Simulated pathogenic conformational switch regions matched well with the biochemical findings

Journal of Biomedical Informatics

Volumn 43, Issue 3, 2010, Pages 365-375

  Liu, Xin ^a   Zhao, Ya Pu ^a  

^a INSTITUTE OF MECHANICS   (China)

Author keywords

Conformational disease; Protein misfolding

Indexed keywords

CLINICAL THERAPY; CONFORMATIONAL CONVERSION; CONFORMATIONAL DISEASE; CONFORMATIONAL SWITCHES; FOLDING PATHWAY; MISFOLDING; NATIVE STRUCTURES; PROTEIN MISFOLDING; RESIDUE LEVEL; SHORT SEGMENTS; SICKLE-CELL ANEMIA; STRUCTURAL CHANGE; TRANSMISSIBLE SPONGIFORM ENCEPHALOPATHIES;

PROTEINS;

APOLIPOPROTEIN A1; BETA 2 MICROGLOBULIN; CALCITONIN; CRYSTALLIN; CYSTATIN C; GELSOLIN; HEMOGLOBIN; INSULIN; LOW DENSITY LIPOPROTEIN RECEPTOR; LYSOZYME; PREALBUMIN; PRION PROTEIN; PROTEIN P53; SERINE PROTEINASE INHIBITOR; SUPEROXIDE DISMUTASE; PRION;

ACCURACY; ALGORITHM; AMYLOIDOSIS; AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; BETA THALASSEMIA; BRAIN HEMORRHAGE; CALCULATION; CATARACT; CORONARY ARTERY DISEASE; EMPHYSEMA; FAMILIAL AMYLOID POLYNEUROPATHY; FAMILIAL AMYLOIDOSIS; FAMILIAL HYPERCHOLESTEROLEMIA; HEART DISEASE; HEMOLYTIC ANEMIA; HUMAN; LIVER CIRRHOSIS; NEOPLASM; PREDICTION; PRION DISEASE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; SIMULATION; THROMBOEMBOLISM; THYROID MEDULLARY CARCINOMA; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PRION; SICKLE CELL ANEMIA;

ALGORITHMS; ANEMIA, SICKLE CELL; COMPUTER SIMULATION; HUMANS; PRION DISEASES; PRIONS; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 77952744962     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2009.12.003     Document Type: Article

References (53)

