{"id":298,"date":"2021-04-18T17:35:23","date_gmt":"2021-04-18T17:35:23","guid":{"rendered":"http:\/\/dlab.clemson.edu\/?p=298"},"modified":"2025-04-28T01:02:50","modified_gmt":"2025-04-28T01:02:50","slug":"protein-folding-misfolding-and-aggregation","status":"publish","type":"post","link":"https:\/\/dlab.clemson.edu\/?p=298","title":{"rendered":"Protein folding, misfolding and aggregation"},"content":{"rendered":"

\"\"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. <\/span>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\u2019, Parkinson\u2019s, Lou Gehrig\u2019s 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.<\/p>\n

 <\/p>\n

78. H. Tang, N. Andrikopoulos, Y. Li, S. Ke, Y. Sun*, F. Ding*, P.C. Ke*, \u201cEmerging biophysical origins and pathogenic implications of amyloid oligomers\u201d, Nature Communications, 16: 2937 (2025) doi: 10.1038\/s41467-025-58335-y<\/p>\n

77. A. Gatch, F. Ding, \u201cCross-interaction with amyloid-\u03b2 drives pathogenic structural transformation within the amyloidogenic core region of TDP-43\u201d, ACS Chemical Neuroscience, 16(8): 1565\u20131581, (2025) doi: 10.1021\/acschemneuro.5c00084<\/p>\n

76. H. Xu, X. Zhang, Z. Lv, F. Huang, Y. Zou, C. Wang, F. Ding*, and Y. Sun*, \u201cComputational exploration of the self-aggregation mechanisms of phenol-soluble modulins \u03b21 and \u03b22 in Staphylococcus aureus biofilms\u201d, Colloids Surf B Biointerfaces, 248: 114498 (2025) doi: 10.1016\/j.colsurfb.2025.114498<\/p>\n

75. F. Huang, X, Fan, H. Xu, Z. Lv, Y. Zou, J. Lian, F. Ding*, Y. Sun*, \u201cComputational insights into the aggregation mechanism of human calcitonin\u201d, International Journal of Biological Macromolecules (Elsevier), 294: 139520 (2025) doi: 10.1016\/j.ijbiomac.2025.139520<\/p>\n

74. F. Huang, J. Yan, H. Xu, Y. Wang, X. Zhang, Y. Zou, J. Lian, F. Ding, Y. Sun, \u201cExploring the Impact of Physiological C-Terminal Truncation on \u03b1-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation\u201d, JCIM, 64(22): 8616\u20138627 (2024) doi: 10.1021\/acs.jcim.4c01839<\/p>\n

73. G. Huang, Z. Song, Y. Xu, Y. Sun, F. Ding, \u201cDeciphering the Morphological Difference of Amyloid-\u03b2 Fibrils in Familial and Sporadic Alzheimer\u2019s Diseases\u201d, JCIM, 64(20): 8024\u20138033 (2024) doi: 10.1021\/acs.jcim.4c01471<\/p>\n

72. H. Tang, Y. Sun, L. Wang, P.C. Ke, F. Ding, \u201cUncovering intermolecular interactions driving the liquid-liquid phase separation of TDP-43 low complexity domain via atomistic dimerization simulations\u201d, JCIM, 64(19):7590-7601 (2024) doi:10.1021\/acs.jcim.4c00943<\/p>\n

71. F. Huang, J. Yan, X. Zhang, H. Xu, J. Lian, X. Yang, C. Wang*, F. Ding*, Y. Sun*, \u201cComputational Insights into the Aggregation Mechanism and Amyloidogenic Core of Aortic Amyloid Medin Polypeptide\u201d, Colloids and Surfaces B: Biointerfaces, 244: 114192(2024) doi:10.1016\/j.colsurfb.2024.114192<\/p>\n

70. Z. Song, H. Tang, A. Gatch, Y. Sun and Feng Ding, \u201cIslet Amyloid Polypeptide Fibril Catalyzes Amyloid-\u03b2 Aggregation by Promoting Fibril Nucleation Rather than Direct Axial Growth\u201d, International Journal of Biological Macromolecules (Elsevier), 279(1): 135137 (2024) doi: 10.1016\/j.ijbiomac.2024.135137<\/p>\n

