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General Protocol for Constructing Molecular Models of Nanodiscs

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  • Lisbeth R. Kjølbye, Aarhus University, Novo Nordisk A/S
  • ,
  • Leonardo De Maria, Novo Nordisk A/S
  • ,
  • Tsjerk A. Wassenaar, University of Groningen
  • ,
  • Haleh Abdizadeh, University of Groningen
  • ,
  • Siewert J. Marrink, University of Groningen
  • ,
  • Jesper Ferkinghoff-Borg, Novo Nordisk A/S
  • ,
  • Birgit Schiøtt

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 languageEnglish
JournalJournal of Chemical Information and Modeling
Pages (from-to)2869-2883
Number of pages15
Publication statusPublished - Jun 2021

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© 2021 The Authors. Published by American Chemical Society.

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