501
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Higashimoto Y, Asanomi Y, Takakusagi S, Lewis MS, Uosaki K, Durell SR, Anderson CW, Appella E, Sakaguchi K. Unfolding, aggregation, and amyloid formation by the tetramerization domain from mutant p53 associated with lung cancer. Biochemistry 2006; 45:1608-19. [PMID: 16460008 PMCID: PMC2536691 DOI: 10.1021/bi051192j] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The p53 tumor suppressor is a tetrameric transcriptional enhancer, and its activity is compromised by mutations that cause amino acid substitutions in its tetramerization domain. Here we analyze the biochemical and biophysical properties of peptides corresponding to amino acids 319-358 of wild-type human p53, which includes the tetramerization domain, and that of a cancer-derived mutant with valine substituted for glycine 334. Unlike the wild-type peptide, the G334V peptide forms amyloid fibrils by a two-step process under physiological conditions of temperature and pH. Nevertheless, the G334V peptide is capable of forming heterooligomers with a wild-type peptide. Computational modeling of the G334V peptide structure suggests that substitution of valine for glycine 334 causes a local distortion that contributes to a beta-dominated structural transition leading to amyloid formation. Since the distortion is mostly on the surface, the mutant peptide is still able to form a pseudonative tetramer complex at higher concentrations and/or lower temperatures. Our study suggests a new potential mechanism by which mutations that compromise tetramer formation inactivate p53 as a tumor suppressor.
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Affiliation(s)
- Yuichiro Higashimoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Hokkaido University, Sapporo 060−0810, Japan
| | - Yuya Asanomi
- Biological Chemistry, Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060−0810, Japan
| | - Satoru Takakusagi
- Physical Chemistry, Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060−0810, Japan
| | - Marc S. Lewis
- Molecular Interactions Resource, Division of Bioengineering and Physical Science, Office of Research Services, Office of Director, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kohei Uosaki
- Physical Chemistry, Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060−0810, Japan
| | - Stewart R. Durell
- Center for Cancer Research Nanobiology Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Carl W. Anderson
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Ettore Appella
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kazuyasu Sakaguchi
- Biological Chemistry, Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060−0810, Japan
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502
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Bader R, Bamford R, Zurdo J, Luisi BF, Dobson CM. Probing the Mechanism of Amyloidogenesis through a Tandem Repeat of the PI3-SH3 Domain Suggests a Generic Model for Protein Aggregation and Fibril Formation. J Mol Biol 2006; 356:189-208. [PMID: 16364365 DOI: 10.1016/j.jmb.2005.11.034] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Revised: 11/07/2005] [Accepted: 11/11/2005] [Indexed: 11/23/2022]
Abstract
Aggregation of the SH3 domain of the PI3 kinase, both as a single domain and as a tandem repeat in which the C terminus of one domain is linked to the N terminus of another by a flexible linker of ten glycine/serine residues, has been studied under a range of conditions in order to investigate the mechanism of protein aggregation and amyloid formation. The tandem repeat was found to form amyloid fibrils much more readily than the single domain under the acidic conditions used here, and the fibrils themselves have higher morphological homogeneity. The folding-unfolding transition of the PI3-SH3 domain shows two-state behaviour and is pH dependent; at pH 3.6, which is near the pH mid-point for folding and only slightly below the isoelectric point of the protein, both the single domain and the tandem repeat spontaneously form broad distributions of soluble oligomers without requirement for nucleation. Under prolonged incubation under these conditions, the oligomers convert into thin, curly fibrils that interact with thioflavin-T, suggesting that they contain an organised beta-sheet structure. Under more acidic conditions (pH 2.0) where the proteins are fully denatured and carry a positive net charge, long, straight fibrils are formed in a process having a pronounced lag phase. The latter was found to be reduced dramatically by the addition of oligomers exceeding a critical size of approximately 20 molecules. The results suggest that the process of aggregation of these SH3 domains can take place by a variety of mechanisms, ranging from downhill formation of relatively amorphous species to nucleated formation of highly organised structures, the relative importance of which varies greatly with solution conditions. Comparison with the behaviour of other amyloidogenic systems suggests that the general mechanistic features outlined here are likely to be common to at least a wide variety of peptides and proteins.
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Affiliation(s)
- Reto Bader
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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503
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Sheng Y, Wang W. Comparative all-atomic study of unfolding pathways for proteins chymotrypsin inhibitor 2 and barnase. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:021915. [PMID: 16605370 DOI: 10.1103/physreve.73.021915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Revised: 10/11/2005] [Indexed: 05/08/2023]
Abstract
The features of transition states and intermediates are important in the study on protein folding. However, transition states and intermediates could not be obviously identified from trajectories obtained by dynamic simulations. In this work, a different method to identify and characterize the transition states and intermediates by combining the root mean square deviation of C(alpha) atoms and the similarity factor Q to the native state is proposed. The unfolding processes based on all-atomic simulations for proteins chymotrypsin inhibitor 2 and barnase are studied, and the related transition states and intermediates are identified by observing an unfolding factor U = 1-F. Comparisons between the conformational cluster analysis and experimental results are also made. The various analyses on the unfolding behaviors indicate that our method can well define the transition states and intermediates, and the factor U (or F) can be used as a reaction coordinate of the folding and unfolding process. It is also found that three-state folding proteins might experience more complicated pathways and have more rugged energy landscapes than two-state folding proteins.
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Affiliation(s)
- Yuebiao Sheng
- National Laboratory of Solid State Microstructure, Institute of Biophysics, and Department of Physics, Nanjing University, Nanjing 210093, China
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504
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Lim KH, Nguyen TN, Damo SM, Mazur T, Ball HL, Prusiner SB, Pines A, Wemmer DE. Solid-state NMR structural studies of the fibril form of a mutant mouse prion peptide PrP89-143(P101L). SOLID STATE NUCLEAR MAGNETIC RESONANCE 2006; 29:183-90. [PMID: 16256316 DOI: 10.1016/j.ssnmr.2005.09.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 09/07/2005] [Indexed: 05/05/2023]
Abstract
The peptide fragment 89-143 of the prion protein (carrying a P101L mutation) is biologically active in transgenic mice when in a fibrillar form. Injection of these fibrils into transgenic mice (expressing full length PrP with the P101L mutation) induces a neurodegenerative prion disease (Kaneko et al., J. Mol. Biol. 295 (2000) 997). Here we present solid-state NMR studies of PrP(89-143)(P101L) fibrils, probing the conformation of residues in the hydrophobic segment 112-124 with chemical shifts. The conformations of glycine residues were analyzed using doubly (13)C=O labeled peptides by two-dimensional (2D) double-quantum correlation, and double-quantum filtered dephasing distance measurements. MQ-NMR experiments were carried out to probe the relative alignment of the individual peptides fibrils. These NMR studies indicate that the 112-124 segment adopts an extended beta-sheet conformation, though not in a parallel, in register alignment. There is evidence for conformational variability at Gly 113. DQ correlation experiments provide useful information in regions with conformational heterogeneity.
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Affiliation(s)
- Kwang Hun Lim
- Department of Chemistry, University of California, USA
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505
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Cecchini M, Curcio R, Pappalardo M, Melki R, Caflisch A. A molecular dynamics approach to the structural characterization of amyloid aggregation. J Mol Biol 2006; 357:1306-21. [PMID: 16483608 DOI: 10.1016/j.jmb.2006.01.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 11/21/2005] [Accepted: 01/04/2006] [Indexed: 10/25/2022]
Abstract
A novel computational approach to the structural analysis of ordered beta-aggregation is presented and validated on three known amyloidogenic polypeptides. The strategy is based on the decomposition of the sequence into overlapping stretches and equilibrium implicit solvent molecular dynamics (MD) simulations of an oligomeric system for each stretch. The structural stability of the in-register parallel aggregates sampled in the implicit solvent runs is further evaluated using explicit water simulations for a subset of the stretches. The beta-aggregation propensity along the sequence of the Alzheimer's amyloid-beta peptide (Abeta(42)) is found to be highly heterogeneous with a maximum in the segment V(12)HHQKLVFFAE(22) and minima at S(8)G(9), G(25)S(26), G(29)A(30), and G(38)V(39), which are turn-like segments. The simulation results suggest that these sites may play a crucial role in determining the aggregation tendency and the fibrillar structure of Abeta(42). Similar findings are obtained for the human amylin, a 37-residue peptide that displays a maximal beta-aggregation propensity at Q(10)RLANFLVHSSNN(22) and two turn-like sites at G(24)A(25) and G(33)S(34). In the third application, the MD approach is used to identify beta-aggregation "hot-spots" within the N-terminal domain of the yeast prion Ure2p (Ure2p(1-94)) and to design a double-point mutant (Ure2p-N4748S(1-94)) with lower beta-aggregation propensity. The change in the aggregation propensity of Ure2p-N4748S(1-94) is verified in vitro using the thioflavin T binding assay.
