Mutational Analysis of the Aggregation-Prone and Disaggregation-Prone Regions of Acylphosphatase

Journal of Molecular Biology

Volumn 387, Issue 4, 2009, Pages 965-974

  Calamai, Martino ^a   Tartaglia, Gian Gaetano ^a   Vendruscolo, Michele ^a   Chiti, Fabrizio ^b,c   Dobson, Christopher M ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF FLORENCE   (Italy)

^c NATIONAL INSTITUTE OF BIOSTRUCTURES AND BIOSYSTEMS   (Italy)

Author keywords

aggregates disassembly; amyloid; computational prediction; protein misfolding; TFE

Indexed keywords

ACYLPHOSPHATASE; AMYLOID; TRIFLUOROETHANOL;

ALGORITHM; ARTICLE; DYNAMICS; GENE MUTATION; INFORMATION; KINETICS; MUTATIONAL ANALYSIS; PHYSIOLOGY; PREDICTION; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN STRUCTURE;

EID: 62649171633     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.09.003     Document Type: Article

References (42)

1. Selkoe D.J. Folding proteins in fatal ways. Nature 426 (2003) 900-904
2. Cohen F.E., and Kelly J.W. Therapeutic approaches to protein-misfolding diseases. Nature 426 (2003) 905-909
3. Chiti F., and Dobson C.M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75 (2006) 333-366
4. Serpell L.C., Sunde M., and Blake C.C. The molecular basis of amyloidosis. Cell. Mol. Life Sci. 53 (1997) 871-887
5. Rochet J.C., and Lansbury Jr. P.T. Amyloid fibrillogenesis: themes and variations. Curr. Opin. Struct. Biol. 10 (2000) 60-68
6. Dobson C.M. Protein folding and misfolding. Nature 426 (2003) 884-890
7. Stefani M., and Dobson C.M. Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. J. Mol. Med. 81 (2003) 678-699
8. Dobson C.M. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24 (1999) 329-332
9. Torok M., Milton S., Kayed R., Wu P., McIntire T., Glabe C.G., and Langen R. Structural and dynamic features of Alzheimer's Abeta peptide in amyloid fibrils studied by site-directed spin labeling. J. Biol. Chem. 277 (2002) 40810-40815
10. Der-Sarkissian A., Jao C.C., Chen J., and Langen R. Structural organization of alpha-synuclein fibrils studied by site-directed spin labeling. J. Biol. Chem. 278 (2003) 37530-37535
11. Margittai M., and Langen R. Template-assisted filament growth by parallel stacking of tau. Proc. Natl Acad. Sci. USA 101 (2004) 10278-10283
12. Williams A.D., Portelius E., Kheterpal I., Guo J.T., Cook K.D., Xu Y., and Wetzel R. Mapping abeta amyloid fibril secondary structure using scanning proline mutagenesis. J. Mol. Biol. 335 (2004) 833-842
13. Shivaprasad S., and Wetzel R. Scanning cysteine mutagenesis analysis of abeta-(1-40) amyloid fibrils. J. Biol. Chem. 281 (2006) 993-1000
14. Ferguson N., Becker J., Tidow H., Tremmel S., Sharpe T.D., Krause G., et al. General structural motifs of amyloid protofilaments. Proc. Natl Acad. Sci. USA 103 (2006) 16248-16253
15. Chiti F., Webster P., Taddei N., Clark A., Stefani M., Ramponi G., and Dobson C.M. Designing conditions for in vitro formation of amyloid protofilaments and fibrils. Proc. Natl Acad. Sci. USA 96 (1999) 3590-3594
16. Chiti F., Taddei N., Bucciantini M., White P., Ramponi G., and Dobson C.M. Mutational analysis of the propensity for amyloid formation by a globular protein. EMBO J. 19 (2000) 1441-1449
17. Chiti F., Taddei N., Baroni F., Capanni C., Stefani M., Ramponi G., and Dobson C.M. Kinetic partitioning of protein folding and aggregation. Nat. Struct. Biol. 9 (2002) 137-143
18. Chiti F., Calamai M., Taddei N., Stefani M., Ramponi G., and Dobson C.M. Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases. Proc. Natl Acad. Sci. USA 99 Suppl 4 (2002) 16419-16426
19. Monti M., Garolla di Bard B.L., Calloni G., Chiti F., Amoresano A., Ramponi G., and Pucci P. The regions of the sequence most exposed to the solvent within the amyloidogenic state of a protein initiate the aggregation process. J. Mol. Biol. 336 (2004) 253-262
