1
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Chao YJ, Wu K, Chang HH, Chien MJ, Chan JCC. Manifold of self-assembly of a de novo designed peptide: amyloid fibrils, peptide bundles, and fractals. RSC Adv 2020; 10:29510-29515. [PMID: 35521097 PMCID: PMC9055936 DOI: 10.1039/d0ra04480f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/02/2020] [Indexed: 12/18/2022] Open
Abstract
We report that a peptide with the sequence of EGAGAAAAGAGE can have different aggregation states, viz., amyloid fibrils, peptide bundles, and fractal assembly under different incubation conditions. The chemical state of the Glu residue played a pivotal regulating role in the aggregation behavior of the peptide. The mechanism of the fractal assembly of this peptide has been unraveled as follows. The peptide fragments adopting the beta-sheet conformation are well dispersed in alkaline solution. In the buffer of sodium bicarbonate, peptide rods are formed with considerable structural rigidity at the C- and N-termini. The peptide rods undergo random trajectory in the solution and form a fractal pattern on a two-dimensional surface via the diffusion-limited aggregation process.
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Affiliation(s)
- Yu-Jo Chao
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
| | - Kan Wu
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
| | - Hsun-Hui Chang
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
| | - Ming-Jou Chien
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
| | - Jerry Chun Chung Chan
- Department of Chemistry, National Taiwan University No. 1, Section 4, Roosevelt Road Taipei 10617 Taiwan
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2
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Teferedegn EY, Yaman Y, Ün C. Novel Variations in Native Ethiopian Goat breeds PRNP Gene and Their Potential Effect on Prion Protein Stability. Sci Rep 2020; 10:6953. [PMID: 32332800 PMCID: PMC7181617 DOI: 10.1038/s41598-020-63874-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/08/2020] [Indexed: 12/22/2022] Open
Abstract
Scrapie is a lethal neurodegenerative disease of sheep and goats caused by the misfolding of the prion protein. Variants such as M142, D145, S146, H154, Q211, and K222 were experimentally found to increase resistance or extend scrapie incubation period in goats. We aimed to identify polymorphisms in the Afar and Arsi-Bale goat breeds of Ethiopia and computationally assess the effect of variants on prion protein stability. In the present study, four non-synonymous novel polymorphisms G67S, W68R, G69D, and R159H in the first octapeptide repeat and the highly conserved C-terminus globular domain of goat PrP were detected. The resistant genotype, S146, was detected in >50% of the present population. The current study population showed a genetic diversity in Ethiopian goat breeds. In the insilico analysis, the R68 variant was predicted to increase stability while S67, D69, and H159 decrease the stability of prion protein. The new variants in the octapeptide repeat motif were predicted to decrease amyloidogenicity but H159 increased the hotspot sequence amyloidogenic propensity. These novel variants could be the source of conformational flexibility that may trigger the gain or loss of function by prion protein. Further experimental study is required to depict the actual effects of variants on prion protein stability.
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Affiliation(s)
| | - Yalçın Yaman
- Department of Biometry and Genetics, Bandırma Sheep Research Institute, Bandırma, Balıkesir, Turkey
| | - Cemal Ün
- Ege University, Department of Biology, Molecular Biology Division, Izmir, Turkey.
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3
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Shen HCH, Chen YH, Lin YS, Chu BKY, Liang CS, Yang CC, Chen RPY. Segments in the Amyloid Core that Distinguish Hamster from Mouse Prion Fibrils. Neurochem Res 2019; 44:1399-1409. [PMID: 30603982 DOI: 10.1007/s11064-018-02709-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/29/2018] [Accepted: 12/23/2018] [Indexed: 10/27/2022]
Abstract
Prion diseases are transmissible fatal neurodegenerative disorders affecting humans and other mammals. The disease transmission can occur between different species but is limited by the sequence homology between host and inoculum. The crucial molecular event in the progression of this disease is prion formation, starting from the conformational conversion of the normal, membrane-anchored prion protein (PrPC) into the misfolded, β-sheet-rich and aggregation-prone isoform (PrPSc), which then self-associates into the infectious amyloid form called prion. Amyloid is the aggregate formed from one-dimensional protein association. As amyloid formation is a key hallmark in prion pathogenesis, studying which segments in prion protein are involved in the amyloid formation can provide molecular details in the cross-species transmission barrier of prion diseases. However, due to the difficulties of studying protein aggregates, very limited knowledge about prion structure or prion formation was disclosed by now. In this study, cross-seeding assay was used to identify the segments involved in the amyloid fibril formation of full-length hamster prion protein, SHaPrP(23-231). Our results showed that the residues in the segments 108-127, 172-194 (helix 2 in PrPC) and 200-227 (helix 3 in PrPC) are in the amyloid core of hamster prion fibrils. The segment 127-143, but not 107-126 (which corresponds to hamster sequence 108-127), was previously reported to be involved in the amyloid core of full-length mouse prion fibrils. Our results indicate that hamster prion protein and mouse prion protein use different segments to form the amyloid core in amyloidogenesis. The sequence-dependent core formation can be used to explain the seeding barrier between mouse and hamster.