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Affiliation(s)
- M Cecchini
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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506
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JiJi RD, Balakrishnan G, Hu Y, Spiro TG. Intermediacy of poly(L-proline) II and beta-strand conformations in poly(L-lysine) beta-sheet formation probed by temperature-jump/UV resonance Raman spectroscopy. Biochemistry 2006; 45:34-41. [PMID: 16388578 PMCID: PMC2596612 DOI: 10.1021/bi051507v] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet resonance Raman spectroscopy (UVRR) in combination with a nanosecond temperature jump (T-jump) was used to investigate early steps in the temperature-induced alpha-helix to beta-sheet conformational transition of poly(L-lysine) [poly(K)]. Excitation at 197 nm from a tunable frequency-quadrupled Ti:sapphire laser provided high-quality UVRR spectra, containing multiple conformation-sensitive amide bands. Although un-ionized poly(K) (pH 11.6) is mainly alpha-helical below 30 degrees C, there is a detectable fraction (approximately 15%) of unfolded polypeptide, which is mainly in the poly(L-proline) II (PPII) conformation. However, deviations from the expected amide I and II signals indicate an additional conformation, suggested to be beta-strand. Above 30 degrees C un-ionized poly(K) forms a beta-sheet at a rate (minutes) which increases with increasing temperature. A 22-44 degrees C T-jump is accompanied by prompt amide I and II difference signals suggested to arise from a rapid shift in the PPII/beta-strand equilibrium. These signals are superimposed on a subsequently evolving difference spectrum which is characteristic of PPII, although the extent of conversion is low, approximately 2% at the 3 micros time limit of the experiment. The rise time of the PPII signals is approximately 250 ns, consistent with melting of short alpha-helical segments. A model is proposed in which the melted PPII segments interconvert with beta-strand conformation, whose association through interstrand H-bonding nucleates the formation of beta-sheet. The intrinsic propensity for beta-strand formation could be a determinant of beta-sheet induction time, with implications for the onset of amyloid diseases.
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Affiliation(s)
- Renee D JiJi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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507
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Abstract
Although abundant evidence suggests that amyloid accumulation plays a significant role in the pathogenesis of degenerative disease, the mechanism of amyloid formation and toxicity remains elusive. Early hypotheses for disease pathogenesis proposed that large amyloid deposits, which are composed primarily of 6-10-nm mature amyloid fibrils, were the primary causative agent in pathogenesis, but this hypothesis required modification to consider the central role of oligomers or aggregation intermediates, because the accumulation of these large aggregates does not correlate well with pathogenesis. Recent evidence supports the hypothesis that small soluble aggregates representing intermediates in the fibril assembly process may represent the primary culprits in a variety of amyloid-related degenerative diseases. Investigating the role of soluble amyloid oligomers in pathogenesis presents a problem for distinguishing these aggregates from the mature fibrils, soluble monomer, and natively folded precursor proteins, especially in vivo and in complex mixtures. Recently, we generated a conformation-specific antibody that recognizes soluble oligomers from many types of amyloid proteins, regardless of sequence. These results indicate that soluble oligomers have a common, generic structure that is distinct from both fibrils and low-molecular-weight soluble monomer/dimer. Conformation-dependent, oligomer-specific antibodies represent powerful tools for understanding the role of oligomers in pathogenesis. The purpose of this chapter is to review the methods for the production, characterization, and application of this antibody to understanding the contribution of amyloid oligomers to the disease process.
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Affiliation(s)
- Rakez Kayed
- UC Irvine, Department of Molecular Biology and Biochemistry, Irvine, CA, USA
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508
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Abstract
Assembly of normally soluble proteins into amyloid fibrils is a cause or associated symptom of numerous human disorders. Although some progress toward understanding the molecular-level details of fibril structure has been made through in vitro experiments, the insoluble nature of fibrils make them difficult to study experimentally. We describe two computational approaches used to investigate fibril formation and structure: intermediate-resolution discontinuous molecular dynamics simulations and atomistic molecular dynamics simulations. Each method has its strengths and weaknesses, but taken together the two approaches provide a useful molecular-level picture of fibril structure and formation.
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Affiliation(s)
- Carol K Hall
- Chemical Engineering Department, North Carolina State University, Raleigh, 27695, USA
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509
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Abstract
The generic tendency of proteins to aggregate into non-functional, and sometimes cytotoxic, structures poses a universal problem for all types of cell. This tendency is greatly exacerbated by the high total concentration of macromolecules found within most intracellular compartments, a phenomenon referred to as macromolecular crowding. This review discusses the quantitative effects of crowding on protein aggregation and the role of molecular chaperones in combating this problem.
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Affiliation(s)
- R John Ellis
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
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510
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Dicko C, Kenney JM, Vollrath F. β‐Silks: Enhancing and Controlling Aggregation. ADVANCES IN PROTEIN CHEMISTRY 2006; 73:17-53. [PMID: 17190610 DOI: 10.1016/s0065-3233(06)73002-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It appears that fiber-forming proteins are not an exclusive group but that, with appropriate conditions, many proteins can potentially aggregate and form fibrils; though only certain proteins, for example, amyloids and silks, do so under normal physiological conditions. Even so, this suggests a ubiquitous aggregation mechanism in which the protein environment is at least as important as the sequence. An ideal model system in which forced and natural aggregation has been observed is silk. Silks have evolved specifically to readily form insoluble ordered structures with a wide range of structural functionality. The animal, be it silkworm or spider, will produce, store, and transport high molecular weight proteins in a complex environment to eventually allow formation of silk fibers with a variety of mechanical properties. Here we review fiber formation and its prerequisites, and discuss the mechanism by which the animal facilitates and modulates silk assembly to achieve controlled protein aggregation.
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Affiliation(s)
- Cedric Dicko
- Zoology Department, Oxford University, OX1 3PS, United Kingdom
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511
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Abstract
Molecular self-assembly has paved the way to create novel, supramolecular, functional biomaterials. Peptide-based biomaterials are gaining interest as a result of their programmability, biodegradability, and bioresorbability. Further, unlike polymeric materials, peptides can be made monodisperse with precise control over sequence, chain length, and stereochemistry. Peptide-based viscoelastic matrices have been designed and characterized for various biomedical applications, such as tissue engineering scaffolds or drug delivery vehicles. The 'holy grail' in designing an ideal tissue engineering scaffold lies in mimicking the cues of the tissue's natural extracellular matrix (ECM). Some of the key elements of ECM that are incorporated into these peptide scaffolds include cell-adhesive and protease-sensitive sequences for enhanced cell-cell and cell-biomaterial interactions. Peptide-based viscoelastic matrices can also be engineered with drug carrying protease-sensitive sequences for controlled and site-specific drug delivery. Molecular-level engineering of simple oligopeptide modules can be used to control the position and density of the bio-mimetic functionalities in the supramolecular structures, which demonstrates the power of the 'bottom-up' approach in self-assembly.
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Affiliation(s)
- Sivakumar Ramachandran
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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512
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Abstract
The ability of proteins to fold into a defined and functional conformation is one of the most fundamental processes in biology. Certain conditions, however, initiate misfolding or unfolding of proteins. This leads to the loss of functional protein or it can result in a wide range of diseases. One group of diseases, which includes Alzheimer's, Parkinson's, Huntington's disease, and the transmissible spongiform encephalopathies (prion diseases), involves deposition of aggregated proteins. Normally, such protein aggregates are not found in properly functioning biological systems, because a variety of mechanisms inhibit their formation. Understanding the nature of these protective mechanisms together with the understanding of factors reducing or deactivating the natural protection machinery will be crucial for developing strategies to prevent and treat these disastrous diseases.
