Journal of Molecular Biology
Prediction of “Aggregation-prone” and “Aggregation-susceptible” Regions in Proteins Associated with Neurodegenerative Diseases
Introduction
Biological macromolecules such as proteins, lipids and nucleic acids have the ability to assemble into functional complexes in a highly regulated manner within densely crowded environments.1, 2 Moreover, the balance between normal and pathological self-association has been carefully tuned by molecular evolution.3, 4 Failures of the regulatory mechanisms do, however, occur and may result in conditions such as Alzheimer's and Creutzfeldt–Jakob diseases, and type II diabetes. Such diseases are associated with the deposition in tissue of pathogenic aggregates that are composed largely of misfolded proteins in the form of amyloid fibrils or plaques.5, 6, 7, 8, 9, 10 Recent work suggests that not only are amyloid aggregates formed in vivo from a group of otherwise unrelated proteins, but they can be induced in vitro from proteins not associated with known deposition diseases.3, 10, 11, 12, 13 Such observations have led to the suggestion that the ability to form amyloid fibrils may be a common characteristic of polypeptide chains,3, 5 although individual propensities vary greatly with the sequence and the environmental conditions.
A range of diverse factors has been reported to influence the rate of amyloid formation. Extrinsic factors that can affect the formation of protein aggregates in vivo include the interaction with cellular or extracellular components such as molecular chaperones that inhibit misfolding,14 proteases that frequently generate or process the amyloidogenic precursors,15 and the effectiveness of quality control mechanisms such as the ubiquitin–proteasome system.16, 17 They also include physicochemical properties that describe the environment of the polypeptide chains, such as pH, temperature, ionic strength, protein concentration, denaturant concentration and pressure.18, 19, 20, 21, 22, 23, 24, 25 Intrinsic factors associated with amyloid formation include a range of fundamental characteristics of polypeptide chains, such as charge,26, 27, 28, 29 hydrophobicity,30, 31, 32 patterns of polar and non-polar residues,33 and the propensities to adopt diverse secondary structure elements.27, 32, 34, 35 In the case of globular proteins, the propensities to form amyloid structures are generally inversely related to the stability of their native states.24, 36, 37, 38, 39, 40, 41, 42 Many of the proteins associated with amyloid diseases are, however, at least partially unfolded under physiological conditions. In addition, it is thought that many globular proteins unfold, at least partially, before aggregating. The present study is therefore focused on the conversion of unfolded or partially unfolded states into amyloid aggregates.
One of the most intriguing recent observations in studies of the kinetics of amyloid formation is that polypeptide sequences appear to contain local regions that are “sensitive” for aggregation.32 Single amino acid mutations in these regions can change the aggregation rates dramatically, while similar changes in other regions may have relatively little effect.32, 43 In addition, it has been shown that it is possible to describe with considerable accuracy the in vitro amyloid aggregation propensities of polypeptides using algorithms that take into account the physico-chemical properties of their sequences and of their environment.44, 45, 46, 47, 48 Here, our purpose is to apply this type of analysis to the rationalisation and the prediction of the sensitive regions of polypeptide sequences in general and of proteins associated with neurodegenerative diseases in particular.
Section snippets
Definition of intrinsic aggregation propensities
We define the intrinsic propensity of an unfolded polypeptide chain to form amyloid aggregates, Pagg, by considering just the intrinsic factors in the formula that we have recently introduced to define the absolute aggregation rates of unstructured polypeptide chains:45where Ihydr represents the hydrophobicity of the sequence,49, 50 Iα is the α-helical propensity,51 Iβ is the β-sheet propensity,51 Ipat is the hydrophobic patterning,52 and Ich is the
Discussion and Conclusions
Here, we describe a method for calculating the intrinsic amyloid aggregation propensities of polypeptide sequences, and we have used this approach to calculate the aggregation propensity profiles for three natively unfolded polypeptide chains associated with neurodegenerative diseases, Aβ42, α-synuclein and tau. These profiles have allowed the regions of these sequences that influence their aggregation behaviour to be identified and compared to the results of experimental studies.
We can
Fitting of the coefficients using known aggregation rates
The intrinsic factors included in the algorithm developed45 were used in this work to calculate Pagg, the intrinsic aggregation propensity of a sequence. The weights of the various intrinsic factors were determined simultaneously by using regression techniques using an extended database of 203 sequences that included the 83 sequences used by DuBay et al.45 We used normalised β-sheet and α-helix propensity scales,51 with the following modifications: for β-sheet propensity calculations, we set
Acknowledgements
We are grateful for support from the Gates Cambridge Trust (A.P.P., K.F.D.), the Leverhulme Trust (to J.Z., M.V. and C.M.D.), the Italian MIUR and CNR (to F.C.), the Royal Society (to M.V.) and the Wellcome Trust (to C.M.D.).
References (100)
Macromolecular crowding: obvious but underappreciated
Trends Biochem.Sci.
(2001)Implications of macromolecular crowding for protein assembly
Curr. Opin. Struct. Biol.
(2000)Protein misfolding, evolution and disease
Trends Biochem. Sci.
(1999)- et al.
Deadly conformations—protein misfolding in prion disease
Cell
(1997) The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways
Curr. Opin. Struct. Biol.
(1998)- et al.
Amyloid fibrillogenesis: themes and variations
Curr. Opin. Struct. Biol.
