Protein folding, misfolding and aggregation

Most proteins fold into specific three-dimensional structures, which determine their functions. The folding process can be described by the free energy landscape as in a first order phase transition. The native state features the lowest free energy and correspond to the most stable and most populated species in physiological conditions. However, due to either environmental changes or mutations, the native states are destabilized. The intermediate(s) and unfolded states are promoted, where protein exposes their hydrophobic core and un-satisfied hydrogen bond donors and acceptors. These non-native species are sticky in nature and tends to aggregate under high concentrations. The aggregation is a nucleation process, and the final aggregates can adopt a fibrillar shape depending on the structural and dynamical properties of the aggregation precursor species. For a long time, the fibrillar aggregation, a.k.a. amyloid fibrils, has been thought to cause a long list of amyloid diseases, including Alzheimers’, Parkinson’s, Lou Gehrig’s diseases. Recent experiments have suggested that the smaller, soluble oligomers are more toxic to cells. We are applying computational modeling approaches to uncover the molecular mechanism of misfolding, to determine  driving forces underlying aggregation, to characterize structures of the oligomers and fibril aggregates, and to design therapeutics against aggregation.

52. Y. Liu, Y. Wang, C. Tong, G. Wei, F. Ding*, Y. Sun*, “Molecular Insights into the Self-assembly of Block Copolymer Suckerin Polypeptides into Nanoconfined β-sheets”, Small, in press, doi: 10.1002/smll.202202642 (2022)

51. H. Tang, Y. Li, A. Kakinen, N. Andrikopoulos, Y. Sun, E. Kwak, T. P. Davis, F. Ding* and P. C. Ke*, “Graphene Quantum Dots Obstruct the Membrane Axis of Alzheimer’s Amyloid Beta”, Physical Chemistry Chemical Physics, 24, 86-97 (2022) doi: 10.1039/D1CP04246G

50. Y. Liu, Y. Zhang, Y. Sun and F. Ding, “A Buried Glutamate in the Cross-β Core Renders β-endorphin Fibrils Reversible”, Nanoscale, 13, 19593-19603 (2021) doi:10.1039/D1NR05679D

49. N. Andrikopoulos, Z. Song, X. Wan, A. Douek, I. Javed, C. Fu, X. Changkui, Y. Xing, F. Xin, Y. Li, A. Kakinen, K. Koppel, R. Qiao, A. Whittaker, J. Kaslin, T. Davis*, Y. Song*, F. Ding*, P.C. Ke*, “Inhibition of Amyloid Aggregation and Toxicity with Janus Iron Oxide Nanoparticles”, Chem. Mater., 33, 16, 6484–6500 (2021) doi: 10.1021/acs.chemmater.1c01947

48. H. He, Y. Liu, Y. Sun, F. Ding, “The Misfolding and Self-assembly Dynamics of Microtubule-binding Repeats of the Alzheimer-related Protein Tau”, J. Chem. Info. Model, 61(6): 2916–2925 (2021) doi: 10.1021/acs.jcim.1c00217

47. Y. Sun, A. Kakinen, X. Wan, N. Moriarty, C.P.J. Hunt, Y. Li, N. Andrikopoulos, A. Nandakumar, T.P. Davis, C.L. Parish, Y. Song, P. C. Ke and F. Ding, “Spontaneous Formation of β-sheet Nano-barrels during the Early Aggregation of Alzheimer’s Amyloid Beta”, Nano Today, 38, 101125 (2021) doi: 10.1016/j.nantod.2021.101125

46. Y. Sun, J. Huang, X. Duan and F. Ding, “Direct Observation of β-barrel Intermediates in the Self-assembly of Toxic SOD128-38 and Absence in Non-toxic Glycine Mutants”, J. Chem. Info. Model, 61, 2, 966–975 (2021) doi: 10.1021/acs.jcim.0c01319

