201
|
Small organic probes as amyloid specific ligands - Past and recent molecular scaffolds. FEBS Lett 2009; 583:2593-9. [DOI: 10.1016/j.febslet.2009.04.016] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 04/08/2009] [Accepted: 04/09/2009] [Indexed: 12/29/2022]
|
202
|
Toupet K, Lehmann S. [The information embedded into protein conformation: the mammalian prion protein is not the only one which "prionized"]. Med Sci (Paris) 2009; 25:307-10. [PMID: 19361397 DOI: 10.1051/medsci/2009253307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Basic research on prions and on protein and peptide aggregation generated a new vision of the pathologic mechanisms of many disorders regrouped under the term "proteinopathies". The latter include several neurodegenerative disorders (Alzheimer, Parkinson disease...) which could benefit for their diagnosis and therapeutics of this type of research. Importantly, the presence of proteins behaving like prions in yeast also contributed to the advance of knowledge in this area by showing that the transmission of a conformational information could be considered as a new epigenetic mechanism. In addition yeast models allow to study the molecular mechanism of protein aggregation, the role of accessory factors, like chaperones, and the screening of therapeutic agents.
Collapse
Affiliation(s)
- Karine Toupet
- Université Montpellier 2, Inserm, U710, 34095 Montpellier, France.
| | | |
Collapse
|
203
|
Maury CPJ. Self-propagating beta-sheet polypeptide structures as prebiotic informational molecular entities: the amyloid world. ORIGINS LIFE EVOL B 2009; 39:141-50. [PMID: 19301141 DOI: 10.1007/s11084-009-9165-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 03/02/2009] [Indexed: 12/13/2022]
Abstract
The idea is advanced that under the extreme earth conditions for ~3.9 billions years ago, protein-based beta-sheet molecular structures were the first self-propagating and information-processing biomolecules that evolved. The amyloid structure of these aggregates provided an effective protection against the harsh conditions known to decompose both polyribonucleotides and natively folded polypeptides. In the prebiotic amyloid world, both the replicative and informational functions were carried out by structurally stable beta-sheet protein aggregates in a prion-like mode involving templated self-propagation and storage of information in the beta-sheet conformation. In this amyloid (protein)-first, hybrid replication-metabolism view, the synthesis of RNA, and the evolvement of an RNA-protein world, were later, but necessary events for further biomolecular evolution to occur. I further argue that in our contemporary DNA<-->RNA-->protein world, the primordial beta-conformation-based information system is preserved in the form of a cytoplasmic epigenetic memory.
Collapse
Affiliation(s)
- C P J Maury
- Department of Medicine, University of Helsinki, Kasarmikatu 11-13, Helsinki FI-00130, Finland.
| |
Collapse
|
204
|
Fang PS, Zhao JH, Liu HL, Liu KT, Chen JT, Lin HY, Huang CH, Fang HW. Molecular Dynamics Simulations to Gain Insights into the Stability and Morphologies of K3 Oligomers from β2-microglobulin. J Biomol Struct Dyn 2009; 26:549-59. [DOI: 10.1080/07391102.2009.10507270] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
205
|
Bryan AW, Menke M, Cowen LJ, Lindquist SL, Berger B. BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis. PLoS Comput Biol 2009; 5:e1000333. [PMID: 19325876 PMCID: PMC2653728 DOI: 10.1371/journal.pcbi.1000333] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 02/12/2009] [Indexed: 11/30/2022] Open
Abstract
Amyloids and prion proteins are clinically and biologically important
β-structures, whose supersecondary structures are difficult to determine
by standard experimental or computational means. In addition, significant
conformational heterogeneity is known or suspected to exist in many amyloid
fibrils. Recent work has indicated the utility of pairwise probabilistic
statistics in β-structure prediction. We develop here a new strategy for
β-structure prediction, emphasizing the determination of
β-strands and pairs of β-strands as fundamental units of
β-structure. Our program, BETASCAN, calculates likelihood scores for
potential β-strands and strand-pairs based on correlations observed in
parallel β-sheets. The program then determines the strands and pairs
with the greatest local likelihood for all of the sequence's potential
β-structures. BETASCAN suggests multiple alternate folding patterns and
assigns relative a priori probabilities based solely on amino
acid sequence, probability tables, and pre-chosen parameters. The algorithm
compares favorably with the results of previous algorithms (BETAPRO, PASTA,
SALSA, TANGO, and Zyggregator) in β-structure prediction and amyloid
propensity prediction. Accurate prediction is demonstrated for experimentally
determined amyloid β-structures, for a set of known
β-aggregates, and for the parallel β-strands of
β-helices, amyloid-like globular proteins. BETASCAN is able both to
detect β-strands with higher sensitivity and to detect the edges of
β-strands in a richly β-like sequence. For two proteins
(Aβ and Het-s), there exist multiple sets of experimental data implying
contradictory structures; BETASCAN is able to detect each competing structure as
a potential structure variant. The ability to correlate multiple alternate
β-structures to experiment opens the possibility of computational
investigation of prion strains and structural heterogeneity of amyloid. BETASCAN
is publicly accessible on the Web at http://betascan.csail.mit.edu. Amyloid is a highly ordered form of protein aggregation that a wide variety of
proteins can form. While the earliest discovered amyloids were associated with
systemic and neurodegenerative diseases, recent findings indicate amyloids may
have myriad roles and functions ranging from learning and memory, to yeast
epigenetics, to biofilm and melanin production. In this study, we expand the
range and flexibility of our ability to understand how amyloid properties arise
from their polypeptide sequence. By taking advantage of the intrinsic properties
of a characteristic amyloid structure—parallel
β-strands—and data from available protein structures, we
construct and test an algorithm to predict the probability that particular
portions of a protein will form amyloid. Our method has the advantage of more
accurate detection of the edges of such zones, as well as the ability to
consider and evaluate the likelihood of multiple folding patterns.
