Modeling Lipid Particles

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Last Updated: Wednesday, 15 December 2021 08:46

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Low-density and high-density lipoproteins (LDL/HDL) consist of a mixture of components including phospholipids, triglycerides, cholesterol, and associated proteins. The Martini model has proven useful to study the structure and dynamics of these particles [1-3].

Other lipid based particles that have been simulated with Martini include a large variety of nanodiscs i.e., lipid bicelles stabilized by scaffolding proteins or DNA [8], or styrene-maleicacid copolymers [6] (figure), as well as liprotides [5] and complex nanoemulsions for vitamin delivery [9].

In addition, the process of triglyceride nanodroplet formation is being addressed with Martini [7], as well as the formation and transfection of lipid/DNA gene delivery vectors (lipoplexes) [10].

To efficiently build lipid-based nanoparticles, a number of dedicated tools are available [4,11].

 

  • [1] A. Catte, J.C. Patterson, D. Bashtovyy, M.K. Jones, F. Gu, L. Li, A. Rampioni, D. Sengupta, T. Vuorela, P. Niemela, M. Karttunen, S.J. Marrink, I. Vattulainen, J.P. Segrest. Structure of spheroidal HDL particles revealed by combined atomistic and coarse grained simulations. Biophys. J., 94:2306-2319, 2008.
  • [2] T.A. Vuorela, A. Catte, P.S. Niemela, A. Hall, M.T. Hyvonen, S.J. Marrink, M. Karttunen, I. Vattulainen. Role of lipids in spheroidal high density lipoproteins. PLoS Comp. Biol., 6:e1000964, 2010.
  • [3] T. Murtola, T.A. Vuorela, M.T. Hyvonen, S.J. Marrink, M. Karttunen, I. Vattulainen. Low density lipoprotein: Structure, dynamics, and interactions of ApoB-100 with lipids. Soft Matter, 7:8135-8141, 2011.
  • [4] Y. Qi, H.I. Ingólfsson, X. Cheng, J. Lee, S.J. Marrink, W. Im. CHARMM-GUI Martini Maker for coarse-grained simulations with the Martini force field. JCTC, 11:4486–4494, 2015. abstract
  • [5] J.N. Pedersen, P.W.J.M. Frederix, J.S. Pedersen, S.J. Marrink, D. Otzen. Role of charge and hydrophobicity in liprotide formation: a molecular dynamics study with experimental constraints. ChemBioChem, 19:263–271, 2018. doi:10.1002/cbic.201700496
  • [6] M. Xue, L. Cheng, I. Faustino, W. Guo, S.J. Marrink. Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers. Biophys. J., 115:494-502, 2018. doi:10.1016/j.bpj.2018.06.018.
  • [7] X. Prasanna, V.T. Salo  et al. Seipin traps triacylglycerols to facilitate their nanoscale clustering in the endoplasmic reticulum membrane. PLoS Biol 19(1): e3000998, 2021. https://doi.org/10.1371/journal.pbio.3000998
  • [8]  V. Maingi, P.W.K. Rothemund. Properties of DNA- and Protein-Scaffolded Lipid Nanodiscs. ACS Nano 15:751–764, 2021. https://doi.org/10.1021/acsnano.0c07128
  • [9] N. Machado, B.M.H. Bruininks, ..., S.J. Marrink, P.C.T. Souza, P.P. Favero. Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes. Nanoscale, 2021, online. https://doi.org/10.1039/D1NR04610A
  • [10] B.M.H. Bruininks, P.C.T. Souza, H. Ingolfsson, S.J. Marrink.  A molecular view on the escape of lipoplexed DNA from the endosome. eLife,  9:e52012, 2020. doi.org/10.7554/eLife.52012
  • [11] L.R. Kjølbye, L. De Maria, T.A. Wassenaar, H. Abdizadeh, S.J. Marrink, J. Ferkinghoff-Borg, B. Schiøtt. General Protocol for Constructing Molecular Models of Nanodiscs. J. Chem. Inf. Model. 61 (6), 2869–2883, 2021. https://doi.org/10.1021/acs.jcim.1c00157

Polymeric systems

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Last Updated: Monday, 31 May 2021 09:00

Coarse-graining has been of fundamental importance in the field of polymer modeling. In order to study the large size of polymer chains and the associated slow relaxation processes, a reduction of the degrees of freedom has proven absolutely necessary.  Although the Martini model has been designed for biomolecular applications, there is no reason why the same philosophy could not be extended to soft matter in general. Indeed there is a growing number of basic polymer systems for which Martini parameters have been derived, including polyethyleneglycol (PEG) [1,11,18], polystyrene [2,9], triblock copolymers [3,10], polyester coatings [4], polymer nanofibres [5], dendrimers [6], amphipols [8], styrene-maleic acid copolymers [17], P3HT and other polymers used in organic photovoltaics [13-16], and many many more with applications across the entire field of materials sciences. For a recent overview, see [20].