69. A. Gatch and F. Ding, \u201cTDP-43 Promotes Amyloid-beta Toxicity by Delaying Fibril Maturation via Direct Molecular Interaction\u201d, ACS Chemical Neuroscience, 15(15): 2936\u20132953 (2024) doi: 10.1021\/acschemneuro.4c00334<\/p>\n

68. X. Fan, X. Zhang, J. Yan, H. Xu, W. Zhao, F. Ding*, F. Huang*, Y. Sun*, \u201cComputational Investigation of Co-Aggregation and Cross-Seeding between A\u03b2 and hIAPP Underpinning the Crosstalk in Alzheimer\u2019s Disease and Type-2 Diabetes\u201d, J. Chem. Inf. Model., 64(13): 5303\u20135316 (2024) doi:10.1021\/acs.jcim.4c00859<\/p>\n

67. F. Huang, J. Huang, J. Yan, Y. Liu, J. Lian, Q. Sun, F. Ding, Y. Sun,\u201dMolecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin\u201d, J. Chem. Inf. Model., 64, 11, 4500\u20134510 (2024) doi:10.1021\/acs.jcim.4c00553<\/p>\n

66. F. Huang, X. Fan, Y. Wang, Y. Zou, J. Lian, C. Wang, F. Ding*, Y. Sun*, \u201cComputational insights into the cross-talk between medin and A\u03b2: implications for age-related vascular risk factors in Alzheimer\u2019s disease\u201d, Brief. Bioinform.,25(2):bbad526 (2024) doi:10.1093\/bib\/bbad526<\/p>\n

65. Y. Li, N. Ni, M. Lee, W. Wei, N. Andrikopoulos, A. Kakinen, T. P. Davis, Y. Song*, F. Ding*, D. T. Leong* and P. Ke*, \u201cEndothelial leakiness elicited by amyloid protein aggregation\u201d, Nature Communications,15, Article number: 613 (2024) doi:10.1038\/s41467-024-44814-1<\/p>\n

64. J. Yan, Y. Wang, X. Fan, Y. Zou, F. Ding*, F. Huang*, Y. Sun*, \u201cDeciphering the influence of Y12L and N17H substitutions on the conformation and oligomerization of human calcitonin\u201d, Soft Matter, 20:693-703 (2024) doi:10.1039\/d3sm01332d<\/p>\n

63. F. Huang, Y. Liu, Y. Wang, J. Xu, J. Lian, Y. Zou, C. Wang*, F. Ding* and Y. Sun*, \u201cCo-aggregation of \u03b1-synuclein with Amyloid-\u03b2 Stabilizes \u03b2-sheet-rich Oligomers and Enhances the Formation of \u03b2-barrels\u201d, Physical Chemistry Chemical Physics, 25(46): 31604-31614 (2023) doi:10.1039\/D3CP04138G<\/p>\n

62. F. Huang, X. Fan, Y. Wang, C. Wang, Y. Zou, J. Lian*, F. Ding*, Y. Sun*, \u201cUnveiling Medin Folding and Dimerization Dynamics and Conformations via Atomistic Discrete Molecular Dynamics Simulations\u201d, Journal of Chemical Information and Modeling, 63(20): 6376\u20136385 (2023) doi: 10.1021\/acs.jcim.3c01267<\/p>\n

61. G. Huang, H. Tang, Y. Liu, C. Zhang, P. C. Ke, Y. Sun, F. Ding, \u201cDirect Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth\u201d, Journal of Chemical Information and Modeling, (63)18: 5863\u20135873 (2023) doi: 10.1021\/acs.jcim.3c00898<\/p>\n

60. S. Cao, Z. Song, J. Rong, N. Andrikopoulos, X. Liang, Y. Wang, G. Peng*, F. Ding*, P. C. Ke*, Spike Protein Fragments Promote Alzheimers Amyloidogenesis, ACS Applied Materials & Interfaces, 15(34): 40317\u201340329 (2023) doi: 10.1021\/acsami.3c09815<\/p>\n

59. Z. Zhang, G. Huang, Z. Song, A.J. Gatch, F. Ding , \u201cAmyloid Aggregation and Liquid-Liquid Phase Separation from the Perspective of Phase Transitions\u201d, J. Phys. Chem. B, 127(28): 6241\u20136250 (2023) doi: 10.1021\/acs.jpcb.3c01426<\/p>\n

58. Huang F., Wang Y., Zhang Y., Wang C., Lian J., Ding F.*, Sun Y.*, \u201cDissecting the Self-assembly Dynamics of Imperfect Repeats in \u03b1-Synuclein\u201d, Journal of Chemical Information and Modeling, 63(11):3591-3600 (2023) doi: 10.1021\/acs.jcim.3c00533<\/p>\n

57. Song Z., Gatch A.J., Sun, Y. and Ding, F., \u201cDifferential binding and conformational dynamics of tau microtubule-binding repeats with a preformed amyloid-\u03b2 fibril seed\u201d, ACS Chemical Neuroscience, 14(7):1321-1330 (2023) doi: 10.1021\/acschemneuro.3c00014<\/p>\n

56. Y. Liu, Y. Wang, Y. Zhang, Y. Zou, G. Wei, F. Ding* and Y. Sun*, \u201cStructural perturbation of monomers determines the amyloid aggregation propensity of calcitonin variants\u201d, Journal of Chemical Information and Modeling, 63, 1, 308\u2013320 doi:10.1021\/acs.jcim.2c01202:(2023)<\/p>\n

55. Y. Zhang, Y. Wang, Y. Liu, G. Wei, F. Ding, Y. Sun, \u201cMolecular Insights into the Misfolding and Dimerization Dynamics of the Full-length \u03b1-synuclein from Atomistic Discrete Molecular Dynamics Simulations\u201d, ACS Chemical Neuroscience, 13, 21, 3126\u20133137 doi:10.1021\/acschemneuro.2c00531(2022)<\/p>\n

54. Y. Xing, N. Andrikopoulos, Z. Zhang, Y. Sun, P.C. Ke, F. Ding, \u201cModulating nanodroplet formation en route to fibrillization of amyloid peptides with designed flanking sequences\u201d, Biomacromolecules, 23(10):4179-4191, doi:10.1021\/acs.biomac.2c00642 (2022)<\/p>\n

53. Y. Wang, Y. Liu, Y. Zhang, G. Wei, F. Ding, Y. Sun, \u201cMolecular Insights into the Oligomerization Dynamics and Conformations of Amyloidogenic and Non-Amyloidogenic Amylin from Discrete Molecular Dynamics Simulations\u201d, Physical Chemistry Chemical Physics, 24, 21773-21785, doi:10.1039\/D2CP02851D (2022)<\/p>\n

52. Y. Liu, Y. Wang, C. Tong, G. Wei, F. Ding*, Y. Sun*, \u201cMolecular Insights into the Self-assembly of Block Copolymer Suckerin Polypeptides into Nanoconfined \u03b2-sheets\u201d, Small, in press, doi: 10.1002\/smll.202202642 (2022)<\/p>\n

51. H. Tang, Y. Li, A. Kakinen, N. Andrikopoulos, Y. Sun, E. Kwak, T. P. Davis, F. Ding* and P. C. Ke*, \u201cGraphene Quantum Dots Obstruct the Membrane Axis of Alzheimer\u2019s Amyloid Beta\u201d, Physical Chemistry Chemical Physics, 24, 86-97 (2022) doi: 10.1039\/D1CP04246G<\/p>\n

50. Y. Liu, Y. Zhang, Y. Sun and F. Ding, \u201cA Buried Glutamate in the Cross-\u03b2 Core Renders \u03b2-endorphin Fibrils Reversible\u201d, Nanoscale, 13, 19593-19603 (2021) doi:10.1039\/D1NR05679D<\/p>\n

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*, \u201cInhibition of Amyloid Aggregation and Toxicity with Janus Iron Oxide Nanoparticles\u201d, Chem. Mater., 33, 16, 6484\u20136500 (2021) doi: 10.1021\/acs.chemmater.1c01947<\/p>\n