Collapse
Affiliation(s)
- Allen W. Bryan
- Harvard/MIT Division of Health Science and Technology, Bioinformatics and
Integrative Genomics, Cambridge, Massachusetts, United States of
America
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,
United States of America
- MIT Computer Science and Artificial Intelligence Laboratory, The Stata
Center, Cambridge, Massachusetts, United States of America
| | - Matthew Menke
- MIT Computer Science and Artificial Intelligence Laboratory, The Stata
Center, Cambridge, Massachusetts, United States of America
| | - Lenore J. Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts,
United States of America
| | - Susan L. Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,
United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of
America
- * E-mail: (SLL); (BB)
| | - Bonnie Berger
- MIT Computer Science and Artificial Intelligence Laboratory, The Stata
Center, Cambridge, Massachusetts, United States of America
- Department of Applied Mathematics, Massachusetts Institute of Technology,
Cambridge, Massachusetts, United States of America
- * E-mail: (SLL); (BB)
| |
Collapse
|
206
|
Levin S, Nowick JS. A new artificial beta-sheet that dimerizes through parallel beta-sheet interactions. Org Lett 2009; 11:1003-6. [PMID: 19173616 DOI: 10.1021/ol802993v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper introduces a chemical model of a beta-sheet that dimerizes through parallel beta-sheet interactions in CDCl(3) solution. The model consists of two C-terminally linked dipeptides connected to a molecular template. (1)H NMR studies establish the beta-sheet folding and dimerization of the model system. This system corroborates that linking two peptide strands and blocking one edge of the assembly creates soluble, easy-to-study systems that participate in the types of interactions that occur widely in peptide and protein aggregates.
Collapse
Affiliation(s)
- Sergiy Levin
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
| | | |
Collapse
|
207
|
Zhou DH, Shah G, Mullen C, Sandoz D, Rienstra CM. Proton-detected solid-state NMR spectroscopy of natural-abundance peptide and protein pharmaceuticals. Angew Chem Int Ed Engl 2009; 48:1253-6. [PMID: 19130513 DOI: 10.1002/anie.200801029] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The natural way: A sensitive NMR spectroscopic method is developed to obtain well-resolved two-dimensional spectra ((15)N-(1)H and (13)C-(1)H) for natural-abundance (that is, without the need for isotopic enrichment) large-molecule samples, such as biopharmaceuticals. This method gives structural insights on two lyophilized aprotinin samples and three insulin samples in lyophilized, microcrystalline suspension formulation (red; see picture) and fibril (green) forms.
Collapse
Affiliation(s)
- Donghua H Zhou
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | | | | | |
Collapse
|
208
|
|
209
|
Fibrils with parallel in-register structure constitute a major class of amyloid fibrils: molecular insights from electron paramagnetic resonance spectroscopy. Q Rev Biophys 2009; 41:265-97. [PMID: 19079806 DOI: 10.1017/s0033583508004733] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The deposition of amyloid- and amyloid-like fibrils is the main pathological hallmark of numerous protein misfolding diseases including Alzheimer's disease, transmissible spongiform encephalopathy, and type 2 diabetes. Besides the well-established role in disease, recent work on a variety of organisms ranging from bacteria to humans suggests that amyloid fibrils can also convey biological functions. To better understand the molecular mechanisms by which amyloidogenic proteins misfold in disease or perform biological functions, structural information is essential. Although high-resolution structural analysis of amyloid fibrils has been challenging, a combination of biophysical approaches is beginning to unravel the various structural features of amyloid fibrils. Here we review these recent developments with particular emphasis on amyloid fibrils that have been studied using site-directed spin labeling and electron paramagnetic resonance spectroscopy. This approach has been used to define the precise location of fibril-forming core regions and identify local secondary structures within such core regions. Perhaps one of the most remarkable findings arrived at by site-directed spin labeling was that most fibrils that contain an extensive core region of 20 amino acids or more share a common parallel in-register arrangement of beta strands. The preference for this arrangement can be explained on topological grounds and may be rationalized by the maximization of hydrophobic contact surface.
Collapse
|
210
|
Couthouis J, Rébora K, Immel F, Berthelot K, Castroviejo M, Cullin C. Screening for toxic amyloid in yeast exemplifies the role of alternative pathway responsible for cytotoxicity. PLoS One 2009; 4:e4539. [PMID: 19262694 PMCID: PMC2650408 DOI: 10.1371/journal.pone.0004539] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 02/02/2009] [Indexed: 11/24/2022] Open
Abstract
The relationship between amyloid and toxic species is a central problem since the discovery of amyloid structures in different diseases. Despite intensive efforts in the field, the deleterious species remains unknown at the molecular level. This may reflect the lack of any structure-toxicity study based on a genetic approach. Here we show that a structure-toxicity study without any biochemical prerequisite can be successfully achieved in yeast. A PCR mutagenesis of the amyloid domain of HET-s leads to the identification of a mutant that might impair cellular viability. Cellular and biochemical analyses demonstrate that this toxic mutant forms GFP-amyloid aggregates that differ from the wild-type aggregates in their shape, size and molecular organization. The chaperone Hsp104 that helps to disassemble protein aggregates is strictly required for the cellular toxicity. Our structure-toxicity study suggests that the smallest aggregates are the most toxic, and opens a new way to analyze the relationship between structure and toxicity of amyloid species.
Collapse
Affiliation(s)
- Julien Couthouis
- IBGC, UMR 5095, CNRS Université Bordeaux 2 “Victor Segalen”, Bordeaux, France
| | - Karine Rébora
- IBGC, UMR 5095, CNRS Université Bordeaux 2 “Victor Segalen”, Bordeaux, France
| | - Françoise Immel
- IBGC, UMR 5095, CNRS Université Bordeaux 2 “Victor Segalen”, Bordeaux, France
| | - Karine Berthelot
- IBGC, UMR 5095, CNRS Université Bordeaux 2 “Victor Segalen”, Bordeaux, France
| | - Michel Castroviejo
- REGER, UMR 5097 CNRS Université Bordeaux 2 “Victor Segalen”, Bordeaux, France
| | - Christophe Cullin
- IBGC, UMR 5095, CNRS Université Bordeaux 2 “Victor Segalen”, Bordeaux, France
- * E-mail:
| |
Collapse
|
211
|
Abstract
Although amyloid has usually been considered a pathological structure, growing evidence indicates that amyloid may also be a productive part of cell biology contributing to normal physiology. In fact, amyloid formation seems to be an intrinsic propensity of polypeptides in general and the amyloid beta-fold an evolutionary highly conserved structure. Functional amyloids have been found in a wide range of organisms, from bacteria to mammals, with functions as diverse as biofilm formation, development of aerial structures, scaffolding, regulation of melanin synthesis, epigenetic control of polyamines and information transfer. Obviously, organisms have evolved taking advantage of the canonical amyloid beta-sheet fold, a conformation that possesses both high resistance to proteolysis, self-replicative properties and capability to function as a molecular memory.