20. Calamai M., Chiti F., and Dobson C.M. Amyloid fibril formation can proceed from different conformations of a partially unfolded protein. Biophys. J. 89 (2005) 4201-4210
21. Bemporad F., Taddei N., Stefani M., and Chiti F. Assessing the role of aromatic residues in the amyloid aggregation of human muscle acylphosphatase. Protein Sci. 15 (2006) 862-870
22. Calamai M., Canale C., Relini A., Stefani M., Chiti F., and Dobson C.M. Reversal of protein aggregation provides evidence for multiple aggregated States. J. Mol. Biol. 346 (2005) 603-616
23. Chiti F., Taddei N., Webster P., Hamada D., Fiaschi T., Ramponi G., and Dobson C.M. Acceleration of the folding of acylphosphatase by stabilization of local secondary structure. Nat. Struct. Biol. 6 (1999) 380-387
24. Chiti F., Stefani M., Taddei N., Ramponi G., and Dobson C.M. Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424 (2003) 805-808
25. West M.W., Wang W., Patterson J., Mancias J.D., Beasley J.R., and Hecht M.H. De novo amyloid proteins from designed combinatorial libraries. Proc. Natl Acad. Sci. USA 96 (1999) 11211-11216
26. 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
27. 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
28. Tartaglia G.G., Cavalli A., Pellarin R., and Caflisch A. Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Sci. 14 (2005) 2723-2734
29. Trovato A., Seno F., and Tosatto S.C. The PASTA server for protein aggregation prediction. Protein Eng. Des. Sel. 20 (2007) 521-523
30. Conchillo-Sole O., de Groot N.S., Aviles F.X., Vendrell J., Daura X., and Ventura S. AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinformatics 8 (2007) 65
31. Tartaglia G.G., Pawar A., Campioni S., Chiti F., Dobson C.M., and Vendruscolo M. Prediction of aggregation-prone regions in structured proteins. J. Mol. Biol. 380 (2008) 425-436
32. Chiti F., Taddei N., White P.M., Bucciantini M., Magherini F., Stefani M., and Dobson C.M. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat. Struct. Biol. 6 (1999) 1005-1009
33. Hortschansky P., Christopeit T., Schroeckh V., and Fandrich M. Thermodynamic analysis of the aggregation propensity of oxidized Alzheimer's beta-amyloid variants. Protein Sci. 14 (2005) 2915-2918
34. Tartaglia G.G., Cavalli A., Pellarin R., and Caflisch A. The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Sci. 13 (2004) 1939-1941
35. Calamai M., Taddei N., Stefani M., Ramponi G., and Chiti F. Relative influence of hydrophobicity and net charge in the aggregation of two homologous proteins. Biochemistry 42 (2003) 15078-15083
36. Castillo G.M., Ngo C., Cummings J., Wight T.N., and Snow A.D. Perlecan binds to the beta-amyloid proteins (A beta) of Alzheimer's disease, accelerates A beta fibril formation, and maintains A beta fibril stability. J. Neurochem. 69 (1997) 2452-2465
37. Yamaguchi I., Suda H., Tsuzuike N., Seto K., Seki M., Yamaguchi Y., et al. Glycosaminoglycan and proteoglycan inhibit the depolymerization of beta2-microglobulin amyloid fibrils in vitro. Kidney Int. 64 (2003) 1080-1088
38. Hartl F.U., and Hayer-Hartl M. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295 (2002) 1852-1858
39. Weibezahn J., Schlieker C., Tessarz P., Mogk A., and Bukau B. Novel insights into the mechanism of chaperone-assisted protein disaggregation. Biol. Chem. 386 (2005) 739-744
40. Taddei N., Stefani M., Magherini F., Chiti F., Modesti A., Raugei G., and Ramponi G. Looking for residues involved in the muscle acylphosphatase catalytic mechanism and structural stabilization: role of Asn41, Thr42, and Thr46. Biochemistry 35 (1996) 7077-7083
41. van Nuland N.A., Chiti F., Taddei N., Raugei G., Ramponi G., and Dobson C.M. Slow folding of muscle acylphosphatase in the absence of intermediates. J. Mol. Biol. 283 (1998) 883-891
42. Wright C.F., Teichmann S.A., Clarke J., and Dobson C.M. The importance of sequence diversity in the aggregation and evolution of proteins. Nature 438 (2005) 878-881