References
- Soriaga AB, Sangwan S, MacDonald R, et al. Crystal structures of IAPP amyloidogenic segments reveal a novel packing motif of out-of-register beta sheets. J Phys Chem B [Internet]. 2016;120:5810–5816. [cited 2017 Nov 23]. Available from: http://pubs.acs.org/doi/10.1021/acs.jpcb.5b09981.
- Sun Y, Wang B, Ge X, et al. Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide. Phys Chem Chem Phys. [Internet]. 2017;19:28414–28423. [cited 2017 Nov 23]. Available from: http://xlink.rsc.org/?DOI=C7CP05695H. doi: 10.1039/C7CP05695H
- Sinopoli A, Magrì A, Milardi D, et al. The role of copper(ii) in the aggregation of human amylin. Metallomics. 2014;6:1841–1852. doi: 10.1039/C4MT00130C
- Glabe CG. Common mechanisms of amyloid oligomer pathogenesis in degenerative disease. Neurobiol Aging. 2006;27:570–575. doi: 10.1016/j.neurobiolaging.2005.04.017
- Kayed R, Bernhagen J, Greenfield N, et al. Conformational transitions of islet amyloid polypeptide (IAPP) in amyloid formation in vitro. J Mol Biol. 1999;287:781–796. doi: 10.1006/jmbi.1999.2646
- Macdonald IA. Amylin and the gastrointestinal tract. Diabet Med. 1997;14:S24–S28. doi: 10.1002/(SICI)1096-9136(199706)14:2+<S24::AID-DIA399>3.3.CO;2-D
- Westermark P, Andersson A, Westermark GT. Islet amyloid polypeptide, islet amyloid, and diabetes mellitus. Physiol Rev. 2011;91:795–826. doi: 10.1152/physrev.00042.2009
- Westermark GT, Krogvold L, Dahl-Jørgensen K, et al. Islet amyloid in recent-onset type 1 diabetes—the DiViD study. Ups J Med Sci. [Internet]. 2017;122:201–203. Available from: https://www.tandfonline.com/doi/full/10.1080/03009734.2017.1359219.
- Marzban L, Park K, Verchere CB. Islet amyloid polypeptide and type 2 diabetes. Exp Gerontol. 2003;38:347–351. doi: 10.1016/S0531-5565(03)00004-4
- Hull RL, Westermark GT, Westermark P, et al. Islet amyloid: A critical entity in the pathogenesis of type 2 diabetes. J Clin Endocrinol Metab. 2004;89:3629–3643. doi: 10.1210/jc.2004-0405
- Jaikaran ETAS, Clark A. Islet amyloid and type 2 diabetes: from molecular misfolding to islet pathophysiology. Biochim Biophys Acta - Mol Basis Dis. [Internet]. 2001;1537:179–203. Available from: http://www.sciencedirect.com/science/article/pii/S0925443901000783. doi: 10.1016/S0925-4439(01)00078-3
- Nielsen JT, Bjerring M, Jeppesen MD, et al. Unique identification of supramolecular structures in amyloid fibrils by solid-state NMR spectroscopy. Angew Chemie - Int Ed. 2009;48:2118–2121. doi: 10.1002/anie.200804198
- Luca S, Yau WM, Leapman R, et al. Peptide conformation and supramolecular organization in amylin fibrils: Constraints from solid-state NMR. Biochemistry. 2007;46:13505–13522. doi: 10.1021/bi701427q
- Akter R, Cao P, Noor H, et al. Islet amyloid polypeptide: structure, function, and pathophysiology. J Diabetes Res. [Internet]. 2016;2016:e2798269. [cited 2017 Jan 31]. Available from: https://www.hindawi.com/journals/jdr/2016/2798269/abs/. doi: 10.1155/2016/2798269
- Srinivasan E, Rajasekaran R. Computational investigation of curcumin, a natural polyphenol that inhibits the destabilization and the aggregation of human SOD1 mutant (Ala4Val). RSC Adv. [Internet]. 2016;6:102744–102753. [cited 2017 Nov 24]. Available from: http://pubs.rsc.org/en/Content/ArticleLanding/2016/RA/C6RA21927F. doi: 10.1039/C6RA21927F
- Rigacci S, Guidotti V, Bucciantini M, et al. Aβ(1-42) aggregates into non-toxic amyloid assemblies in the presence of the natural polyphenol oleuropein aglycon. Curr Alzheimer Res. 2011;8:841–852. doi: 10.2174/156720511798192682
- Wobst HJ, Sharma A, Diamond MI, et al. The green tea polyphenol (-)-epigallocatechin gallate prevents the aggregation of tau protein into toxic oligomers at substoichiometric ratios. FEBS Lett. [Internet]. 2015;589:77–83. Available from: http://onlinelibrary.wiley.com/doi/10.1016/j.febslet.2014.11.026/abstract. doi: 10.1016/j.febslet.2014.11.026
- Ip P, Sharda PR, Cunningham A, et al. Quercitrin and quercetin 3-β-d-glucoside as chemical chaperones for the A4V SOD1 ALS-causing mutant. Protein Eng Des Sel. [Internet]. 2017;30:431–440. [cited 2017 Jul 24]. Available from: https://academic.oup.com/peds/article-lookup/doi/10.1093/protein/gzx025.