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Affiliation(s)
- Howard C-H Shen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Yung-Han Chen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan
| | - Yu-Sheng Lin
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.,Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Brett K-Y Chu
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Ching-Shin Liang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chien-Chih Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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4
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Sengupta I, Udgaonkar JB. Structural mechanisms of oligomer and amyloid fibril formation by the prion protein. Chem Commun (Camb) 2018; 54:6230-6242. [PMID: 29789820 DOI: 10.1039/c8cc03053g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Misfolding and aggregation of the prion protein is responsible for multiple neurodegenerative diseases. Works from several laboratories on folding of both the WT and multiple pathogenic mutant variants of the prion protein have identified several structurally dissimilar intermediates, which might be potential precursors to misfolding and aggregation. The misfolded aggregates themselves are morphologically distinct, critically dependent on the solution conditions under which they are prepared, but always β-sheet rich. Despite the lack of an atomic resolution structure of the infectious pathogenic agent in prion diseases, several low resolution models have identified the β-sheet rich core of the aggregates formed in vitro, to lie in the α2-α3 subdomain of the prion protein, albeit with local stabilities that vary with the type of aggregate. This feature article describes recent advances in the investigation of in vitro prion protein aggregation using multiple spectroscopic probes, with particular focus on (1) identifying aggregation-prone conformations of the monomeric protein, (2) conditions which trigger misfolding and oligomerization, (3) the mechanism of misfolding and aggregation, and (4) the structure of the misfolded intermediates and final aggregates.
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Affiliation(s)
- Ishita Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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5
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Iłowska E, Sawicka J, Szymańska A. Synthesis and physicochemical studies of amyloidogenic hexapeptides derived from human cystatin C. J Pept Sci 2018; 24:e3073. [PMID: 29573035 DOI: 10.1002/psc.3073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/06/2018] [Accepted: 02/12/2018] [Indexed: 01/20/2023]
Abstract
Human cystatin C (hCC) is a low molecular mass protein that belongs to the cystatin superfamily. It is an inhibitor of extracellular cysteine proteinases, present in all human body fluids. At physiological conditions, hCC is a monomer, but it has a tendency to dimerization. Naturally occurring hCC mutant, with leucine in position 68 substituted by glutamine (L68Q), is directly involved in the formation of amyloid deposits, independently of other proteins. This process is the primary cause of hereditary cerebral amyloid angiopathy, observed mainly in the Icelandic population. Oligomerization and fibrillization processes of hCC are not explained equally well, but it is proposed that domain swapping is involved in both of them. Research carried out on the fibrillization process led to new hypothesis about the existence of a steric zipper motif in amyloidogenic proteins. In the hCC sequence, there are 2 fragments which may play the role of a steric zipper: the loop L1 region and the C-terminal fragment. In this work, we focused on the first of these. Nine hexapeptides covering studied hCC fragment were synthesized, and their fibrillogenic potential was assessed using an array of biophysical methods. The obtained results showed that the studied hCC fragment has strong profibrillogenic propensities because it contains 2 fragments fulfilling the requirements for an effective steric zipper located next to each other, forming 1 super-steric zipper motif. This hCC fragment might therefore be responsible for the enhanced amyloidogenic properties of dimeric or partially unfolded hCC.
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Affiliation(s)
- Emilia Iłowska
- Faculty of Chemistry, Department of Biomedical Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Justyna Sawicka
- Faculty of Chemistry, Department of Biomedical Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Aneta Szymańska
- Faculty of Chemistry, Department of Biomedical Chemistry, University of Gdańsk, Gdańsk, Poland
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6
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Cheng CJ, Koldsø H, Van der Kamp MW, Schiøtt B, Daggett V. Simulations of membrane-bound diglycosylated human prion protein reveal potential protective mechanisms against misfolding. J Neurochem 2017; 142:171-182. [PMID: 28407243 DOI: 10.1111/jnc.14044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/06/2023]
Abstract
Prion diseases are associated with the misfolding of the prion protein (PrP) from its normal cellular form (PrPC ) to its infectious scrapie form (PrPSc ). Post-translational modifications in PrP in vivo can play an important role in modulating the process of misfolding. To gain more insight into the effects of post-translational modifications in PrP structure and dynamics and to test the hypothesis that such modifications can interact with the protein, we have performed molecular dynamics simulations of diglycosylated human PrPC bound to a lipid bilayer via a glycophosphatidylinositol anchor. Multiple simulations were performed at three different pH ranges to explore pH effects on structure and dynamics. In contrast to simulations of protein-only PrPC , no large effects were observed upon lowering the pH of the system. The protein tilted toward the membrane surface in all of the simulations and the putative PrPSc oligomerization sites became inaccessible, thereby offering a possible protective mechanism against PrPSc -induced misfolding of PrPC .
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Affiliation(s)
- Chin Jung Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Heidi Koldsø
- Department of Bioengineering, University of Washington, Seattle, Washington, USA.,Department of Chemistry, inSPIN and iNANO Centers, Aarhus University, Aarhus C, Denmark
| | - Marc W Van der Kamp
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Birgit Schiøtt
- Department of Chemistry, inSPIN and iNANO Centers, Aarhus University, Aarhus C, Denmark
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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7
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Ning L, Wang Q, Zheng Y, Liu H, Yao X. Effects of the A117V mutation on the folding and aggregation of palindromic sequences (PrP113–120) in prion: insights from replica exchange molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2015; 11:647-55. [DOI: 10.1039/c4mb00546e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The A117V mutation enhances the aggregation propensity of the palindromic sequences in prion protein.
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Affiliation(s)
- Lulu Ning
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Qianqian Wang
- School of Pharmacy
- Lanzhou University
- Lanzhou 730000
- China
| | - Yang Zheng
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Huanxiang Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- School of Pharmacy
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- State Key Laboratory of Quality Research in Chinese Medicine
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8
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Gill AC. β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides. PLoS One 2014; 9:e87354. [PMID: 24498083 PMCID: PMC3909104 DOI: 10.1371/journal.pone.0087354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/19/2013] [Indexed: 01/09/2023] Open
Abstract
Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109-122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109-122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109-122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106-126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new atomic-level model for the formation of oligomers and fibrils of the prion protein and suggest that stabilization of β-hairpin structure may enhance cellular toxicity by altering the balance between oligomeric and fibrillar protein assemblies.
