Protein sequences encode safeguards against aggregation

Human Mutation

Volumn 30, Issue 3, 2009, Pages 431-437

  Reumers, Joke ^a   Maurer Stroh, Sebastian ^a,b   Schymkowitz, Joost ^a   Rousseau, Fréderic ^a  

^a VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^b BIOINFORMATICS INSTITUTE   (Singapore)

Author keywords

Aggregation gatekeepers; Conformational disease; Disease mutations; In silico analysis; Nonsynonymous SNPs; Protein aggregation; TANGO algorithm

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DISEASE PREDISPOSITION; FABRY DISEASE; LIMB GIRDLE MUSCULAR DYSTROPHY; MUTATION; PRIORITY JOURNAL; PROTEIN AGGREGATION; VAN DER WOUDE SYNDROME;

ALGORITHMS; CALPAIN; HUMANS; HYDROPHOBICITY; MODELS, MOLECULAR; MUSCLE PROTEINS; MUSCULAR DYSTROPHIES, LIMB-GIRDLE; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SELECTION (GENETICS);

PYRONIA TITHONUS;

EID: 61649092809     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20905     Document Type: Article

References (43)

1. Carrell RW. 2005. Cell toxicity and conformational disease. Trends Cell Biol 15:574-580.
2. Chen L, Sigler PB. 1999. The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity. Cell 99:757-768.
3. Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM. 2003. Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424:805-808.
4. Conway KA, Harper JD, Lansbury Jr PT. 2000. Fibrils formed in vitro from alpha-synuclein and two mutant forms linked to Parkinson's disease are typical amyloid. Biochemistry 39:2552-2563.
5. Cooper DN, Youssoufian H. 1988. The CpG dinucleotide and human genetic disease. Hum Genet 78:151-155.
6. Dehay B, Bertolotti A. 2006. Critical role of the proline-rich region in Huntingtin for aggregation and cytotoxicity in yeast. J Biol Chem 281:35608-35615.
7. Dobson CM. 2004. Principles of protein folding, misfolding and aggregation. Semin Cell Dev Biol 15:3-16.
8. Eng CM, Desnick RJ. 1994. Molecular basis of Fabry disease: mutations and polymorphisms in the human alpha-galactosidase A gene. Hum Mutat 3:103-111.
9. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L. 2004. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22:1302-1306.
10. Garman SC. 2007. Structure-function relationships in alpha-galactosidase A. Acta Paediatr Suppl 96:6-16.
11. Hardy J. 2002. Testing times for the "amyloid cascade hypothesis". Neurobiol Aging 23:1073-1074.
12. Henikoff JG, Henikoff S. 1996. Blocks database and its applications. Methods Enzymol 266:88-105.
13. Kall L, Krogh A, Sonnhammer EL. 2007. Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res 35(Web Server issue):W429-W432.
14. Khan S, Vihinen M. 2007. Spectrum of disease-causing mutations in protein secondary structures. BMC Struct Biol 7:56.
15. Kondo S, Schutte BC, Richardson RJ, Bjork BC, Knight AS, Watanabe Y, Howard E, de Lima RL, Daack-Hirsch S, Sander A, McDonald-McGinn DM, Zackai EH, Lammer EJ, Aylsworth AS, Ardinger HH, Lidral AC, Pober BR, Moreno L, Arcos-Burgos M, Valencia C, Houdayer C, Bahuau M, Moretti-Ferreira D, Richieri-Costa A, Dixon MJ, Murray JC. 2002. Mutations in IRF6 cause Van der Woude and popliteal pterygium syndromes. Nat Genet 32:285-289.
16. Krieger E, Koraimann G, Vriend G. 2002. Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field. Proteins 47:393-402.
17. Li W, Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
18. Linding R, Schymkowitz J, Rousseau F, Diella F, Serrano L. 2004. A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. J Mol Biol 342:345-353.
19. Lopez-Bigas N, Ouzounis CA. 2004. Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res 32:3108-3114.
20. Monsellier E, Chiti F. 2007. Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep 8:737-742.
21. Monsellier E, Ramazzotti M, de Laureto PP, Tartaglia GG, Taddei N, Fontana A, Vendruscolo M, Chiti F. 2007. The distribution of residues in a polypeptide sequence is a determinant of aggregation optimized by evolution. Biophys J 93:4382-4391.
