Computational and experimental characterizations of silver nanoparticle-apolipoprotein biocorona

Journal of Physical Chemistry B

Volumn 117, Issue 43, 2013, Pages 13451-13456

  Li, Rongzhong ^a   Chen, Ran ^b   Chen, Pengyu ^b   Wen, Yimei ^b   Ke, Pu Chun ^b   Cho, Samuel S ^a  

^a WAKE FOREST UNIVERSITY   (United States)

^b CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DICHROISM SPECTRA; ENVIRONMENTAL HEALTH AND SAFETY; EXPERIMENTAL CHARACTERIZATION; ION CONCENTRATIONS; MOLECULAR DYNAMICS SIMULATIONS; NANOPARTICLE (NPS); NEGATIVELY CHARGED; SILVER NANOPARTICLES;

CIRCULAR DICHROISM SPECTROSCOPY; LIPOPROTEINS; MEDICAL NANOTECHNOLOGY; MOLECULAR DYNAMICS; NANOPARTICLES;

SILVER;

APOLIPOPROTEIN; METAL NANOPARTICLE; SILVER;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; HYDRODYNAMICS; MOLECULAR DYNAMICS; PARTICLE SIZE; PROTEIN FOLDING; SURFACE PROPERTY; ULTRASTRUCTURE;

APOLIPOPROTEINS; CIRCULAR DICHROISM; HYDRODYNAMICS; METAL NANOPARTICLES; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PARTICLE SIZE; PROTEIN FOLDING; SILVER; SURFACE PROPERTIES;

EID: 84887041026     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4061158     Document Type: Article

References (42)

