Outline and computational approaches of protein misfolding

Abstract

Protein misfolding is a general causation of classical conformational diseases and many pathogenic changes that are the result of structural conversion. Here I review recent progress in clinical and computational approaches for each stage of the misfolding process, aiming to present readers an outline for swift comprehension of this field.

Keywords

computational approaches / protein misfolding / conformational diseases

References

[1] Abrahamson M (1996). Molecular basis for amyloidosis related to hereditary brain hemorrhage. Scand J Clin Lab Invest, 226: 47–56

[2] Bemporad F, Calloni G, Campioni S, Plakoutsi G, Taddei N, Chiti F (2006). Sequence and structural determinants of amyloid fibril formation. Acc Chem Res, 39: 620–627

[3] Bitan G, Vollers S S, Teplow D B (2003). Elucidation of primary structure elements controlling early amyloid-beta protein oligomerisation. J Biol Chem, 278: 34882–34889

[4] Bonvin A M (2006). Flexible protein-protein docking. Curr Opin Struct Biol, 16: 194–200

[5] Bornholdt Z A, Prasad B V V (2008). X-ray structure of NS1 from a highly pathogenic H5N1 influenza virus. Nature, 456: 985–988

[6] Brändén C I, Tooze J (1999). Introduction to protein structure. 2nd ed. New York: Garland Publishing

[7] Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo J, Taddei N, Ramponi G, Dobson CM, Stefani M (2002). Inherent cytotoxicity of aggregates implies a common origin for protein misfolding diseases. Nature, 416: 507–511

[8] Caflisch A (2006). Computational models for the prediction of polypeptide aggregation propensity. Curr Opin Chem Biol, 10: 437–444

[9] Capaldi A P, Kleanthous C, Radford S E (2002). Im7 folding mechanism: misfolding on a path to the native state. Nat Struct Biol, 9: 209–216

[10] Carrell R W, Gooptu B (1998). Conformational changes and diseases-serpins, prions, and Alzheimer's. Curr Opin Struct Biol, 8: 799–809

[11] Carrell R W, Lomas D A (1997). Conformational disease. Lancet, 350: 134–138

[12] Castillo V, Ventura S (2009). Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases. PLoS Comput Biol, 5: e1000476

[13] Caughey B, Lansbury P T (2003). Protofibrils, pores, fibrils, and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. Annu Rev Neurosci, 26: 267–298

[14] Chiti F, Taddei N, Baroni F, Capanni C, Stefani M, Ramponi G, Dobson C M (2002). Kinetic partitioning of protein folding and aggregation. Nat Struct Biol, 9:137–143

[15] Davis R, Dobson C M, Vendruscolo M (2002). Determination of the structures of distinct transition state ensembles for a β-sheet peptide with parallel folding pathways. J Chem Phys, 117: 9510–9517

[16] DeMarco M L, Daggett V (2004). From conversion to aggregation: Protofibril formation of the prion protein. Proc Natl Acad Sci USA, 101:2293–2298

[17] Dill K A, Chan H S (1997). From Levinthal to pathways to funnels. Nat Struct Biol, 4: 10–19

[18] Dinner A R, Sali A, Smith L J, Dobson C M, Karplus M (2000). Understanding protein folding via free energy surfaces from theory and experiment. Trends Biochem Sci, 25: 331–339

[19] Dobson C M (1999). Protein misfolding, evolution and disease. Trends Biochem Sci, 24: 329–332

[20] Dobson C M (2002). Getting out of shape-protein misfolding diseases. Nature, 418: 729–730

[21] Dobson C M (2003). Protein folding and disease: a view from the first Horizon symposium. Nat Rev Drug Discov, 2: 154–160

[22] Dobson C M (2004). Principles of protein folding, misfolding and aggregation. Semin Cell Dev Bio, 15: 3–16

[23] Dobson C M, Sali A, Karplus M (1998). Protein folding: a perspective from theory and experiment. Angew Chem Int Ed Eng, 37: 868–893

[24] Fernandez-Escamilla A M, 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

[25] Fersht A (1999). Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding. New York: WH Freeman

[26] Fersht A R (2000). Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc Natl Acad Sci USA, 97:1525–1529

[27] Galzitskaya O V, Garbuzynskiy S O, Lobanov M Y (2006). Is it possible to predict amyloidogenic regions from sequence alone? J Bioinform Comput Biol, 4: 373–388

