Colonic amyloidosis, computational analysis of the major amyloidogenic species, Serum Amyloid A

Computational Biology and Chemistry

Volumn 39, Issue , 2012, Pages 29-34

  Nordling, Erik ^a   Abraham Nordling, Mirna ^b  

^a LINKÖPING UNIVERSITY   (Sweden)

^b DANDERYD HOSPITAL   (Sweden)

Author keywords

Ab initio structure prediction; Amyloid A amyloidosis; Colonic amyloidosis; Fibril; Molecular dynamics simulation; Serum Amyloid A

Indexed keywords

AB INITIO STRUCTURE; AMYLOID A AMYLOIDOSIS; COLONIC AMYLOIDOSIS; FIBRIL; MOLECULAR DYNAMICS SIMULATIONS; SERUM AMYLOID A;

AMINO ACIDS; BODY FLUIDS; CONFORMATIONS; GLYCOPROTEINS; MOLECULAR DYNAMICS; PROTEINS; UNCERTAINTY ANALYSIS;

DISEASES;

SERUM AMYLOID A;

AMINO ACID SEQUENCE; AMYLOIDOSIS; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COLON DISEASE; GENETICS; HUMAN; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PATHOLOGY; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

AMINO ACID SEQUENCE; AMYLOIDOSIS; COLONIC DISEASES; HUMANS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SERUM AMYLOID A PROTEIN;

EID: 84864551681     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2012.06.005     Document Type: Article

References (33)

