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.
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References
Sharifi S, Behzadi S, Laurent S, Forrest ML, Stroevee P, Mahmoudi M (2012) Toxicity of nanomaterials. Chem Soc Rev 41:2323
Borm PJA et al (2006) The potential risks of nanomaterials. Part Fibre Toxicol 3:11
Johnston HJ, Hutchison GR, Christensen FM et al (2009) Identification of the mechanisms that drive the toxicity of tio2 particulates: the contribution of physicochemical characteristics. Part Fibre Toxicol 6:33
Nel AE, Maedler L, Velegol D et al (2009) Understanding biophysicochemical interactions at the nano-bio interface. Nat Mater 8:543
Verma A, Uzun O, Hu Y et al (2008) Surface-structure-regulated cell-membrane penetration by monolayer-protected nanoparticles. Nat Mater 7:588
Schlick T, Collepardo-Guevara R, Halvorsen LA et al (2011) Biomolecular modeling and simulation: a field coming of age. Q Rev Biol 44:191
Valerio LG Jr (2009) In silico toxicology for the pharmaceutical sciences. Toxicol Appl Pharmacol 241:356
Nigsch F, Macaluso NJ, Mitchell JB, Zmuidinavicius D (2009) Computational toxicology: an overview of the sources of data and of modelling methods. Expert Opin Drug Metab Toxicol 5:1
Dearden JC (2003) In silico prediction of drug toxicity. J Comput Aided Mol Des 17:119
Lyubartsev AP, Rabinovich AL (2011) Recent development in computer simulations of lipid bilayers. Soft Matter 7:25
Wong-Ekkabut J, Baoukina S, Triampo W, Tang I-M, Tieleman DP (2008) Computer simulation study of fullerene translocation through lipid membranes. Nat Nanotechnol 3:363
Hou WC, Moghadam BY, Westerhoff P, Posner JD (2011) Distribution of fullerene nanomaterials between water and model biological membranes. Langmuir 27:11899
Yang K, Ma YQ (2010) Computer simulation of the translocation of nanoparticles with different shapes across a lipid bilayer. Nat Nanotechnol 5:579
Monticelli L, Salonen E, Ke PC, Vattulainen I (2009) Effects of carbon nanoparticles on lipid membranes: a molecular simulation perspective. Soft Matter 5:4433
Izvekov S, Voth GA (2005) Multiscale coarse-graining method for biomolecular systems. J Phys Chem B 109:2469
Ayton GS, Noid WG, Voth GA (2007) Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol 17:192
Lyubartsev AP, Laaksonen A (1995) Calculation of effective interaction potentials from radial distribution functions: a reverse monte carlo approach. Phys Rev E 52:3730
Lyubartsev AP, Mirzoev A, Chen L-J, Laaksonen A (2010) Systematic coarse-graining of molecular models by the newton inversion method. Faraday Discuss 144:43
Lyubartsev AP, Laaksonen A (1999) Effective potentials for ion-DNA interactions. J Chem Phys 111:11207
Tozzini V (2005) Coarse-grained models for proteins. Curr Opin Struct Biol 15(2):144–150
Bereau T, Deserno M (2009) Generic coarse-grained model for protein folding and aggregation. J Chem Phys 130(23):235106
Takada S (2012) Coarse-grained molecular simulations of large biomolecules. Curr Opin Struct Biol 22(2):130–137
Wei S, Knotts T (2013) A coarse grain model for protein-surface interactions. J Chem Phys 139(9):095102
Lobaskin V, Lyubartsev AP, Linse P (2001) Effective macroion-macroion potentials in asymmetric electrolytes. Phys Rev E 63:020401
Brunner M, Bechinger C, Strepp W, Lobaskin V, von Gruenberg HH (2002) Density-dependent pair interactions in 2D colloidal dispersions. Europhys Lett 58:926
Lynch I, Salvati A, Dawson KA (2009) Protein-nanoparticle interactions. What does the cell see? Nat Nanotechnol 4:546
Lynch I, Dawson KA, Linse S (2006) Detecting cryptic epitopes created by nanoparticles. Sci STKE 2006:14
Cedervall T et al (2007) Understanding the nanoparticle protein corona using methods to quantify exchange rates and affinities of proteins for nanoparticles. Proc Natl Acad Sci U S A 104:2050
Lindman S et al (2007) Systematic investigation of the thermodynamics of HSA adsorption to n-iso-propylacrylamide/n-tert-butylacrylamide copolymer nanoparticles. effects of particle size and hydrophobicity. Nanoletters 7:914
Allen LT et al (2006) Surface-induced changes in protein adsorption and implications for cellular phenotypic responses to surface interaction. Biomaterials 27:3096
Radke CE, Prausnitz JM (1972) Thermodynamics of multisolute adsorption from dilute liquid solutions. AIChE J 18:761
Lesniak A, Campbell A, Monopoli MP, Lynch I, Salvati A, Dawson KA (2010) Serum heat inactivation affects protein corona composition and nanoparticle uptake. Biomaterials 31:9511
Kamath P, Fernandez A, Giralt F, Rallo R (2015) Predicting cell association of surface-modified nanoparticles using protein corona structure – activity relationships (PCSAR). Curr Top Med Chem 15(18):1930–1937
