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Wu H, Zhang F, Williamson N, Jian J, Zhang L, Liang Z, Wang J, An L, Tunnacliffe A, Zheng Y. Effects of secondary metabolite extract from Phomopsis occulta on β-amyloid aggregation. PLoS One 2014; 9:e109438. [PMID: 25275648 PMCID: PMC4183696 DOI: 10.1371/journal.pone.0109438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 09/02/2014] [Indexed: 11/19/2022] Open
Abstract
Inhibition of β-amyloid (Aβ) aggregation is an attractive therapeutic and preventive strategy for the discovery of disease-modifying agents in Alzheimer's disease (AD). Phomopsis occulta is a new, salt-tolerant fungus isolated from mangrove Pongamia pinnata (L.) Pierre. We report here the inhibitory effects of secondary metabolites from Ph. occulta on the aggregation of Aβ42. It was found that mycelia extracts (MEs) from Ph. occulta cultured with 0, 2, and 3 M NaCl exhibited inhibitory activity in an E. coli model of Aβ aggregation. A water-soluble fraction, ME0-W-F1, composed of mainly small peptides, was able to reduce aggregation of an Aβ42-EGFP fusion protein and an early onset familial mutation Aβ42E22G-mCherry fusion protein in transfected HEK293 cells. ME0-W-F1 also antagonized the cytotoxicity of Aβ42 in the neural cell line SH-SY5Y in dose-dependent manner. Moreover, SDS-PAGE and FT-IR analysis confirmed an inhibitory effect of ME0-W-F1 on the aggregation of Aβ42 in vitro. ME0-W-F1 blocked the conformational transition of Aβ42 from α-helix/random coil to β-sheet, and thereby inhibited formation of Aβ42 tetramers and high molecular weight oligomers. ME0-W-F1 and other water-soluble secondary metabolites from Ph. occulta therefore represent new candidate natural products against aggregation of Aβ42, and illustrate the potential of salt tolerant fungi from mangrove as resources for the treatment of AD and other diseases.
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Affiliation(s)
- Haiqiang Wu
- College of Life Sciences, Shenzhen University, Shenzhen, China
| | - Fang Zhang
- College of Life Sciences, Shenzhen University, Shenzhen, China
| | - Neil Williamson
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Jie Jian
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
- College of Pharmacy, Guilin Medical University, Guilin, China
| | - Liao Zhang
- College of Life Sciences, Shenzhen University, Shenzhen, China
| | - Zeqiu Liang
- College of Life Sciences, Shenzhen University, Shenzhen, China
| | - Jinyu Wang
- College of Life Sciences, Shenzhen University, Shenzhen, China
| | - Linkun An
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou, China
| | - Alan Tunnacliffe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AT); (YZ)
| | - Yizhi Zheng
- College of Life Sciences, Shenzhen University, Shenzhen, China
- * E-mail: (AT); (YZ)
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52
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Susa AC, Wu C, Bernstein SL, Dupuis NF, Wang H, Raleigh DP, Shea JE, Bowers MT. Defining the molecular basis of amyloid inhibitors: human islet amyloid polypeptide-insulin interactions. J Am Chem Soc 2014; 136:12912-9. [PMID: 25144879 PMCID: PMC4183647 DOI: 10.1021/ja504031d] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Indexed: 11/28/2022]
Abstract
Human islet amyloid polypeptide (hIAPP or Amylin) is a 37 residue hormone that is cosecreted with insulin from the pancreatic islets. The aggregation of hIAPP plays a role in the progression of type 2 diabetes and contributes to the failure of islet cell grafts. Despite considerable effort, little is known about the mode of action of IAPP amyloid inhibitors, and this has limited rational drug design. Insulin is one of the most potent inhibitors of hIAPP fibril formation, but its inhibition mechanism is not understood. In this study, the aggregation of mixtures of hIAPP with insulin, as well as with the separate A and B chains of insulin, were characterized using ion mobility spectrometry-based mass spectrometry and atomic force microscopy. Insulin and the insulin B chain target the hIAPP monomer in its compact isoform and shift the equilibrium away from its extended isoform, an aggregation-prone conformation, and thus inhibit hIAPP from forming β-sheets and subsequently amyloid fibrils. All-atom molecular modeling supports these conclusions.