1. G. Bussi, D. Donadio, and M. Parrinello Canonical sampling through velocity rescaling The Journal of Chemical Physics 126 2007 014101
2. J.H. Chen, S.J. Lai, P.P. Tsai, and Y.F. Chen Localized amyloidosis mimicking carcinoma of the colon American Journal of Roentgenology 179 2002 536 537
3. T. Darden, L. Perera, L. Li, and L. Pedersen New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations Structure 7 1999 R55 R60
4. F.C. De Beer, R.K. Mallya, E.A. Fagan, J.G. Lanham, G.R. Hughes, and M.B. Pepys Serum amyloid-A protein concentration in inflammatory diseases and its relationship to the incidence of reactive systemic amyloidosis Lancet 2 1982 231 234
5. D. De Casa, and J.J. Bocian Primary systemic amyloidosis simulating acute idiopathic ulcerative colitis: report of a case American Journal of Digestive Diseases 10 1965 63 74
6. E.C. Ebert, and M. Nagar Gastrointestinal manifestations of amyloidosis American Journal of Gastroenterology 103 2008 776 787 (Pubitemid 351405997)
7. M. Egashira, H. Takase, I. Yamamoto, M. Tanaka, and H. Saito Identification of regions responsible for heparin-induced amyloidogenesis of human serum amyloid A using its fragment peptides Archives of Biochemistry and Biophysics 511 2011 101 106
8. E. Elimova, R. Kisilevsky, and J.B. Ancsin Heparan sulfate promotes the aggregation of HDL-associated serum amyloid A: evidence for a proamyloidogenic histidine molecular switch FASEB Journal 23 2009 3436 3448
9. M. Fandrich, M. Schmidt, and N. Grigorieff Recent progress in understanding Alzheimer's beta-amyloid structures Trends in Biochemical Sciences 36 2011 338 345
10. N. Ferguson, J. Becker, H. Tidow, S. Tremmel, T.D. Sharpe, G. Krause, J. Flinders, M. Petrovich, J. Berriman, H. Oschkinat, and A.R. Fersht General structural motifs of amyloid protofilaments Proceedings of the National Academy of Sciences of the United States of America 103 2006 16248 16253 (Pubitemid 44715182)
11. J. Gotz, A. Eckert, M. Matamales, L.M. Ittner, and X. Liu Modes of Abeta toxicity in Alzheimer's disease Cellular and Molecular Life Sciences 68 2011 3359 3375
12. A. Husebekk, B. Skogen, G. Husby, and G. Marhaug Transformation of amyloid precursor SAA to protein AA and incorporation in amyloid fibrils in vivo Scandinavian Journal of Immunology 21 1985 283 287 (Pubitemid 15108055)
13. K. Iwata, T. Fujiwara, Y. Matsuki, H. Akutsu, S. Takahashi, H. Naiki, and Y. Goto 3D structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR Proceedings of the National Academy of Sciences of the United States of America 103 2006 18119 18124 (Pubitemid 44871622)
14. D.H. Johnson, T.H. Guthrie, F.J. Tedesco, J.W. Griffin, and H.F. Anthony Jr. Amyloidosis masquerading as inflammatory bowel disease with a mass lesion simulating a malignancy American Journal of Gastroenterology 77 1982 141 145 (Pubitemid 12145402)
15. D.T. Jones Protein secondary structure prediction based on position-specific scoring matrices Journal of Molecular Biology 292 1999 195 202 (Pubitemid 29435759)
16. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
17. G.A. Kaminski, R.A. Friesner, J. Tirado-Rives, and W.L. Jorgensen Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides The Journal of Physical Chemistry B 105 2001 6474 6487 (Pubitemid 35339015)
18. R. Kisilevsky, and P.N. Manley Acute-phase serum amyloid A: perspectives on its physiological and pathological roles Amyloid 19 2012 5 14
19. S. Kumar, A. Dispenzieri, M.Q. Lacy, M.R. Litzow, and M.A. Gertz High incidence of gastrointestinal tract bleeding after autologous stem cell transplant for primary systemic amyloidosis Bone Marrow Transplantation 28 2001 381 385 (Pubitemid 32834357)
20. P.G. Kusalik, and I.M. Svishchev The spatial structure in liquid water Science 265 1994 1219 1221 (Pubitemid 24292788)
21. T. Luhrs, C. Ritter, M. Adrian, D. Riek-Loher, B. Bohrmann, H. Dobeli, D. Schubert, and R. Riek 3D structure of Alzheimer's amyloid-beta(1-42) fibrils Proceedings of the National Academy of Sciences of the United States of America 102 2005 17342 17347
22. O. Mardinger, L. Rotenberg, G. Chaushu, and S. Taicher Surgical management of macroglossia due to primary amyloidosis International Journal of Oral and Maxillofacial Surgery 28 1999 129 131
23. R. Nelson, and D. Eisenberg Recent atomic models of amyloid fibril structure Current Opinion in Structural Biology 16 2006 260 265
24. R.J. O'Brien, and P.C. Wong Amyloid precursor protein processing and Alzheimer's disease Annual Review of Neuroscience 34 2011 185 204
25. S. Ohta, M. Tanaka, K. Sakakura, T. Kawakami, S. Aimoto, and H. Saito Defining lipid-binding regions of human serum amyloid A using its fragment peptides Chemistry and Physics of Lipids 162 2009 62 68
26. M. Parrinello, and A. Rahman Polymorphic transitions in single crystals: a new molecular dynamics method Journal of Applied Physics 52 1981 7182 7190 (Pubitemid 12456820)
27. P.T. Sattianayagam, P.N. Hawkins, and J.D. Gillmore Systemic amyloidosis and the gastrointestinal tract Nature Reviews Gastroenterology & Hepatology 6 2009 608 617
28. G. Seliger, R.L. Krassner, E.R. Beranbaum, and F. Miller The spectrum of roentgen appearance in amyloidosis of the small and large bowel: radiologic-pathologic correlation Radiology 100 1971 63 70
29. F.J. Stevens Hypothetical structure of human serum amyloid A protein Amyloid 11 2004 71 80 (Pubitemid 39222403)
30. C.M. Uhlar, and A.S. Whitehead Serum amyloid A, the major vertebrate acute-phase reactant European Journal of Biochemistry 265 1999 501 523 (Pubitemid 29488982)
31. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J. Berendsen GROMACS: fast, flexible, and free Journal of Computational Chemistry 26 2005 1701 1718 (Pubitemid 43076182)
32. C. Wasmer, A. Lange, H. Van Melckebeke, A.B. Siemer, R. Riek, and B.H. Meier Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core Science 319 2008 1523 1526 (Pubitemid 351398180)
33. Y. Zhang I-TASSER server for protein 3D structure prediction BMC Bioinformatics 9 2008 40