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Affiliation(s)
- T Scheibel
- Department Chemie, Lehrstuhl für Biotechnologie, Technische Universität München, Garching, Germany
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513
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Malmo C, Vilasi S, Iannuzzi C, Tacchi S, Cametti C, Irace G, Sirangelo I. Tetracycline inhibits W7FW14F apomyoglobin fibril extension and keeps the amyloid protein in a pre-fibrillar, highly cytotoxic state. FASEB J 2005; 20:346-7. [PMID: 16317065 DOI: 10.1096/fj.05-4652fje] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A significant number of fatal diseases are classified as protein deposition disorders, in which a normally soluble protein is deposited in an insoluble amyloid form. It has been reported that tetracycline exhibits anti-amyloidogenic activity by inhibiting aggregate formation and disaggregating preformed fibrils. In this work, we examined the effect induced by the presence of tetracycline on the fibrillogenesis and cytotoxicity of the amyloid-forming apomyoglobin mutant W7FW14F. Like other amyloid-forming proteins, early prefibrillar aggregates formed by this protein are highly cytotoxic, whereas insoluble mature fibrils are not. The effect induced by tetracycline on the fibrillation process has been examined by atomic force microscopy, light scattering, DPH staining, and thioflavin T fluorescence. The cytotoxicity of the amyloid aggregates was estimated by measuring cell viability using MTT assay. The results show that tetracycline acts as anti-aggregating agent, which inhibits the fibril elongation process but not the early aggregation steps leading to the formation of soluble oligomeric aggregates. Thus, this inhibition keeps the W7FW14F mutant in a prefibrillar, highly cytotoxic state. In this respect, a careful usage of tetracycline as fibril inhibitor is indicated.
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Affiliation(s)
- Clorinda Malmo
- Dipartimento di Biochimica e Biofisica, Seconda Università di Napoli, Naples, Italy
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514
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Ji ZS, Müllendorff K, Cheng IH, Miranda RD, Huang Y, Mahley RW. Reactivity of apolipoprotein E4 and amyloid beta peptide: lysosomal stability and neurodegeneration. J Biol Chem 2005; 281:2683-92. [PMID: 16298992 DOI: 10.1074/jbc.m506646200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously demonstrated that apolipoprotein E4 (apoE4) potentiates lysosomal leakage and apoptosis induced by amyloid beta (Abeta) peptide in cultured Neuro-2a cells and hypothesized that the low pH of lysosomes accentuates the conversion of apoE4 to a molten globule, inducing reactive intermediates capable of destabilizing cellular membranes. Here we report that neutralizing lysosomal pH with bafilomycin or NH4Cl abolished the apoE4 potentiation of Abeta-induced lysosomal leakage and apoptosis in Neuro-2a cells. Consistent with these results, apoE4 at acidic pH bound more avidly to phospholipid vesicles and disrupted them to a greater extent than at pH 7.4. Comparison of "Arctic" mutant Abeta, which forms multimers, and GM6 mutant Abeta, which remains primarily monomeric, showed that aggregation is essential for apoE4 to potentiate Abeta-induced lysosomal leakage and apoptosis. Both apoE4 and Abeta1-42 had to be internalized to exert these effects. Blocking the low density lipoprotein receptor-related protein with small interfering RNA abolished the enhanced effects of apoE4 and Abeta on lysosomes and apoptosis. In cultured Neuro-2a cells, Abeta1-42 increased lysosome formation to a greater extent in apoE3- or apoE4-transfected cells than in Neo-transfected cells, as shown by immunostaining for lysosome-associated membrane protein 1. Similarly, in transgenic mice expressing apoE and amyloid precursor protein, hippocampal neurons displayed increased numbers of lysosomes. Thus, apoE4 and Abeta1-42 may work in concert in neurons to increase lysosome formation while increasing the susceptibility of lysosomal membranes to disruption, release of lysosomal enzymes into the cytosol, and neuronal degeneration.
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Affiliation(s)
- Zhong-Sheng Ji
- Gladstone Institute of Neurological Disease, Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, California 94158,USA
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515
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Ricklefs RE, Swanson BL, Fallon SM, MartÍnez-AbraÍn A, Scheuerlein A, Gray J, Latta SC. COMMUNITY RELATIONSHIPS OF AVIAN MALARIA PARASITES IN SOUTHERN MISSOURI. ECOL MONOGR 2005. [DOI: 10.1890/04-1820] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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516
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Yagi H, Kusaka E, Hongo K, Mizobata T, Kawata Y. Amyloid Fibril Formation of α-Synuclein Is Accelerated by Preformed Amyloid Seeds of Other Proteins. J Biol Chem 2005; 280:38609-16. [PMID: 16162499 DOI: 10.1074/jbc.m508623200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alpha-synuclein is one of the causative proteins of familial Parkinson disease, which is characterized by neuronal inclusions named Lewy bodies. Lewy bodies include not only alpha-synuclein but also aggregates of other proteins. This fact raises a question as to whether the formation of alpha-synuclein amyloid fibrils in Lewy bodies may occur via interaction with fibrils derived from different proteins. To probe this hypothesis, we investigated in vitro fibril formation of human alpha-synuclein in the presence of preformed fibril seeds of various different proteins. We used three proteins, Escherichia coli chaperonin GroES, hen lysozyme, and bovine insulin, all of which have been shown to form amyloid fibrils. Very surprisingly, the formation of alpha-synuclein amyloid fibril was accelerated markedly in the presence of preformed seeds of GroES, lysozyme, and insulin fibrils. The structural characteristics of the natively unfolded state of alpha-synuclein may allow binding to various protein particles, which in turn triggers the formation (extension) of alpha-synuclein amyloid fibrils. This finding is very important for understanding the molecular mechanism of Parkinson disease and also provides interesting implications into the mechanism of transmissible conformational diseases.
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Affiliation(s)
- Hisashi Yagi
- Department of Biotechnology, Faculty of Engineering, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan
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517
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Griffin MA, Friedel M, Shea JE. Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice β-barrel protein. J Chem Phys 2005; 123:174707. [PMID: 16375557 DOI: 10.1063/1.2101458] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the effects of confinement, sequence frustration, and surface interactions on the thermodynamics of dimerization of an off-lattice minimalist beta-barrel protein using replica exchange molecular dynamics. We vary the degree of frustration of the protein by tuning the specificity of the hydrophobic interactions and investigate dimerization in confining spheres of different radii. We also investigate surface effects by tethering the first residue of one of the proteins to a uniformly repulsive surface. We find that increasing the confinement and frustration stabilize the dimer, while adding a repulsive surface decreases its stability. Different ensembles of structures, including properly dimerized and various partially dimerized states, are observed at the association transition temperature T(a), depending on the amount of frustration and whether a surface is present. The presence of a surface is predicted to alter the morphology of larger aggregates formed from partially unfolded dimeric conformations.
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Affiliation(s)
- Mary A Griffin
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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518
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Paci E, Greene LH, Jones RM, Smith LJ. Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach. FEBS J 2005; 272:4826-38. [PMID: 16156801 DOI: 10.1111/j.1742-4658.2005.04898.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Retinol-binding protein transports retinol, and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic conditions retinol-binding protein undergoes a transition to the molten globule state, and releases the bound retinol ligand. A biased molecular dynamics simulation method has been used to generate models for the ensemble of conformers populated within this molten globule state. Simulation conformers, with a radius of gyration at least 1.1 A greater than that of the native state, contain on average 37%beta-sheet secondary structure. In these conformers the central regions of the two orthogonal beta-sheets that make up the beta-barrel in the native protein are highly persistent. However, there are sizable fluctuations for residues in the outer regions of the beta-sheets, and large variations in side chain packing even in the protein core. Significant conformational changes are seen in the simulation conformers for residues 85-104 (beta-strands E and F and the E-F loop). These changes give an opening of the retinol-binding site. Comparisons with experimental data suggest that the unfolding in this region may provide a mechanism by which the complex of retinol-binding protein and transthyretin dissociates, and retinol is released at the cell surface.
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Affiliation(s)
- Emanuele Paci
- Institute of Molecular Biophysics, School of Physics and Astronomy, University of Leeds, UK.