Collapse
Affiliation(s)
- C P J Maury
- Department of Medicine, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
212
|
Berthelot K, Immel F, Géan J, Lecomte S, Oda R, Kauffmann B, Cullin C. Driving amyloid toxicity in a yeast model by structural changes: a molecular approach. FASEB J 2009; 23:2254-63. [DOI: 10.1096/fj.08-125724] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Karine Berthelot
- Institut de Biochimie et Génétique CellulairesUniversité Bordeaux 2 “Victor Segalen”BordeauxFrance
| | - Franşoise Immel
- Institut de Biochimie et Génétique CellulairesUniversité Bordeaux 2 “Victor Segalen”BordeauxFrance
| | - Julie Géan
- Chimie et Biochimie des Membranes et Nano‐objetsUniversité Bordeaux 1PessacFrance
| | - Sophie Lecomte
- Chimie et Biochimie des Membranes et Nano‐objetsUniversité Bordeaux 1PessacFrance
| | - Reiko Oda
- Chimie et Biochimie des Membranes et Nano‐objetsUniversité Bordeaux 1PessacFrance
| | - Brice Kauffmann
- Chimie et Biochimie des Membranes et Nano‐objetsUniversité Bordeaux 1PessacFrance
| | - Christophe Cullin
- Institut de Biochimie et Génétique CellulairesUniversité Bordeaux 2 “Victor Segalen”BordeauxFrance
| |
Collapse
|
213
|
Nanomechanical Characterization of the Triple β-Helix Domain in the Cell Puncture Needle of Bacteriophage T4 Virus. Cell Mol Bioeng 2009. [DOI: 10.1007/s12195-009-0047-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
214
|
Sivertsen AC, Bayro MJ, Belenky M, Griffin RG, Herzfeld J. Solid-state NMR evidence for inequivalent GvpA subunits in gas vesicles. J Mol Biol 2009; 387:1032-9. [PMID: 19232353 DOI: 10.1016/j.jmb.2009.02.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 02/04/2009] [Accepted: 02/10/2009] [Indexed: 11/18/2022]
Abstract
Gas vesicles are organelles that provide buoyancy to the aquatic microorganisms that harbor them. The gas vesicle shell consists almost exclusively of the hydrophobic 70-residue gas vesicle protein A, arranged in an ordered array. Solid-state NMR spectra of intact collapsed gas vesicles from the cyanobacterium Anabaena flos-aquae show duplication of certain gas vesicle protein A resonances, indicating that specific sites experience at least two different local environments. Interpretation of these results in terms of an asymmetric dimer repeat unit can reconcile otherwise conflicting features of the primary, secondary, tertiary, and quaternary structures of the gas vesicle protein. In particular, the asymmetric dimer can explain how the hydrogen bonds in the beta-sheet portion of the molecule can be oriented optimally for strength while promoting stabilizing aromatic and electrostatic side-chain interactions among highly conserved residues and creating a large hydrophobic surface suitable for preventing water condensation inside the vesicle.
Collapse
Affiliation(s)
- Astrid C Sivertsen
- Department of Chemistry, Brandeis University, Waltham, MA 02454-9110, USA
| | | | | | | | | |
Collapse
|
215
|
Zhou D, Shah G, Mullen C, Sandoz D, Rienstra C. Proton-Detected Solid-State NMR Spectroscopy of Natural-Abundance Peptide and Protein Pharmaceuticals. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200801029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
216
|
Abstract
As hamster scrapie cannot infect mice, due to sequence differences in their PrP proteins, we find "species barriers" to transmission of the [URE3] prion in Saccharomyces cerevisiae among Ure2 proteins of S. cerevisiae, paradoxus, bayanus, cariocanus, and mikatae on the basis of differences among their Ure2p prion domain sequences. The rapid variation of the N-terminal Ure2p prion domains results in protection against the detrimental effects of infection by a prion, just as the PrP residue 129 Met/Val polymorphism may have arisen to protect humans from the effects of cannibalism. Just as spread of bovine spongiform encephalopathy prion variant is less impaired by species barriers than is sheep scrapie, we find that some [URE3] prion variants are infectious to another yeast species while other variants (with the identical amino acid sequence) are not. The species barrier is thus prion variant dependent as in mammals. [URE3] prion variant characteristics are maintained even on passage through the Ure2p of another species. Ure2p of Saccharomyces castelli has an N-terminal Q/N-rich "prion domain" but does not form prions (in S. cerevisiae) and is not infected with [URE3] from Ure2p of other Saccharomyces. This implies that conservation of its prion domain is not for the purpose of forming prions. Indeed the Ure2p prion domain has been shown to be important, though not essential, for the nitrogen catabolism regulatory role of the protein.
Collapse
|
217
|
Paramagnetic shifts in solid-state NMR of proteins to elicit structural information. Proc Natl Acad Sci U S A 2008; 105:17284-9. [PMID: 18988744 DOI: 10.1073/pnas.0708460105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent observation of pseudocontact shifts (pcs) in (13)C high-resolution solid-state NMR of paramagnetic proteins opens the way to their application as structural restraints. Here, by investigating a microcrystalline sample of cobalt(II)-substituted matrix metalloproteinase 12 [CoMMP-12 (159 AA, 17.5 kDa)], it is shown that a combined strategy of protein labeling and dilution of the paramagnetic species (i.e., (13)C-,(15)N-labeled CoMMP-12 diluted in unlabeled ZnMMP-12, and (13)C-,(15)N-labeled ZnMMP-12 diluted in unlabeled CoMMP-12) allows one to easily separate the pcs contributions originated from the protein internal metal (intramolecular pcs) from those due to the metals in neighboring proteins in the crystal lattice (intermolecular pcs) and that both can be used for structural purposes. It is demonstrated that intramolecular pcs are significant structural restraints helpful in increasing both precision and accuracy of the structure, which is a need in solid-state structural biology nowadays. Furthermore, intermolecular pcs provide unique information on positions and orientations of neighboring protein molecules in the solid phase.
Collapse
|
218
|
Wang L, Maji SK, Sawaya MR, Eisenberg D, Riek R. Bacterial inclusion bodies contain amyloid-like structure. PLoS Biol 2008; 6:e195. [PMID: 18684013 DOI: 10.1371/journal.pbio.0060195] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2007] [Accepted: 06/25/2008] [Indexed: 11/19/2022] Open
Abstract
Protein aggregation is a process in which identical proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are generally classified as amorphous, lacking any long-range order, or highly ordered fibrils. Protein fibrils can be composed of native globular molecules, such as the hemoglobin molecules in sickle-cell fibrils, or can be reorganized beta-sheet-rich aggregates, termed amyloid-like fibrils. Amyloid fibrils are associated with several pathological conditions in humans, including Alzheimer disease and diabetes type II. We studied the structure of bacterial inclusion bodies, which have been believed to belong to the amorphous class of aggregates. We demonstrate that all three in vivo-derived inclusion bodies studied are amyloid-like and comprised of amino-acid sequence-specific cross-beta structure. These findings suggest that inclusion bodies are structured, that amyloid formation is an omnipresent process both in eukaryotes and prokaryotes, and that amino acid sequences evolve to avoid the amyloid conformation.
