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*

*Bijbehorende auteur voor dit werk

OnderzoeksoutputAcademicpeer review

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Samenvatting

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.

Originele taal-2English
Artikelnummeracs.jcim.1c00157
Pagina's (van-tot)2869-2883
Aantal pagina's15
TijdschriftJournal of chemical information and modeling
Volume61
Nummer van het tijdschrift6
Vroegere onlinedatum28-mei-2021
DOI's
StatusPublished - jul-2021

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