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519
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Heise H, Hoyer W, Becker S, Andronesi OC, Riedel D, Baldus M. Molecular-level secondary structure, polymorphism, and dynamics of full-length alpha-synuclein fibrils studied by solid-state NMR. Proc Natl Acad Sci U S A 2005; 102:15871-6. [PMID: 16247008 PMCID: PMC1276071 DOI: 10.1073/pnas.0506109102] [Citation(s) in RCA: 523] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 140-residue protein alpha-synuclein (AS) is able to form amyloid fibrils and as such is the main component of protein inclusions involved in Parkinson's disease. We have investigated the structure and dynamics of full-length AS fibrils by high-resolution solid-state NMR spectroscopy. Homonuclear and heteronuclear 2D and 3D spectra of fibrils grown from uniformly (13)C/(15)N-labeled AS and AS reverse-labeled for two of the most abundant amino acids, K and V, were analyzed. (13)C and (15)N signals exhibited linewidths of <0.7 ppm. Sequential assignments were obtained for 48 residues in the hydrophobic core region. We identified two different types of fibrils displaying chemical-shift differences of up to 13 ppm in the (15)N dimension and up to 5 ppm for backbone and side-chain (13)C chemical shifts. EM studies suggested that molecular structure is correlated with fibril morphology. Investigation of the secondary structure revealed that most amino acids of the core region belong to beta-strands with similar torsion angles in both conformations. Selection of regions with different mobility indicated the existence of monomers in the sample and allowed the identification of mobile segments of the protein within the fibril in the presence of monomeric protein. At least 35 C-terminal residues were mobile and lacked a defined secondary structure, whereas the N terminus was rigid starting from residue 22. Our findings agree well with the overall picture obtained with other methods and provide insight into the amyloid fibril structure and dynamics with residue-specific resolution.
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Affiliation(s)
- Henrike Heise
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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520
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Del Mar C, Greenbaum EA, Mayne L, Englander SW, Woods VL. Structure and properties of alpha-synuclein and other amyloids determined at the amino acid level. Proc Natl Acad Sci U S A 2005; 102:15477-82. [PMID: 16223878 PMCID: PMC1266128 DOI: 10.1073/pnas.0507405102] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structure of alpha-synuclein (alpha-syn) amyloid was studied by hydrogen-deuterium exchange by using a fragment separation-MS analysis. The conditions used made it possible to distinguish the exchange of unprotected and protected amide hydrogens and to define the order/disorder boundaries at close to amino acid resolution. The soluble alpha-syn monomer exchanges its amide hydrogens with water hydrogens at random coil rates, consistent with its natively unstructured condition. In assembled amyloid, long N-terminal and C-terminal segments remain unprotected (residues 1- approximately 38 and 102-140), although the N-terminal segment shows some heterogeneity. A continuous middle segment (residues approximately 39-101) is strongly protected by systematically H-bonded cross-beta structure. This segment is much too long to fit the amyloid ribbon width, but non-H-bonded amides expected for direction-changing loops are not apparent. These results and other known constraints specify that alpha-syn amyloid adopts a chain fold like that suggested before for amyloid-beta [Petkova et al. (2002) Proc. Natl. Acad Sci. USA 99, 16742-16747] but with a short, H-bonded interlamina turn. More generally, we suggest that the prevalence of accidental amyloid formation derives mainly from the exceptional ability of the main chain in a structurally relaxed beta-conformation to adapt to and energy-minimize side-chain mismatching. Seeding specificity, strain variability, and species barriers then arise because newly added parallel in-register chains must faithfully reproduce the same set of adaptations.
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Affiliation(s)
- Charyl Del Mar
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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521
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Rogers SS, Venema P, van der Ploeg JPM, Sagis LMC, Donald AM, van der Linden E. Electric birefringence study of an amyloid fibril system: the short end of the length distribution. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2005; 18:207-17. [PMID: 16228124 DOI: 10.1140/epje/i2005-10038-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Accepted: 08/25/2005] [Indexed: 05/04/2023]
Abstract
In this article, a system of amyloid fibrils, based on the protein beta-lactoglobulin, is studied by transient electric birefringence. Single pulses of an electric field were applied to the solution, and the initial rise and subsequent decay of birefringence analysed. The decay takes place on a range of relaxation times, and therefore contains information about the length distribution of fibrils in the system. The information can be extracted using theories of the electric polarisability of polyelectrolyte rods, since the fibrils are an example of these. Despite the long-standing complications of such theories, useful quantitative information about the system can still be obtained. Using the Fixman model of polyelectrolyte polarisability, we obtain a measurement of the short end of the length distribution which shows the fibril concentration as a function of length rising linearly from 0.02-2 microm. The short end of the length distribution was unobtainable in our previous study using rheo-optics (S.S. Rogers et al., Macromolecules 38, 2948 (2005)), but reasonable agreement between the two techniques shows they are complementary.
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Affiliation(s)
- S S Rogers
- Department of Physics, Cambridge University, Cambridge, UK
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522
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Hortschansky P, Christopeit T, Schroeckh V, Fändrich M. Thermodynamic analysis of the aggregation propensity of oxidized Alzheimer's beta-amyloid variants. Protein Sci 2005; 14:2915-8. [PMID: 16199659 PMCID: PMC2253225 DOI: 10.1110/ps.051585905] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We have determined the critical concentrations of a set of 18 variants of Alzheimer's Abeta(1-40) peptide, each carrying a different residue at position 18. We find that the critical concentrations depend on the hydrophobicity and beta-sheet propensity of residue 18, and therefore on properties that we identified previously to affect also the kinetics by which these peptides aggregate. Since the critical concentrations can be related to the Gibbs free energy of aggregation (DeltaG), these data imply a link between the thermodynamics and the kinetics of aggregation in that sequences that form very stable aggregates are also those that form such aggregates very rapidly.
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Affiliation(s)
- Peter Hortschansky
- Leibniz-Institut für Naturstoff-Forschung une Infektionsbiologie, Hans-Knöll-Institut, D-07745 Jena, Germany
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523
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Abstract
Sup35NM, the prion determining domain of the protein responsible for the yeast prion phenomenon [Psi], has become a powerful model for studying key processes in amyloid-related human diseases. One of these processes is a conformational conversion of soluble precursor protein into insoluble fibrillar structures. In this study, we created a set of Sup35NM mutants and used proteolytic digestion coupled with mass spectroscopy to monitor local structure of the protein during polymerization. Experimental data were compared to a network model and showed that during the conformational conversion residue Arg-28 became highly protected from cleavage, residue Arg-98 remained partially solvent exposed, and residues between 28 and 98 showed an intermediate degree of protection. In addition, we found that a distinct subset of proteolytic polypeptides spanning 28-98 residues segment spontaneously formed stable dimers. This finding suggests that the [29-98] region is the key interacting region of Sup35NM responsible for amyloid conversion.
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Affiliation(s)
- Vladimir A Goncharov
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.
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524
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Surgucheva I, Ninkina N, Buchman VL, Grasing K, Surguchov A. Protein aggregation in retinal cells and approaches to cell protection. Cell Mol Neurobiol 2005; 25:1051-66. [PMID: 16392036 PMCID: PMC11529641 DOI: 10.1007/s10571-005-8474-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Accepted: 04/21/2005] [Indexed: 10/25/2022]
Abstract
1. Retinal dystrophies (RD) comprise a group of clinically and genetically heterogeneous retinal disorders, which typically result in the degeneration of photoreceptors followed by the impairment or loss of vision. Although age-related macular degeneration (AMD) and retinitis pigmentosa (RP) are among the most common forms of RD, currently, there is no effective treatment for either disorder. 2. Recently, abnormal protein accumulation and aggregation due to protein misfolding and proteasome inhibition have been implicated in the pathogenesis of RD. In this paper we describe effects of several factors on protein aggregation and survival of photoreceptor cells. 3. Expression of rhodopsin carrying P23H mutation causes its accumulation in intracellular inclusion bodies in a perinuclear area of photoreceptor cells. beta- and gamma-synucleins and heat shock protein Hsp-70, but not alpha-synuclein, protect cultured ocular cells from mutant opsin accumulation. This effect might be explained by their chaperonic activity. 4. Knock-out of alpha- and gamma-synucleins does not affect gross retinal morphology, but induces tyrosine hydroxylase in the inner prexiform layer of the retina. Selegiline-a monoamine oxidase inhibitor used for the treatment of Parkinson's disease, reduces apoptosis and increases viability in cultured retinal pigment epithelium cells (APRE-19). 5. These results suggest that chaperones and selegiline may be considered promising candidates for the protection of ocular cells from the accumulation of misfolded and aggregated proteins.