Collapse
Affiliation(s)
- Lei Wang
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
| | | | | | | | | |
Collapse
|
219
|
Wickner RB, Shewmaker F, Kryndushkin D, Edskes HK. Protein inheritance (prions) based on parallel in-register beta-sheet amyloid structures. Bioessays 2008; 30:955-64. [PMID: 18798523 DOI: 10.1002/bies.20821] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Most prions (infectious proteins) are self-propagating amyloids (filamentous protein multimers), and have been found in both mammals and fungal species. The prions [URE3] and [PSI+] of yeast are disease agents of Saccharomyces cerevisiae while [Het-s] of Podospora anserina may serve a normal cellular function. The parallel in-register beta-sheet structure shown by prion amyloids makes possible a templating action at the end of filaments which explains the faithful transmission of variant differences in these molecules. This property of self-reproduction, in turn, allows these proteins to act as de facto genes, encoding heritable information.
Collapse
Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
| | | | | | | |
Collapse
|
220
|
Abstract
Beta-sheets consist of extended polypeptide strands (beta-strands) connected by a network of hydrogen bonds and occur widely in proteins. Although the importance of beta-sheets in the folded structures of proteins has long been recognized, there is a growing recognition of the importance of intermolecular interactions among beta-sheets. Intermolecular interactions between the hydrogen-bonding edges of beta-sheets constitute a fundamental form of biomolecular recognition (like DNA base pairing) and are involved protein quaternary structure, protein-protein interactions, and peptide and protein aggregation. The importance of beta-sheet interactions in biological processes makes them potential targets for intervention in diseases such as AIDS, cancer, and Alzheimer's disease. This Account describes my research group's use of chemical model systems to study the structure and interactions of beta-sheets. Chemical model systems provide an excellent vehicle with which to explore beta-sheets, because they are smaller, simpler, and easier to manipulate than proteins. Synthetic chemical models also provide the opportunity to control or modulate natural systems or to develop other useful applications and may eventually lead to new drugs with which to treat diseases. In our "artificial beta-sheets", molecular template and turn units are combined with peptides to mimic the structures of parallel and antiparallel beta-sheets. The templates and turn units form folded, hydrogen-bonded structures with the peptide groups and help prevent the formation of complex, ill-defined aggregates. Templates that duplicate the hydrogen-bonding pattern of one edge of a peptide beta-strand while blocking the other edge have proven particularly valuable in preventing aggregate formation and in promoting the formation of simple monomeric and dimeric structures. Artificial beta-sheets that present exposed hydrogen-bonding edges can form well-defined hydrogen-bonded dimers. Dimerization occurs readily in chloroform solutions but requires additional hydrophobic interactions to occur in aqueous solution. Interactions among the side chains, as well as hydrogen bonding among the main chains, are important in dimer formation. NMR studies of artificial beta-sheets have elucidated the importance of hydrogen-bonding complementarity, size complementarity, and chiral complementarity in these interactions. These pairing preferences demonstrate sequence selectivity in the molecular recognition between beta-sheets. These studies help illustrate the importance of intermolecular edge-to-edge interactions between beta-sheets in peptides and proteins. Ultimately, these model systems may lead to new ways of controlling beta-sheet interactions and treating diseases in which they are involved.
Collapse
Affiliation(s)
- James S Nowick
- Department of Chemistry University of California, Irvine, Irvine, California 92617-4048, USA.
| |
Collapse
|
221
|
Curtis-Fisk J, Spencer RM, Weliky DP. Native conformation at specific residues in recombinant inclusion body protein in whole cells determined with solid-state NMR spectroscopy. J Am Chem Soc 2008; 130:12568-9. [PMID: 18759389 DOI: 10.1021/ja8039426] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inclusion bodies are insoluble aggregates that are formed by bacteria to store excess recombinant protein produced during expression. The structure of the protein in inclusion bodies is poorly understood but it has been hypothesized that the protein may form misfolded beta sheet aggregates. This paper presents an isotopic labeling and solid-state nuclear magnetic resonance approach to determine the secondary structure of individual residues within a recombinant influenza virus "FHA2" protein in inclusion bodies. The inclusion bodies were studied either in the context of the unlysed hydrated E. coli cells or in the hydrated pellet formed from centrifugation of the material insoluble in the cell lysate. The native structure of FHA2 is predominantly helical and native helical structure was also observed for several specific residues in the inclusion body FHA2. This approach will be applicable to structural analysis of many inclusion body proteins and should provide useful information for optimizing solubilization and purification protocols of these proteins.
Collapse
Affiliation(s)
- Jaime Curtis-Fisk
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | | | | |
Collapse
|
222
|
Wasmer C, Soragni A, Sabaté R, Lange A, Riek R, Meier BH. Infectious and noninfectious amyloids of the HET-s(218-289) prion have different NMR spectra. Angew Chem Int Ed Engl 2008; 47:5839-41. [PMID: 18548467 DOI: 10.1002/anie.200704896] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christian Wasmer
- Laboratorium für Physikalische Chemie, ETH Zurich, 8093 Zurich, Switzerland
| | | | | | | | | | | |
Collapse
|
223
|
Becker J, Ferguson N, Flinders J, van Rossum BJ, Fersht AR, Oschkinat H. A Sequential Assignment Procedure for Proteins that have Intermediate Line Widths in MAS NMR Spectra: Amyloid Fibrils of Human CA150.WW2. Chembiochem 2008; 9:1946-52. [DOI: 10.1002/cbic.200700706] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
224
|
Okada T, Ikeda K, Wakabayashi M, Ogawa M, Matsuzaki K. Formation of toxic Abeta(1-40) fibrils on GM1 ganglioside-containing membranes mimicking lipid rafts: polymorphisms in Abeta(1-40) fibrils. J Mol Biol 2008; 382:1066-74. [PMID: 18692507 DOI: 10.1016/j.jmb.2008.07.072] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2008] [Revised: 07/24/2008] [Accepted: 07/24/2008] [Indexed: 02/02/2023]
Abstract
The abnormal aggregation and deposition of amyloid beta protein (Abeta) on neuronal cells are critical to the onset of Alzheimer's disease. The entity (oligomers or fibrils) of toxic Abeta species responsible for the pathogenesis of the disease has been controversial. We have reported that the Abeta aggregates on ganglioside-rich domains of neuronal PC12 cells as well as in raft-like model membranes. Here, we identified toxic Abeta(1-40) aggregates formed with GM1-ganglioside-containing membranes. Abeta(1-40) was incubated with raft-like liposomes composed of GM1/cholesterol/sphingomyelin at 1:2:2 and 37 degrees C. After a lag period, toxic amyloid fibrils with a width of 12 nm were formed and subsequently laterally assembled with slight changes in their secondary structure as confirmed by viability assay, thioflavin-T fluorescence, circular dichroism, and transmission electron microscopy. In striking contrast, Abeta fibrils formed without membranes were thinner (6.7 nm) and much less toxic because of weaker binding to cell membranes and a smaller surface hydrophobicity. This study suggests that toxic Abeta(1-40) species formed on membranes are not soluble oligomers but amyloid fibrils and that Abeta(1-40) fibrils exhibit polymorphisms.
Collapse
Affiliation(s)
- Takuma Okada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | | | | | | | | |
Collapse
|
225
|
Abstract
Amyloid fibrils are elongated protein aggregates well known for their association with many human diseases. However, similar structures have also been found in other organisms and amyloid fibrils can also be formed in vitro by other proteins usually under non-physiological conditions. In all cases, these fibrils assemble in a nucleated polymerization reaction with a pronounced lag phase that can be eliminated by supplying pre-formed fibrils as seeds. Once formed, the fibrils are usually very stable, except for their tendency to break into smaller pieces forming more growing ends in the process. These properties give amyloid fibers a self-replicating character dependent only on a source of soluble protein. For some systems and under certain circumstances this can lead to infectious protein structures, so-called prions, that can be passed from one organism to another as in the transmissible spongiform encephalopathies and in fungal prion systems. Structural details about these processes have emerged only recently, mostly on account of the inability of traditional high-resolution methods to deal with insoluble, filamentous specimens. In consequence, current models for amyloid fibrils are based on fewer constraints than common atomic-resolution structures. This review gives an overview of the constraints used for the development of amyloid models and the methods used to derive them. The principally possible structures will be introduced by discussing current models of amyloid fibrils from Alzheimer's beta-peptide, amylin and several fungal systems. The infectivity of some amyloids under specific conditions might not be due to a principal structural difference between infectious and non-infectious amyloids, but could result from an interplay of the rates for filament nucleation, growth, fragmentation, and clearance.
Collapse
Affiliation(s)
- Ulrich Baxa
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
226
|
Wasmer C, Soragni A, Sabaté R, Lange A, Riek R, Meier B. Infektiöse und nichtinfektiöse Amyloide des HET‐s(218‐289)‐Prions haben unterschiedliche NMR‐Spektren. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
227
|
Loquet A, Laage S, Gardiennet C, Elena B, Emsley L, Böckmann A, Lesage A. Methyl Proton Contacts Obtained Using Heteronuclear Through-Bond Transfers in Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:10625-32. [DOI: 10.1021/ja801464g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Ségolène Laage
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Bénédicte Elena
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Lyndon Emsley
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Anne Lesage
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| |
Collapse
|
228
|
Scrapie prion protein structural constraints obtained by limited proteolysis and mass spectrometry. J Mol Biol 2008; 382:88-98. [PMID: 18621059 DOI: 10.1016/j.jmb.2008.06.070] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 05/16/2008] [Accepted: 06/24/2008] [Indexed: 01/30/2023]
Abstract
Elucidation of the structure of scrapie prion protein (PrP(Sc)), essential to understand the molecular mechanism of prion transmission, continues to be one of the major challenges in prion research and is hampered by the insolubility and polymeric character of PrP(Sc). Limited proteolysis is a useful tool to obtain insight on structural features of proteins: proteolytic enzymes cleave proteins more readily at exposed sites, preferentially within loops, and rarely in beta-strands. We treated PrP(Sc) isolated from brains of hamsters infected with 263K and drowsy prions with varying concentrations of proteinase K (PK). After PK deactivation, PrP(Sc) was denatured, reduced, and cleaved at Cys179 with 2-nitro-5-thiocyanatobenzoic acid. Fragments were analyzed by nano-HPLC/mass spectrometry and matrix-assisted laser desorption/ionization. Besides the known cleavages at positions 90, 86, and 92 for 263K prions and at positions 86, 90, 92, 98, and 101 for drowsy prions, our data clearly demonstrate the existence of additional cleavage sites at more internal positions, including 117, 119, 135, 139, 142, and 154 in both strains. PK concentration dependence analysis and limited proteolysis after partial unfolding of PrP(Sc) confirmed that only the mentioned cleavage sites at the N-terminal side of the PrP(Sc) are susceptible to PK. Our results indicate that besides the "classic" amino-terminal PK cleavage points, PrP(Sc) contains, in its middle core, regions that show some degree of susceptibility to proteases and must therefore correspond to subdomains with some degree of structural flexibility, interspersed with stretches of amino acids of high resistance to proteases. These results are compatible with a structure consisting of short beta-sheet stretches connected by loops and turns.
Collapse
|
229
|
Tartaglia GG, Pawar AP, Campioni S, Dobson CM, Chiti F, Vendruscolo M. Prediction of Aggregation-Prone Regions in Structured Proteins. J Mol Biol 2008; 380:425-36. [DOI: 10.1016/j.jmb.2008.05.013] [Citation(s) in RCA: 378] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 05/02/2008] [Accepted: 05/08/2008] [Indexed: 11/17/2022]
|
230
|
Linser R, Fink U, Reif B. Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 193:89-93. [PMID: 18462963 DOI: 10.1016/j.jmr.2008.04.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 04/04/2008] [Accepted: 04/14/2008] [Indexed: 05/10/2023]
Abstract
Assignment of proteins in MAS (magic angle spinning) solid-state NMR relies so far on correlations among heteronuclei. This strategy is based on well dispersed resonances in the (15)N dimension. In many complex cases like membrane proteins or amyloid fibrils, an additional frequency dimension is desirable in order to spread the amide resonances. We show here that proton detected HNCO, HNCA, and HNCACB type experiments can successfully be implemented in the solid-state. Coherences are sufficiently long lived to allow pulse schemes of a duration greater than 70 ms before incrementation of the first indirect dimension. The achieved resolution is comparable to the resolution obtained in solution-state NMR experiments. We demonstrate the experiments using a triply labeled sample of the SH3 domain of chicken alpha-spectrin, which was re-crystallized in H(2)O/D(2)O using a ratio of 1/9. We employ paramagnetic relaxation enhancement (PRE) using EDTA chelated Cu(II) to enable rapid data acquisition.