[28] Garten R J, Davis C T, Russell C A, Shu B, Lindstrom S, Balish A, Sessions W M, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith C B, Emery S L, Hillman M J, Rivailler P, Smagala J, de Graaf M, Burke D F, Fouchier R A, Pappas C, Alpuche-Aranda C M, López-Gatell H, Olivera H, López I, Myers C A, Faix D, Blair P J, Yu C, Keene K M, Dotson P D Jr, Boxrud D, Sambol A R, Abid S H, St George K, Bannerman T, Moore A L, Stringer D J, Blevins P, Demmler-Harrison G J, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara H F, Belongia E A, Clark P A, Beatrice S T, Donis R, Katz J, Finelli L, Bridges C B, Shaw M, Jernigan D B, Uyeki T M, Smith D J, Klimov A I, Cox N J (2009). Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science, 325: 197–201

[29] Gething M J, Sambrook J (1992). Protein folding in the cell. Nature, 355: 33–45

[30] Govaerts C, Wille H, Prusiner S B, Cohen F E (2004). Evidence for assembly of prions with left-handed beta-helices into trimers. Proc Natl Acad Sci USA, 101: 8342–8347

[31] Gray J J (2006). High-resolution protein-protein docking. Curr Opin Struct Biol, 16: 183–193

[32] Hardesty B, Kramer G (2001). Folding of a nascent peptide on the ribosome. Prog Nucleic Acid Res Mol Biol, 66:41–66

[33] Hardy J, Cai H, Cookson M R, Gwinn-Hardy K, Singleton A (2006). Genetics of Parkinson's disease and parkinsonism. Ann Neurol, 60: 389–398

[34] Hardy J, Selkoe D J (2002). The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science, 297: 353–356

[35] Hartl F U, Hayer-Hartl M (2002). Molecular chaperones in the cytosol: from nascent chain to folded protein. Science, 295: 1852–1858

[36] Hore P J, Winder S L, Roberts C H, Dobson C M (1997). Stopped-flow photo-CIDNP observation of protein folding. J Am Chem Soc, 119: 5049–5050

[37] Höppener J W, Nieuwenhuis M G, Vroom T M, Ahrén B, Lips C J (2002). Role of islet amyloid in type 2 diabetes mellitus: consequence or cause? Mol Cell Endocrinol, 197: 205–212

[38] Huang Z W, Prusiner S B, Cohen F E (1996). Scrapie prions: a three-dimensional model of an infectious fragment. Fold Des, 1: 13–19

[39] Ivanova M I, Sawaya M R, Gingery M, Attinger A, Eisenberg D (2004). An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril. Proc Natl Acad Sci USA, 101: 10584–10589

[40] Karplus M (1997). The Levinthal paradox, yesterday and today. Fold Des, 2: S69–S76

[41] Kelly J W (1996). Alternative conformations of amyloidogenic proteins govern their behavior. Curr Opin Struct Biol, 6: 11–17

[42] Koo E H, Lansbury P T Jr, Kelly J W (1999). Amyloid diseases: abnormal protein aggregation in neurodegeneration. Proc Natl Acad Sci USA, 96: 9989–9990

[43] Kuwata K, Nishida N, Matsumoto T, Kamatari Y O, Hosokawa-Muto J, Kodama K, Nakamura H K, Kimura K, Kawasaki M, Takakura Y, Shirabe S, Takata J, Kataoka Y, Katamine S (2007). Hot spots in prion protein for pathogenic conversion. Proc Natl Acad Sci USA, 104: 11921–11926

[44] Liu X, Zhao Y P (2009a). A scheme for multiple sequence alignment optimization-- an improvement based on family representative mechanics features. J Theor Biol, 261: 593–597

[45] Liu X, Zhao Y P (2009b). Donut-shaped fingerprint in homologous polypeptide relationships--a topological feature related to pathogenic structural conversion of conformational disease. J Theor Biol, 258: 294–301

[46] Liu X, Zhao Y P (2010a). Generating artificial homologous proteins according to the representative family characteristic in molecular mechanics properties. FEBS Lett, (in press)

[47] Liu X, Zhao Y P (2010b). Simulated pathogenic conformational switch regions matched well with the biochemical findings. J Biomed Inform, (in press)

[48] Liu X, Zhao Y P (2010c). Switch region for pathogenic structural change in conformational disease and its prediction. Plos One, 5(1): e8441

[49] López de la Paz M, Goldie K, Zurdo J, Lacroix E, Dobson C M, Hoenger A, Serrano L (2002). De novo designed peptide-based amyloid fibrils. Proc Natl Acad Sci USA, 99: 16052–16057

[50] López de la Paz M, Serrano L (2004). Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci USA, 101: 87–92

