Interactions between Nanoparticles and Biomolecules at the Nano-Bio interface

The advancement of nanomedicine and increasing applications of nanoparticles (NPs) in consumer products have led to administered biological exposure and unintentional environmental accumulation of NPs, causing concerns over the safety and sustainability of nanotechnology. Other sources of NP pollutions include combustion processes from human activities, such as petroleum-fueled vehicles. Therefore, there is a crucial need to understand the molecular mechanism of nanotoxicity to ensure safe nanotechnology and enable the vast applications of nanomedicine.

Upon entering biological systems, NPs form molecular complexes with their encountered proteins, termed as the NP-protein corona. Protein corona shields the surface of an exogenous NP and determines its biological identifies. On the other hand, interactions with NP can alter the structure, dynamics, and function of the NP-bound proteins, which may further impact recognition by membrane receptors and the immune system. We hypothesize that the conformational changes of NP-bound proteins are an important determinant of nanotoxicity in additional to other accepted factors, such as ion dissolution and ability for lipid membrane translocation. We apply multiscale computer simulations to understand the structure and dynamics of NP-protein corona, and to evaluate the corresponding conformational changes of the NP-bound proteins. Correlation between computational studies of NP-protein corona and experimental evaluations of NP cytotoxicity will help the development of a predictive metric of nanotoxicity for advancing nanomedicine and environmental remediation of the hazardous by-products of the petroleum industry.

35. Koppel K, Tang H, Javed I, Parsa M, Mortimer M, Davis TP, Lin S, Chaffee AL, Ding F and Ke P, “Elevated Amyloidoses of Human IAPP and Amyloid Beta by Lipopolysaccharide and Their Mitigation by Carbon Quantum Dots”, Nanoscale, in press (2020)

34. Y. Xing, Y. Sun, B. Wang, & F. Ding, “Morphological Determinants of Carbon Nanomaterial-Induced Amyloid Peptide Self-Assembly”, Frontiers in Chemistry, in press (2020)

33. Z Huma,I Javed, Z Zhang, H Bilal, Y Sun, SZ Hussain, TP Davis, DE Otzen, CB Landersdorfer, F Ding, I Hussain and PC Ke, “Nano Silver Mitigates Biofilm Formation via FapC Amyloidosis Inhibition”, Small, 1906674-1906683 (2019) DOI: 10.1002/smll.201906674

32. A Faridi, Y Sun, M Mortimer, RR Aranha, A Nandakumar, Y Li, I Javed, A Kakinen, Q Fan, AW Purcell, TP Davis,* F Ding,* P Faridi,* and P Ke*, “Graphene quantum dots rescue protein dysregulation of pancreatic β-cells exposed to human islet amyloid polypeptide”, Nano Research, in press (2019)

31. I Javed, G Peng, Y Xing, T Yu, M Zhao, A Kakinen, A Faridi, CL Parish, F Ding*, TP Davis*, P Ke* and S Lin*, “Inhibition of Amyloid Beta Toxicity in Zebrafish with A Chaperone-Gold Nanoparticle Dual Strategy”, Nature Commun, in press (2019)

30. Y. Sun, A. Kakinen, C. Zhang, Y. Yang, A. Faridi, T. P. Davis, W. Cao, P. C. Ke and F. Ding, “Amphiphilic Surface Chemistry of Fullerenols Is Necessary for Inhibiting the Amyloid Aggregation of Alpha-Synuclein NACore”, Nanoscale, in press, (2019)

29. P. C. Ke, E. H. Pilkington, Y. Sun, I. Javed, A. Kakinen, G. Peng, F. Ding, . P. Davisa, “Mitigation of Amyloidosis with Nanomaterials”, Advanced Materials, in press, (2019)

28. M. Wang, Y. Sun, X. Cao, G. Peng, I. Javed, A. Kakinen, T.P. Davis, S. Lin, J. Liu, F. Ding, and P. Ke, “Graphene Quantum Dots against Human IAPP Aggregation and Toxicity in Vivo”, Nanoscale 10, 19995, DOI: 10.1039/C8NR07180B (2018)