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Affiliation(s)
- Andrew C. Gill
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus, University of Edinburgh, Roslin, Edinburgh, United Kingdom
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9
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Abskharon RNN, Giachin G, Wohlkonig A, Soror SH, Pardon E, Legname G, Steyaert J. Probing the N-terminal β-sheet conversion in the crystal structure of the human prion protein bound to a nanobody. J Am Chem Soc 2014; 136:937-44. [PMID: 24400836 DOI: 10.1021/ja407527p] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prions are fatal neurodegenerative transmissible agents causing several incurable illnesses in humans and animals. Prion diseases are caused by the structural conversion of the cellular prion protein, PrP(C), into its misfolded oligomeric form, known as prion or PrP(Sc). The canonical human PrP(C) (HuPrP) fold features an unstructured N-terminal part (residues 23-124) and a well-defined C-terminal globular domain (residues 125-231). Compelling evidence indicates that an evolutionary N-terminal conserved motif AGAAAAGA (residues 113-120) plays an important role in the conversion to PrP(Sc). The intrinsic flexibility of the N-terminal has hampered efforts to obtain detailed atomic information on the structural features of this palindromic region. In this study, we crystallized the full-length HuPrP in complex with a nanobody (Nb484) that inhibits prion propagation. In the complex, the prion protein is unstructured from residue 23 to 116. The palindromic motif adopts a stable and fully extended configuration to form a three-stranded antiparallel β-sheet with the β1 and β2 strands, demonstrating that the full-length HuPrP(C) can adopt a more elaborate β0-β1-α1-β2-α2-α3 structural organization than the canonical β1-α1-β2-α2-α3 prion-like fold. From this structure, it appears that the palindromic motif mediates β-enrichment in the PrP(C) monomer as one of the early events in the conversion of PrP(C) into PrP(Sc).
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Affiliation(s)
- Romany N N Abskharon
- Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
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10
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Baral PK, Swayampakula M, Rout MK, Kav NNV, Spyracopoulos L, Aguzzi A, James MNG. Structural basis of prion inhibition by phenothiazine compounds. Structure 2013; 22:291-303. [PMID: 24373770 DOI: 10.1016/j.str.2013.11.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/10/2023]
Abstract
Conformational transitions of the cellular form of the prion protein, PrP(C), into an infectious isoform, PrP(Sc), are considered to be central events in the progression of fatal neurodegenerative diseases known as transmissible spongiform encephalopathies. Tricyclic phenothiazine compounds exhibit antiprion activity; however, the underlying molecular mechanism of PrP(Sc) inhibition remains elusive. We report the molecular structures of two phenothiazine compounds, promazine and chlorpromazine bound to a binding pocket formed at the intersection of the structured and the unstructured domains of the mouse prion protein. Promazine binding induces structural rearrangement of the unstructured region proximal to β1, through the formation of a "hydrophobic anchor." We demonstrate that these molecules, promazine in particular, allosterically stabilize the misfolding initiator-motifs such as the C terminus of α2, the α2-α3 loop, as well as the polymorphic β2-α2 loop. Hence, the stabilization effects of the phenothiazine derivatives on initiator-motifs induce a PrP(C) isoform that potentially resists oligomerization.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Manoj Kumar Rout
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Adriano Aguzzi
- Department of Pathology, Institute of Neuropathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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11
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Do TD, Economou NJ, LaPointe NE, Kincannon WM, Bleiholder C, Feinstein SC, Teplow DB, Buratto SK, Bowers MT. Factors that drive peptide assembly and fibril formation: experimental and theoretical analysis of Sup35 NNQQNY mutants. J Phys Chem B 2013; 117:8436-46. [PMID: 23802812 DOI: 10.1021/jp4046287] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Residue mutations have substantial effects on aggregation kinetics and propensities of amyloid peptides and their aggregate morphologies. Such effects are attributed to conformational transitions accessed by various types of oligomers such as steric zipper or single β-sheet. We have studied the aggregation propensities of six NNQQNY mutants: NVVVVY, NNVVNV, NNVVNY, VIQVVY, NVVQIY, and NVQVVY in water using a combination of ion-mobility mass spectrometry, transmission electron microscopy, atomic force microscopy, and all-atom molecular dynamics simulations. Our data show a strong correlation between the tendency to form early β-sheet oligomers and the subsequent aggregation propensity. Our molecular dynamics simulations indicate that the stability of a steric zipper structure can enhance the propensity for fibril formation. Such stability can be attained by either hydrophobic interactions in the mutant peptide or polar side-chain interdigitations in the wild-type peptide. The overall results display only modest agreement with the aggregation propensity prediction methods such as PASTA, Zyggregator, and RosettaProfile, suggesting the need for better parametrization and model peptides for these algorithms.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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12
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Chatterjee B, Lee CY, Lin C, Chen EHL, Huang CL, Yang CC, Chen RPY. Amyloid core formed of full-length recombinant mouse prion protein involves sequence 127-143 but not sequence 107-126. PLoS One 2013; 8:e67967. [PMID: 23844138 PMCID: PMC3700907 DOI: 10.1371/journal.pone.0067967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/23/2013] [Indexed: 12/23/2022] Open
Abstract
The principal event underlying the development of prion disease is the conversion of soluble cellular prion protein (PrP(C)) into its disease-causing isoform, PrP(Sc). This conversion is associated with a marked change in secondary structure from predominantly α-helical to a high β-sheet content, ultimately leading to the formation of aggregates consisting of ordered fibrillar assemblies referred to as amyloid. In vitro, recombinant prion proteins and short prion peptides from various species have been shown to form amyloid under various conditions and it has been proposed that, theoretically, any protein and peptide could form amyloid under appropriate conditions. To identify the peptide segment involved in the amyloid core formed from recombinant full-length mouse prion protein mPrP(23-230), we carried out seed-induced amyloid formation from recombinant prion protein in the presence of seeds generated from the short prion peptides mPrP(107-143), mPrP(107-126), and mPrP(127-143). Our results showed that the amyloid fibrils formed from mPrP(107-143) and mPrP(127-143), but not those formed from mPrP(107-126), were able to seed the amyloidogenesis of mPrP(23-230), showing that the segment residing in sequence 127-143 was used to form the amyloid core in the fibrillization of mPrP(23-230).