[51] Makarov D E, Plaxco K W (2003). The topomer search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci, 12: 17–26

[52] Mastrangelo I, Ahmed M, Sato T, Liu W, Wang C, Hough P, Smith S O (2006). High-resolution atomic force microscopy of soluble Abeta42 oligomers. J Mol Biol, 358: 106–109

[53] Matouschek A, Kellis J T, Serrano L, Fersht A R (1989). Mapping the transition state and pathway of protein folding by protein engineering. Nature, 342: 122–126

[54] Meiering E M (2008). The threat of instability: neurodegeneration predicted by protein destabilization and aggregation propensity. Plos Biol, 6: e193

[55] Nelson R, Sawaya M R, Balbirnie M, Madsen A Ø, Riekel C, Grothe R, Eisenberg D (2005). Structure of the cross-beta spine of amyloid-like fibrils. Nature, 435: 773–778

[56] Ólafsson Í, Grubb A (2000). Hereditary cystatin C amyloid angiopathy. Amyloid, 7: 70–79

[57] Pawar A P, Dubay K F, Zurdo J, Chiti F, Vendruscolo M, Dobson C M (2005). Prediction of “aggregation-prone” and “aggregation-susceptible” regions in proteins associated with neurodegenerative diseases. J Mol Biol, 350: 379–392

[58] Pepys M B (1995). The Oxford textbook of medicine. 3rd ed. Oxford: Oxford University Press, 1512–1524

[59] Polverino de Laureto P, Taddei N, Frare E, Capanni C, Costantini S, Zurdo J, Chiti F, Dobson C M, Fontana A (2003). Protein aggregation and amyloid fibril formation by an SH3 domain probed by limited proteolysis. J Mol Biol, 334: 129–141

[60] Prusiner S B (1997). Prion diseases and the BSE crisis. Science, 278: 245–251

[61] Saiki M, Konakahara T, Morii H (2006). Interaction-based evaluation of the propensity for amyloid formation with cross-beta structure. Biochem Biophys Res Commun, 343: 1262–1271

[63] Sánchez de Groot N, Pallarés I, Avilés FX, Vendrell J, Ventura S (2005). Prediction of “hot spots” of aggregation in disease-linked polypeptides. BMC Struct Biol, 5: 18

[64] Sawaya M R, Sambashivan S, Nelson R, Ivanova M I, Sievers S A, Apostol M I, Thompson MJ, Balbirnie M, Wiltzius J J, McFarlane H T, Madsen A Ø, Riekel C, Eisenberg D (2007). Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature, 447(7143): 453–457

[65] Smirnovas V, Kim J I, Lu X, Atarashi R, Caughey B, Surewicz W K (2009). Distinct structures of Scrapie Prion Protein (PrPSc)-seeded versus spontaneous recombinant prion protein fibrils revealed by hydrogen/deuterium exchange. J Biol Chem, 284(36): 24233–24241

[66] Soto C (2001). Protein misfolding and disease; protein refolding and therapy. FEBS lett, 498: 204–207

[67] Stefani M, Dobson C M (2003). Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. J Mol Med, 81: 678–699

[68] Thomas P J, Qu B H, Pedersen P L (1995). Defective protein folding as a basis of human disease. Trends Biochem Sci, 20: 456–459

[69] Walsh D M, Klyubin I, Fadeeva J V, Cullen W K, Anwyl R, Wolfe M S, Rowan M J, Selkoe D J (2002). Naturally secreted oligomers of amyloid beta protein potently inhibit hippocampal long-term potentiation in vivo. Nature, 416: 535–539

[70] Wei G, Mousseau N, Derreumaux P (2007). Computational simulations of the early steps of pProtein aggregation. Prion, 1: 3–8

[71] Wolynes P G, Onuchic J N, Thirumalai D (1995). Navigating the folding routes. Science, 267: 1619–1623

[72] Vendruscolo M, Paci E, Dobson C M, Karplus M (2001). Three key residues form a critical contact network in a transition state for protein folding. Nature, 409: 641–645

[73] Ventura S, Zurdo J, Narayanan S, Parreño M, Mangues R, Reif B, Chiti F, Giannoni E, Dobson C M, Aviles F X, Serrano L (2004). Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc Natl Acad Sci USA, 101: 7258–7263

[74] Yoon S, Welsh W J (2004). Detecting hidden sequence propensity for amyloid fibril formation. Protein Sci, 13: 2149–2160

[75] Zhang Z, Chen H, Lai L (2007). Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential. Bioinformatics, 23: 2218–2225

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg