Amyloidogenic peptides of yeast cell wall glucantransferase Bgl2p as a model for the investigation of its pH-dependent fibril formation

References

• Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006; 75:333 - 66; http://dx.doi.org/10.1146/annurev.biochem.75.101304.123901; PMID: 16756495
   PubMed Web of Science ®Google Scholar
• Westermark P, Benson MD, Buxbaum JN, Cohen AS, Frangione B, Ikeda S, et al. A primer of amyloid nomenclature. Amyloid 2007; 14:179 - 83; http://dx.doi.org/10.1080/13506120701460923; PMID: 17701465
   PubMed Web of Science ®Google Scholar
• Wösten HA, de Vocht ML. Hydrophobins, the fungal coat unravelled. Biochim Biophys Acta 2000; 1469:79 - 86; http://dx.doi.org/10.1016/S0304-4157(00)00002-2; PMID: 10998570
   PubMed Web of Science ®Google Scholar
• Chapman MR, Robinson LS, Pinkner JS, Roth R, Heuser J, Hammar M, et al. Role of Escherichia coli curli operons in directing amyloid fiber formation. Science 2002; 295:851 - 5; http://dx.doi.org/10.1126/science.1067484; PMID: 11823641
   PubMed Web of Science ®Google Scholar
• Shewmaker F, McGlinchey RP, Wickner RB. Structural insights into functional and pathological amyloid. J Biol Chem 2011; 286:16533 - 40; http://dx.doi.org/10.1074/jbc.R111.227108; PMID: 21454545
   PubMed Web of Science ®Google Scholar
• Fowler DM, Koulov AV, Alory-Jost C, Marks MS, Balch WE, Kelly JW. Functional amyloid formation within mammalian tissue. PLoS Biol 2006; 4:e6; http://dx.doi.org/10.1371/journal.pbio.0040006; PMID: 16300414
   PubMed Web of Science ®Google Scholar
• Larsen P, Nielsen JL, Dueholm MS, Wetzel R, Otzen D, Nielsen PH. Amyloid adhesins are abundant in natural biofilms. Environ Microbiol 2007; 9:3077 - 90; http://dx.doi.org/10.1111/j.1462-2920.2007.01418.x; PMID: 17991035
   PubMed Web of Science ®Google Scholar
• Otzen D, Nielsen PH. We find them here, we find them there: functional bacterial amyloid. Cell Mol Life Sci 2008; 65:910 - 27; http://dx.doi.org/10.1007/s00018-007-7404-4; PMID: 18034321
   PubMed Web of Science ®Google Scholar
• Gebbink MF, Claessen D, Bouma B, Dijkhuizen L, Wösten HA. Amyloids--a functional coat for microorganisms. Nat Rev Microbiol 2005; 3:333 - 41; http://dx.doi.org/10.1038/nrmicro1127; PMID: 15806095
   PubMed Web of Science ®Google Scholar
• Teertstra WR, van der Velden GJ, de Jong JF, Kruijtzer JA, Liskamp RM, Kroon-Batenburg LM, et al. The filament-specific Rep1-1 repellent of the phytopathogen Ustilago maydis forms functional surface-active amyloid-like fibrils. J Biol Chem 2009; 284:9153 - 9; http://dx.doi.org/10.1074/jbc.M900095200; PMID: 19164282
   PubMed Web of Science ®Google Scholar
• Otoo HN, Lee KG, Qiu W, Lipke PN. Candida albicans Als adhesins have conserved amyloid-forming sequences. Eukaryot Cell 2008; 7:776 - 82; http://dx.doi.org/10.1128/EC.00309-07; PMID: 18083824
   PubMed Web of Science ®Google Scholar
• Teertstra WR, Krijgsheld P, Wösten HA. Absence of repellents in Ustilago maydis induces genes encoding small secreted proteins. Antonie Van Leeuwenhoek 2011; 100:219 - 29; http://dx.doi.org/10.1007/s10482-011-9581-2; PMID: 21626092
   PubMed Web of Science ®Google Scholar
• Lundmark K, Westermark GT, Olsén A, Westermark P. Protein fibrils in nature can enhance amyloid protein A amyloidosis in mice: Cross-seeding as a disease mechanism. Proc Natl Acad Sci U S A 2005; 102:6098 - 102; http://dx.doi.org/10.1073/pnas.0501814102; PMID: 15829582
   PubMed Web of Science ®Google Scholar
• Klebl F, Tanner W. Molecular cloning of a cell wall exo-beta-1,3-glucanase from Saccharomyces cerevisiae.. J Bacteriol 1989; 171:6259 - 64; PMID: 2509432
   PubMed Web of Science ®Google Scholar
• Mrša V, Klebl F, Tanner W. Purification and characterization of the Saccharomyces cerevisiae BGL2 gene product, a cell wall endo-beta-1,3-glucanase. J Bacteriol 1993; 175:2102 - 6; PMID: 8458852
   PubMed Web of Science ®Google Scholar
• Kalebina TS, Plotnikova TA, Gorkovskii AA, Selyakh IO, Galzitskaya OV, Bezsonov EE, et al. Amyloid-like properties of Saccharomyces cerevisiae cell wall glucantransferase Bgl2p: prediction and experimental evidences. Prion 2008; 2:91 - 6; http://dx.doi.org/10.4161/pri.2.2.6645; PMID: 19098439