Collapse
Affiliation(s)
- Rasmus Linser
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle Strasse 10, 13125 Berlin, Germany
| | | | | |
Collapse
|
231
|
Svane ASP, Jahn K, Deva T, Malmendal A, Otzen DE, Dittmer J, Nielsen NC. Early stages of amyloid fibril formation studied by liquid-state NMR: the peptide hormone glucagon. Biophys J 2008; 95:366-77. [PMID: 18339765 PMCID: PMC2426625 DOI: 10.1529/biophysj.107.122895] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 02/21/2008] [Indexed: 11/18/2022] Open
Abstract
The 29-residue peptide hormone glucagon forms amyloid fibrils within a few hours at low pH. In this study, we use glucagon as a model system to investigate fibril formation by liquid-state (1)H-NMR spectroscopy One-dimensional, correlation, and diffusion experiments monitoring the fibril formation process provide insight into the early stages of the pathway on which the molecules aggregate to fibrils. In conjunction with these techniques, exchange experiments give information about the end-state conformation. Within the limits of detection, there are no signs of larger oligomeric intermediates in the course of the fibril formation process. Kinetic information is extracted from the time course of the residual free glucagon signal decay. This suggests that glucagon amyloids form by a nucleated growth mechanism in which trimers (rather than monomers) of glucagon interact directly with the growing fibrils rather than with each other. The results of proton/deuterium exchange experiments on mature fibrils with subsequent dissolution show that the N-terminal of glucagon is the least amenable to exchange, which indicates that this part is strongly involved in the intermolecular bonds of the fibrils.
Collapse
Affiliation(s)
- Anna Sigrid Pii Svane
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Denmark
| | | | | | | | | | | | | |
Collapse
|
232
|
Abstract
The aggregation of proteins into amyloid fibrils is associated with several neurodegenerative diseases. In Parkinson's disease it is believed that the aggregation of alpha-synuclein (alpha-syn) from monomers by intermediates into amyloid fibrils is the toxic disease-causative mechanism. Here, we studied the structure of alpha-syn in its amyloid state by using various biophysical approaches. Quenched hydrogen/deuterium exchange NMR spectroscopy identified five beta-strands within the fibril core comprising residues 35-96 and solid-state NMR data from amyloid fibrils comprising the fibril core residues 30-110 confirmed the presence of beta-sheet secondary structure. The data suggest that beta1-strand interacts with beta2, beta2 with beta3, beta3 with beta4, and beta4 with beta5. High-resolution cryoelectron microscopy revealed the protofilament boundaries of approximately 2 x 3.5 nm. Based on the combination of these data and published structural studies, a fold of alpha-syn in the fibrils is proposed and discussed.
Collapse
|
233
|
Heise H, Celej MS, Becker S, Riedel D, Pelah A, Kumar A, Jovin TM, Baldus M. Solid-state NMR reveals structural differences between fibrils of wild-type and disease-related A53T mutant alpha-synuclein. J Mol Biol 2008; 380:444-50. [PMID: 18539297 DOI: 10.1016/j.jmb.2008.05.026] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 05/07/2008] [Accepted: 05/13/2008] [Indexed: 11/30/2022]
Abstract
Fibrils from the Parkinson's-disease-related A53T mutant of alpha-synuclein were investigated by solid-state NMR spectroscopy, electron microscopy, and atomic force microscopy. Sequential solid-state NMR resonance assignments were obtained for a large fraction of the fibril core. Experiments conducted above and below the freezing point suggest that the fibrils contain regions with increased mobility and structural elements different from beta-strand character, in addition to the rigid beta-sheet-rich core region. As in earlier studies on wild-type alpha-synuclein, the C-terminus was found to be flexible and unfolded, whereas the main core region was highly rigid and rich in beta-sheets. Compared to fibrils from wild-type alpha-synuclein, the well-ordered beta-sheet region extends to at least L38 and L100. These results demonstrate that a disease-related mutant of alpha-synuclein differs in both aggregation kinetics and fibril structure.
Collapse
Affiliation(s)
- Henrike Heise
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Solid-State NMR Group, Am Fassberg 11, D-37077 Göttingen, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
234
|
Sackewitz M, Scheidt HA, Lodderstedt G, Schierhorn A, Schwarz E, Huster D. Structural and Dynamical Characterization of Fibrils from a Disease-Associated Alanine Expansion Domain Using Proteolysis and Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:7172-3. [DOI: 10.1021/ja800120s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mirko Sackewitz
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Holger A. Scheidt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Grit Lodderstedt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Angelika Schierhorn
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Elisabeth Schwarz
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Daniel Huster
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| |
Collapse
|
235
|
Paired beta-sheet structure of an Abeta(1-40) amyloid fibril revealed by electron microscopy. Proc Natl Acad Sci U S A 2008; 105:7462-6. [PMID: 18483195 DOI: 10.1073/pnas.0712290105] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease is a neurodegenerative disorder that is characterized by the cerebral deposition of amyloid fibrils formed by Abeta peptide. Despite their prevalence in Alzheimer's and other neurodegenerative diseases, important details of the structure of amyloid fibrils remain unknown. Here, we present a three-dimensional structure of a mature amyloid fibril formed by Abeta(1-40) peptide, determined by electron cryomicroscopy at approximately 8-A resolution. The fibril consists of two protofilaments, each containing approximately 5-nm-long regions of beta-sheet structure. A local twofold symmetry within each region suggests that pairs of beta-sheets are formed from equivalent parts of two Abeta(1-40) peptides contained in each protofilament. The pairing occurs via tightly packed interfaces, reminiscent of recently reported steric zipper structures. However, unlike these previous structures, the beta-sheet pairing is observed within an amyloid fibril and includes significantly longer amino acid sequences.
Collapse
|
236
|
Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses. Biophys J 2008; 95:1965-73. [PMID: 18469082 DOI: 10.1529/biophysj.108.129213] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deposition of insoluble amyloid plaques is frequently associated with a large variety of neurodegenerative diseases. However, data collected in the last decade have suggested that the neurotoxic action is exerted by prefibrillar, soluble assemblies of amyloid-forming proteins and peptides. The scarcity of structural data available for both amyloid-like fibrils and soluble oligomers is a major limitation for the definition of the molecular mechanisms linked to the onset of these diseases. Recently, the structural characterization of GNNQQNY and other peptides has shown a general feature of amyloid-like fibers, the so-called steric zipper motif. However, very little is known still about the prefibrillar oligomeric forms. By using replica exchange molecular dynamics we carried out extensive analyses of the properties of several small and medium GNNQQNY aggregates arranged through the steric zipper motif. Our data show that the assembly formed by two sheets, each made of two strands, arranged as in the crystalline states are highly unstable. Conformational free energy surfaces indicate that the instability of the model can be ascribed to the high reactivity of edge backbone hydrogen bonding donors/acceptors. On the other hand, data on larger models show that steric zipper interactions may keep small oligomeric forms in a stable state. These models simultaneously display two peculiar structural motifs: a tightly packed steric zipper interface and a large number of potentially reactive exposed strands. The presence of highly reactive groups on these assemblies likely generates two distinct evolutions. On one side the reactive groups quickly lead, through self-association, to the formation of ordered fibrils, on the other they may interfere with several cellular components thereby generating toxic effects. In this scenario, fiber formation propensity and toxicity of oligomeric states are two different manifestations of the same property: the hyper-reactivity of the exposed strands.