48. H. He, Y. Liu, Y. Sun, F. Ding, \u201cThe Misfolding and Self-assembly Dynamics of Microtubule-binding Repeats of the Alzheimer-related Protein Tau\u201d, J. Chem. Info. Model, 61(6): 2916\u20132925 (2021) doi: 10.1021\/acs.jcim.1c00217<\/p>\n

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, \u201cSpontaneous Formation of \u03b2-sheet Nano-barrels during the Early Aggregation of Alzheimer\u2019s Amyloid Beta\u201d, Nano Today, 38, 101125 (2021) doi: 10.1016\/j.nantod.2021.101125<\/p>\n

46. Y. Sun, J. Huang, X. Duan and F. Ding, \u201cDirect Observation of \u03b2-barrel Intermediates in the Self-assembly of Toxic SOD128-38 and Absence in Non-toxic Glycine Mutants\u201d, J. Chem. Info. Model, 61, 2, 966\u2013975 (2021) doi: 10.1021\/acs.jcim.0c01319<\/p>\n

45. Y. Xing, A. Nandakumar, A. Kakinen, Y. Sun, T.P. Davis, P. C. Ke, and F. Ding, \u201cAmyloid Aggregation under the Lens of Liquid-Liquid Phase Separation\u201d, J. Phys. Chem. Lett., 12, XXX, 368\u2013378 (2021)doi: doi.org\/10.1021\/acs.jpclett.0c02567<\/p>\n

44. Chen P, Ding F, Cai R, Javed I, Yang W, Zhang Z, Li Y, Davis TP, Ke PC, Chen C., \u201cAmyloidosis Inhibition, a New Frontier of the Protein Corona\u201d, Nano Today, 35:100937 (2020) doi: 10.1016\/j.nantod.2020.100937<\/p>\n

43. Y. Sun, F. Ding, \u201c\u03b1B-Crystallin Chaperone Inhibits A\u03b2 Aggregation by Capping the \u03b2-Sheet-Rich Oligomers and Fibrils\u201d, J. Phys. Chem. B, 124:10138-10146 (2020) doi: 10.1021\/acs.jpcb.0c07256.<\/p>\n

42. I Javed,Z Zhang, J Adamcik, N Andrikopoulos, Y Li, DE Otzen, S Lin, R Mezzenga, TP Davis, F Ding* and P Ke*, \u201cAccelerated Amyloid Beta Pathogenesis by Bacterial Amyloid FapC\u201d, Advanced Science, 7, 2001299 (2020) doi: doi.org\/10.1002\/advs.202001299
\n\u2013 Featured as the Cover.<\/p>\n

41. Koppel K, Tang H, Javed I, Parsa M, Mortimer M, Davis TP, Lin S, Chaffee AL, Ding F and Ke P, \u201cElevated Amyloidoses of Human IAPP and Amyloid Beta by Lipopolysaccharide and Their Mitigation by Carbon Quantum Dots\u201d, Nanoscale, in press (2020)<\/p>\n

40. Y. Sun, F. Ding, \u201cThermo- and pH-Responsive Fibrillization of Squid Suckerin A1H1 Peptide\u201d, Nanoscale, in press (2020) DOI: 10.1039\/C9NR09271D<\/p>\n

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*, \u201cGraphene quantum dots rescue protein dysregulation of pancreatic \u03b2-cells exposed to human islet amyloid polypeptide\u201d, Nano Research, in press (2019)<\/p>\n

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*, \u201cSingle-molecular hetero-amyloidosis of human islet amyloid polypeptide\u201d, Nano Lett, in press, (2019) Just Accepted<\/p>\n

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*, \u201cInhibition of Amyloid Beta Toxicity in Zebrafish with A Chaperone-Gold Nanoparticle Dual Strategy\u201d, Nature Commun, in press (2019)<\/p>\n

36. Y. Sun, A. Kakinen, C. Zhang, Y. Yang, A. Faridi, T. P. Davis, W. Cao, P. C. Ke and F. Ding, \u201cAmphiphilic Surface Chemistry of Fullerenols Is Necessary for Inhibiting the Amyloid Aggregation of Alpha-Synuclein NACore\u201d, Nanoscale, in press, (2019)<\/p>\n