- Srinivasan E, Rajasekaran R. Probing the inhibitory activity of epigallocatechin-gallate on toxic aggregates of mutant (L84F) SOD1 protein through geometry based sampling and steered molecular dynamics. J Mol Graph Model. 2017;74:288–295. doi: 10.1016/j.jmgm.2017.04.019
- Churches QI, Caine J, Cavanagh K, et al. Naturally occurring polyphenolic inhibitors of amyloid beta aggregation. Bioorganic Med Chem Lett. [Internet]. 2014;24:3108–3112. Available from: https://www.sciencedirect.com/science/article/pii/S0960894X14004958. doi: 10.1016/j.bmcl.2014.05.008
- Caruana M, Högen T, Levin J, et al. Inhibition and disaggregation of α-synuclein oligomers by natural polyphenolic compounds. FEBS Lett. 2011;585:1113–1120. doi: 10.1016/j.febslet.2011.03.046
- Srinivasan E, Rajasekaran R. Comparative binding of kaempferol and kaempferide on inhibiting the aggregate formation of mutant (G85R) SOD1 protein in familial amyotrophic lateral sclerosis: A quantum chemical and molecular mechanics study. BioFactors [Internet]. 2018;44:431–442. [cited 2018 Nov 5]. Available from: http://doi.wiley.com/10.1002/biof.1441.
- Srinivasan E, Rajasekaran R. Quantum chemical and molecular mechanics studies on the assessment of interactions between resveratrol and mutant SOD1 (G93A) protein. J Comput Aided Mol Des. [Internet]. 2018;32(12):1347–1361. [cited 2018 Nov 5]; Available from: http://www.ncbi.nlm.nih.gov/pubmed/30368622. doi: 10.1007/s10822-018-0175-1
- Figueira I, Garcia G, Pimpão RC, et al. Polyphenols journey through blood-brain barrier towards neuronal protection. Sci Rep. [Internet]. 2017;7:11456. [cited 2017 Nov 24]. Available from: https://www.nature.com/articles/s41598-017-11512-6. doi: 10.1038/s41598-017-11512-6
- Vauzour D. Dietary polyphenols as modulators of brain functions: biological actions and molecular mechanisms underpinning their beneficial effects. Oxid Med Cell Longev. [Internet]. 2012;2012:1–16. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372091/. doi: 10.1155/2012/914273
- Guo J, Sun W, Li L, et al. Brazilin inhibits fibrillogenesis of human islet amyloid polypeptide, disassembles mature fibrils, and alleviates cytotoxicity. RSC Adv. [Internet]. 2017;7:43491–43501. [cited 2017 Nov 23]. Available from: http://xlink.rsc.org/?DOI=C7RA05742C. doi: 10.1039/C7RA05742C
- Wang Q, Zhou S, Wei W, et al. Computational insights into the inhibition and destabilization of morin on the oligomer of full-length human islet amyloid polypeptide. Phys Chem Chem Phys. [Internet]. 2015;17:29103–29112. [cited 2016 Aug 18]. Available from: http://xlink.rsc.org/?DOI=C5CP03991F. doi: 10.1039/C5CP03991F
- Nedumpully-Govindan P, Kakinen A, Pilkington EH, et al. Stabilizing off-pathway oligomers by polyphenol nanoassemblies for IAPP aggregation inhibition. Sci Rep. [Internet]. 2016;6:19463. [cited 2016 Feb 8]. Available from: http://www.nature.com/articles/srep19463. doi: 10.1038/srep19463
- Wang Q, Guo J, Jiao P, et al. Exploring the influence of egcg on the b-sheet-rich oligomers of human islet amyloid polypeptide (hiapp and identifying its possible binding sites from molecular dynamics simulation. PLoS One [Internet]. 2014;9:e94796. [cited 2017 Nov 23]. Available from: http://dx.plos.org/10.1371/journal.pone.0094796.
