Free energy of PAMAM dendrimer adsorption onto model biological membranes

Journal of Physical Chemistry B

Volumn 118, Issue 24, 2014, Pages 6792-6802

  Kim, Yongbin ^a   Kwak, Yongkyu ^a   Chang, Rakwoo ^a  

^a Kwangwoon University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ADSORPTION; CELL MEMBRANES; CYTOLOGY; FREE ENERGY; LIPID BILAYERS; MEMBRANES; VAN DER WAALS FORCES;

ATOMISTIC INTERACTIONS; ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS; BILAYER LIPID MEMBRANE; DOMINANT CONTRIBUTIONS; LIPID BILAYER MEMBRANES; MINIMUM FREE ENERGIES; POLYAMIDOAMINE DENDRIMERS; VAN DER WAALS ATTRACTION;

DENDRIMERS;

1-PALMITOYL-2-OLEOYLGLYCERO-3-PHOSPHOGLYCEROL; DENDRIMER; DIPALMITOYLPHOSPHATIDYLCHOLINE; ETHYLENEDIAMINE; ETHYLENEDIAMINE DERIVATIVE; LIPID BILAYER; PAMAM STARBURST; PHOSPHATIDYLGLYCEROL;

ADSORPTION; CHEMICAL STRUCTURE; CHEMISTRY; LIPID BILAYER; MOLECULAR DYNAMICS; THERMODYNAMICS;

1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE; ADSORPTION; DENDRIMERS; ETHYLENEDIAMINES; LIPID BILAYERS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PHOSPHATIDYLGLYCEROLS; THERMODYNAMICS;

EID: 84902970226     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp501755k     Document Type: Article

References (53)