(2000) - et al.
Conformational constraints for amyloid fibrillation: the importance of being unfolded
BBA-Proteins Proteomics
(2004) Protein misfolding, amyloid formation, and neurodegeneration: a critical role for molecular chaperones?
Neuron
(2002)- et al.
Acidic pH promotes the formation of toxic fibrils from beta-amyloid peptide
Brain Res.
(2001) - et al.
Dependence on solution conditions of aggregation and amyloid formation by an SH3 domain
J. Mol. Biol.
(2001)
Charge attraction and beta propensity are necessary for amyloid fibril formation from tetrapeptides
J. Biol. Chem.
Prediction of amyloid fibril-forming proteins
J. Biol. Chem.
The tetrameric protein transthyretin dissociates to a non-native monomer in solution—a novel model for amyloidogenesis
J. Biol. Chem.
A systematic investigation into the effect of protein destabilisation on beta 2-microglobulin amyloid formation
J. Mol. Biol.
Mapping A beta amyloid fibril secondary structure using scanning proline mutagenesis
J. Mol. Biol.
Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains
J. Mol. Biol.
A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins
J. Mol. Biol.
Hydrophilicity of polar amino-acid side-chains is markedly reduced by flanking peptide-bonds
J. Mol. Biol.
Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis
J. Mol. Biol.
Analysis of the minimal amyloid-forming fragment of the islet amyloid polypeptide—an experimental support for the key role of the phenylalanine residue in amyloid formation
J. Biol. Chem.
A molecular model of Alzheimer amyloid beta-peptide fibril formation
J. Biol. Chem.
Structural and dynamic features of Alzheimer's A beta peptide in amyloid fibrils studied by site-directed spin labeling
J. Biol. Chem.
Mutations that reduce aggregation of the Alzheimer's A beta 42 peptide: an unbiased search for the sequence determinants of A beta amyloidogenesis
J. Mol. Biol.
Elucidation of primary structure elements controlling early amyloid beta-protein oligomerization
J. Biol. Chem.
Amyloid beta-protein oligomerization—prenucleation interactions revealed by photo-induced cross-linking of unmodified proteins
J. Biol. Chem.
Substitutions at codon 22 of Alzheimer's A beta peptide induce diverse conformational changes and apoptotic effects in human cerebral endothelial cells
J. Biol. Chem.
Pathogenic effects of D23N Iowa mutant amyloid beta-protein
J. Biol. Chem.
The core Alzheimers peptide Nac forms amyloid fibrils which seed and are seeded by beta-amyloid—is Nac a common trigger or target in neurodegenerative disease
Chem. Biol.
A hydrophobic stretch of 12 amino acid residues in the middle of alpha-synuclein is essential for filament assembly
J. Biol. Chem.
Intrinsically disordered protein
J. Mol. Graph.
Structural organization of alpha-synuclein fibrils studied by site-directed spin labeling
J. Biol. Chem.
Mutation E46K increases phospholipid binding and assembly into filaments of human alpha-synuclein
FEBS Letters
Tissue-dependent alternative splicing of messenger-Rna For Nacp, the precursor of non-A-beta component of Alzheimer's-disease amyloid
Biochem. Biophys. Res. Commun.
Tau gene mutations: dissecting the pathogenesis of FTDP-17
Trends Mol. Med.
Multiple isoforms of human microtubule-associated protein-Tau—sequences and localization in neurofibrillary tangles of Alzheimers disease
Neuron
Protein folding and misfolding: a paradigm of self-assembly and regulation in complex biological systems
Phil. Trans. Roy. Soc. ser. A
The structural basis of protein folding and its links with human disease
Phil. Trans. Roy. Soc. ser. B
Alzheimer's disease is a synaptic failure
Science
Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution
J. Mol. Med.
Designing conditions for in vitro formation of amyloid protofilaments and fibrils
Proc. Natl Acad. Sci. USA
Amyloid fibril formation by an SH3 domain
Proc. Natl Acad. Sci. USA
Mutant presenilins of Alzheimer's disease increase production of 42-residue amyloid beta-protein in both transfected cells and transgenic mice
Nature Med.
Impairment of the ubiquitin-proteasome system by protein aggregation
Science
Increased body-temperature accelerates aggregation of the Leu-68-Gln mutant cystatin-C, the amyloid-forming protein in hereditary cystatin-C amyloid angiopathy
Proc. Natl Acad. Sci. USA
On the nucleation and growth of amyloid beta-protein fibrils: detection of nuclei and quantitation of rate constants
Proc. Natl Acad. Sci. USA
Models of amyloid seeding in Alzheimier's disease and scrapie: mechanistic truths and physiological consequences of the time-dependent solubility of amyloid proteins
Annu. Rev. Biochem.
Temperature dependence of amyloid beta-protein fibrillization
Proc. Natl Acad. Sci. USA
Mutational analysis of the propensity for amyloid formation by a globular protein
EMBO J.
The preaggregated state of an amyloidogenic protein: hydrostatic pressure converts native transthyretin into the amyloidogenic state
Proc. Natl Acad. Sci. USA
Cited by (0)
- †
A.P.P. & K.F.D. contributed equally to this work.
- ‡
Present address: K. F. DuBay, Department of Chemistry, UC Berkeley, 419 Latimer Hall, Berkeley, CA 94720-1460, USA.