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Affiliation(s)
| | - Chung-Yu Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chen Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Eric H.-L. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chao-Li Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chien-Chih Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Rita P.-Y. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- * E-mail:
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13
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Cheng H, Huang WYC, Tsai TWT, Mou Y, Chao JCH, Chan JCC. Depletion of Water Molecules Near the End Stage of Steric Zipper Formation. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hsin‐Mei Cheng
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - William Y. C. Huang
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Tim W. T. Tsai
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - John Chin Hao Chao
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Jerry C. C. Chan
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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14
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Huang P, Lian F, Wen Y, Guo C, Lin D. Prion protein oligomer and its neurotoxicity. Acta Biochim Biophys Sin (Shanghai) 2013; 45:442-51. [PMID: 23557632 DOI: 10.1093/abbs/gmt037] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The prion diseases, also known as transmissible spongiform encephalopathies, are fatal neurodegenerative disorders. According to the 'protein only' hypothesis, the key molecular event in the pathogenesis of prion disease is the conformational conversion of the host-derived cellular prion protein (PrP(C)) into a misfolded form (scrapie PrP, PrP(Sc)). Increasing evidence has shown that the most infectious factor is the smaller subfibrillar oligomers formed by prion proteins. Both the prion oligomer and PrP(Sc) are rich in β-sheet structure and resistant to the proteolysis of proteinase K. The prion oligomer is soluble in physiologic environments whereas PrP(Sc) is insoluble. Various prion oligomers are formed in different conditions. Prion oligomers exhibited more neurotoxicity both in vitro and in vivo than the fibrillar forms of PrP(Sc), implying that prion oligomers could be potential drug targets for attacking prion diseases. In this article, we describe recent experimental evidence regarding prion oligomers, with a special focus on prion oligomer formation and its neurotoxicity.
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Affiliation(s)
- Pei Huang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 21009, China
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15
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Zhang J, Zhang Y. Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136). Acta Biochim Biophys Sin (Shanghai) 2013; 45:509-19. [PMID: 23563221 DOI: 10.1093/abbs/gmt031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Prion diseases, traditionally referred to as transmissible spongiform encephalopathies, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species, manifesting as scrapie in sheep, bovine spongiform encephalopathy (or 'mad-cow' disease) in cattle, and Creutzfeldt-Jakob disease, Gerstmann-Strussler-Scheinker syndrome, fatal familial insomnia (FFI), and Kulu in humans, etc. These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)) into insoluble abnormally folded infectious prions (PrP(Sc)). The hydrophobic region PrP(109-136) controls the formation of diseased prions: the normal PrP(113-120) AGAAAAGA palindrome is an inhibitor/blocker of prion diseases and the highly conserved glycine-xxx-glycine motif PrP(119-131) can inhibit the formation of infectious prion proteins in cells. This article gives detailed reviews on the PrP(109-136) region and presents the studies of its three-dimensional structures and structural dynamics.
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Affiliation(s)
- Jiapu Zhang
- Graduate School of Sciences, Information Technology and Engineering, CIAO, The University of Ballarat, MT Helen Campus, Victoria 3353, Australia.
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16
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Comellas G, Rienstra CM. Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils. Annu Rev Biophys 2013; 42:515-36. [DOI: 10.1146/annurev-biophys-083012-130356] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology,
- Department of Chemistry, and
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; ,
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17
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Chou FC, Tsai TWT, Cheng HM, Chan JCC. Measurements of 13C multiple-quantum coherences in amyloid fibrils under magic-angle spinning. J Phys Chem B 2012; 116:7162-7. [PMID: 22632418 DOI: 10.1021/jp303455w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The excitation and detection of high-order multiple quantum coherences among (13)C nuclear spins are demonstrated in the samples of [1-(13)C]-L-alanine and (13)C labeled amyloid fibrils at a spinning frequency of 20 kHz. The technique is based on the double-quantum average Hamiltonian prepared by the DRAMA-XY4 pulse sequence. Empirically, we find that multiple supercycles are required to suppress the higher-order effects for real applications. Measurements for the fibril samples formed by the polypeptides of PrP(113-127) provide the first solid-state NMR evidence for the stacking of multiple β-sheet layers at the structural core of amyloid fibrils.