27. A. Faridi,Y. Sun, Y. Okazaki, G. Peng, J. Gao, A. Kakinen, P. Faridi, M. Zhao, I. Javed, A.W. Purcell, T.P. Davis, S. Lin, R. Oda, F. Ding, P. Ke, “Mitigating Human IAPP Amyloidogenesis in Vivo with Chiral Silica Nanoribbons”, Small, 14, 1802825, DOI: 10.1002/smll.201802825 (2018)

26. B. Wang, Y. Sun, T. Davis, P.C. Ke, Y. Wu, and F. Ding, “Understanding the Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations”, ACS Sustainable Chemistry & Engineering, 6 (9),11704–11715, DOI: 10.1021/acssuschemeng.8b01959 , (2018)

25. Pilkington E.P., Gustafsson O.J.R., Xing Y., Hernandez-Fernaud J., Zampronio C., Kakinen A., Faridi A., Ding F., Wilson P., Ke P.C. and Davis T.P., “Profiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide”, ACS Nano, 12, 6066−6078 (2018) DOI: 10.1021/acsnano.8b02346
-Featured as Journal Front Cover .

24. A. Kakinen, J. Adamcik, B. Wang, X. Ge, R. Mezzenga, T.P. Davis, F. Ding, and P. Ke, “Nanoscale inhibition of polymorphic and ambidextrous IAPP amyloid aggregation with small molecules”, Nano Research, 11(7): 3636–3647 (2017)[download]DOI: 10.1007/s12274-017-1930-7

23. I. Javed, Y. Sun, J. Adamcik, B. Wang, A. Kakinen, E. Pilkington, F. Ding, R. Mezzenga, T. Davis, Thomas; P. Ke, “Co-fibrillization of pathogenic and functional amyloid proteins with gold nanoparticles against amyloidogenesis”, Biomacromolecules, in press (2017) DOI: 10.1021/acs.biomac.7b01359

22. E. Pilkington, M. Lai, X. Ge, W. Stanley, B. Wang, M. Wang, A. Kakinen, M. Sani, M. Whittaker, E. Gurzov, F. Ding, J. Quinn, T. Davis, P. Ke, “Star Polymers Reduce IAPP Toxicity via Accelerated Amyloid Aggregation”, Biomacromolecules, in press (2017)

21. J. Yang, B. Wang, Y. You, W. Chang, K. Tang, Y. Wang, W. Zhang, F. Ding, S. Gunasekaran, “Probing the modulated formation of gold nanoparticle-beta lactoglobulin corona complexes and its applications”, Nanoscale, in press (2017) [link]

20. B. Wang, E.H. Pilkington, Y. Sun, T.P. Davis, P.C. Ke and F. Ding, Modulating protein amyloid aggregation with nanomaterials, Environmental Science Nano, in press (2017)

19. N.K. Geitner, W. Zhao, F. Ding, W. Chen, M. R. Wiesner, “Mechanistic Insights from Discrete Molecular Dynamics Simulations of PesticideNanoparticle Interactions”, Environmental Science & Technology, in press (2017) [link]

18. S. Lin, M. Mortimer, R. Chen, A. Kakinen, J.E. Riviere, T.P. Davis, F. Ding,* and P. C. Ke*, “NanoEHS beyond Toxicity – Focusing on Biocorona”, Env. Sci. Nano, in press (2017) [link]

17. Pilkington E.H., Xing Y., Wang B., Kakinen A., Wang M., Davis T.P., Ding F., Ke P.C., “Effects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity”, Scientific Reports, in press (2017)

16. B. Wang,T. Blin, A. Käkinen, X. Ge, E.H. Pilkington, J.F. Quinn, M.R. Whittaker, T.P. Davis, P.C. Ke and F. Ding, “Brushed polyethylene glycol and phosphorylcholine for grafting nanoparticles against protein binding”, Polymer Chemistry, in press (2016)

15. T. Blin, A. Kakinen, E.H. Pilkington, A. Ivask, F. Ding, J.F. Quinn. M.R. Whittaker, P.C. Ke and T.P. Davis, “Synthesis and In Vitro Properties of Iron Oxide Nanoparticles Grafted with Brushed Phosphorylcholine and Polyethylene Glycol”, Polymer Chemistry, in press (2016)