22. Ollila J, Lappalainen I, Vihinen M. 1996. Sequence specificity in CpG mutation hotspots. FEBS Lett 396:119-122.
23. Otzen DE, Oliveberg M. 1999. Salt-induced detour through compact regions of the protein folding landscape. Proc Natl Acad Sci USA 96:11746-11751.
24. Otzen DE, Kristensen O, Oliveberg M. 2000. Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly. Proc Natl Acad Sci USA 97:9907-9912.
25. Pal GP, Elce JS, Jia Z. 2001. Dissociation and aggregation of calpain in the presence of calcium. J Biol Chem 276:47233-47238.
26. Patzelt H, Rüdiger S, Brehmer D, Kramer G, Vorderwülbecke S, Schaffitzel E, Waitz A, Hesterkamp T, Dong L, Schneider-Mergener J, Bukau B, Deuerling E. 2001. Binding specificity of Escherichia coli trigger factor. Proc Natl Acad Sci USA 98:14244-14249.
27. Raser KJ, Buroker-Kilgore M, Wang KK. 1996. Binding and aggregation of human mu-calpain by terbium ion. Biochim Biophys Acta 1292:9-14.
28. Reumers J, Conde L, Medina I, Maurer-Stroh S, Van Durme J, Dopazo J, Rousseau F, Schymkowitz J. 2008. Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res 36(Database issue):D825-D829.
29. Richard I, Roudaut C, Saenz A, Pogue R, Grimbergen JE, Anderson LV, Beley C, Cobo AM, de Diego C, Eymard B, Gallano P, Ginjaar HB, Lasa A, Pollitt C, Topaloglu H, Urtizberea JA, de Visser M, van der Kooi A, Bushby K, Bakker E, Lopez de Munain A, Fardeau M, Beckmann JS. 1999. Calpainopathy - a survey of mutations and polymorphisms. Am J Hum Genet 64:1524-1540.
30. Rousseau F, Schymkowitz J, Serrano L. 2006a. Protein aggregation and amyloidosis: confusion of the kinds? Curr Opin Struct Biol 16:118-126.
31. Rousseau F, Serrano L, Schymkowitz JW. 2006b. How evolutionary pressure against protein aggregation shaped chaperone specificity. J Mol Biol 355:1037-1047.
32. Rudiger S, Germeroth L, SchneiderMergener J, Bukau B. 1997. Substrate specificity of the DnaK chaperone determined by screening cellulose-bound peptide libraries. EMBO J 16:1501-1507.
33. Schlieker C, Weibezahn J, Patzelt H, Tessarz P, Strub C, Zeth K, Erbse A, Schneider-Mergener J, Chin JW, Schultz PG, Bukau B, Mogk A. 2004. Substrate recognition by the AAA+ chaperone ClpB. Nat Struct Mol Biol 11:607-615.
34. Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L. 2005. The FoldX web server: an online force field. Nucleic Acids Res 33(Web Server issue):W382-W388.
35. Shabbeer J, Yasuda M, Benson SD, Desnick RJ. 2006. Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations. Hum Genomics 2:297-309.
36. Stefani M, Dobson CM. 2003. Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. J Mol Med 81:678-699.
37. Stefani M. 2004. Protein misfolding and aggregation: new examples in medicine and biology of the dark side of the protein world. Biochim Biophys Acta 1739:5-25.
38. Vitkup D, Sander C, Church GM. 2003. The amino-acid mutational spectrum of human genetic disease. Genome Biol 4:R72.
39. von Bergen M, Barghorn S, Li L, Marx A, Biernat J, Mandelkow EM, Mandelkow E. 2001. Mutations of tau protein in frontotemporal dementia promote aggregation of paired helical filaments by enhancing local beta-structure. J Biol Chem 276:48165-48174.
40. Wang Q, Buckle AM, Fersht AR. 2000. From minichaperone to GroEL 1: information on GroEL-polypeptide interactions from crystal packing of minichaperones. J Mol Biol 304:873-881.
41. Wang J, Chen L. 2003. Domain motions in GroEL upon binding of an oligopeptide. J Mol Biol 334:489-499.
42. Wong P, Fritz A, Frishman D. 2005. Designability, aggregation propensity and duplication of disease-associated proteins. Protein Eng Des Sel 18:503-508.
43. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B. 2006. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34(Database issue):D187-D191.