Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes

Bioinformatics

Volumn 31, Issue 14, 2015, Pages 2294-2302

  Smaoui, Mohamed Raef ^a,b   Orland, Henri ^c   Waldispühl, Jérôme ^a,b  

^a MCGILL UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c CEA SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLIN; AMYLOID; ANTIDIABETIC AGENT; GLUCOSE BLOOD LEVEL; INSULIN; PRAMLINTIDE;

BIOLOGY; CHEMISTRY; DIABETES MELLITUS; GENETICS; GLUCOSE BLOOD LEVEL; HUMAN; METABOLISM; MUTATION; PANCREAS ISLET BETA CELL; PROCEDURES;

AMYLOID; BLOOD GLUCOSE; COMPUTATIONAL BIOLOGY; DIABETES MELLITUS; HUMANS; HYPOGLYCEMIC AGENTS; INSULIN; INSULIN-SECRETING CELLS; ISLET AMYLOID POLYPEPTIDE; MUTATION;

EID: 84941627304     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv143     Document Type: Article

References (36)

1. Bolie, V. W. (1961) Coefficients of normal blood glucose regulation. J. Appl. Physiol., 16, 783-788.
2. Boutayeb, A. and Chetouani, A. (2006) A critical review of mathematical models and data used in diabetology. Biomed. Eng. Online, 5, 43.
3. Bryan, A. W. Jr. et al. (2009) Betascan: probable beta-amyloids identified by pairwise probabilistic analysis. PLoS Comput. Biol., 5, e1000333.
4. Cort, J. R. et al. (2009) Solution state structures of human pancreatic amylin and pramlintide. Protein Eng. Des. Sel., 22, 497-513.
5. Darden, T. et al. (1993) Particle mesh ewald-an n. log(n) method for ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
6. Essmann, U. et al. (1995) A smooth particle mesh ewald method. J. Chem. Phys., 103, 8577-8593.
7. Fernandez-Escamilla, A.-M. et al. (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat. Biotechnol., 22, 1302-1306.
8. He, L. et al. (2014) Inhibition of human amylin fibril formation by insulin-mimetic vanadium complexes. Metallomics, 6, 1087-1096.
9. Kahn, S. E. et al. (1990) Evidence of cosecretion of islet amyloid polypeptide and insulin by beta-cells. Diabetes, 39, 634-638.
10. Koehl, P. and Delarue, M. (2010) Aquasol: An efficient solver for the dipolar poisson-boltzmann-langevin equation. J. Chem. Phys., 132, 064101.
11. Lashuel, H. A. et al. (2002) Neurodegenerative disease: Amyloid pores from pathogenic mutations. Nature, 418, 291.
12. Li, X. et al. (2014) Inhibition of islet amyloid polypeptide fibril formation by selenium-containing phycocyanin and prevention of beta cell apoptosis. Biomaterials, 35, 8596-8604.
13. Lutz, T. A. et al. (1995) Amylin decreases meal size in rats. Physiol. Behav., 58, 1197-1202.
14. MacArthur, D. L. et al. (1999) Amyloid fibril formation is progressive and correlates with beta-cell secretion in transgenic mouse isolated islets. Diabetologia, 42, 1219-1227.
15. Meier, J. J. et al. (2006). Inhibition of human iapp fibril formation does not prevent beta-cell death: evidence for distinct actions of oligomers and fibrils of human iapp. Am. J. Physiol. Endocrinol. Metab., 291, E1317-E1324.
16. Mirzabekov, T. A. et al. (1996) Pore formation by the cytotoxic islet amyloid peptide amylin. J. Biol. Chem., 271, 1988-1992.
17. Mishra, R. et al. (2009) Inhibiting islet amyloid polypeptide fibril formation by the red wine compound resveratrol. Chembiochem, 10, 445-449.
18. O'Donnell, C. W. et al. (2011) A method for probing the mutational landscape of amyloid structure. Bioinformatics, 27, i34-i42.
19. Pick, A. et al. (1998) Role of apoptosis in failure of beta-cell mass compensation for insulin resistance and beta-cell defects in the male zucker diabetic fatty rat. Diabetes, 47, 358-364.
20. Porat, Y. et al. (2004) Inhibition of islet amyloid polypeptide fibril formation: A potential role for heteroaromatic interactions. Biochemistry, 43, 14454-14462.
21. Porat, Y. et al. (2006) Inhibition of amyloid fibril formation by polyphenols: structural similarity and aromatic interactions as a common inhibition mechanism. Chem. Biol. Drug Des., 67, 27-37.
22. Pronk, S. et al. (2013) Gromacs 4. 5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29, 845-854.
23. Riddle, M. et al. (2007) Pramlintide improved glycemic control and reduced weight in patients with type 2 diabetes using basal insulin. Diabetes Care, 30, 2794-2799.
24. Ritzel, R. A. et al. (2007) Human islet amyloid polypeptide oligomers disrupt cell coupling, induce apoptosis, and impair insulin secretion in isolated human islets. Diabetes, 56, 65-71.
25. Rushing, P. A. et al. (2000) Amylin: A novel action in the brain to reduce body weight. Endocrinology, 141, 850-853.
26. Schrodinger, L. (2010) The PyMOL molecular graphics system, version 1. 3r1.
27. Schymkowitz, J. et al. (2005) The foldx web server: An online force field. Nucleic Acids Res., 33, W382-W388.
28. Smaoui, M. R. et al. (2013) Computational assembly of polymorphic amyloid fibrils reveals stable aggregates. Biophys. J., 104, 683-693.
29. Tartaglia, G. G. et al. (2008) Prediction of aggregation-prone regions in structured proteins. J. Mol. Biol., 380, 425-436.
30. Tatarek-Nossol, M. et al. (2005) Inhibition of hiapp amyloid-fibril formation and apoptotic cell death by a designed hiapp amyloid-core-containing hexapeptide. Chem. Biol., 12, 797-809.
31. Tomiyama, T. et al. (1997) Rifampicin inhibits the toxicity of pre-aggregated amyloid peptides by binding to peptide fibrils and preventing amyloid-cell interaction. Biochem. J., 322, 859-865.
32. Walsh, I. et al. (2014) Pasta 2. 0: An improved server for protein aggregation prediction. Nucleic Acids Res., 42, W301-W307.
33. Wang, Q. et al. (2008) Scwrl and molide: computer programs for side-chain conformation prediction and homology modeling. Nat. Protoc., 3, 1832-1847.
34. Weir, G. C. and Bonner-Weir, S. (2004) Five stages of evolving beta-cell dysfunction during progression to diabetes. Diabetes, 53, S16-S21.
35. Westermark, P. et al. (2011) Islet amyloid polypeptide, islet amyloid, and diabetes mellitus. Physiol. Rev., 91, 795-826.
36. Wiltzius, J. J. W. et al. (2008) Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin). Protein Sci., 17, 1467-1474.