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Affiliation(s)
- Fang-Chieh Chou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan
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18
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Zhang J, Hou Y, Wang Y, Wang C, Zhang X. The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ns.2012.412a138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Daidone I, Di Nola A, Smith JC. Molecular origin of Gerstmann-Sträussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide. Biophys J 2011; 100:3000-7. [PMID: 21689534 DOI: 10.1016/j.bpj.2011.04.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 04/11/2011] [Accepted: 04/25/2011] [Indexed: 01/02/2023] Open
Abstract
Prion proteins become pathogenic through misfolding. Here, we characterize the folding of a peptide consisting of residues 109-122 of the Syrian hamster prion protein (the H1 peptide) and of a more amyloidogenic A117V point mutant that leads in humans to an inheritable form of the Gerstmann-Sträussler-Scheinker syndrome. Atomistic molecular dynamics simulations are performed for 2.5 μs. Both peptides lose their α-helical starting conformations and assume a β-hairpin that is structurally similar in both systems. In each simulation several unfolding/refolding events occur, leading to convergence of the thermodynamics of the conformational states to within 1 kJ/mol. The similar stability of the β-hairpin relative to the unfolded state is observed in the two peptides. However, substantial differences are found between the two unfolded states. A local minimum is found within the free energy unfolded basin of the A117V mutant populated by misfolded collapsed conformations of comparable stability to the β-hairpin state, consistent with increased amyloidogenicity. This population, in which V117 stabilizes a hydrophobic core, is absent in the wild-type peptide. These results are supported by simulations of oligomers showing a slightly higher stability of the associated structures and a lower barrier to association for the mutated peptide. Hence, a single point mutation carrying only two additional methyl groups is here shown to be responsible for rather dramatic differences of structuring within the unfolded (misfolded) state.
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Affiliation(s)
- Isabella Daidone
- Department of Chemistry, Chemical Engineering and Materials, University of L'Aquila, L'Aquila, Italy.
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20
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Jones EM, Wu B, Surewicz K, Nadaud PS, Helmus JJ, Chen S, Jaroniec CP, Surewicz WK. Structural polymorphism in amyloids: new insights from studies with Y145Stop prion protein fibrils. J Biol Chem 2011; 286:42777-42784. [PMID: 22002245 PMCID: PMC3234922 DOI: 10.1074/jbc.m111.302539] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/05/2011] [Indexed: 11/06/2022] Open
Abstract
The C-terminally-truncated human prion protein variant Y145Stop (or PrP23-144), associated with a familial prion disease, provides a valuable model for studying the fundamental properties of protein amyloids. In previous solid-state NMR experiments, we established that the β-sheet core of the PrP23-144 amyloid is composed of two β-strand regions encompassing residues ∼113-125 and ∼130-140. The former segment contains a highly conserved hydrophobic palindrome sequence, (113)AGAAAAGA(120), which has been considered essential to PrP conformational conversion. Here, we examine the role of this segment in fibrillization of PrP23-144 using a deletion variant, Δ113-120 PrP23-144, in which the palindrome sequence is missing. Surprisingly, we find that deletion of the palindrome sequence affects neither the amyloidogenicity nor the polymerization kinetics of PrP23-144, although it does alter amyloid conformation and morphology. Using two-dimensional and three-dimensional solid-state NMR methods, we find that Δ113-120 PrP23-144 fibrils contain an altered β-core extended N-terminally to residue ∼106, encompassing residues not present in the core of wild-type PrP23-144 fibrils. The C-terminal β-strand of the core, however, is similar in both fibril types. Collectively, these data indicate that amyloid cores of PrP23-144 variants contain "essential" (i.e. nucleation-determining) and "nonessential" regions, with the latter being "movable" in amino acid sequence space. These findings reveal an intriguing new mechanism for structural polymorphism in amyloids and suggest a potential means for modulating the physicochemical properties of amyloid fibrils without compromising their polymerization characteristics.
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Affiliation(s)
- Eric M Jones
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Bo Wu
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Philippe S Nadaud
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Jonathan J Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Shugui Chen
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | | | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106.
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21
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Cheng HM, Tsai TWT, Huang WYC, Lee HK, Lian HY, Chou FC, Mou Y, Chan JCC. Steric zipper formed by hydrophobic peptide fragment of Syrian hamster prion protein. Biochemistry 2011; 50:6815-23. [PMID: 21749158 DOI: 10.1021/bi200712z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Steric zippers, where the residues of two neighboring β-sheet layers are tightly interdigitated, have been proposed as fundamental structural units of amyloid fibrils by Eisenberg and co-workers. The steric zipper formed by polypeptides containing the palindromic sequence AGAAAAGA has a distinctive feature that the distance between two interdigitated β-sheet layers is comparable to the interstrand distance of the individual β-sheet. This structural motif is of great interest in the study of prion disease because the AGAAAAGA sequence is highly conserved in prion proteins of different species. In this work, the amyloid fibrils formed by the polypeptides of PrP(113-127), viz. Ac-AGAAAAGAVVGGLGG-NH(2), are taken as the model compound to investigate the biophysical principles governing the steric zipper formation. The target fibrils adopt the structural motif of class 7 steric zipper, which is formed by stacking of antiparallel β-sheet layers with residue 117 + k forming backbone hydrogen bonds to residue 120 - k. Implication of our results in the infectivity of scrapie prion is briefly discussed.
