python and based on geometric equations, making it fast and easy to modify, enabling automation and customization of nanodiscs in silico. The novelty being the ability to construct any membrane scaffold protein (MSP) variant fast and easy given only an input sequence. We validated and tested the protocol by simulating seven different nanodiscs of various sizes and with different membrane scaffold proteins, both circularized and noncircularized. The structural and biophysical properties were analyzed and shown to be in good agreement with previously reported experimental data and simulation studies.",

author = "Kj{\o}lbye, {Lisbeth R.} and {De Maria}, Leonardo and Wassenaar, {Tsjerk A.} and Haleh Abdizadeh and Marrink, {Siewert J.} and Jesper Ferkinghoff-Borg and Birgit Schi{\o}tt",

note = "Publisher Copyright: {\textcopyright} 2021 The Authors. Published by American Chemical Society.",

year = "2021",

month = jun,

doi = "10.1021/acs.jcim.1c00157",

language = "English",

volume = "61",

pages = "2869--2883",

journal = "Journal of Chemical Information and Modeling",

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publisher = "American Chemical Society",

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General Protocol for Constructing Molecular Models of Nanodiscs. / Kjølbye, Lisbeth R.; De Maria, Leonardo; Wassenaar, Tsjerk A. et al.
In: Journal of Chemical Information and Modeling, Vol. 61, No. 6, 06.2021, p. 2869-2883.

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

TY - JOUR

T1 - General Protocol for Constructing Molecular Models of Nanodiscs

AU - Kjølbye, Lisbeth R.

AU - De Maria, Leonardo

AU - Wassenaar, Tsjerk A.

AU - Abdizadeh, Haleh

AU - Marrink, Siewert J.

AU - Ferkinghoff-Borg, Jesper

AU - Schiøtt, Birgit

PY - 2021/6

Y1 - 2021/6

N2 - Nanodisc technology is increasingly being applied for structural and biophysical studies of membrane proteins. In this work, we present a general protocol for constructing molecular models of nanodiscs for molecular dynamics simulations. The protocol is written in python and based on geometric equations, making it fast and easy to modify, enabling automation and customization of nanodiscs in silico. The novelty being the ability to construct any membrane scaffold protein (MSP) variant fast and easy given only an input sequence. We validated and tested the protocol by simulating seven different nanodiscs of various sizes and with different membrane scaffold proteins, both circularized and noncircularized. The structural and biophysical properties were analyzed and shown to be in good agreement with previously reported experimental data and simulation studies.

AB - Nanodisc technology is increasingly being applied for structural and biophysical studies of membrane proteins. In this work, we present a general protocol for constructing molecular models of nanodiscs for molecular dynamics simulations. The protocol is written in python and based on geometric equations, making it fast and easy to modify, enabling automation and customization of nanodiscs in silico. The novelty being the ability to construct any membrane scaffold protein (MSP) variant fast and easy given only an input sequence. We validated and tested the protocol by simulating seven different nanodiscs of various sizes and with different membrane scaffold proteins, both circularized and noncircularized. The structural and biophysical properties were analyzed and shown to be in good agreement with previously reported experimental data and simulation studies.

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U2 - 10.1021/acs.jcim.1c00157

DO - 10.1021/acs.jcim.1c00157

M3 - Journal article

C2 - 34048229

AN - SCOPUS:85108424873

SN - 1549-9596

VL - 61

SP - 2869

EP - 2883

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

IS - 6

ER -

General Protocol for Constructing Molecular Models of Nanodiscs

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