1. Tomalia, D. A.; Naylor, A. M.; Goddard, W. A. Starburst Dendrimers: Molecular-Level Control of Size, Shape, Surface Chemistry, Topology, and Flexibility from Atoms to Macroscopic Matter Angew. Chem., Int. Ed. Engl. 1990, 29, 138-175
2. Esfand, R.; Tomalia, D. A. Poly(amidoamine) (PAMAM) Dendrimers: from Biomimicry to Drug Delivery and Biomedical Applications Drug Discovery Today 2001, 6, 427-436
3. Cagin, T.; Wang, G. F.; Martin, R.; Zamanakos, G.; Vaidehi, N.; Mainz, D. T.; Goddard, W. A. Multiscale Modeling and Simulation Methods with Applications to Dendritic Polymers Comput. Theor. Polym. Sci. 2001, 11, 345-356
4. Lee, I.; Athey, B. D.; Wetzel, A. W.; Meixner, W.; Baker, J. R. Structural Molecular Dynamics Studies on Polyamidoamine Dendrimers for a Therapeutic Application: Effects of pH and Generation Macromolecules 2002, 35, 4510-4520
5. Fischer, D.; Li, Y.; Ahlemeyer, B.; Krieglstein, J.; Kissel, T. In vitro Cytotoxicity Testing of Polycations: Influence of Polymer Structure on Cell Viability and Hemolysis Biomaterials 2003, 24, 1121-1131
6. Hong, S.; Bielinska, A. U.; Mecke, A.; Keszler, B.; Beals, J. L.; Shi, X.; Balogh, L.; Orr, B. G.; Baker, J. R., Jr.; Holl, M. M. B. Interaction of Poly(amidoamine) Dendrimers with Supported Lipid Bilayers and Cells: Hole Formation and the Relation to Transport Bioconjugate Chem. 2004, 15, 774-782
7. Mecke, A.; Lee, D.-K.; Ramamoorthy, A.; Orr, B. G.; Holl, M. M. B. Synthetic and Natural Polycationic Polymer Nanoparticles Interact Selectively with Fluid-Phase Domains of DMPC Lipid Bilayers Langmuir 2005, 21, 8588-8590
8. Mecke, A.; Majoros, I. J.; Patri, A. K.; Baker, J. R., Jr.; Holl, M. M. B.; Orr, B. G. Lipid Bilayer Disruption by Polycationic Polymers: The Roles of Size and Chemical Functional Group Langmuir 2005, 21, 10348-10354
9. Hong, S.; Leroueil, P. R.; Janus, E. K.; Peters, J. L.; Kober, M.-M.; Islam, M. T.; Orr, B. G.; James R Baker, J.; Holl, M. M. B. Interaction of Polycationic Polymers with Supported Lipid Bilayers and Cells: Nanoscale Hole Formation and Enhanced Membrane Permeability Bioconjugate Chem. 2006, 17, 728-734
10. Leroueil, P. R.; Hong, S.; Mecke, A. Nanoparticle Interaction with Biological Membranes: Does Nanotechnology Present a Janus Face? Acc. Chem. Res. 2007, 40, 335-342
11. Leroueil, P. R.; Berry, S. A.; Duthie, K.; Han, G.; Rotello, V. M.; McNerny, D. Q.; Baker, J. R., Jr.; Orr, B. G.; Holl, M. M. B. Wide Varieties of Cationic Nanoparticles Induce Defects in Supported Lipid Bilayers Nano Lett. 2008, 8, 420-424
12. Zhang, Z.-Y.; Smith, B. D. High-Generation Polycationic Dendrimers Are Unusually Effective at Disrupting Anionic Vesicles: Membrane Bending Model Bioconjugate Chem. 2000, 11, 805-814
13. Karoonuthaisiri, N.; Titiyevskiy, K.; Thomas, J. L. Destabilization of Fatty Acid-Containing Liposomes by Polyamidoamine Dendrimers Colloids Surf., B 2003, 27, 365-375
14. Nyitrai, G.; Keszthelyi, T.; Bóta, A.; Simon, A.; Töke, O.; Horváth, G.; Pál, I.; Kardos, J.; Héja, L. Sodium Selective Ion Channel Formation in Living Cell Membranes by Polyamidoamine Dendrimer Biochim. Biophys. Acta, Biomembr. 2013, 1828, 1873-1880
15. Jain, K.; Kesharwani, P.; Gupta, U.; Jain, N. K. Dendrimer Toxicity: Let's Meet the Challenge Int. J. Pharm. 2010, 394, 122-142
16. Kim, Y.; Klutz, A. M.; Jacobson, K. A. Systematic Investigation of Polyamidoamine Dendrimers Surface-Modified with Poly(ethylene glycol) for Drug Delivery Applications: Synthesis, Characterization, and Evaluation of Cytotoxicity Bioconjugate Chem. 2008, 19, 1660-1672
17. Akesson, A.; Lind, T. K.; Barker, R.; Hughes, A.; Cárdenas, M. Unraveling Dendrimer Translocation across Cell Membrane Mimics Langmuir 2012, 28, 13025-13033
18. Lee, H.; Larson, R. G. Molecular Dynamics Simulations of PAMAM Dendrimer-Induced Pore Formation in DPPC Bilayers with a Coarse-Grained Model J. Phys. Chem. B 2006, 110, 18204-18211
19. Lee, H.; Larson, R. G. 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 2008, 112, 7778-7784
20. Lee, H.; Larson, R. G. Lipid Bilayer Curvature and Pore Formation Induced by Charged Linear Polymers and Dendrimers: The Effect of Molecular Shape J. Phys. Chem. B 2008, 112, 12279-12285
21. Lee, H.; Larson, R. G. Multiscale Modeling of Dendrimers and Their Interactions with Bilayers and Polyelectrolytes Molecules 2009, 14, 423-438
22. Lee, H.; Larson, R. G. Membrane Pore Formation Induced by Acetylated and Polyethylene Glycol-Conjugated Polyamidoamine Dendrimers J. Phys. Chem. C 2011, 115, 5316-5322
23. Lee, H. Self-Assembly of Mixtures of a Dendrimer and Lipids: Effects of Hydrophobicity and Electrostatics Mol. Simul. 2012, 38, 534-539