35. P. C. Ke, E. H. Pilkington, Y. Sun, I. Javed, A. Kakinen, G. Peng, F. Ding, . P. Davisa, \u201cMitigation of Amyloidosis with Nanomaterials\u201d, Advanced Materials, in press, (2019)<\/p>\n

34. Y. Sun, A. Kakinen, Y. Xing, P. Faridi, A. Nandakumar, A.W. Purcell, T.P. Davis, P. Ke, and F. Ding, \u201cAmyloid self-assembly of hIAPP8-20 via the accumulation of helical oligomers, alpha-helix to beta-sheet transition, and formation of beta-barrel intermediates\u201d, Small, in press, (2019)<\/p>\n

33. Y. Sun, A. Kakinen, Y. Xing, E.H. Pilkington, T.P. Davis, P. Ke, & F. Ding, \u201cNucleation of \u03b2-rich Oligomers and \u03b2-barrels in the Early Aggregation of Human Islet Amyloid Polypeptide\u201d, BBA-Molecular Basis of Disease, 1865 (2), 434-444, DOI: 10.1016\/j.bbadis.2018.11.021 <\/a> (2019)<\/p>\n

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, \u201cPhysical and Toxicological Profiles of Human IAPP Amyloids and Plaques\u201d, Science Bulletin, in press, DOI: 10.1016\/j.scib.2018.11.012<\/a> (2018)<\/p>\n

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, \u201cGraphene Quantum Dots against Human IAPP Aggregation and Toxicity in Vivo\u201d, Nanoscale 10, 19995, DOI: 10.1039\/C8NR07180B <\/a> (2018)<\/p>\n

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, \u201cMitigating Human IAPP Amyloidogenesis in Vivo with Chiral Silica Nanoribbons\u201d, Small, 14, 1802825, DOI: 10.1002\/smll.201802825 <\/a>(2018)<\/p>\n

29. Y. Sun, X. Ge , Y. Xing, Bo Wang, and F. Ding, \u201c\u03b2-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-\u03b2 Aggregates\u201d, Scientific Reports 8: 10353, DOI: 10.1038\/s41598-018-28649-7<\/a> (2018)<\/p>\n

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., \u201cProfiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide\u201d, ACS Nano, in press (2018)<\/p>\n

27. X. Ge., Y. Sun and F. Ding, \u201cStructures and Dynamics of \u03b2-barrel Oligomer Intermediates of Amyloid-beta16-22 Aggregation\u201d, BBA Biomembranes, in press (2018)<\/p>\n

26. X. Ge., Y. Yang, Y. Sun, W. Cao and F. Ding, \u201cIslet Amyloid Polypeptide Promotes Amyloid-beta Aggregation by Binding-induced Helix- unfolding of the Amyloidogenic Core\u201d, ACS Chem. Neurosci., in press (2018)<\/p>\n

25. Y. Sun, B. Wang, X. Ge and F. Ding, \u201cDistinct Oligomerization and Fibrillization Dynamics of Amyloid Core Sequences of Amyloid-beta and Islet Amyloid Polypeptide\u201d, PCCP, in press (2017)<\/p>\n

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)<\/p>\n

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)<\/p>\n

22. Pilkington E.H., Xing Y., Wang B., Kakinen A., Wang M., Davis T.P., Ding F., Ke P.C., \u201cEffects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity\u201d, Scientific Reports, in press (2017)<\/p>\n

21. Hadi-Alijanvand, H., Proctor, E. A., Ding, F., Dokholyan, N. V. and Moosavi-Movahedi, A. A. \u201cA Hidden Aggregation-Prone Structure in the Heart of Hypoxia Inducible Factor Prolyl Hydroxylase\u201d, Proteins: Structure, Function and Bioinformatics, in press, (2016)<\/p>\n

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, \u201cInhibition of hIAPP Amyloid Aggregation and Pancreatic \u03b2-cell Toxicity by OH-terminated PAMAM Dendrimer\u201d, Small, in press (2016)<\/p>\n