Collapse
|
237
|
Steric Zipper of the Amyloid Fibrils Formed by Residues 109–122 of the Syrian Hamster Prion Protein. J Mol Biol 2008; 378:1142-54. [DOI: 10.1016/j.jmb.2008.03.035] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 03/04/2008] [Accepted: 03/16/2008] [Indexed: 11/20/2022]
|
238
|
Andronesi OC, Bergen MV, Biernat J, Seidel K, Griesinger C, Mandelkow E, Baldus M. Characterization of Alzheimer’s-like Paired Helical Filaments from the Core Domain of Tau Protein Using Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:5922-8. [DOI: 10.1021/ja7100517] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
239
|
Bourguet E, Correia I, Dorgeret B, Chassaing G, Sicsic S, Ongeri S. Synthesis and conformational studies of pseudopeptides containing an unsymmetrical triazine scaffold. J Pept Sci 2008; 14:596-609. [DOI: 10.1002/psc.944] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
240
|
Molecular conformation and dynamics of the Y145Stop variant of human prion protein in amyloid fibrils. Proc Natl Acad Sci U S A 2008; 105:6284-9. [PMID: 18436646 DOI: 10.1073/pnas.0711716105] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A C-terminally truncated Y145Stop variant of the human prion protein (huPrP23-144) is associated with a hereditary amyloid disease known as PrP cerebral amyloid angiopathy. Previous studies have shown that recombinant huPrP23-144 can be efficiently converted in vitro to the fibrillar amyloid state, and that residues 138 and 139 play a critical role in the amyloidogenic properties of this protein. Here, we have used magic-angle spinning solid-state NMR spectroscopy to provide high-resolution insight into the protein backbone conformation and dynamics in fibrils formed by (13)C,(15)N-labeled huPrP23-144. Surprisingly, we find that signals from approximately 100 residues (i.e., approximately 80% of the sequence) are not detected above approximately -20 degrees C in conventional solid-state NMR spectra. Sequential resonance assignments revealed that signals, which are observed, arise exclusively from residues in the region 112-141. These resonances are remarkably narrow, exhibiting average (13)C and (15)N linewidths of approximately 0.6 and 1 ppm, respectively. Altogether, the present findings indicate the existence of a compact, highly ordered core of huPrP23-144 amyloid encompassing residues 112-141. Analysis of (13)C secondary chemical shifts identified likely beta-strand segments within this core region, including beta-strand 130-139 containing critical residues 138 and 139. In contrast to this relatively rigid, beta-sheet-rich amyloid core, the remaining residues in huPrP23-144 amyloid fibrils under physiologically relevant conditions are largely unordered, displaying significant conformational dynamics.
Collapse
|
241
|
The beta-strand-loop-beta-strand conformation is marginally populated in beta2-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations. Biophys J 2008; 95:510-7. [PMID: 18408040 DOI: 10.1529/biophysj.107.125054] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Solid-state NMR study shows that the 22-residue K3 peptide (Ser(20)-Lys(41)) from beta(2)-microglobulin (beta(2)m) adopts a beta-strand-loop-beta-strand conformation in its fibril state. Residue Pro(32) has a trans conformation in the fibril state of the peptide, while it adopts a cis conformation in the native state of full-length beta(2)m. To get insights into the structural properties of the K3 peptide, and determine whether the strand-loop-strand conformation is encoded at the monomeric level, we run all-atom explicit solvent replica exchange molecular dynamics on both the cis and trans variants. Our simulations show that the conformational space of the trans- and cis-K3 peptides is very different, with 1% of the sampled conformations in common at room temperature. In addition, both variants display only 0.3-0.5% of the conformations with beta-strand-loop-beta-strand character. This finding, compared to results on the Alzheimer's Abeta peptide, suggests that the biases toward aggregation leading to the beta-strand-loop-beta-strand conformation in fibrils are peptide-dependent.
Collapse
|
242
|
Helmus JJ, Nadaud PS, Höfer N, Jaroniec CP. Determination of methyl 13C-15N dipolar couplings in peptides and proteins by three-dimensional and four-dimensional magic-angle spinning solid-state NMR spectroscopy. J Chem Phys 2008; 128:052314. [PMID: 18266431 DOI: 10.1063/1.2817638] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We describe three- and four-dimensional semiconstant-time transferred echo double resonance (SCT-TEDOR) magic-angle spinning solid-state nuclear magnetic resonance (NMR) experiments for the simultaneous measurement of multiple long-range (15)N-(13)C(methyl) dipolar couplings in uniformly (13)C, (15)N-enriched peptides and proteins with high resolution and sensitivity. The methods take advantage of (13)C spin topologies characteristic of the side-chain methyl groups in amino acids alanine, isoleucine, leucine, methionine, threonine, and valine to encode up to three distinct frequencies ((15)N-(13)C(methyl) dipolar coupling, (15)N chemical shift, and (13)C(methyl) chemical shift) within a single SCT evolution period of initial duration approximately 1(1)J(CC) (where (1)J(CC) approximately 35 Hz, is the one-bond (13)C(methyl)-(13)C J-coupling) while concurrently suppressing the modulation of NMR coherences due to (13)C-(13)C and (15)N-(13)C J-couplings and transverse relaxation. The SCT-TEDOR schemes offer several important advantages over previous methods of this type. First, significant (approximately twofold to threefold) gains in experimental sensitivity can be realized for weak (15)N-(13)C(methyl) dipolar couplings (corresponding to structurally interesting, approximately 3.5 A or longer, distances) and typical (13)C(methyl) transverse relaxation rates. Second, the entire SCT evolution period can be used for (13)C(methyl) and/or (15)N frequency encoding, leading to increased spectral resolution with minimal additional coherence decay. Third, the experiments are inherently "methyl selective," which results in simplified NMR spectra and obviates the use of frequency-selective pulses or other spectral filtering techniques. Finally, the (15)N-(13)C cross-peak buildup trajectories are purely dipolar in nature (i.e., not influenced by J-couplings or relaxation), which enables the straightforward extraction of (15)N-(13)C(methyl) distances using an analytical model. The SCT-TEDOR experiments are demonstrated on a uniformly (13)C, (15)N-labeled peptide, N-acetyl-valine, and a 56 amino acid protein, B1 immunoglobulin-binding domain of protein G (GB1), where the measured (15)N-(13)C(methyl) dipolar couplings provide site-specific information about side-chain dihedral angles and the packing of protein molecules in the crystal lattice.