1. Colvin, V. L. The Potential Environmental Impact of Engineered Nanomaterials Nat. Biotechnol. 2003, 21, 1166-1170
2. Lynch, I.; Dawson, K. A.; Linse, S. Detecting Cryptic Epitopes Created by Nanoparticles Sci. STKE 2006, 2006, pe14
3. Cedervall, T.; Lynch, I.; Lindman, S.; BerggaÌŠrd, T.; Thulin, E.; Nilsson, H.; Dawson, K. A.; Linse, S. Understanding the Nanoparticle-protein Corona Using Methods to Quantify Exchange Rates and Affinities of Proteins for Nanoparticles Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2050-2055
4. Li, Y.; Budamagunta, M. S.; Luo, J.; Xiao, W.; Voss, J. C.; Lam, K. S. Probing of the Assembly Structure and Dynamics Within Nanoparticles During Interaction with Blood Proteins ACS Nano 2012, 6, 9485-9495
5. Monopoli, M. P.; Åberg, C.; Salvati, A.; Dawson, K. A. Biomolecular Coronas Provide the Biological Identity of Nanosized Materials Nat. Nano 2012, 7, 779-786
6. Lundqvist, M.; Stigler, J.; Cedervall, T.; BerggaÌŠrd, T.; Flanagan, M. B.; Lynch, I.; Elia, G.; Dawson, K. The Evolution of the Protein Corona Around Nanoparticles: A Test Study ACS Nano 2011, 5, 7503-7509
7. Wang, F.; Yu, L.; Salvati, A.; Dawson, K. A. The Biomolecular Corona Is Retained During Nanoparticle Uptake and Protects the Cells from the Damage Induced by Cationic Nanoparticles Until Degraded in the Lysosomes. Nanomed.: Nanotechnol., Biol. Med. 2013, in press
8. Salvati, A.; Pitek, A. S.; Monopoli, M. P.; Prapainop, K.; Bombelli, F. B.; Hristov, D. R.; Kelly, P. M.; Åberg, C.; Mahon, E.; Dawson, K. A. Transferrin-Functionalized Nanoparticles Lose Their Targeting Capabilities When a Biomolecule Corona Adsorbs on the Surface Nat. Nano 2013, 8, 137-143
9. Anfinsen, C. B. Principles That Govern the Folding of Protein Chains Science 1973, 181, 223-230
10. Bryngelson, J. D.; Wolynes, P. G. Spin Glasses and the Statistical Mechanics of Protein Folding Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 7524-7528
11. Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Funnels, Pathways, and the Energy Landscape of Protein Folding: a Synthesis Proteins 1995, 21, 167-195
12. Leopold, P. E.; Montal, M.; Onuchic, J. N. Protein Folding Funnels: a Kinetic Approach to the Sequence-Structure Relationship Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 8721-8725
13. Onuchic, J. N.; Wolynes, P. G. Theory of Protein Folding Curr. Opin. Struct. Biol. 2004, 14, 70-75
14. Levy, Y.; Cho, S. S.; Onuchic, J. N.; Wolynes, P. G. A Survey of Flexible Protein Binding Mechanisms and Their Transition States Using Native Topology Based Energy Landscapes J. Mol. Biol. 2005, 346, 1121-1145
15. Shea, J. E.; Brooks, C. L. From Folding Theories to Folding Proteins: a Review and Assessment of Simulation Studies of Protein Folding and Unfolding Annu. Rev. Phys. Chem. 2001, 52, 499-535
16. Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S. Principles of Protein Folding: a Perspective from Simple Exact Models Protein Sci. 1995, 4, 561-602
17. Clementi, C.; Nymeyer, H.; Onuchic, J. N. Topological and Energetic Factors: What Determines the Structural Details of the Transition State Ensemble and "En-route" Intermediates for Protein Folding? An Investigation for Small Globular Proteins J. Mol. Biol. 2000, 298, 937-953
18. Hills, R. D.; Brooks, C. L. Insights from Coarse-Grained GoÌ... Models for Protein Folding and Dynamics Int. J. Mol. Sci. 2009, 10, 889-905
19. Cho, S. S.; Levy, Y.; Wolynes, P. G. Quantitative Criteria for Native Energetic Heterogeneity Influences in the Prediction of Protein Folding Kinetics Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 434-439
20. Karanicolas, J.; Brooks, C. L. The Origins of Asymmetry in the Folding Transition States of Protein L and Protein G Protein Sci. 2002, 11, 2351-2361
21. Ejtehadi, M. R.; Avall, S. P.; Plotkin, S. S. Three-Body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15088-15093
22. Thirumalai, D.; Hyeon, C. RNA and Protein Folding: Common Themes and Variations Biochemistry 2005, 44, 4957-4970
23. Cho, S. S.; Pincus, D. L.; Thirumalai, D. Assembly Mechanisms of RNA Pseudoknots Are Determined by the Stabilities of Constituent Secondary Structures Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 17349-17354
24. Hyeon, C.; Thirumalai, D. Capturing the Essence of Folding and Functions of Biomolecules Using Coarse-Grained Models Nat. Commun. 2011, 2, 487
25. Bailor, M. H.; Mustoe, A. M.; Brooks, C. L., III; Al-Hashimi, H. M. Topological Constraints: Using RNA Secondary Structure to Model 3D Conformation, Folding Pathways, and Dynamic Adaptation Curr. Opin. Struct. Biol. 2011, 21, 296-305
26. Cheung, M. S.; Klimov, D.; Thirumalai, D. Molecular Crowding Enhances Native State Stability and Refolding Rates of Globular Proteins Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 4753-4758
27. Morriss-Andrews, A.; Shea, J.-E. Kinetic Pathways to Peptide Aggregation on Surfaces: The Effects of B-Sheet Propensity and Surface Attraction J. Chem. Phys. 2012, 136, 065103-065111
28. Morriss-Andrews, A.; Bellesia, G.; Shea, J.-E. B-Sheet Propensity Controls the Kinetic Pathways and Morphologies of Seeded Peptide Aggregation J. Chem. Phys. 2012, 137, 145104-145109
29. Vilaseca, P.; Dawson, K. A.; Franzese, G. Understanding and Modulating the Competitive Surface-Adsorption of Proteins through Coarse-Grained Molecular Dynamics Simulations Soft Matter 2013, 9, 6978-6985
30. Zannis, V. I.; Chroni, A.; Krieger, M. Role of apoA-I, ABCA1, LCAT, and SR-BI in the Biogenesis of HDL J. Mol. Med 2006, 84, 276-294
31. Dagher, G.; Donne, N.; Klein, C.; Ferré, P.; Dugail, I. HDL-mediated Cholesterol Uptake and Targeting to Lipid Droplets in Adipocytes J. Lipid Res. 2003, 44, 1811-1820
32. Pincus, D. L.; Cho, S. S.; Hyeon, C.; Thirumalai, D. Minimal Models for Proteins and RNA from Folding to Function Prog. Mol. Biol. Transl. Sci. 2008, 84, 203-250
33. Cho, S. S.; Levy, Y.; Wolynes, P. G. P Versus Q: Structural Reaction Coordinates Capture Protein Folding on Smooth Landscapes Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 586-591
34. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules 0.1. The Method J. Comput. Chem. 1992, 13, 1011-1021
35. Lipscomb, T. J.; Zou, A.; Cho, S. S. Parallel Verlet Neighbor List Algorithm for GPU-optimized MD Simulations. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine; BCB '12; ACM: New York, 2012; pp 321-328.
36. Proctor, A. J.; Lipscomb, T. J.; Zou, A.; Anderson, J. A.; Cho, S. S. GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly Science J. 2012, 1, 1-11
37. Cho, S. S.; Weinkam, P.; Wolynes, P. G. Origins of Barriers and Barrierless Folding in BBL Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 118-123
38. Biyun, S.; Cho, S. S.; Thirumalai, D. Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations J. Am. Chem. Soc. 2011, 133, 20634-20643
39. Veitshans, T.; Klimov, D.; Thirumalai, D. Protein Folding Kinetics: Timescales, Pathways and Energy Landscapes in Terms of Sequence-dependent Properties Folding Des. 1997, 2, 1-22
40. Shen, X.-C.; Liou, X.-Y.; Ye, L.-P.; Liang, H.; Wang, Z.-Y. Spectroscopic Studies on the Interaction Between Human Hemoglobin and CdS Quantum Dots J. Colloid Interface Sci. 2007, 311, 400-406
41. Kaufman, E. D.; Belyea, J.; Johnson, M. C.; Nicholson, Z. M.; Ricks, J. L.; Shah, P. K.; Bayless, M.; Pettersson, T.; Feldotö, Z.; Blomberg, E. Probing Protein Adsorption onto Mercaptoundecanoic Acid Stabilized Gold Nanoparticles and Surfaces by Quartz Crystal Microbalance and ζ-Potential Measurements Langmuir 2007, 23, 6053-6062
42. Darabi Sahneh, F.; Scoglio, C.; Riviere, J. Dynamics of Nanoparticle-Protein Corona Complex Formation: Analytical Results from Population Balance Equations PLoS One 2013, 8, e64690