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Affiliation(s)
- Irina Surgucheva
- Retinal Disease Research Laboratory, Veterans Administration Medical Center, Kansas City, Missouri
- Department of Neurology, Kansas University Medical Center, Kansas City, Kansas
| | | | | | - Kenneth Grasing
- Retinal Disease Research Laboratory, Veterans Administration Medical Center, Kansas City, Missouri
- Department of Medicine, Kansas University Medical Center, Kansas City, Kansas
| | - Andrei Surguchov
- Retinal Disease Research Laboratory, Veterans Administration Medical Center, Kansas City, Missouri
- Department of Neurology, Kansas University Medical Center, Kansas City, Kansas
- Retinal Disease Research Laboratory, VA Medical Center and Kansas University Medical Center, 4801 Linwood Boulevard, Kansas City, Missouri 66148
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525
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Higurashi T, Yagi H, Mizobata T, Kawata Y. Amyloid-like Fibril Formation of Co-chaperonin GroES: Nucleation and Extension Prefer Different Degrees of Molecular Compactness. J Mol Biol 2005; 351:1057-69. [PMID: 16054644 DOI: 10.1016/j.jmb.2005.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 06/01/2005] [Accepted: 07/03/2005] [Indexed: 10/25/2022]
Abstract
The molecular chaperone GroES, together with GroEL from Escherichia coli, is the best characterized protein of the molecular chaperone family. Here, we report on the in vitro formation of GroES amyloid-like fibrils and the mechanism of formation. When incubated for several weeks at neutral pH in the presence of the denaturant guanidine hydrochloride, GroES formed a typical amyloid fibril; unbranched, twisted, and extended filaments stainable by thioflavin T and Congo red. GroES fibril formation was accelerated by the addition of preformed fibril seeds, in accordance with a nucleation-extension mechanism. Interestingly, whereas the spontaneous formation of GroES fibrils was favored in the structural transition region of GroES dissociation/unfolding, the extension of fibrils from preformed fibril seeds was favored in the region corresponding to an expanded molecular state. We concluded that the two stages of GroES fibril formation prefer different molecular states of the same protein. The significance of this preference is discussed.
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Affiliation(s)
- Takashi Higurashi
- Department of Biotechnology, Faculty of Engineering, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan
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526
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Ab initio conformational analysis of N- and C-terminally-protected valyl-alanine dipeptide model. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.02.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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527
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Cellmer T, Bratko D, Prausnitz JM, Blanch H. Protein-folding landscapes in multichain systems. Proc Natl Acad Sci U S A 2005; 102:11692-7. [PMID: 16081531 PMCID: PMC1188005 DOI: 10.1073/pnas.0505342102] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out by using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the thermodynamics of folding for a Miyazawa-Jernigan model 64-mer in isolation to results obtained in the presence of additional chains. The melting temperature falls as the chain concentration increases. In multichain systems, free-energy landscapes for folding show an increased preference for misfolded states. Misfolding is accompanied by an increase in interprotein interactions; however, near the folding temperature, the transition from folded chains to misfolded and associated chains is entropically driven. A majority of the most probable interprotein contacts are also native contacts, suggesting that native topology plays a role in early stages of aggregation.
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Affiliation(s)
- Troy Cellmer
- Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
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528
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Pawar AP, Dubay KF, Zurdo J, Chiti F, Vendruscolo M, Dobson CM. Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases. J Mol Biol 2005; 350:379-92. [PMID: 15925383 DOI: 10.1016/j.jmb.2005.04.016] [Citation(s) in RCA: 484] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 04/11/2005] [Accepted: 04/11/2005] [Indexed: 02/08/2023]
Abstract
Increasing evidence indicates that many peptides and proteins can be converted in vitro into highly organised amyloid structures, provided that the appropriate experimental conditions can be found. In this work, we define intrinsic propensities for the aggregation of individual amino acids and develop a method for identifying the regions of the sequence of an unfolded peptide or protein that are most important for promoting amyloid formation. This method is applied to the study of three polypeptides associated with neurodegenerative diseases, Abeta42, alpha-synuclein and tau. In order to validate the approach, we compare the regions of proteins that are predicted to be most important in driving aggregation, either intrinsically or as the result of mutations, with those determined experimentally. The knowledge of the location and the type of the "sensitive regions" for aggregation is important both for rationalising the effects of sequence changes on the aggregation of polypeptide chains and for the development of targeted strategies to combat diseases associated with amyloid formation.
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Affiliation(s)
- Amol P Pawar
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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529
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Cheung JK, Truskett TM. Coarse-grained strategy for modeling protein stability in concentrated solutions. Biophys J 2005; 89:2372-84. [PMID: 16040749 PMCID: PMC1366737 DOI: 10.1529/biophysj.105.062067] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a coarse-grained approach for modeling the thermodynamic stability of single-domain globular proteins in concentrated aqueous solutions. Our treatment derives effective protein-protein interactions from basic structural and energetic characteristics of the native and denatured states. These characteristics, along with the intrinsic (i.e., infinite dilution) thermodynamics of folding, are calculated from elementary sequence information using a heteropolymer collapse theory. We integrate this information into Reactive Canonical Monte Carlo simulations to investigate the connections between protein sequence hydrophobicity, protein-protein interactions, protein concentration, and the thermodynamic stability of the native state. The model predicts that sequence hydrophobicity can affect how protein concentration impacts native-state stability in solution. In particular, low hydrophobicity proteins are primarily stabilized by increases in protein concentration, whereas high hydrophobicity proteins exhibit richer nonmonotonic behavior. These trends appear qualitatively consistent with the available experimental data. Although factors such as pH, salt concentration, and protein charge are also important for protein stability, our analysis suggests that some of the nontrivial experimental trends may be driven by a competition between destabilizing hydrophobic protein-protein attractions and entropic crowding effects.
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Affiliation(s)
- Jason K Cheung
- Department of Chemical Engineering, and Institute of Theoretical Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
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530
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Chen P. Self-assembly of ionic-complementary peptides: a physicochemical viewpoint. Colloids Surf A Physicochem Eng Asp 2005. [DOI: 10.1016/j.colsurfa.2004.12.048] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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531
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Christopeit T, Hortschansky P, Schroeckh V, Gührs K, Zandomeneghi G, Fändrich M. Mutagenic analysis of the nucleation propensity of oxidized Alzheimer's beta-amyloid peptide. Protein Sci 2005; 14:2125-31. [PMID: 15987892 PMCID: PMC2279324 DOI: 10.1110/ps.051470405] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The formation of polypeptide aggregates represents a nucleated polymerization reaction in which an initial nucleation event (lag phase) is followed by the extension of newly formed nuclei into larger aggregates, including fibrils (growth phase). The efficiencies of these reactions relate to the lag time (lag phase) and to the rate of aggregation (growth phase), which can be determined from experimental aggregation curves. Here we present a mutagenic analysis in which we replace valine 18 of the Alzheimer's Abeta (1-40) peptide with 17 different amino acids and determine its effect on the lag time, and therefore, on the propensity of nucleation. Comparison with various physico-chemical properties shows that nucleation is affected in a predictable manner depending on the beta-sheet propensity and hydrophobicity of residue 18. In addition, we observe a direct proportionality between the lag time and the rate of aggregation. These data imply that the two reactions, nucleation and polymerization, are governed by very similar physicochemical principles and that they involve the formation of the same types of noncovalent interactions.
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532
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Abstract
Receptors, hormones, enzymes, ion channels, and structural components of the cell are created by the act of protein synthesis. Synthesis alone is insufficient for proper function, of course; for a cell to operate effectively, its components must be correctly compartmentalized. The mechanism by which proteins maintain the fidelity of localization warrants attention in light of the large number of different molecules that must be routed to distinct subcellular loci, the potential for error, and resultant disease. This review summarizes diseases known to have etiologies based on defective protein folding or failure of the cell's quality control apparatus and presents approaches for therapeutic intervention.