   PubMed Web of Science ®Google Scholar
• Belli M, Ramazzotti M, Chiti F. Prediction of amyloid aggregation in vivo.. EMBO Rep 2011; 12:657 - 63; http://dx.doi.org/10.1038/embor.2011.116; PMID: 21681200
   PubMed Web of Science ®Google Scholar
• López De La Paz M, Goldie K, Zurdo J, Lacroix E, Dobson CM, Hoenger A, et al. De novo designed peptide-based amyloid fibrils. Proc Natl Acad Sci U S A 2002; 99:16052 - 7; http://dx.doi.org/10.1073/pnas.252340199; PMID: 12456886
   PubMed Web of Science ®Google Scholar
• Ohhashi Y, Hasegawa K, Naiki H, Goto Y. Optimum amyloid fibril formation of a peptide fragment suggests the amyloidogenic preference of β2-microglobulin under physiological conditions. J Biol Chem 2004; 279:10814 - 21; http://dx.doi.org/10.1074/jbc.M310334200; PMID: 14699107
   PubMed Web of Science ®Google Scholar
• Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. Prediction of amyloidogenic and disordered regions in protein chains. PLoS Comput Biol 2006; 2:e177; http://dx.doi.org/10.1371/journal.pcbi.0020177; PMID: 17196033
   PubMed Web of Science ®Google Scholar
• Garbuzynskiy SO, Lobanov MY, Galzitskaya OV. FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence. Bioinformatics 2010; 26:326 - 32; http://dx.doi.org/10.1093/bioinformatics/btp691; PMID: 20019059
   PubMed Web of Science ®Google Scholar
• Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. Is it possible to predict amyloidogenic regions from sequence alone?. J Bioinform Comput Biol 2006; 4:373 - 88; http://dx.doi.org/10.1142/S0219720006002004; PMID: 16819789
   PubMedGoogle Scholar
• Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 2004; 22:1302 - 6; http://dx.doi.org/10.1038/nbt1012; PMID: 15361882
   PubMed Web of Science ®Google Scholar
• Sánchez de Groot N, Pallarés I, Avilés FX, Vendrell J, Ventura S. Prediction of “hot spots” of aggregation in disease-linked polypeptides. BMC Struct Biol 2005; 5:18; http://dx.doi.org/10.1186/1472-6807-5-18; PMID: 16197548
   PubMed Web of Science ®Google Scholar
• Conchillo-Solé O, de Groot NS, Avilés FX, Vendrell J, Daura X, Ventura S. AGGRESCAN: a server for the prediction and evaluation of “hot spots” of aggregation in polypeptides. BMC Bioinformatics 2007; 8:65; http://dx.doi.org/10.1186/1471-2105-8-65; PMID: 17324296
   PubMed Web of Science ®Google Scholar
• Trovato A, Chiti F, Maritan A, Seno F. Insight into the structure of amyloid fibrils from the analysis of globular proteins. PLoS Comput Biol 2006; 2:e170; http://dx.doi.org/10.1371/journal.pcbi.0020170; PMID: 17173479
   PubMed Web of Science ®Google Scholar
• Maurer-Stroh S, Debulpaep M, Kuemmerer N, Lopez de la Paz M, Martins IC, Reumers J, et al. Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods 2010; 7:237 - 42; http://dx.doi.org/10.1038/nmeth.1432; PMID: 20154676
   PubMed Web of Science ®Google Scholar
• Zimmermann O, Hansmann UH. Support vector machines for prediction of dihedral angle regions. Bioinformatics 2006; 22:3009 - 15; http://dx.doi.org/10.1093/bioinformatics/btl489; PMID: 17005536
   PubMed Web of Science ®Google Scholar
• Groenning M. Binding mode of Thioflavin T and other molecular probes in the context of amyloid fibrils-current status. J Chem Biol 2010; 3:1 - 18; http://dx.doi.org/10.1007/s12154-009-0027-5; PMID: 19693614
   PubMedGoogle Scholar
• Frid P, Anisimov SV, Popovic N. Congo red and protein aggregation in neurodegenerative diseases. Brain Res Rev 2007; 53:135 - 60; http://dx.doi.org/10.1016/j.brainresrev.2006.08.001; PMID: 16959325
   PubMed Web of Science ®Google Scholar
• Tzotzos S, Doig AJ. Amyloidogenic sequences in native protein structures. Protein Sci 2010; 19:327 - 48; http://dx.doi.org/10.1002/pro.314; PMID: 20027621
   PubMed Web of Science ®Google Scholar
• Inouye H, Kirschner DA. X-Ray fiber and powder diffraction of PrP prion peptides. Adv Protein Chem 2006; 73:181 - 215; http://dx.doi.org/10.1016/S0065-3233(06)73006-6; PMID: 17190614
   PubMedGoogle Scholar
• Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, et al. Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 2007; 447:453 - 7; http://dx.doi.org/10.1038/nature05695; PMID: 17468747
   PubMed Web of Science ®Google Scholar
• Sánchez de Groot N, Pallarés I, Avilés FX, Vendrell J, Ventura S. Prediction of “hot spots” of aggregation in disease-linked polypeptides. BMC Struct Biol 2005; 5:18; http://dx.doi.org/10.1186/1472-6807-5-18; PMID: 16197548
   PubMed Web of Science ®Google Scholar
• Kalebina TS, Egorov SN, Arbatskii NP, Bezsonov EE, Gorkovskii AA, Kulaev IS. The role of high-molecular-weight polyphosphates in activation of glucan transferase Bgl2p from Saccharomyces cerevisiae cell wall. Dokl Biochem Biophys 2008; 420:142 - 5; http://dx.doi.org/10.1134/S1607672908030125; PMID: 18680912
   PubMed Web of Science ®Google Scholar
• Wang X, Zhou Y, Ren JJ, Hammer ND, Chapman MR. Gatekeeper residues in the major curlin subunit modulate bacterial amyloid fiber biogenesis. Proc Natl Acad Sci U S A 2010; 107:163 - 8; http://dx.doi.org/10.1073/pnas.0908714107; PMID: 19966296
   PubMed Web of Science ®Google Scholar
• Gorkovskii AA, Bezsonov EE, Plotnikova TA, Kalebina TS, Kulaev IS. Revealing of Saccharomyces cerevisiae yeast cell wall proteins capable of binding thioflavin T, a fluorescent dye specifically interacting with amyloid fibrils. Biochemistry (Mosc) 2009; 74:1219 - 24; http://dx.doi.org/10.1134/S0006297909110066; PMID: 19916936
   PubMed Web of Science ®Google Scholar
• Tartaglia GG, Caflisch A. Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins. Proteins 2007; 68:273 - 8; http://dx.doi.org/10.1002/prot.21427; PMID: 17407164
   PubMed Web of Science ®Google Scholar
• Andersen CB, Yagi H, Manno M, Martorana V, Ban T, Christiansen G, et al. Branching in amyloid fibril growth. Biophys J 2009; 96:1529 - 36; http://dx.doi.org/10.1016/j.bpj.2008.11.024; PMID: 19217869
   PubMed Web of Science ®Google Scholar
• Harper JD, Lieber CM, Lansbury PT Jr.. Atomic force microscopic imaging of seeded fibril formation and fibril branching by the Alzheimer’s disease amyloid-beta protein. Chem Biol 1997; 4:951 - 9; http://dx.doi.org/10.1016/S1074-5521(97)90303-3; PMID: 9427660
   PubMed Web of Science ®Google Scholar
• Hammer ND, Schmidt JC, Chapman MR. The curli nucleator protein, CsgB, contains an amyloidogenic domain that directs CsgA polymerization. Proc Natl Acad Sci U S A 2007; 104:12494 - 9; http://dx.doi.org/10.1073/pnas.0703310104; PMID: 17636121
   PubMed Web of Science ®Google Scholar
• Fominov GV, Ter-Avanesian MD. [Caffeine sensitivity of the yeast Saccharomyces cerevisiae MCD4 mutant is related to alteration of calcium homeostasis and degradation of misfolded proteins]. Mol Biol (Mosk) 2005; 39:464 - 76; http://dx.doi.org/10.1007/s11008-005-0056-2; PMID: 15981576
   PubMed Web of Science ®Google Scholar
• Foderà V, Librizzi F, Groenning M, van de Weert M, Leone M. Secondary nucleation and accessible surface in insulin amyloid fibril formation. J Phys Chem B 2008; 112:3853 - 8; http://dx.doi.org/10.1021/jp710131u; PMID: 18311965
   PubMed Web of Science ®Google Scholar
• Wellings DA, Atherton E. Standard Fmoc protocols. Methods Enzymol 1997; 289:44 - 67; http://dx.doi.org/10.1016/S0076-6879(97)89043-X; PMID: 9353717
   PubMed Web of Science ®Google Scholar
• Scopes RK. Measurement of protein by spectrophotometry at 205 nm. Anal Biochem 1974; 59:277 - 82; http://dx.doi.org/10.1016/0003-2697(74)90034-7; PMID: 4407487
   PubMed Web of Science ®Google Scholar
• Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970; 227:680 - 5; http://dx.doi.org/10.1038/227680a0; PMID: 5432063
   PubMed Web of Science ®Google Scholar
• Morenkov OS, Mantsygin IuA, Sergeev VA, Sobko IuA, Morenkova MA, Panchenko OA. [The isolation and characteristics of monoclonal antibodies to the glycoprotein GII of Aujeszky’s disease virus and their use for the epitopic mapping of GII]. Vopr Virusol 1994; 39:174 - 7; PMID: 7527989
   PubMed Web of Science ®Google Scholar