Collapse
Affiliation(s)
- Jonathan J Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
243
|
|
244
|
Wasmer C, Lange A, Van Melckebeke H, Siemer AB, Riek R, Meier BH. Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core. Science 2008; 319:1523-6. [PMID: 18339938 DOI: 10.1126/science.1151839] [Citation(s) in RCA: 814] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Prion and nonprion forms of proteins are believed to differ solely in their three-dimensional structure, which is therefore of paramount importance for the prion function. However, no atomic-resolution structure of the fibrillar state that is likely infectious has been reported to date. We present a structural model based on solid-state nuclear magnetic resonance restraints for amyloid fibrils from the prion-forming domain (residues 218 to 289) of the HET-s protein from the filamentous fungus Podospora anserina. On the basis of 134 intra- and intermolecular experimental distance restraints, we find that HET-s(218-289) forms a left-handed beta solenoid, with each molecule forming two helical windings, a compact hydrophobic core, at least 23 hydrogen bonds, three salt bridges, and two asparagine ladders. The structure is likely to have broad implications for understanding the infectious amyloid state.
Collapse
|
245
|
Hetényi A, Fülöp L, Martinek TA, Wéber E, Soós K, Penke B. Ligand-Induced Flocculation of Neurotoxic Fibrillar Aβ(1–42) by Noncovalent Crosslinking. Chembiochem 2008; 9:748-57. [DOI: 10.1002/cbic.200700351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
246
|
Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR. Proc Natl Acad Sci U S A 2008; 105:4621-6. [PMID: 18344321 DOI: 10.1073/pnas.0712393105] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.
Collapse
|
247
|
Shewmaker F, Ross ED, Tycko R, Wickner RB. Amyloids of shuffled prion domains that form prions have a parallel in-register beta-sheet structure. Biochemistry 2008; 47:4000-7. [PMID: 18324784 DOI: 10.1021/bi7024589] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The [URE3] and [PSI (+)] prions of Saccharomyces cerevisiae are self-propagating amyloid forms of Ure2p and Sup35p, respectively. The Q/N-rich N-terminal domains of each protein are necessary and sufficient for the prion properties of these proteins, forming in each case their amyloid cores. Surprisingly, shuffling either prion domain, leaving amino acid content unchanged, does not abrogate the ability of the proteins to become prions. The discovery that the amino acid composition of a polypeptide, not the specific sequence order, determines prion capability seems contrary to the standard folding paradigm that amino acid sequence determines protein fold. The shuffleability of a prion domain further suggests that the beta-sheet structure is of the parallel in-register type, and indeed, the normal Ure2 and Sup35 prion domains have such a structure. We demonstrate that two shuffled Ure2 prion domains capable of being prions form parallel in-register beta-sheet structures, and our data indicate the same conclusion for a single shuffled Sup35 prion domain. This result confirms our inference that shuffleability indicates parallel in-register structure.
Collapse
Affiliation(s)
- Frank Shewmaker
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
| | | | | | | |
Collapse
|
248
|
Affiliation(s)
- Henrike Heise
- Institute for Physical Biology, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
| |
Collapse
|
249
|
Amyloid of Rnq1p, the basis of the [PIN+] prion, has a parallel in-register beta-sheet structure. Proc Natl Acad Sci U S A 2008; 105:2403-8. [PMID: 18268327 DOI: 10.1073/pnas.0712032105] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The [PIN(+)] prion, a self-propagating amyloid form of Rnq1p, increases the frequency with which the [PSI(+)] or [URE3] prions arise de novo. Like the prion domains of Sup35p and Ure2p, Rnq1p is rich in N and Q residues, but rnq1Delta strains have no known phenotype except for inability to propagate the [PIN(+)] prion. We used solid-state NMR methods to examine amyloid formed in vitro from recombinant Rnq1 prion domain (residues 153-405) labeled with Tyr-1-(13)C (14 residues), Leu-1-(13)C (7 residues), or Ala-3-(13)C (13 residues). The carbonyl chemical shifts indicate that most Tyr and Leu residues are in beta-sheet conformation. Experiments designed to measure the distance from each labeled residue to the next nearest labeled carbonyl showed that almost all Tyr and Leu carbonyl carbon atoms were approximately 0.5 nm from the next nearest Tyr and Leu residues, respectively. This result indicates that the Rnq1 prion domain forms amyloid consisting of parallel beta-strands that are either in register or are at most one amino acid out of register. Similar experiments with Ala-3-(13)C indicate that the beta-strands are indeed in-register. The parallel in-register structure, now demonstrated for each of the yeast prions, explains the faithful templating of prion strains, and suggests as well a mechanism for the rare hetero-priming that is [PIN(+)]'s defining characteristic.
Collapse
|
250
|
Ecroyd H, Koudelka T, Thorn DC, Williams DM, Devlin G, Hoffmann P, Carver JA. Dissociation from the oligomeric state is the rate-limiting step in fibril formation by kappa-casein. J Biol Chem 2008; 283:9012-22. [PMID: 18245081 DOI: 10.1074/jbc.m709928200] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibrils are aggregated and precipitated forms of protein in which the protein exists in highly ordered, long, unbranching threadlike formations that are stable and resistant to degradation by proteases. Fibril formation is an ordered process that typically involves the unfolding of a protein to partially folded states that subsequently interact and aggregate through a nucleation-dependent mechanism. Here we report on studies investigating the molecular basis of the inherent propensity of the milk protein, kappa-casein, to form amyloid fibrils. Using reduced and carboxymethylated kappa-casein (RCMkappa-CN), we show that fibril formation is accompanied by a characteristic increase in thioflavin T fluorescence intensity, solution turbidity, and beta-sheet content of the protein. However, the lag phase of RCMkappa-CN fibril formation is independent of protein concentration, and the rate of fibril formation does not increase upon the addition of seeds (preformed fibrils). Therefore, its mechanism of fibril formation differs from the archetypal nucleation-dependent aggregation mechanism. By digestion with trypsin or proteinase K and identification by mass spectrometry, we have determined that the region from Tyr(25) to Lys(86) is incorporated into the core of the fibrils. We suggest that this region, which is predicted to be aggregation-prone, accounts for the amyloidogenic nature of kappa-casein. Based on these data, we propose that fibril formation by RCMkappa-CN occurs through a novel mechanism whereby the rate-limiting step is the dissociation of an amyloidogenic precursor from an oligomeric state rather than the formation of stable nuclei, as has been described for most other fibril-forming systems.
Collapse
Affiliation(s)
- Heath Ecroyd
- School of Chemistry and the Physics, University of Adelaide, Adelaide, South Australia.
| | | | | | | | | | | | | |
Collapse
|