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Affiliation(s)
- Cecilia Castro-Fernández
- Oregon National Primate Research Center/Oregon Health and Science University, 505 NW 185th Avenue, Beaverton, Oregon 97006, USA
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533
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Abstract
Bovine Spongiform Encephalopathy (BSE) is typical of the dementias that affect both animals and man; Scrapie in sheep, Creutzfeldt-Jakob disease in man. Global efforts have been made to determine the nature of the active agents in these diseases. At present the 'protein only hypothesis' of Prusiner holds. It was a surprise that a protein could per se be the active agent but other surprises for our traditional teaching of biochemistry arose. These are explained in a brief summary of our present understanding of the biochemistry of the active agents that cause the diseases.
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Affiliation(s)
- Peter N Campbell
- Department of Biochemistry and Molecular Biology, University College London, London, UK
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534
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Murali J, Jayakumar R. Spectroscopic studies on native and protofibrillar insulin. J Struct Biol 2005; 150:180-9. [PMID: 15866741 DOI: 10.1016/j.jsb.2005.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 02/18/2005] [Indexed: 11/16/2022]
Abstract
The structure of insulin in amyloid fibrillar form has been recently shown as a well folded conformation using cryoelectron microscopy [Jimenez, J.L., Nettleton, E.J., Bouchard, M., Robinson, C.V., Dobson, C.M., Saibil H.R., 2002. The protofilament structure of insulin amyloid fibrils. Proc. Natl. Acad. Sci. USA. 99 9196-9201.]. Most of the amyloid aggregates elicit maximum toxicity in the protofibrillar (PF) intermediate state. Here, we describe PF intermediates of insulin are made-up monomers with flexible conformers. We also show protofibrils have three-dimensionally extended hydrophobic cavity to bind with 1-anilinonaphthalene-8-sulphonate (ANS) molecules. Energy transfer measurement revealed that ANS dye binding site of PF is within the range of FRET distance of insulin tyrosine residues. Significant proportion of beta-sheet, helical, and turn structures in the PF form indicate conformational dynamics in the folded chain of insulin in the PF assembled form. Though the conformational flexibility is noticeably present in the assembly, addition of GdnHCl could completely unfold PF into disordered structure suggesting structural "zipping" in the PF form. We have also shown that helical conformer inducing solvent 2,2,2-trifluoroethanol (TFE) could dissociate the PF aggregate indicating possible involvement of beta-sheets in contributing to PF stability.
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Affiliation(s)
- J Murali
- Bioorganic and Neurochemistry Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
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535
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de Chiara C, Menon RP, Adinolfi S, de Boer J, Ktistaki E, Kelly G, Calder L, Kioussis D, Pastore A. The AXH Domain Adopts Alternative Folds. Structure 2005; 13:743-53. [PMID: 15893665 DOI: 10.1016/j.str.2005.02.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 02/20/2005] [Accepted: 02/22/2005] [Indexed: 11/24/2022]
Abstract
AXH is a protein module identified in two unrelated families that comprise the transcriptional repressor HBP1 and ataxin-1 (ATX1), the protein responsible for spinocerebellar ataxia type-1 (SCA1). SCA1 is a neurodegenerative disorder associated with protein misfolding and formation of toxic intranuclear aggregates. We have solved the structure in solution of monomeric AXH from HBP1. The domain adopts a nonclassical permutation of an OB fold and binds nucleic acids, a function previously unidentified for this region of HBP1. Comparison of HBP1 AXH with the crystal structure of dimeric ATX1 AXH indicates that, despite the significant sequence homology, the two proteins have different topologies, suggesting that AXH has chameleon properties. We further demonstrate that HBP1 AXH remains monomeric, whereas the ATX1 dimer spontaneously aggregates and forms fibers. Our results describe an entirely novel, to our knowledge, example of a chameleon fold and suggest a link between these properties and the SCA1 pathogenesis.
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Affiliation(s)
- Cesira de Chiara
- National Institute for Medical Research, The Ridgeway, London, United Kingdom
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536
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Tcherkasskaya O, Davidson EA, Schmerr MJ, Orser CS. Conformational biosensor for diagnosis of prion diseases. Biotechnol Lett 2005; 27:671-5. [PMID: 15977076 DOI: 10.1007/s10529-005-4478-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Accepted: 03/18/2005] [Indexed: 11/24/2022]
Abstract
A fluorescence technology to monitor the proliferation of amyloidogenic neurological disorders is proposed. A crude brain homogenate (0.01%) from animals infected with a transmissible spongiform encephalopathy is employed as a catalytic medium initiating conformational changes in 520 nM polypeptide biosensors (Tris/trifluoroethanol 50% mixture at pH 7). The fluorescence methods utilize pyrene residues covalently attached to the peptide ends. The coil-to-beta-strand transitions in biosensor molecules cause elevation of a distinct fluorescence band of the pyrene aggregates (i.e. excimers). This approach enables the detection of infectious prion proteins at fmol, does not require antibody binding or protease treatment. Technology might be adopted for diagnosing a large variety of conformational disorders as well as for generic high-throughput screening of the amyloidogenic potential in plasma.
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Affiliation(s)
- Olga Tcherkasskaya
- Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, DC 20057, USA.
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537
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Cellmer T, Bratko D, Prausnitz JM, Blanch H. The competition between protein folding and aggregation: off-lattice minimalist model studies. Biotechnol Bioeng 2005; 89:78-87. [PMID: 15540197 DOI: 10.1002/bit.20302] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein aggregation has been associated with a number of human diseases, and is a serious problem in the manufacture of recombinant proteins. Of particular interest to the biotechnology industry is deleterious aggregation that occurs during the refolding of proteins from inclusion bodies. As a complement to experimental efforts, computer simulations of multi-chain systems have emerged as a powerful tool to investigate the competition between folding and aggregation. Here we report results from Langevin dynamics simulations of minimalist model proteins. Order parameters are developed to follow both folding and aggregation. By mapping natural units to real units, the simulations are shown to be carried out under experimentally relevant conditions. Data pertaining to the contacts formed during the association process show that multiple mechanisms for aggregation exist, but certain pathways are statistically preferred. Kinetic data show that there are multiple time scales for aggregation, although most association events take place at times much shorter than those required for folding. Last, we discuss results presented here as a basis for future work aimed at rational design of mutations to reduce aggregation propensity, as well as for development of small-molecular weight refolding enhancers.
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Affiliation(s)
- Troy Cellmer
- Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
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538
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Gellermann GP, Appel TR, Tannert A, Radestock A, Hortschansky P, Schroeckh V, Leisner C, Lütkepohl T, Shtrasburg S, Röcken C, Pras M, Linke RP, Diekmann S, Fändrich M. Raft lipids as common components of human extracellular amyloid fibrils. Proc Natl Acad Sci U S A 2005; 102:6297-302. [PMID: 15851687 PMCID: PMC1088351 DOI: 10.1073/pnas.0407035102] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils are fibrillar polypeptide aggregates from several degenerative human conditions, including Alzheimer's and Creutzfeldt-Jakob diseases. Analysis of amyloid fibrils derived from various human diseases (AA, ATTR, Abeta2M, ALlambda, and ALkappa amyloidosis) shows that these are associated with a common lipid component that has a conserved chemical composition and that is specifically rich in cholesterol and sphingolipids, the major components of cellular lipid rafts. This pattern is not notably affected by the purification procedure, and no tight lipid interactions can be detected when preformed fibrils are mixed with lipids. By contrast, the early and prefibrillar aggregates formed in an AA amyloid-producing cell system interact with the raft marker ganglioside-1, and amyloid formation is impaired by addition of cholesterol-reducing agents. These data suggest the existence of common cellular mechanisms in the generation of different types of clinical amyloid deposits.
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Affiliation(s)
- Gerald P Gellermann
- Institut für Molekulare Biotechnologie, Beutenbergstrasse 11, 07745 Jena, Germany
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539
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Dumoulin M, Dobson CM. Probing the origins, diagnosis and treatment of amyloid diseases using antibodies. Biochimie 2005; 86:589-600. [PMID: 15556268 DOI: 10.1016/j.biochi.2004.09.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2004] [Revised: 07/12/2004] [Accepted: 09/16/2004] [Indexed: 01/21/2023]
Abstract
The deposition of proteins in the form of amyloid fibrils is the characteristic feature of more than 20 medical conditions affecting the central nervous system or a variety of peripheral tissues. These disorders, which include Alzheimer's disease, the prion diseases and type II diabetes, are of enormous importance in the context of present-day human health and welfare. Extensive research is therefore being carried out to define the molecular details of the mechanism of the pathological conversion of amyloidogenic proteins from their soluble forms into fibrillar structures. This review focuses on recent studies that demonstrate the power of using antibodies or antibody fragments to probe the process of fibril formation, and discusses the emerging potential of these species as diagnostic and therapeutic agents.