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Affiliation(s)
- Hsin-Mei Cheng
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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22
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Zanetti Polzi L, Amadei A, Aschi M, Daidone I. New Insight into the IR-Spectra/Structure Relationship in Amyloid Fibrils: A Theoretical Study on a Prion Peptide. J Am Chem Soc 2011; 133:11414-7. [DOI: 10.1021/ja2028662] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Laura Zanetti Polzi
- Department of Chemistry, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Amadei
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Massimiliano Aschi
- Department of Chemistry, Chemical Engineering and Materials, University of L’Aquila, Via Vetoio (Coppito 1), 67010 L’Aquila, Italy
| | - Isabella Daidone
- Department of Chemistry, Chemical Engineering and Materials, University of L’Aquila, Via Vetoio (Coppito 1), 67010 L’Aquila, Italy
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23
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Tycko R, Savtchenko R, Ostapchenko VG, Makarava N, Baskakov IV. The α-helical C-terminal domain of full-length recombinant PrP converts to an in-register parallel β-sheet structure in PrP fibrils: evidence from solid state nuclear magnetic resonance. Biochemistry 2011; 49:9488-97. [PMID: 20925423 DOI: 10.1021/bi1013134] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report the results of solid state nuclear magnetic resonance (NMR) measurements on amyloid fibrils formed by the full-length prion protein PrP (residues 23−231, Syrian hamster sequence). Measurements of intermolecular 13C−13C dipole−dipole couplings in selectively carbonyl-labeled samples indicate that β-sheets in these fibrils have an in-register parallel structure, as previously observed in amyloid fibrils associated with Alzheimer’s disease and type 2 diabetes and in yeast prion fibrils. Two-dimensional 13C−13C and 15N−13C solid state NMR spectra of a uniformly 15N- and 13C-labeled sample indicate that a relatively small fraction of the full sequence, localized to the C-terminal end, forms the structurally ordered, immobilized core. Although unique site-specific assignments of the solid state NMR signals cannot be obtained from these spectra, analysis with a Monte Carlo/simulated annealing algorithm suggests that the core is comprised primarily of residues in the 173−224 range. These results are consistent with earlier electron paramagnetic resonance studies of fibrils formed by residues 90−231 of the human PrP sequence, formed under somewhat different conditions [Cobb, N. J., Sonnichsen, F. D., McHaourab, H., and Surewicz, W. K. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 18946−18951], suggesting that an in-register parallel β-sheet structure formed by the C-terminal end may be a general feature of PrP fibrils prepared in vitro.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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24
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Wagoner VA, Cheon M, Chang I, Hall CK. Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides. Proteins 2011; 79:2132-45. [PMID: 21557317 DOI: 10.1002/prot.23034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 01/26/2011] [Accepted: 02/11/2011] [Indexed: 11/11/2022]
Abstract
We simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113-120 (AGAAAAGA) and the mouse prion protein MoPrP 111-120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)(4) , A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV The first two peptides are thought to act as the Velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves. Kinetic events along the fibrillization pathway influence the types of structures that occur and variations in the sequence affect aggregation kinetics and fibrillar structure. Discontinuous molecular dynamics simulations using the PRIME20 force field are performed on systems containing 48 peptides starting from a random coil configuration. Depending on the sequence, fibrillar structures form spontaneously over a range of temperatures, below which amorphous aggregates form and above which no aggregation occurs. AGAAAAGA forms well organized fibrillar structures whereas VAGAAAAGAV forms less well organized structures that are partially fibrillar and partially amorphous. The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV. The ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. However as the hydrophobicity of the sequence increases, the ability to form well-ordered structures decreases. Thus, longer hydrophobic sequences form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures.
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Affiliation(s)
- Victoria A Wagoner
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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25
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Formation of β-sheets in glutamine and alanine tripeptides. Biochem Biophys Res Commun 2011; 406:348-52. [DOI: 10.1016/j.bbrc.2011.02.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 02/10/2011] [Indexed: 11/20/2022]
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26
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Prion protein and its conformational conversion: a structural perspective. Top Curr Chem (Cham) 2011; 305:135-67. [PMID: 21630136 DOI: 10.1007/128_2011_165] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The key molecular event in the pathogenesis of prion diseases is the conformational conversion of a cellular prion protein, PrP(C), into a misfolded form, PrP(Sc). In contrast to PrP(C) that is monomeric and α-helical, PrP(Sc) is oligomeric in nature and rich in β-sheet structure. According to the "protein-only" model, PrP(Sc) itself represents the infectious prion agent responsible for transmissibility of prion disorders. While this model is supported by rapidly growing experimental data, detailed mechanistic and structural aspects of prion protein conversion remain enigmatic. In this chapter we describe recent advances in understanding biophysical and biochemical aspects of prion diseases, with a special focus on structural underpinnings of prion protein conversion, the structural basis of prion strains, and generation of prion infectivity in vitro from bacterially-expressed recombinant PrP.
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27
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Chan JCC. Solid-state NMR techniques for the structural determination of amyloid fibrils. Top Curr Chem (Cham) 2011; 306:47-88. [PMID: 21630137 DOI: 10.1007/128_2011_154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.
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Affiliation(s)
- Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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28
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Zhang J. Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing. J Mol Model 2010; 17:173-9. [PMID: 20411399 DOI: 10.1007/s00894-010-0691-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 02/11/2010] [Indexed: 02/04/2023]
Abstract
To date, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins, although many experimental studies have shown that this region has amyloid fibril forming properties. This region belongs to the N-terminal unstructured region (1-123) of prions, the structure of which has proved hard to determine using NMR or X-ray crystallography. This paper reports the successful construction of three amyloid fibril models for this region. The models were formatted by standard simulated annealing using suitable templates from the Protein Data Bank, and were refined using several traditional optimization methods within AMBER. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, these models can be used as a reference for experimental studies on this region. The results presented here confirm standard simulated annealing as an effective tool in molecular modeling. The three constructed models for amyloid fibrils may be useful in furthering the goals of medicinal chemistry in this field.
