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Multiscale Modelling of Bionano Interface

  • Hender Lopez
  • Erik G. Brandt
  • Alexander Mirzoev
  • Dmitry Zhurkin
  • Alexander Lyubartsev
  • Vladimir LobaskinEmail author
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 947)

Abstract

We present a framework for coarse-grained modelling of the interface between foreign nanoparticles (NP) and biological fluids and membranes. Our model includes united-atom presentations of membrane lipids and globular proteins in implicit solvent, which are based on all-atom structures of the corresponding molecules and parameterised using experimental data or atomistic simulation results. The NPs are modelled by homogeneous spheres that interact with the beads of biomolecules via a central force that depends on the NP size. The proposed methodology is used to predict the adsorption energies for human blood plasma proteins on NPs of different sizes as well as the preferred orientation of the molecules upon adsorption. Our approach allows one to rank the proteins by their binding affinity to the NP, which can be used for predicting the composition of the NP-protein corona for the corresponding material. We also show how the model can be used for studying NP interaction with a lipid bilayer membrane and thus can provide a mechanistic insight for modelling NP toxicity.

Keywords

Nanoparticle Toxicity Coarse-grained molecular dynamics Protein corona Cell membrane 

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Hender Lopez
    • 1
  • Erik G. Brandt
    • 2
  • Alexander Mirzoev
    • 2
  • Dmitry Zhurkin
    • 2
  • Alexander Lyubartsev
    • 2
  • Vladimir Lobaskin
    • 1
    Email author
  1. 1.School of Physics, Complex and Adaptive Systems LabUniversity College DublinDublin 4Ireland
  2. 2.Department of Materials and Environmental ChemistryStockholm UniversityStockholmSweden

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