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Affiliation(s)
- Mireille Dumoulin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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540
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Lu JR, Perumal S, Zhao X, Miano F, Enea V, Heenan RR, Penfold J. Surface-induced unfolding of human lactoferrin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:3354-3361. [PMID: 15807574 DOI: 10.1021/la047162j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We have determined the structural conformations of human lactoferrin adsorbed at the air/water interface by neutron reflectivity (NR) and its solution structure by small angle neutron scattering (SANS). The neutron reflectivity measurements revealed a strong structural unfolding of the molecule when adsorbed at the interface from a pH 7 phosphate buffer solution (PBS with a total ionic strength at 4.5 mM) over a wide concentration range. Two distinct regions, a top dense layer of 15-20 angstroms on the air side and a bottom diffuse layer of some 50 angstroms into the aqueous subphase, characterized the unfolded interfacial layer. At a concentration around 1 g dm(-3), close to the physiological concentration of lactoferrin in biological fluids, the adsorbed amount was 5.5 x 10(-8) mol m(-2) in the absence of NaCl, but the addition of 0.3 M NaCl reduced protein adsorption to 3.5 x 10(-8) mol m(-2). Although the polypeptide distributions at the interface remained similar, quantitative analysis showed that the addition of NaCl reduced the layer thickness. Parallel measurements of lactoferrin adsorption in D2O instead of null reflecting water confirmed the unfolded structure at the interface. Furthermore, the D2O data indicated that the polypeptide in the top layer was predominantly protruded out of water, consistent with it being hydrophobic. In contrast, the scattering intensity profiles from SANS were well described by a cylindrical model with a diameter of 47 angstroms and a length of 105 angstroms in the presence of 0.3 M NaCl, indicating a retention of the globular framework in the bulk solution. In the absence of NaCl but with the same amount of phosphate buffer, the length of the cylinder increased to some 190 angstroms and the diameter remained constant. The length increase is indicative of changes in distance and orientation between the bilobal monomers due to the change in charge interactions. The results thus demonstrate that the surface structural unfolding was caused by the exposure of the protein molecule to the unsymmetrical energetic balance following surface adsorption.
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Affiliation(s)
- Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, the University of Manchester, Sackville Street Building, Sackville Street, Manchester M60 1QD, UK.
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541
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Foss TR, Kelker MS, Wiseman RL, Wilson IA, Kelly JW. Kinetic Stabilization of the Native State by Protein Engineering: Implications for Inhibition of Transthyretin Amyloidogenesis. J Mol Biol 2005; 347:841-54. [PMID: 15769474 DOI: 10.1016/j.jmb.2005.01.050] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Revised: 01/19/2005] [Accepted: 01/21/2005] [Indexed: 11/23/2022]
Abstract
The amyloidogenic homotetrameric protein transthyretin (TTR) must undergo rate-limiting dissociation to partially denatured monomers in order to aggregate. TTR contains two distinct quaternary interfaces, one of which defines the binding sites for thyroxine and small-molecule amyloidogenesis inhibitors. Kinetic stabilization of the tetramer can be accomplished either by the binding of amyloidogenesis inhibitors selectively to the native state over the dissociative transition state or by the introduction of trans-suppressor subunits (T119M) into heterotetramers to destabilize the dissociative transition state. In each case, increasing the dissociation activation barrier prevents tetramer dissociation. Herein, we demonstrate that tethering two subunits whose quaternary interface defines the thyroxine binding site also dramatically increases the barrier for tetramer dissociation, apparently by destabilization of the dissociative transition state. The tethered construct (TTR-L-TTR)2 is structurally and functionally equivalent to wild-type TTR. Urea is unable to denature (TTR-L-TTR)2, yet it is able to maintain the denatured state once denaturation is achieved by GdnHCl treatment, suggesting that (TTR-L-TTR)2 is kinetically rather than thermodynamically stabilized, consistent with the identical wild-type TTR and (TTR-L-TTR)2 GdnHCl denaturation curves. Studies focused on a construct containing a single TTR-L-TTR chain and two normal monomer subunits establish that alteration of only one quaternary structural interface is sufficient to impose kinetic stabilization on the entire quaternary structure.
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Affiliation(s)
- Ted R Foss
- Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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542
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Tanaka M, Chien P, Yonekura K, Weissman JS. Mechanism of Cross-Species Prion Transmission. Cell 2005; 121:49-62. [PMID: 15820678 DOI: 10.1016/j.cell.2005.03.008] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 02/22/2005] [Accepted: 03/10/2005] [Indexed: 11/22/2022]
Abstract
Efficiency of interspecies prion transmission decreases as the primary structures of the infectious proteins diverge. Yet, a single prion protein can misfold into multiple infectious conformations, and such differences in "strain conformation" also alter infection specificity. Here, we explored the relationship between prion strains and species barriers by creating distinct synthetic prion forms of the yeast prion protein Sup35. We identified a strain conformation of Sup35 that allows transmission from the S. cerevisiae (Sc) Sup35 to the highly divergent C. albicans (Ca) Sup35 both in vivo and in vitro. Remarkably, cross-species transmission leads to a novel Ca strain that in turn can infect the Sc protein. Structural studies reveal strain-specific conformational differences in regions of the prion domain that are involved in intermolecular contacts. Our findings support a model whereby strain conformation is the critical determinant of cross-species prion transmission while primary structure affects transmission specificity by altering the spectrum of preferred amyloid conformations.
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Affiliation(s)
- Motomasa Tanaka
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
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543
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Komaru K, Ishida Y, Amaya Y, Goseki-Sone M, Orimo H, Oda K. Novel aggregate formation of a frame-shift mutant protein of tissue-nonspecific alkaline phosphatase is ascribed to three cysteine residues in the C-terminal extension. FEBS J 2005; 272:1704-17. [PMID: 15794757 DOI: 10.1111/j.1742-4658.2005.04597.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the majority of hypophosphatasia patients, reductions in the serum levels of alkaline phosphatase activity are caused by various missense mutations in the tissue-nonspecific alkaline phosphatase (TNSALP) gene. A unique frame-shift mutation due to a deletion of T at cDNA number 1559 [TNSALP (1559delT)] has been reported only in Japanese patients with high allele frequency. In this study, we examined the molecular phenotype of TNSALP (1559delT) using in vitro translation/translocation system and COS-1 cells transiently expressing this mutant protein. We showed that the mutant protein not only has a larger molecular size than the wild type enzyme by approximately 12 kDa, reflecting an 80 amino acid-long extension at its C-terminus, but that it also lacks a glycosylphosphatidylinositol anchor. In support of this, alkaline phosphatase activity of the cells expressing TNSALP (1559delT) was localized at the juxtanucleus position, but not on the cell surface. However, only a limited amount of the newly synthesized protein was released into the medium and the rest was polyubiquitinated, followed by degradation in the proteasome. SDS/PAGE and analysis by sucrose-density-gradient analysis indicated that TNSALP (1559delT) forms a disulfide-bonded high-molecular-mass aggregate. Interestingly, the aggregate form of TNSALP (1559delT) exhibited a significant enzyme activity. When all three cysteines at positions of 506, 521 and 577 of TNSALP (1559delT) were replaced with serines, the aggregation disappeared and instead this modified mutant protein formed a noncovalently associated dimer, strongly indicating that these cysteine residues in the C-terminal region are solely responsible for aggregate formation by cross-linking the catalytically active dimers. Thus, complete absence of TNSALP on cell surfaces provides a plausible explanation for a severe lethal phenotype of a homozygote hypophosphatasia patient carrying TNSALP (1559delT).