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Affiliation(s)
- Jiapu Zhang
- Victorian Life Sciences Computation Initiative, The University of Melbourne, 1-3 Hull Road, Croydon, Victoria, VIC 3136, Australia.
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29
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Molecular Structure of Amyloid Fibrils Formed by Residues 127 to 147 of the Human Prion Protein. Chemistry 2010; 16:5492-9. [DOI: 10.1002/chem.200903290] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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30
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Abstract
Demonstrated successes of protein design and engineering suggest significant potential to produce diverse protein architectures and assemblies beyond those found in nature. Here, we describe a new class of synthetic protein architecture through the successful design and atomic structures of water-soluble cross-beta proteins. The cross-beta motif is formed from the lamination of successive beta-sheet layers, and it is abundantly observed in the core of insoluble amyloid fibrils associated with protein-misfolding diseases. Despite its prominence, cross-beta has been designed only in the context of insoluble aggregates of peptides or proteins. Cross-beta's recalcitrance to protein engineering and conspicuous absence among the known atomic structures of natural proteins thus makes it a challenging target for design in a water-soluble form. Through comparative analysis of the cross-beta structures of fibril-forming peptides, we identified rows of hydrophobic residues ("ladders") running across beta-strands of each beta-sheet layer as a minimal component of the cross-beta motif. Grafting a single ladder of hydrophobic residues designed from the Alzheimer's amyloid-beta peptide onto a large beta-sheet protein formed a dimeric protein with a cross-beta architecture that remained water-soluble, as revealed by solution analysis and x-ray crystal structures. These results demonstrate that the cross-beta motif is a stable architecture in water-soluble polypeptides and can be readily designed. Our results provide a new route for accessing the cross-beta structure and expanding the scope of protein design.
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31
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Expression and purification of a recombinant amyloidogenic peptide from transthyretin for solid-state NMR spectroscopy. Protein Expr Purif 2009; 70:101-8. [PMID: 19796687 DOI: 10.1016/j.pep.2009.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 09/22/2009] [Accepted: 09/23/2009] [Indexed: 11/17/2022]
Abstract
We describe the expression and purification of a model amyloidogenic peptide comprising residues 105-115 of human transthyretin (TTR105-115). Recombinant TTR105-115, which does not contain any non-native residues, was prepared as part of a fusion protein construct with a highly soluble B1 immunoglobulin binding domain of protein G (GB1), with typical yields of approximately 4 mg/L of uniformly (13)C,(15)N-enriched HPLC-purified peptide per liter of minimal media culture. Amyloid fibrils formed by recombinant TTR105-115 were characterized by transmission electron microscopy and solid-state NMR spectroscopy, and found to be comparable to synthetic TTR105-115 fibrils. These results establish recombinant TTR105-115 as a valuable model system for the development of new solid-state NMR techniques for the atomic-level characterization of amyloid architecture.
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32
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Structural insights into alternate aggregated prion protein forms. J Mol Biol 2009; 393:1033-42. [PMID: 19720066 DOI: 10.1016/j.jmb.2009.08.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Revised: 08/11/2009] [Accepted: 08/22/2009] [Indexed: 11/21/2022]
Abstract
The conversion of the cellular form of the prion protein (PrP(C)) to an abnormal, alternatively folded isoform (PrP(Sc)) is the central event in prion diseases or transmissible spongiform encephalopathies. Recent studies have demonstrated de novo generation of murine prions from recombinant prion protein (recPrP) after inoculation into transgenic and wild-type mice. These so-called synthetic prions lead to novel prion diseases with unique neuropathological and biochemical features. Moreover, the use of recPrP in an amyloid seeding assay can specifically detect and amplify various strains of prions. We employed this assay in our experiments and analyzed in detail the morphology of aggregate structures produced under defined chemical constraints. Our results suggest that changes in the concentration of guanidine hydrochloride can lead to different kinetic traces in a typical thioflavin T(ThT) assay. Morphological and structural analysis of these aggregates by atomic force microscopy indicates a variation in the structure of the PrP molecular assemblies. In particular, ThT positive PrP aggregates produced from rec mouse PrP residues 89 to 230 lead to mostly oligomeric structures at low concentrations of guanidine hydrochloride, while more amyloidal structures were observed at higher concentrations of the denaturant. These findings highlight the presence of numerous and complex pathways in deciphering prion constraints for infectivity and toxicity.
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33
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Antiparallel beta-sheet: a signature structure of the oligomeric amyloid beta-peptide. Biochem J 2009; 421:415-23. [PMID: 19435461 DOI: 10.1042/bj20090379] [Citation(s) in RCA: 385] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AD (Alzheimer's disease) is linked to Abeta (amyloid beta-peptide) misfolding. Studies demonstrate that the level of soluble Abeta oligomeric forms correlates better with the progression of the disease than the level of fibrillar forms. Conformation-dependent antibodies have been developed to detect either Abeta oligomers or fibrils, suggesting that structural differences between these forms of Abeta exist. Using conditions which yield well-defined Abeta-(1-42) oligomers or fibrils, we studied the secondary structure of these species by ATR (attenuated total reflection)-FTIR (Fourier-transform infrared) spectroscopy. Whereas fibrillar Abeta was organized in a parallel beta-sheet conformation, oligomeric Abeta displayed distinct spectral features, which were attributed to an antiparallel beta-sheet structure. We also noted striking similarities between Abeta oligomers spectra and those of bacterial outer membrane porins. We discuss our results in terms of a possible organization of the antiparallel beta-sheets in Abeta oligomers, which may be related to reported effects of these highly toxic species in the amyloid pathogenesis associated with AD.