19. S. Radic, T.P. Davis, P.C. Ke and F. Ding, \u201cContrasting effects of nanoparticle-protein attraction on amyloid aggregation\u201d, RSC Advances, in press (2015)<\/p>\n

18. P. Nedumpully-Govindan, A. Kakinen, E.H. Pilkington, T.P. Davis, P.C. Ke and F. Ding, \u201cStabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition\u201d, Scientific Reports, in press (2015)<\/p>\n

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, \u201cGraphene Oxide Inhibits hIAPP Amyloid Fibrillation and Toxicity in Insulin-Producing NIT-1 Cells\u201d, PCCP, in press (2015)<\/p>\n

16. S. Radic, T.P. Davis, P.C. Ke and F. Ding, \u201cContrasting effects of nanoparticle-protein attraction on amyloid aggregation\u201d, RSC Advances, in press (2015)<\/p>\n

15. Nedumpully-Govindan P. and Ding F., \u201cInhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration\u201d, Scientific Reports, in press (2015)<\/p>\n

14. F. Ding, Y. Furukawa, N. Nukina, and Dokholyan, N.V., \u201cLocal unfolding of Cu, Zn superoxide Dismutase monomer determines the morphology of fibrillar aggregates\u201d, Journal of Molecular Biology, 421:548-560 (2012) [download]<\/a><\/p>\n

13. Proctor, E. A., F. Ding, and Dokholyan, N. V. \u201cStructural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase\u201d, Journal of Molecular Biology, 408:555-567 (2011). [download]<\/a><\/p>\n

12. V. V. Lakhani, F. Ding and N. V. Dokholyan, \u201cPoly-glutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences\u201d Public Library of Science Computational Biology:e1000772 (2010) [download]<\/a><\/p>\n

11. F. Ding and N. V. Dokholyan, \u201cDynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation\u201d Proceedings of the National Academy of Sciences USA, 105:19696-19701 (2008) [download]<\/a><\/p>\n

10. S. Sharma, F. Ding, and N. V. Dokholyan, \u201cProbing protein aggregation using simplified models and discrete molecular dynamics\u201d Frontiers in Bioscience, 13: 4795-4808 (2008) [download]<\/a><\/p>\n

9. S. Barton, R. Jacak, S. D. Khare, F. Ding*, and N. V. Dokholyan*, \u201cThe length dependence of the polyQ-mediated protein aggregation\u201d Journal of Biological Chemistry, 282: 25487-25492 (2007)[download]<\/a><\/p>\n

8. F. Ding, K. C. Prutzman, S. L. Campbell, and N. V. Dokholyan, \u201cTopological determinants of protein domain swapping\u201d, Structure, 14: 5-14 (2005). [download]<\/a><\/a>[service]<\/a><\/p>\n

7. F. Ding, J. J. LaRocque, and N. V. Dokholyan, \u201cDirect observation of protein folding, aggregation and a prion-like conformational transition\u201d, Journal of Biological Chemistry, 280: 40235-40240 (2005)[download]<\/a><\/p>\n

6. S. D. Khare, F. Ding, K. N. Gwanmesia, and N. V. Dokholyan, \u201cMolecular origin of polyglutamine-mediated protein aggregation in neurodegenerative diseases\u201d, PLoS Computational Biology, 1, e30 (2005). [download]<\/a><\/p>\n

5. B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, \u201cMolecular dynamics simulation of Amyloid beta dimer formation\u201d Biophys. J., 87: 2310-2321 (2004). [download]<\/a><\/p>\n

4. S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz , H. E. Stanley, and N. V. Dokholyan, \u201cDiscrete molecular dynamics simulations of peptide aggregation\u201d Phys. Rev. E 69: 041908 (2004)[download]<\/a><\/p>\n

3. S. D. Khare, F. Ding and N. V. Dokholyan, \u201cFolding of Cu,Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis.\u201d J. Mol. Biol, 334, 515-525, 2003[download]<\/a><\/p>\n

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]<\/a><\/p>\n

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]<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

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 … <\/p>\n

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