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Affiliation(s)
- Keiichi Komaru
- Division of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Gakkocho-dori, Niigata, Japan
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544
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Rogers SS, Venema P, Sagis LMC, van der Linden E, Donald AM. Measuring the Length Distribution of a Fibril System: A Flow Birefringence Technique Applied to Amyloid Fibrils. Macromolecules 2005. [DOI: 10.1021/ma0474224] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Salman S. Rogers
- Department of Physics, Cambridge University, Cavendish Laboratory, Cambridge CB3 0HE, UK, and Laboratory of Food Physics, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Paul Venema
- Department of Physics, Cambridge University, Cavendish Laboratory, Cambridge CB3 0HE, UK, and Laboratory of Food Physics, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Leonard M. C. Sagis
- Department of Physics, Cambridge University, Cavendish Laboratory, Cambridge CB3 0HE, UK, and Laboratory of Food Physics, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Erik van der Linden
- Department of Physics, Cambridge University, Cavendish Laboratory, Cambridge CB3 0HE, UK, and Laboratory of Food Physics, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Athene M. Donald
- Department of Physics, Cambridge University, Cavendish Laboratory, Cambridge CB3 0HE, UK, and Laboratory of Food Physics, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
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545
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Pokala N, Handel TM. Energy Functions for Protein Design: Adjustment with Protein–Protein Complex Affinities, Models for the Unfolded State, and Negative Design of Solubility and Specificity. J Mol Biol 2005; 347:203-27. [PMID: 15733929 DOI: 10.1016/j.jmb.2004.12.019] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 12/05/2004] [Accepted: 12/09/2004] [Indexed: 11/16/2022]
Abstract
The development of the EGAD program and energy function for protein design is described. In contrast to most protein design methods, which require several empirical parameters or heuristics such as patterning of residues or rotamers, EGAD has a minimalist philosophy; it uses very few empirical factors to account for inaccuracies resulting from the use of fixed backbones and discrete rotamers in protein design calculations, and describes the unfolded state, aggregates, and alternative conformers explicitly with physical models instead of fitted parameters. This approach unveils important issues in protein design that are often camouflaged by heuristic-emphasizing methods. Inter-atom energies are modeled with the OPLS-AA all-atom forcefield, electrostatics with the generalized Born continuum model, and the hydrophobic effect with a solvent-accessible surface area-dependent term. Experimental characterization of proteins designed with an unmodified version of the energy function revealed problems with under-packing, stability, aggregation, and structural specificity. Under-packing was addressed by modifying the van der Waals function. By optimizing only three parameters, the effects of >400 mutations on protein-protein complex formation were predicted to within 1.0 kcal mol(-1). As an independent test, this modified energy function was used to predict the stabilities of >1500 mutants to within 1.0 kcal mol(-1); this required a physical model of the unfolded state that includes more interactions than traditional tripeptide-based models. Solubility and structural specificity were addressed with simple physical approximations of aggregation and conformational equilibria. The complete energy function can design protein sequences that have high levels of identity with their natural counterparts, and have predicted structural properties more consistent with soluble and uniquely folded proteins than the initial designs.
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Affiliation(s)
- Navin Pokala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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546
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Vendruscolo M, Dobson CM. Towards complete descriptions of the free-energy landscapes of proteins. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:433-452. [PMID: 15664892 DOI: 10.1098/rsta.2004.1501] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In recent years increasingly detailed information about the structures and dynamics of protein molecules has been obtained by innovative applications of experimental techniques, in particular nuclear magnetic resonance spectroscopy and protein engineering, and theoretical methods, notably molecular dynamics simulations. In this article we discuss how such approaches can be combined by incorporating a wide range of different types of experimental data as restraints in computer simulations to provide unprecedented detail about the ensembles of structures that describe proteins in a wide variety of states from the native structure to highly unfolded species. Knowledge of these ensembles is beginning to enable the complete free-energy landscapes of individual proteins to be defined at atomic resolution. This strategy has provided new insights into the mechanism by which proteins are able to fold into their native states, or by which they fail to do so and give rise to harmful aggregates that are associated with a wide range of debilitating human diseases.
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Affiliation(s)
- Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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547
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Clark LA. Protein aggregation determinants from a simplified model: cooperative folders resist aggregation. Protein Sci 2005; 14:653-62. [PMID: 15689507 PMCID: PMC2279276 DOI: 10.1110/ps.041017305] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Two-chain aggregation simulations using minimalist models of proteins G, L, and mutants were used to investigate the fundamentals of protein aggregation. Mutations were selected to break up repeats of hydrophobic beads in the sequence while maintaining native topology and folding ability. Data are collected under conditions in which all chain types have similar folded populations and after equilibrating the separated chains to minimize competition between folding and aggregation. Folding cooperativity stands out as the best single-chain determinant under these conditions and for these simple models. It can be experimentally measured by the width of the unfolding transition during thermal denaturation and loosely related to population of intermediate-like states during folding. Additional measures of cooperativity and other properties such as radius of gyration fluctuations and patterning of hydrophobic residues are also examined. Initial contact system states with transition-state characteristics can be identified and are more expanded than average initial contact states. Two-chain minimalist model aggregates are considerably less structured than their native states and have minimal domain-swapping features.
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Affiliation(s)
- Louis A Clark
- Biogen Idec, Inc., Computational Drug Design Group, 14 Cambridge Center, Cambridge, MA 02142, USA.
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548
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Soto P, Cladera J, Mark AE, Daura X. Stability of SIV gp32 Fusion‐Peptide Single‐Layer Protofibrils as Monitored by Molecular‐Dynamics Simulations. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461935] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Patricia Soto
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Josep Cladera
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Alan E. Mark
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Xavier Daura
- Catalan Institution for Research and Advanced Studies (ICREA), Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, Fax: (+34) 93‐581‐2011
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549
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Krebs MRH, Morozova-Roche LA, Daniel K, Robinson CV, Dobson CM. Observation of sequence specificity in the seeding of protein amyloid fibrils. Protein Sci 2005; 13:1933-8. [PMID: 15215533 PMCID: PMC2279934 DOI: 10.1110/ps.04707004] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
It is well established that the rate of formation of fibrils by amyloidogenic proteins is enhanced by the addition of preformed fibrils, a phenomenon known as seeding. We show that the efficiency of seeding fibril formation from solutions of hen lysozyme by a series of other proteins depends strongly on the similarity of their sequences. This observation is consistent with the importance of long-range interactions in stabilizing the core structure of amyloid fibrils and may be associated with the existence of a species barrier observed in the transmissible spongiform encephalopathies. In addition, it is consistent with the observation of a single dominant type of protein in the deposits associated with each form of amyloid disease.
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Affiliation(s)
- Mark R H Krebs
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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550
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Ohkuri T, Shioi S, Imoto T, Ueda T. Effect of the structure of the denatured state of lysozyme on the aggregation reaction at the early stages of folding from the reduced form. J Mol Biol 2005; 347:159-68. [PMID: 15733925 DOI: 10.1016/j.jmb.2005.01.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Revised: 01/06/2005] [Accepted: 01/07/2005] [Indexed: 11/25/2022]
Abstract
We previously demonstrated that the hydrophobic clusters present in hen lysozyme under denaturing conditions were disrupted by the mutation of Trp62 to Gly (W62G). In order to examine the effects of the structure of the denatured state of W62G lysozyme on folding, we analyzed the early events in the folding of reduced W62G lysozyme in detail. From the exchange measurements of disulfide bonds using the variants containing a pair of cysteine residues (1SS), it was found that the formation of disulfide bond in the W62G1SS lysozyme was not accompanied by a prominent interaction between amino acid residues, indicating that the disruption of the hydrophobic core led to the random folding at the early stages in the process of folding of the reduced lysozyme. On the other hand, analyses of the oxidative-renaturation of reduced W62G lysozymes, as well as measurements of the extent of aggregation of the reduced and carboxy amido methylated W62G lysozyme, indicated that the formation of an aggregate is more prominent in the reduced W62G lysozyme than in the reduced wild-type lysozyme. Moreover, a lag phase was detected in the oxidative-renaturation of reduced W62G lysozyme, as based on observations of the recovery of activity. The simulation of the folding process indicated that intermediates were present at the early stages in the folding of the reduced W62G lysozyme. These results suggest that the presence of the intermediates was derived from the random folding at the early stages in the folding process of reduced W62G lysozyme due to the disruption of the structure of the denatured state. Folding thus appears to have been kinetically delayed by these processes, which then led to the significant aggregation of reduced lysozyme. Moreover, from the analysis of amyloid aggregation of the reduced lysozymes, it was suggested that the disruption of the residual structure in denatured state by W62G mutation deterred the formation of the amyloid fibrils of lysozyme.
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Affiliation(s)
- Takatoshi Ohkuri
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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