- Wang Q, Ning L, Niu Y, et al. Molecular mechanism of the inhibition and remodeling of human islet amyloid polypeptide (hIAPP1-37) oligomer by resveratrol from molecular dynamics simulation. J Phys Chem B. [Internet]. 2015;119:15–24. [cited 2016 Aug 18]. Available from: http://pubs.acs.org/doi/abs/10.1021/jp507529f.
- Dinda B, Dinda S, DasSharma S, et al. Therapeutic potentials of baicalin and its aglycone, baicalein against inflammatory disorders. Eur J Med Chem. [Internet]. 2017;131:68–80. Available from: http://www.sciencedirect.com/science/article/pii/S0223523417301538. doi: 10.1016/j.ejmech.2017.03.004
- Velander P, Wu L, Ray WK, et al. Amylin amyloid inhibition by Flavonoid baicalein: key roles of Its Vicinal Dihydroxyl groups of the catechol moiety. Biochemistry [Internet]. 2016;55:4255–4258. [cited 2016 Aug 18]. Available from: http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00578.
- Mahalingam R, Peng HP, Yang AS. Prediction of fatty acid-binding residues on protein surfaces with three-dimensional probability distributions of interacting atoms. Biophys Chem. [Internet]. 2014;192:10–19. [cited 2019 Mar 19]. Available from: https://www.sciencedirect.com/science/article/pii/S0022519313005195. doi: 10.1016/j.bpc.2014.05.002
- Rajasekaran M, Chen C. Structural effect of the L16Q, K50E, and R53P mutations on homeodomain of pituitary homeobox protein 2. Int J Biol Macromol. [Internet]. 2012;51:305–313. [cited 2019 Mar 19]. Available from: https://www.sciencedirect.com/science/article/pii/S0141813012001699. doi: 10.1016/j.ijbiomac.2012.05.008
- Srinivasan E, Rajasekaran R. Computational simulation analysis on human SOD1 mutant (H80R) exposes the structural destabilization and the deviation of Zn binding that directs familial amyotrophic lateral sclerosis. J Biomol Struct Dyn. 2017;35:2645–2653. doi: 10.1080/07391102.2016.1227723
- Hess B, Kutzner C, Van Der Spoel D, et al. GRGMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. [Internet]. 2008;4:435–447. [cited 2015 Oct 24]. Available from: http://pubs.acs.org/doi/abs/10.1021/ct700301q.
- Darden T, York D, Pedersen L. Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. J Chem Phys. [Internet]. 1993;98:10089–10092. [cited 2015 Oct 30]. Available from: http://scitation.aip.org/content/aip/journal/jcp/98/12/10.1063/1.464397.
- Kim S, Chen J, Cheng T, et al. Pubchem 2019 update: improved access to chemical data. Nucleic Acids Res. [Internet]. 2019;47:D1102–D1109. [cited 2019 Jul 2]. Available from: http://www.ncbi.nlm.nih.gov/pubmed/30371825. doi: 10.1093/nar/gky1033
- Morris GM, Ruth H, Lindstrom W, et al. Software news and updates AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. [Internet]. 2009;30:2785–2791. [cited 2016 Jan 27]. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760638/. doi: 10.1002/jcc.21256
- Morris GM, Goodsell DS, Halliday RS, et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem. 1998;19:1639–1662. doi: 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
- Fedorov DG, Kitaura K. The importance of three-body terms in the fragment molecular orbital method. J Chem Phys. [Internet]. 2004;120:6832–6840. Available from: http://aip.scitation.org/doi/abs/10.1063/1.1687334.
- Dokholyan NV, Buldyrev SV, Stanley HE, et al. Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des. [Internet]. 1998;3:577–587. [cited 2016 Mar 8]. Available from: http://www.sciencedirect.com/science/article/pii/S1359027898000728. doi: 10.1016/S1359-0278(98)00072-8
- Shirvanyants D, Ding F, Tsao D, et al. Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. J Phys Chem B. [Internet]. 2012;116:8375–8382. doi:10.1021/jp2114576.
- Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins. 1999;35:133–152. doi: 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N
- Ding F, Tsao D, Nie H, et al. Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure [Internet]. 2008;16:1010–1018. [cited 2016 Apr 27] [cited 2016 Mar 8]. Available from: http://www.sciencedirect.com/science/article/pii/S0969212608001780. doi: 10.1016/j.str.2008.03.013
- Andersen HC. Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys. [Internet]. 1980;72:2384–2393. [cited 2016 Jul 10]. Available from: http://scitation.aip.org/content/aip/journal/jcp/72/4/10.1063/1.439486.
- Papaleo E, Mereghetti P, Fantucci P, et al. Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case. J Mol Graph Model. [Internet]. 2009;27:889–899. Available from: http://www.sciencedirect.com/science/article/pii/S1093326309000175. doi: 10.1016/j.jmgm.2009.01.006
- Amadei A, Linssen AB, Berendsen HJ. Essential dynamics of proteins. Proteins. 1993;17(4):412–425. DOI:10.1002/prot.340170408.
- Nahm FS. Nonparametric statistical tests for the continuous data: the basic concept and the practical use. Korean J Anesthesiol. [Internet]. 2016;69:8–14. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754273/. doi: 10.4097/kjae.2016.69.1.8
- Mo Y, Lei J, Sun Y, et al. Conformational ensemble of hIAPP dimer: insight into the molecular mechanism by which a green tea extract inhibits hIAPP aggregation. Sci Rep. 2016;6:33076. DOI:10.1038/srep33076.
- Bhatia NK, Srivastava A, Katyal N, et al. Curcumin binds to the pre-fibrillar aggregates of Cu/Zn superoxide dismutase (SOD1) and alters its amyloidogenic pathway resulting in reduced cytotoxicity. Biochim Biophys Acta - Proteins Proteomics. 2015;1854:426–436. doi: 10.1016/j.bbapap.2015.01.014
- Prudencio M, Hart PJ, Borchelt DR, et al. Variation in aggregation propensities among ALS-associated variants of SOD1: correlation to human disease. Hum Mol Genet. [Internet]. 2009;18:3217–3226. [cited 2016 Feb 1]. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722984/. doi: 10.1093/hmg/ddp260
- Lu J-H, Ardah MT, Durairajan SSK, et al. Baicalein inhibits formation of α-synuclein oligomers within living cells and prevents Aβ peptide fibrillation and oligomerisation. Chembiochem A Eur J Chem Biol. 2011;12:615–624. doi: 10.1002/cbic.201000604
- Zhu M, Rajamani S, Kaylor J, et al. The flavonoid baicalein Inhibits fibrillation of α-Synuclein and disaggregates existing fibrils. J Biol Chem. 2004;279:26846–26857. doi: 10.1074/jbc.M403129200
- Hu Q, Uversky VN, Huang M, et al. Baicalein inhibits α-synuclein oligomer formation and prevents progression of α-synuclein accumulation in a rotenone mouse model of Parkinson’s disease. Biochim Biophys Acta - Mol Basis Dis. [Internet]. 2016;1862:1883–1890. Available from: http://www.sciencedirect.com/science/article/pii/S0925443916301685. doi: 10.1016/j.bbadis.2016.07.008
- Jiang P, Li W, Shea JE, et al. Resveratrol inhibits the formation of multiple-layered β-sheet oligomers of the human islet amyloid polypeptide segment 22-27. Biophys J. 2011;100(6):1550–1558. DOI:10.1016/j.bpj.2011.02.010.
- Porat Y, Mazor Y, Efrat S, et al. Inhibition of islet amyloid polypeptide fibril formation: A potential role for heteroaromatic interactions. Biochemistry. 2004;43(45):14454–14462. DOI:10.1021/bi048582a.
- Meiering EM. The threat of instability: neurodegeneration predicted by protein destabilization and aggregation propensity. PLoS Biol. [Internet]. 2008;6:1383–1385. [cited 2016 Apr 1]. Available from: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060193.
- Gómez-Gallego F, Garrido-Pertierra A, Bautista JM. Structural defects underlying protein dysfunction in human Glucose-6-phosphate dehydrogenase a− deficiency. J Biol Chem. 2000;275:9256–9262. doi: 10.1074/jbc.275.13.9256