Noid WG (2013) Perspective: Coarse-grained models for biomolecular systems. J Chem Phys 139(9):090901
Lopez H, Lobaskin V (2015) Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles. J Chem Phys 143:243138
Miyazawa S, Jernigan RL (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256(3):623–644
Kim Y, Tang C, Clore G, Hummer G (2008) Replica exchange simulations of transient encounter complexes in protein-protein association. Proc Natl Acad Sci U S A 105(35):12855–12860
Kim Y, Hummer G (2008) Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol 375(5):1416–1433
Agashe M, Raut V, Stuart S, Latour R (2005) Molecular simulation to characterize the adsorption behavior of a Fibrinogen γ-chain fragment. Langmuir 21(3):1103–1117
Sun Y, Welsh W, Latour R (2005) Prediction of the orientations of adsorbed protein using an empirical energy function with implicit solvation. Langmuir 21(12):5616–5626
Kokh D, Corni S, Winn P, Hoefling M, Gottschalk K, Wade R (2010) Prometcs: An atomistic force field for modeling proteinmetal surface interactions in a continuum aqueous solvent. J Chem Theory Comput 6(5):1753–1768
Limbach H, Arnold A, Mann B, Holm C (2006) ESPResSo – an extensible simulation package for research on soft matter systems. Comput Phys Commun 174(9):704–727
Chen W, Huang H, Lin C, Lin F, Chan Y (2003) Effect of temperature on hydrophobic interaction between proteins and hydrophobic adsorbents: studies by isothermal titration calorimetry and the van’t Hoff equation. Langmuir 19(22):9395–9403
Lacerda S, Park JJ, Meuse C, Pristinski D, Becker M, Karim A, Douglas J (2010) Interaction of gold nanoparticles with common human blood proteins. ACS Nano 4(1):365–379
Vilaseca P, Dawson K, Franzese G (2013) Understanding and modulating the competitive surface-adsorption of proteins through coarse-grained molecular dynamics simulations. Soft Matter 9:6978–6985
Vijay-Kumar S, Bugg C, Cook W (1987) Structure of ubiquitin refined at 1.8 resolution. J Mol Biol 194:531–544
Momma K, Izumi F (2011) VESTA3 for three-dimensional visualization of crystal, volumetric and morphology data. J Appl Cryst 44:1272–1276
Brandt EG, Lyubartsev A (2015) Systematic optimization of a force field for classical simulations of TiO2-water interfaces. J Phys Chem C 119:18110–18125
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690
Hoover W (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev A 31:1695–1697
Nose S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 81:511–519
Jämbeck JPM, Lyubartsev AP (2012) Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J Phys Chem B 116(10):3164–3179
Jämbeck JPM, Lyubartsev AP (2013) Another piece of the membrane puzzle: extending Slipids further. J Chem Theory Comput 9(1):774–784
Mirzoev A, Lyubartsev AP (2013) MagiC: software package for multiscale modeling. J Chem Theory Comput 9(3):1512–1520
Qin S-S, Yu ZW, Yu Y-X (2009) Structural characterization on the gel to liquid-crystal phase transition of fully hydrated DSPC and DSPE bilayers. J Phys Chem B 113:8114–8123
Kučerka N, Liu Y, Chu N, Petrache HI, Tristram-Nagle S, Nagle JF (2005) Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles. Biophys J 88:2626–2637
Koenig BW, Strey HH, Gawrisch K (1997) Membrane lateral compressibility determined by NMR and X-ray diffraction: effect of acyl chain polyunsaturation. Biophys J 73(4):1954–1966
Kučerka N, Nagle JF, Sachs JN, Feller SE, Pencer J, Jackson A, Katsaras J (2008) Lipid bilayer structure determined by the simultaneous analysis of neutron and X-Ray scattering data. Biophys J 95(5):2356–2367
Bereau T, Wang Z-J, Deserno M (2014) More than the sum of its parts: Coarse-grained peptide-lipid interactions from a simple cross-parametrization. J Chem Phys 140(11):115101
Lin J, Zhang H, Chen Z, Zheng Y (2010) Penetration of lipid membranes by gold nanoparticles: Insights into cellular uptake, cytotoxicity, and their relationship. ACS Nano 4(9):5421–5429
Hong-Ming D, Yu-Qiang M (2014) Computer simulation of the role of protein corona in cellular delivery of nanoparticles. Biomaterials 35(30):8703–8710
Monopoli M, Aberg C, Salvati A, Dawson KA (2012) Biomolecular coronas provide the biological identity of nanosized materials. Nat Nanotechnol 7(12):779–786
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Lopez, H., Brandt, E.G., Mirzoev, A., Zhurkin, D., Lyubartsev, A., Lobaskin, V. (2017). Multiscale Modelling of Bionano Interface. In: Tran, L., Bañares, M., Rallo, R. (eds) Modelling the Toxicity of Nanoparticles. Advances in Experimental Medicine and Biology, vol 947. Springer, Cham. https://doi.org/10.1007/978-3-319-47754-1_7
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DOI: https://doi.org/10.1007/978-3-319-47754-1_7
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