1. Carrell R.W., and Lomas D.A. Conformational disease. Lancet 350 (1997) 134-138
2. Dobson C.M. Protein misfolding, evolution and disease. Trends Biochem Sci 24 (1999) 329-332
3. Xin L., and Ya-Pu Z. Donut-shaped fingerprint in homologous polypeptide relationships-a topological feature related to pathogenic structural conversion of conformational disease. J Theor Biol 258 (2009) 294-301
4. Carrell R.W., and Gooptu B. Conformational changes and diseases-serpins, prions, and Alzheimer's. Curr Opin Struct Biol 8 (1998) 799-809
5. Soto C. Protein misfolding and disease; protein refolding and therapy. FEBS Lett 498 (2001) 204-207
6. Kelly J.W. Alternative conformations of amyloidogenic proteins govern their behavior. Curr Opin Struct Biol 6 (1996) 11-17
7. Thomas P.J., Qu B.H., and Pedersen P.L. Defective protein folding as a basis of human disease. Trends Biochem Sci 20 (1995) 456-459
8. Dische F.E., Wernstedt C., Westermark G.T., Westermark P., Pepys M.B., Rennie J.A., et al. Insulin as an amyloid-fibril protein at sites of repeated insulin injections in a diabetic patient. Diabetologia 31 (1988) 158-161
9. Jiménez J.L., Nettleton E.J., Bouchard M., Robinson C.V., Dobson C.M., and Saibil H.R. The protofilament structure of insulin amyloid fibrils. Proc Natl Acad Sci USA 99 (2002) 9196-9201
10. Fass D., Blacklow S., Kim P.S., and Berger J.M. Molecular basis of familial hypercholesterolaemia from structure of LDL receptor module. Nature 388 (1997) 691-693
11. Ajees A.A., Anantharamaiah G.M., Mishra V.K., Hussain M.M., and Murthy H.M.K. Crystal structure of human apolipoprotein A-I: insights into its protective effect against cardiovascular diseases. Proc Natl Acad Sci USA 103 (2006) 2126-2131
12. Frank P.G., and Marcel Y.L. Apoliproprotein A-I: structure-function relationship. J Lipid Res 41 (2000) 853-872
13. Haspel N., Zanuy D., Ma B., Wolfson H., and Nussinov R. A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single β-sheet model with a small hydrophobic core. J Mol Biol 345 (2005) 1213-1227
14. Kazantzis A., Waldner M., Taylor J.W., and Kapurniotu A. Conformationally constrained human calcitonin (hCt) analogues reveal a critical role of sequence 17-21 for the oligomerization state and bioactivity of hCt. Eur J Biochem 269 (2002) 780-791
15. Andreotti G, Vitale RM, Avidan-Shpalter C, Amodeo P, Gazit E, Motta A. Designing aggregation-resistant bioactive peptides by three-dimensional structure homology with a non-amyloidogenic analogue. Submitted for publication.
16. Janowski R., et al. Human cystatin C, an amyloidogenic protein, dimerizes through threedimensional domain swapping. Nat Struct Biol 8 (2001) 316-320
17. Abrahamson M. Molecular basis for amyloidosis related to hereditary brain hemorrhage. Scand J Clin Lab Invest 226 (1996) 47-56
18. Olafsson I., and Grubb A. Hereditary cystatin C amyloid angiopathy. Amyloid Int J Exp Clin Invest 7 (2000) 70-79
19. Outeirino J., Casey R., White J.M., and Lehmann H. Haemoglobin Madrid beta 115 (G17) alanine-proline: an unstable variant associated with haemolytic anaemia. Acta Haematol 52 (1974) 53-60
20. Available from: http://globin.cse.psu.edu/html/huisman/variants/beta/index.html.
21. Page L.J., Suk J.Y., Huff M.E., Lim H.J., Venable III J., Kelly J.Y., et al. Metalloendoprotease cleavage triggers gelsolin amyloidogenesis. EMBO J 24 (2005) 4124-4132
22. Johnson R.J.K., et al. Rationalising lysozyme amyloidosis: insights from the structure and solution dynamics of T70N lysozyme. J Mol Biol 352 (2005) 823-836
23. Bjorkman P.J., et al. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329 (1987) 506-512
24. Floege J., and Ketteler M. β2-Microglobulin-derived amyloidosis: an update. Kidney Int 59 (2001) 164-171
25. Gejyo F., et al. A new form of amyloid protein associated with chronic hemodialysis was identified as beta 2-microglobulin. Biochem Biophys Res Commun 129 (1985) 701-706
26. Hasegawa K., et al. Amyloidogenic synthetic peptides of β2-microglobulina role of the disulfide bond. Biochem Biophys Res Commun 304 (2003) 101-106