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Affiliation(s)
- Anna C. Susa
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Chun Wu
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Summer L. Bernstein
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Nicholas F. Dupuis
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Hui Wang
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Daniel P. Raleigh
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Joan-Emma Shea
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
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53
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Bowers MT. Ion mobility spectrometry: A personal view of its development at UCSB. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014; 370:75-95. [PMID: 25147478 PMCID: PMC4135396 DOI: 10.1016/j.ijms.2014.06.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Ion mobility is not a newly discovered phenomenon. It has roots going back to Langevin at the beginning of the 20th century. Our group initially got involved by accident around 1990 and this paper is a brief account of what has transpired here at UCSB the past 25 years in response to this happy accident. We started small, literally, with transition metal atomic ions and transitioned to carbon clusters, synthetic polymers, most types of biological molecules and eventually peptide and protein oligomeric assembly. Along the way we designed and built several generations of instruments, a process that is still ongoing. And perhaps most importantly we have incorporated theory with experiment from the beginning; a necessary wedding that allows an atomistic face to be put on the otherwise interesting but not fully informative cross section measurements.
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54
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Sitkiewicz E, Kłoniecki M, Poznański J, Bal W, Dadlez M. Factors Influencing Compact–Extended Structure Equilibrium in Oligomers of Aβ1–40 Peptide—An Ion Mobility Mass Spectrometry Study. J Mol Biol 2014; 426:2871-85. [DOI: 10.1016/j.jmb.2014.05.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/08/2014] [Accepted: 05/15/2014] [Indexed: 12/15/2022]
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55
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Sitkiewicz E, Olędzki J, Poznański J, Dadlez M. Di-tyrosine cross-link decreases the collisional cross-section of aβ peptide dimers and trimers in the gas phase: an ion mobility study. PLoS One 2014; 9:e100200. [PMID: 24945725 PMCID: PMC4063900 DOI: 10.1371/journal.pone.0100200] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/22/2014] [Indexed: 01/04/2023] Open
Abstract
Oligomeric forms of Aβ peptide are most likely the main synaptotoxic and neurotoxic agent in Alzheimer’s disease. Toxicity of various Aβ oligomeric forms has been confirmed in vivo and also in vitro. However, in vitro preparations were found to be orders of magnitude less toxic than oligomers obtained from in vivo sources. This difference can be explained by the presence of a covalent cross-link, which would stabilize the oligomer. In the present work, we have characterized the structural properties of Aβ dimers and trimers stabilized by di- and tri-tyrosine cross-links. Using ion mobility mass spectrometry we have compared the collisional cross-section of non-cross-linked and cross-linked species. We have found that the presence of cross-links does not generate new unique forms but rather shifts the equilibrium towards more compact oligomer types that can also be detected for non-cross-linked peptide. In consequence, more extended forms, probable precursors of off-pathway oligomeric species, become relatively destabilized in cross-linked oligomers and the pathway of oligomer evolution becomes redirected towards fibrillar structures.