45. Y. Xing, A. Nandakumar, A. Kakinen, Y. Sun, T.P. Davis, P. C. Ke, and F. Ding, “Amyloid Aggregation under the Lens of Liquid-Liquid Phase Separation”, J. Phys. Chem. Lett., 12, XXX, 368–378 (2021)doi:

44. Chen P, Ding F, Cai R, Javed I, Yang W, Zhang Z, Li Y, Davis TP, Ke PC, Chen C., “Amyloidosis Inhibition, a New Frontier of the Protein Corona”, Nano Today, 35:100937 (2020) doi: 10.1016/j.nantod.2020.100937

43. Y. Sun, F. Ding, “αB-Crystallin Chaperone Inhibits Aβ Aggregation by Capping the β-Sheet-Rich Oligomers and Fibrils”, J. Phys. Chem. B, 124:10138-10146 (2020) doi: 10.1021/acs.jpcb.0c07256.

42. I Javed,Z Zhang, J Adamcik, N Andrikopoulos, Y Li, DE Otzen, S Lin, R Mezzenga, TP Davis, F Ding* and P Ke*, “Accelerated Amyloid Beta Pathogenesis by Bacterial Amyloid FapC”, Advanced Science, 7, 2001299 (2020) doi:
– Featured as the Cover.

41. 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)

40. Y. Sun, F. Ding, “Thermo- and pH-Responsive Fibrillization of Squid Suckerin A1H1 Peptide”, Nanoscale, in press (2020) DOI: 10.1039/C9NR09271D

39. 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)

38. A Kakinen, Y Xing, NDH Arachchi, I Javed, L Feng, A Faridi, AM Douek, Y Sun, J Kaslin, TP Davis*, MJ Higgins*, F Ding*, and P Ke*, “Single-molecular hetero-amyloidosis of human islet amyloid polypeptide”, Nano Lett, in press, (2019) Just Accepted

37. 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)

36. 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)

35. 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)

34. Y. Sun, A. Kakinen, Y. Xing, P. Faridi, A. Nandakumar, A.W. Purcell, T.P. Davis, P. Ke, and F. Ding, “Amyloid self-assembly of hIAPP8-20 via the accumulation of helical oligomers, alpha-helix to beta-sheet transition, and formation of beta-barrel intermediates”, Small, in press, (2019)

33. Y. Sun, A. Kakinen, Y. Xing, E.H. Pilkington, T.P. Davis, P. Ke, & F. Ding, “Nucleation of β-rich Oligomers and β-barrels in the Early Aggregation of Human Islet Amyloid Polypeptide”, BBA-Molecular Basis of Disease, 1865 (2), 434-444, DOI: 10.1016/j.bbadis.2018.11.021 (2019)

32. A. Kakinen, Y. Sun, I. Javed, A. Faridi, E.H. Pilkington, P. Faridi, A.W. Purcell, R. Zhou, F. Ding, S. Lin, P. Ke, and T. P. Davis, “Physical and Toxicological Profiles of Human IAPP Amyloids and Plaques”, Science Bulletin, in press, DOI: 10.1016/j.scib.2018.11.012 (2018)

31. 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)

30. 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)

29. Y. Sun, X. Ge , Y. Xing, Bo Wang, and F. Ding, “β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates”, Scientific Reports 8: 10353, DOI: 10.1038/s41598-018-28649-7 (2018)

28. 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, in press (2018)

27. X. Ge., Y. Sun and F. Ding, “Structures and Dynamics of β-barrel Oligomer Intermediates of Amyloid-beta16-22 Aggregation”, BBA Biomembranes, in press (2018)

26. X. Ge., Y. Yang, Y. Sun, W. Cao and F. Ding, “Islet Amyloid Polypeptide Promotes Amyloid-beta Aggregation by Binding-induced Helix- unfolding of the Amyloidogenic Core”, ACS Chem. Neurosci., in press (2018)

25. Y. Sun, B. Wang, X. Ge and F. Ding, “Distinct Oligomerization and Fibrillization Dynamics of Amyloid Core Sequences of Amyloid-beta and Islet Amyloid Polypeptide”, PCCP, in press (2017)