27. Hiramatsu H., Goto Y., Naiki H., and Kitagawa T. Core structure of amyloid fibril proposed from IR-microscope linear dichroism. J Am Chem Soc 126 (2004) 3008-3009
28. 2-microglobulin #21-31 fragment based on vibrational spectroscopy. J Am Chem Soc 127 (2005) 7988-7989
29. 2-microglobulin and its deamidated variant, N17D form amyloid fibrils with a range of morphologies in vitro. J Mol Biol 313 (2001) 559-571
30. de Belleroche J., Orrell R., and King A. Familial amyotrophic lateral sclerosis/motor neurone disease (FALS): a review of current developments. J Med Genet 32 (1995) 841-847
31. Saraiva M.J.M. Transthyretin mutations in health and disease. Hum Mutat 5 (1995) 191-196
32. Jacobson D.R., McFarlin D.E., Kane I., and Buxbaum J.N. Transthyretin Pro55, a variant associated with early-onset, aggressive, diffuse amyloidosis with cardiac and neurologic involvement. Hum Genet 89 (1992) 353-356
33. Sebastiao M.P., Saraiva M.J., and Damas A.M. The crystal structure of amyloidogenic Leu55 → Pro transthyretin variant reveals a possible pathway for transthyretin polymerization into amyloid fibrils. J Biol Chem 273 (1998) 24715-24722
34. Jarvis J.A., Kirkpatrick A., and Craik D.J. 1H NMR analysis of fibril-forming peptide fragments of transthyretin. Int J Pept Protein Res 44 (1994) 388-398
35. Jaroniec C.P., MacPhee C.E., Astrof N.S., Dobson C.M., and Griffin R.G. Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril. Proc Natl Acad Sci USA 99 (2002) 16748-16753
36. Ventura S., et al. Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc Natl Acad Sci USA 101 (2004) 7258-7263
37. Ivanova M.I., Sawaya M.R., Gingery M., Attinger A., and Eisenberg D. An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril. Proc Natl Acad Sci USA 101 (2004) 10584-10589
38. Available from: http://p53.free.fr/Database/p53_database.html.
39. Joerger A.C., Ang H.C., and Fersht A.R. Structural basis for understanding oncogenic p53 mutations and designing rescue drugs. Proc Natl Acad Sci USA 103 (2006) 15056-15061
40. Available from: http://www-p53.iarc.fr/stability.html.
41. Johnson D.J.D., and Huntington J.A. The influence of hinge region residue Glu-381 on antithrombin allostery and metastability. J Biol Chem 279 (2004) 4913-4921
42. Jung J, Byeon IJ, Wang Y, King J, Gronenborn A. The structure of the cataract causing P23T mutant of HgD crystallin exhibits local distinctive conformational and dynamic changes. Biochemistry. doi: 10.1021/bi802292q.
43. Lopez de la Paz M., and Serrano L. Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci USA 101 (2004) 87-92
44. Fernandez-Escamilla A.M., Rousseau F., Schymkowitz J., and Serrano L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22 (2004) 1302-1306
45. Yoon S., and Welsh W.J. Detecting hidden sequence propensity for amyloid fibril formation. Protein Sci 13 (2004) 2149-2160
46. Pawar A.P., Dubay K.F., Zurdo J., Chiti F., Vendruscolo M., and Dobson C.M. Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases. J Mol Biol 350 (2005) 379-392
47. de Groot N.S., Pallarés I., Avilés F.X., Vendrell J., and Ventura S. Prediction of "hot spots" of aggregation in disease-linked polypeptides. BMC Struct Biol 5 (2005) 18
48. Bemporad F., Calloni G., Campioni S., Plakoutsi G., Taddei N., and Chiti F. Sequence and structural determinants of amyloid fibril formation. Acc Chem Res 39 (2006) 620-627
49. Caflisch A. Computational models for the prediction of polypeptide aggregation propensity. Curr Opin Chem Biol 10 (2006) 437-444
50. Saiki M., Konakahara T., and Morii H. Interaction-based evaluation of the propensity for amyloid formation with cross-beta structure. Biochem Biophys Res Commun 343 (2006) 1262-1271
51. Galzitskaya O.V., Garbuzynskiy S.O., and Lobanov M.Y. Is it possible to predict amyloidogenic regions from sequence alone?. J Bioinform Comput Biol 4 (2006) 373-388
52. Zhuqing Z., Hao C., and Luhua L. Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential. Bioinformatics 23 (2007) 2218-2225
53. Xin L, Ya-Pu Z. Switch region for pathogenic structural change in conformational disease and its prediction. PLoS One, in press.