Multiscale Modelling of Bionano Interface.
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.
School of Physics, Complex and Adaptive Systems Lab, University College Dublin, Belfield, Dublin 4, Ireland.
Hender
H
Lopez
Department of Materials and Environmental Chemistry, Stockholm University, SE-10691, Stockholm, Sweden.
Erik G
EG
Brandt
Department of Materials and Environmental Chemistry, Stockholm University, SE-10691, Stockholm, Sweden.
Alexander
A
Mirzoev
Department of Materials and Environmental Chemistry, Stockholm University, SE-10691, Stockholm, Sweden.
Dmitry
D
Zhurkin
Department of Materials and Environmental Chemistry, Stockholm University, SE-10691, Stockholm, Sweden.
Alexander
A
Lyubartsev
School of Physics, Complex and Adaptive Systems Lab, University College Dublin, Belfield, Dublin 4, Ireland. vladimir.lobaskin@ucd.ie.
Vladimir
V
Lobaskin
D001798:Blood Proteins / Q000737:chemistry; D006801:Humans; D008051:Lipid Bilayers / Q000737:chemistry; D008566:Membranes / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D053758:Nanoparticles / Q000737:chemistry*; D010316:Particle Size
D001798:Blood Proteins; D008051:Lipid Bilayers
Cell membrane; Coarse-grained molecular dynamics; Nanoparticle; Protein corona; Toxicity