24. 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)

23. P.C. Ke, M. Sani, F. Ding, A. Kakinen, I. Javed, F. Separovic, T. P. Davis, and R. Mezzenga, Implications of Peptide Assemblies in Amyloid Diseases, Chem. Soc. Rev., in press (2017)

22. 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)

21. Hadi-Alijanvand, H., Proctor, E. A., Ding, F., Dokholyan, N. V. and Moosavi-Movahedi, A. A. “A Hidden Aggregation-Prone Structure in the Heart of Hypoxia Inducible Factor Prolyl Hydroxylase”, Proteins: Structure, Function and Bioinformatics, in press, (2016)

20. 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)

19. 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)

18. P. Nedumpully-Govindan, A. Kakinen, E.H. Pilkington, T.P. Davis, P.C. Ke and F. Ding, “Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition”, Scientific Reports, in press (2015)

17. 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)

16. 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)

15. Nedumpully-Govindan P. and Ding F., “Inhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration”, Scientific Reports, in press (2015)

14. F. Ding, Y. Furukawa, N. Nukina, and Dokholyan, N.V., “Local unfolding of Cu, Zn superoxide Dismutase monomer determines the morphology of fibrillar aggregates”, Journal of Molecular Biology, 421:548-560 (2012) [download]

13. Proctor, E. A., F. Ding, and Dokholyan, N. V. “Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase”, Journal of Molecular Biology, 408:555-567 (2011). [download]

12. V. V. Lakhani, F. Ding and N. V. Dokholyan, “Poly-glutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences” Public Library of Science Computational Biology:e1000772 (2010) [download]

11. F. Ding and N. V. Dokholyan, “Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation” Proceedings of the National Academy of Sciences USA, 105:19696-19701 (2008) [download]

10. S. Sharma, F. Ding, and N. V. Dokholyan, “Probing protein aggregation using simplified models and discrete molecular dynamics” Frontiers in Bioscience, 13: 4795-4808 (2008) [download]

9. S. Barton, R. Jacak, S. D. Khare, F. Ding*, and N. V. Dokholyan*, “The length dependence of the polyQ-mediated protein aggregation” Journal of Biological Chemistry, 282: 25487-25492 (2007)[download]

8. F. Ding, K. C. Prutzman, S. L. Campbell, and N. V. Dokholyan, “Topological determinants of protein domain swapping”, Structure, 14: 5-14 (2005). [download][service]

7. F. Ding, J. J. LaRocque, and N. V. Dokholyan, “Direct observation of protein folding, aggregation and a prion-like conformational transition”, Journal of Biological Chemistry, 280: 40235-40240 (2005)[download]

6. S. D. Khare, F. Ding, K. N. Gwanmesia, and N. V. Dokholyan, “Molecular origin of polyglutamine-mediated protein aggregation in neurodegenerative diseases”, PLoS Computational Biology, 1, e30 (2005). [download]

5. B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, “Molecular dynamics simulation of Amyloid beta dimer formation” Biophys. J., 87: 2310-2321 (2004). [download]

4. S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz , H. E. Stanley, and N. V. Dokholyan, “Discrete molecular dynamics simulations of peptide aggregation” Phys. Rev. E 69: 041908 (2004)[download]

3. S. D. Khare, F. Ding and N. V. Dokholyan, “Folding of Cu,Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis.” J. Mol. Biol, 334, 515-525, 2003[download]

2. F. Ding*, Borreguero J.M., Buldyrev S.V., Stangley H.E. and Dokholyan N.V., A mechanism for alpha-helix to beta-hairpin transition, Proteins: Structure, Function and Genetics, 53:220-228 (2003)[download]

1. F. Ding, Dokholyan N.V., Buldyrev S.V., Stanley H.E. and Shakhnovich E.I. Molecular dynamics simulation of C-Src SH3 aggregation suggests a generic amyloidogenesis mechanism J Mol Biol, 324:851-857 (2002) [download]