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One of the advantages of the broad scope of Martini is the ability to easily combine different systems. In the context of polymers, this is demonstrated by studies of dendrimers and copolymers interacting with lipid membranes [6,10, 12, 17], simulations of pegylated lipids [7,19], partitioning of compounds in complex coacervates [21], and blends of polymers with other nanoparticles (see Figure) [13]. We expect many more of these Martini  hybrid simulations in the near future ...
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  • [1] H. Lee, A.H. de Vries, S.J. Marrink, R.W. Pastor. A coarse-grained model for polyethylene oxide: conformation and hydrodynamics. J. Phys. Chem. B, 113:13186-13194, 2009. abstract
  • [2] G. Rossi, L. Monticelli, S. R. Puisto, I. Vattulainen and T. Ala-Nissila. Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case. Soft Matter, 7:698-708, 2011.
  • [3] M. Hatakeyama, R. Faller. Coarse-grained simulations of ABA amphiphilic triblock copolymer solutions in thin films, Phys Chem Chem Phys 9:4662-4672, 2007.
  • [4] G. Rossi, I. Giannakopoulos, L. Monticelli, N.K.J. Rostedt, S.R. Puisto, C. Lowe, A.C. Taylor, I. Vattulainen, T. Ala-Nissila. A MARTINI coarse-grained model of a thermoset polyester coating. Macromolecules, ASAP, 2011.
  • [5] A. Milani, M. Casalegno, C. Castiglioni, G. Raos. Coarse-grained simulations of model polymer nanofibres, Macromol. Th. Sim. ASAP, 2011.
  • [6] H. Lee, R.G. Larson, Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer, J Phys Chem B 112:7778-7784, 2008.
  • [7] H. Lee, R.W. Pastor. Coarse-grained model for PEGylated lipids: effect of PEGylation on the size and shape of self-assembled structures. J. Phys. Chem. B, ASAP, 2011
  • [8] J.D. Perlmutter, W.J. Drasler, W. Xie, J. Gao, J.L. Popot , J. Sachs. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer. Langmuir, ASAP, 2011.
  • [9] G Rossi, I.G. Elliott, T. Ala-Nissila, R. Faller. Molecular dynamics study of a MARTINI coarse-grained polystyrene brush in good solvent: structure and dynamics. Macromolecules, ASAP, 2011. DOI: 10.1021/ma201980k
  • [10] S. Hezaveh, S. Samanta, A. De Nicola, G. Milano, D. Roccatano. Understanding the Interaction of Block Copolymers with DMPC Lipid Bilayer using Coarse-Grained Molecular Dynamics Simulations. J. Phys. Chem. B, Just Accepted Manuscript, 2012. DOI: 10.1021/jp306565e
  • [11] G. Rossi, P. François, J. Fuchs, J. Barnoud, L. Monticelli.A Coarse-Grained Martini Model of Polyethylene Glycol and of Polyoxyethylene Alkyl Ether Surfactants. J. Phys. Chem. B, Just Accepted Manuscript, 2012. DOI: 10.1021/jp3095165
  • [12] J. Barnoud, G. Rossi, S.J. Marrink, L. Monticelli. Hydrophobic compounds reshape membrane domains. PLoS Comp. Biol., 10: e1003873, 2014. open access
  • [13] R. Alessandri, J.J. Uusitalo, A.H. De Vries, R.W.A. Havenith, S.J. Marrink. Bulk heterojunction morphologies with atomistic resolution from coarse-grain solvent evaporation simulations. JACS, 139:3697–3705, 2017. open access
  • [14] L. Qiu, J. Liu, R. Alessandri, X. Qiu, M. Koopmans, R.W.A. Havenith, S.J. Marrink, R.C. Chiechi, L.J.A. Koster, J.C. Hummelen. Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics. Journal of Material Chemistry A, 5:21234-2124, 2017. abstract
  • [15] J. Liu, L. Qiu, R. Alessandri, X. Qiu, G. Portale, J. Dong, W. Talsma, G. Ye, A.A. Sengrian, P.C.T. Souza, M.A. Loi, R.C. Chiechi, S.J. Marrink, J.C. Hummelen, L.J.A. Koster. Enhancing Molecular n-Type Doping of Donor–Acceptor Copolymers by Tailoring Side Chains. Advanced Materials, 30:1704630, 2018. doi:10.1002/adma.201704630
  • [16] R. Alessandri, S. Sami, J. Barnoud, A.H. de Vries, S.J. Marrink, R.W.A. Havenith. Resolving donor–acceptor interfaces and charge carrier energy levels of organic semiconductors with polar side chains. Advanced Funct. Materials, 2004799, 2020 .doi:10.1002/adfm.202004799
  • [17] M. Xue, L. Cheng, I. Faustino, W. Guo, S.J. Marrink. Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers. Biophys. J., 115:494-502, 2018. doi:10.1016/j.bpj.2018.06.018.
  • [18] F. Grunewald, G. Rossi, A.H. De Vries, S.J. Marrink, L. Monticelli. A Transferable MARTINI Model of Polyethylene Oxide. JPCB, 122:7436–7449, 2018. doi:10.1021/acs.jpcb.8b04760
  • [19] F. Grünewald, P.C. Kroon, P.C.T. Souza, S.J. Marrink. Protocol for Simulations of PEGylated Proteins with Martini 3. Structural Genomics: Methods in Molecular Biology 2199:315-335, 2021. reprint
  • [20] R. Alessandri, F. Grünewald, S.J. Marrink. Martini Perspective in Materials Science, Adv. Materials, 2021. https://doi.org/10.1002/adma.202008635 
  • [21] M. Tsanai, P.W.J.M. Frederix, C.F.E. Schroer, P.C.T. Souza, S.J. Marrink. Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chemical Science, 2021. pubs.rsc.org/en/content/art