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34
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Maji SK, Wang L, Greenwald J, Riek R. Structure-activity relationship of amyloid fibrils. FEBS Lett 2009; 583:2610-7. [PMID: 19596006 DOI: 10.1016/j.febslet.2009.07.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/02/2009] [Accepted: 07/07/2009] [Indexed: 11/18/2022]
Abstract
Protein aggregation is a process in which proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are generally classified as either amorphous or highly ordered, the most common form of the latter being amyloid fibrils. Amyloid fibrils composed of cross-beta-sheet structure are the pathological hallmarks of several diseases including Alzheimer's disease, but are also associated with functional states such as the fungal HET-s prion. This review aims to summarize the recent high-resolution structural studies of amyloid fibrils in light of their (potential) activities. We propose that the repetitive nature of the cross-beta-sheet structure of amyloids is key for their multiple properties: the repeating motifs can translate a rather non-specific interaction into a specific one through cooperativity.
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Affiliation(s)
- Samir K Maji
- School of Bioscience and Bioengineering, IIT-Bombay, Powai, Mumbai, India.
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35
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Saracino GA, Villa A, Moro G, Cosentino U, Salmona M. Spontaneous β-helical fold in prion protein: The case of PrP(82-146). Proteins 2009; 75:964-76. [DOI: 10.1002/prot.22306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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36
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Core structure of amyloid fibrils formed by residues 106-126 of the human prion protein. Structure 2009; 17:417-26. [PMID: 19278656 DOI: 10.1016/j.str.2008.12.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/24/2008] [Accepted: 12/21/2008] [Indexed: 11/21/2022]
Abstract
Peptides comprising residues 106-126 of the human prion protein (PrP) exhibit many features of the full-length protein. PrP(106-126) induces apoptosis in neurons, forms fibrillar aggregates, and can mediate the conversion of native cellular PrP (PrP(C)) to the scrapie form (PrP(Sc)). Despite a wide range of biochemical and biophysical studies on this peptide, including investigation of its propensity for aggregation, interactions with cell membranes, and PrP-like toxicity, the structure of amyloid fibrils formed by PrP(106-126) remains poorly defined. In this study we use solid-state nuclear magnetic resonance to define the secondary and quaternary structure of PrP(106-126) fibrils. Our results reveal that PrP(106-126) forms in-register parallel beta sheets, stacked in an antiparallel fashion within the mature fibril. The close intermolecular contacts observed in the fibril core provide a rational for the sequence-dependent behavior of PrP(106-126), and provide a basis for further investigation of its biological properties.
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Microscopic factors that control beta-sheet registry in amyloid fibrils formed by fragment 11-25 of amyloid beta peptide: insights from computer simulations. J Mol Biol 2009; 389:921-37. [PMID: 19414017 DOI: 10.1016/j.jmb.2009.04.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 04/27/2009] [Accepted: 04/28/2009] [Indexed: 01/21/2023]
Abstract
Short fragments of amyloidogenic proteins are widely used as model systems in studies of amyloid formation. Fragment 11-25 of the amyloid beta protein involved in Alzheimer's disease (Abeta11-25) was recently shown to form amyloid fibrils composed of anti-parallel beta-sheets. Interestingly, fibrils grown under neutral and acidic conditions were seen to possess different registries of their inter-beta-strand hydrogen bonds. In an effort to explain the microscopic origin of this pH dependence, we studied Abeta11-25 fibrils using methods of theoretical modeling. Several structural models were built for fibrils at low and neutral pH levels and these were examined in short molecular dynamics simulations in explicit water. The models that displayed the lowest free energy, as estimated using an implicit solvent model, were selected as representative of the true fibrillar structure. It was shown that the registry of these models agrees well with the experimental results. At neutral pH, the main contribution to the free energy difference between the two registries comes from the electrostatic interactions. The charge group of the carboxy terminus makes a large contribution to these interactions and thus appears to have a critical role in determining the registry.
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Madine J, Copland A, Serpell LC, Middleton DA. Cross-β Spine Architecture of Fibrils Formed by the Amyloidogenic Segment NFGSVQFV of Medin from Solid-State NMR and X-ray Fiber Diffraction Measurements. Biochemistry 2009; 48:3089-99. [DOI: 10.1021/bi802164e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jillian Madine
- School of Biological Sciences, University of Liverpool,
Crown Street, Liverpool L69 7ZB, United Kingdom, and Department of
Biochemistry, School of Life Sciences, University of Sussex, Falmer,
Brighton BN1 9QG, United Kingdom
| | - Alastair Copland
- School of Biological Sciences, University of Liverpool,
Crown Street, Liverpool L69 7ZB, United Kingdom, and Department of
Biochemistry, School of Life Sciences, University of Sussex, Falmer,
Brighton BN1 9QG, United Kingdom
| | - Louise C. Serpell
- School of Biological Sciences, University of Liverpool,
Crown Street, Liverpool L69 7ZB, United Kingdom, and Department of
Biochemistry, School of Life Sciences, University of Sussex, Falmer,
Brighton BN1 9QG, United Kingdom
| | - David A. Middleton
- School of Biological Sciences, University of Liverpool,
Crown Street, Liverpool L69 7ZB, United Kingdom, and Department of
Biochemistry, School of Life Sciences, University of Sussex, Falmer,
Brighton BN1 9QG, United Kingdom
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