14. E.N. Gurzov, B. Wang, E.H. Pilkington, P. Chen,A. Kakinen, W.J. Stanley, S.A. Litwak, E.G. Hanssen,T.P. Davis, F. Ding, and P.Chun Ke, “Inhibition of hIAPP Amyloid Aggregation and Pancreatic β-cell Toxicity by OH-terminated PAMAM Dendrimer”, Small, in press (2016)

13. S. Radic, T.P. Davis, P.C. Ke and F. Ding, “Contrasting effects of nanoparticle-protein attraction on amyloid aggregation”, RSC Advances, in press (2015)

12. P. Nedumpully-Govindan, E.N. Gurzov, P. Chen, E.H. Pilkington, W.J. Stanley, S.A. Litwak, T.P. Davis, P.C. Ke, and F. Ding, “Graphene Oxide Inhibits hIAPP Amyloid Fibrillation and Toxicity in Insulin-Producing NIT-1 Cells”, PCCP, in press (2015)

11. Wang B, Geitner NK, Davis TP, Ke PC, Ladner DL and Ding F, “Deviation from the Unimolecular Micelle Paradigm of PAMAM Dendrimers Induced by Strong Inter-Ligand Interactions”, Journal of Physical Chemistry C, in press (2015)

10. Ge XW, Ke PC, Davis TP and Ding F, “A Thermodynamics Model for the Emergence of a Stripe-like Binary SAM on a Nanoparticle Surface”, Small, in press (2015)

9. DeFever R., Geitner N., Bhattacharya P., Ding F., Ke P.C., Sarupria S., “PAMAM dendrimers and graphene: Materials for removing aromatic contaminants from water”, Environmental Science & Technology, in press (2015)

8. Geitner N., Wang B., Andorfer R.; Ladner D.; Ke P.K.; Ding F., “The structure-function relationship of PAMAM dendrimers as robust oil dispersants”, Environmental Science & Technology, 48(21):12868-75, (2014)

7. Wang B., Seabrook S.A., Nedumpully-Govindan P., Chen P., Yin H., Waddington L., Epa V.C., Winkler D.A., Kirby J.K., Ding F., Ke P.C., “Thermostability and Reversibility of Silver Nanoparticle-Protein Binding”, Physical Chemistry Chemical Physics, in press (2014)

6. S. Radic, P. Nedumpully-Govindan,R. Chen, E. Salonen, J.M. Brown, P.C. Ke, and F. Ding, “Effect of Fullerenol Surface Chemistry on Nanoparticle Binding-induced Protein Misfolding”, Nanoscale, in press (2014)

5. Y. Wen, N.K. Geitner, R. Chen, F. Ding, P. Chen, R.E. Andorfer, P.N. Govindan, and P.C. Ke, Binding of Cytoskeletal Proteins with Silver Nanoparticles, RSC Adcances, in press, (2013).

4. EE. Salonen, F. Ding, and P.C. Ke, “Fate, behavior and biophysical modeling of nanoparticles in living systems” in “Engineered Nanoparticles and the Environment: Biophysicochemical Processes and Toxicity”, Edited by B. Xing, C.D. Vecitis, & N. Senesi, Wiley-IUPAC (2016) [download]

3. A. Kakinen, F. Ding, P. Chen, A. Kahru*, and P.C. Ke, “Interaction of Silver Nanoparticles and Firefly Luciferase and Its Impact on Enzyme Luminescence”, Nanotechnology, in press. (2013)

2. S. Radic, N. Geitner, R. Podila, A. Kakinen, P. Chen, P.C. Ke*, and F. Ding*, “Competitive Binding of Natural Amphiphiles with Graphene Derivatives”, Scientific Reports, in press. (2013)

1. F. Ding*, S. Radic, R. Chen, P. Chen, J.M. Brown and P.C. Ke*, “Direct observation of silver nanoparticle-ubiquitin corona formation”, Nanoscale, in press (2012)