24. Smith, K. A.; Jasnow, D.; Balazs, A. C. Designing Synthetic Vesicles that Engulf Nanoscopic Particles J. Chem. Phys. 2007, 127, 084703
25. Wang, Y.-L. Y.; Lu, Z.-Y. Z.; Laaksonen, A. A. Specific Binding Structures of Dendrimers on Lipid Bilayer Membranes Phys. Chem. Chem. Phys. 2012, 14, 8348-8359
26. Mecke, A.; Uppuluri, S.; Sassanella, T. M.; Lee, D.-K.; Ramamoorthy, A.; Baker, J. R., Jr.; Orr, B. G.; Banaszak Holl, M. M. Direct Observation of Lipid Bilayer Disruption by Poly(amidoamine) Dendrimers Chem. Phys. Lipids 2004, 132, 3-14
27. Mecke, A.; Lee, I.; Baker, J. R., Jr.; Holl, M. M. B.; Orr, B. G. Deformability of Poly(amidoamine) Dendrimers Eur. Phys. J. E 2004, 14, 7-17
28. Kelly, C. V.; Leroueil, P. R.; Nett, E. K.; Wereszczynski, J. M.; Baker, J. R., Jr.; Orr, B. G.; Holl, M. M. B.; Andricioaei, I. Poly(amidoamine) Dendrimers on Lipid Bilayers I: Free Energy and Conformation of Binding J. Phys. Chem. B 2008, 112, 9337-9345
29. Kelly, C. V.; Leroueil, P. R.; Orr, B. G.; Holl, M. M. B.; Andricioaei, I. Poly(amidoamine) Dendrimers on Lipid Bilayers II: Effects of Bilayer Phase and Dendrimer Termination J. Phys. Chem. B 2008, 112, 9346-9353
30. Torrie, G. M.; Valleau, J. P. Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling J. Comput. Phys. 1977, 23, 187-199
31. Roux, B. The Calculation of the Potential of Mean Force Using Computer Simulations Comput. Phys. Commun. 1995, 91, 275-282
32. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. I. The method J. Comput. Chem. 1992, 13, 1011-1021
33. Epand, R. M.; Epand, R. F. Domains in Bacterial Membranes and the Action of Antimicrobial Agents Mol. BioSyst. 2009, 5, 580-587
34. Schuettelkopf, A. W.; van Aalten, D. M. F. PRODRG: A Tool for High-Throughput Crystallography of Protein-Ligand Complexes Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 1355
35. 2-Terminated PAMAM Dendrimers: A Microscopic View from Atomistic Computer Simulations Mol. Pharmaceutics 2014, 11, 1459-1470
36. Elmore, D. E. Molecular Dynamics Simulation of a Phosphatidylglycerol Membrane FEBS Lett. 2006, 580, 144-148
37. Tieleman, D. P.; Berendsen, H. J. C. Molecular Dynamics Simulations of a Fully Hydrated Dipalmitoyl Phosphatidylcholine Bilayer with Different Macroscopic Boundary Conditions and Parameters J. Chem. Phys. 1996, 105, 4871-4880
38. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The Missing Term in Effective Pair Potentials J. Phys. Chem. 1987, 91, 6269-6271
39. Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, Flexible, and Free J. Comput. Chem. 2005, 26, 1701-1718
40. Nose, S.; Klein, M. L. Constant Pressure Molecular-Dynamics for Molecular Systems Mol. Phys. 1983, 50, 1055-1076
41. Parrinello, M.; Rahman, A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method J. Appl. Phys. 1981, 52, 7182-7190
42. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N·log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089
43. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577
44. Chang, R.; Violi, A. Insights into the Effect of Combustion-Generated Carbon Nanoparticles on Biological Membranes: A Computer Simulation Study J. Phys. Chem. B 2006, 110, 5073-5083
45. Choe, S.; Chang, R.; Jeon, J.; Violi, A. Molecular Dynamics Simulation Study of a Pulmonary Surfactant Film Interacting with a Carbonaceous Nanoparticle Biophys. J. 2008, 95, 4102-4114
46. 60 Molecules in Biological Membranes: Computer Simulation Studies Bull. Korean Chem. Soc. 2010, 31, 3195-3200
47. 1 and P c Periodic Boundary Conditions Biophys. J. 2002, 82, 2317-2325
48. Prosa, T. J.; Bauer, B. J.; Amis, E. J.; Tomalia, D. A.; Scherrenberg, R. A SAXS Study of the Internal Structure of Dendritic Polymer Systems J. Polym. Sci., Part B: Polym. Phys. 1997, 35, 2913-2924
49. Prosa, T. J.; Bauer, B. J.; Amis, E. J. From Stars to Spheres: A SAXS Analysis of Dilute Dendrimer Solutions Macromolecules 2001, 34, 4897-4906
50. Rathgeber, S.; Monkenbusch, M. Dynamics of Star-Burst Dendrimers in Solution in Relation to Their Structural Properties J. Chem. Phys. 2002, 117, 4047
51. Porcar, L.; Liu, Y.; Verduzco, R.; Hong, K.; Butler, P. D.; Magid, L. J.; Smith, G. S.; Chen, W.-R. Structural Investigation of PAMAM Dendrimers in Aqueous Solutions Using Small-Angle Neutron Scattering: Effect of Generation J. Phys. Chem. B 2008, 112, 14772-14778
52. Opitz, A. W.; Wagner, N. J. Structural Investigations of Poly(amido amine) Dendrimers in Methanol Using Molecular Dynamics J. Polym. Sci., Part B: Polym. Phys. 2006, 44, 3062-3077
53. Maingi, V.; Jain, V.; Bharatam, P. V.; Maiti, P. K. Dendrimer Building Toolkit: Model Building and Characterization of Various Dendrimer Architectures J. Comput. Chem. 2012, 33, 1997-2011