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Affiliation(s)
- Ewa Sitkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Warszawa, Poland
| | - Jacek Olędzki
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Warszawa, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Warszawa, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Warszawa, Poland
- Institute of Genetics and Biotechnology, Biology Department, Warsaw University, Warszawa, Poland
- * E-mail:
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56
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Lanucara F, Holman SW, Gray CJ, Eyers CE. The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat Chem 2014; 6:281-94. [DOI: 10.1038/nchem.1889] [Citation(s) in RCA: 655] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 02/11/2014] [Indexed: 02/07/2023]
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57
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Shen X, Deng X, Pang Y. Self-assembly of Cu(ii) with amyloid β19–20 peptide: relevant to Alzheimer's disease. RSC Adv 2014. [DOI: 10.1039/c4ra02758b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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58
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Lee S, Zheng X, Krishnamoorthy J, Savelieff MG, Park HM, Brender JR, Kim JH, Derrick JS, Kochi A, Lee HJ, Kim C, Ramamoorthy A, Bowers MT, Lim MH. Rational design of a structural framework with potential use to develop chemical reagents that target and modulate multiple facets of Alzheimer's disease. J Am Chem Soc 2013; 136:299-310. [PMID: 24397771 DOI: 10.1021/ja409801p] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Alzheimer's disease (AD) is characterized by multiple, intertwined pathological features, including amyloid-β (Aβ) aggregation, metal ion dyshomeostasis, and oxidative stress. We report a novel compound (ML) prototype of a rationally designed molecule obtained by integrating structural elements for Aβ aggregation control, metal chelation, reactive oxygen species (ROS) regulation, and antioxidant activity within a single molecule. Chemical, biochemical, ion mobility mass spectrometric, and NMR studies indicate that the compound ML targets metal-free and metal-bound Aβ (metal-Aβ) species, suppresses Aβ aggregation in vitro, and diminishes toxicity induced by Aβ and metal-treated Aβ in living cells. Comparison of ML to its structural moieties (i.e., 4-(dimethylamino)phenol (DAP) and (8-aminoquinolin-2-yl)methanol (1)) for reactivity with Aβ and metal-Aβ suggests the synergy of incorporating structural components for both metal chelation and Aβ interaction. Moreover, ML is water-soluble and potentially brain permeable, as well as regulates the formation and presence of free radicals. Overall, we demonstrate that a rational structure-based design strategy can generate a small molecule that can target and modulate multiple factors, providing a new tool to uncover and address AD complexity.
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Affiliation(s)
- Sanghyun Lee
- Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109-2216, United States
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59
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Bleiholder C, Do TD, Wu C, Economou NJ, Bernstein SS, Buratto SK, Shea JE, Bowers MT. Ion mobility spectrometry reveals the mechanism of amyloid formation of Aβ(25-35) and its modulation by inhibitors at the molecular level: epigallocatechin gallate and scyllo-inositol. J Am Chem Soc 2013; 135:16926-37. [PMID: 24131107 DOI: 10.1021/ja406197f] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Amyloid cascades leading to peptide β-sheet fibrils and plaques are central to many important diseases. Recently, intermediate assemblies of these cascades were identified as the toxic agents that interact with the cellular machinery. The relationship between the transformation from natively unstructured assembly to the β-sheet oligomers to disease is important in understanding disease onset and the development of therapeutic agents. Research on this early oligomeric region has largely been unsuccessful since traditional techniques measure only ensemble average oligomer properties. Here, ion mobility methods are utilized to deduce the modulation of peptide self-assembly pathways in the amyloid-β protein fragment Aβ(25-35) by two amyloid inhibitors (epigallocatechin gallate and scyllo-inositol) that are currently in clinical trials for Alzheimer's Disease. We provide evidence that suppression of β-extended oligomers from the onset of the conversion into β-oligomer conformations is essential for effective attenuation of β-structured amyloid oligomeric species often associated with oligomer toxicity. Furthermore, we demonstrate the ease with which ion mobility spectrometry-mass spectrometry can guide the development of therapeutic agents and drug evaluation by providing molecular level insight into the amyloid formation process and its modulation by small molecule assembly modulators.
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Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
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60
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Niu S, Rabuck JN, Ruotolo BT. Ion mobility-mass spectrometry of intact protein–ligand complexes for pharmaceutical drug discovery and development. Curr Opin Chem Biol 2013; 17:809-17. [DOI: 10.1016/j.cbpa.2013.06.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/17/2013] [Accepted: 06/18/2013] [Indexed: 11/30/2022]
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61
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Pulsed hydrogen-deuterium exchange mass spectrometry probes conformational changes in amyloid beta (Aβ) peptide aggregation. Proc Natl Acad Sci U S A 2013; 110:14604-9. [PMID: 23959898 DOI: 10.1073/pnas.1309175110] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Probing the conformational changes of amyloid beta (Aβ) peptide aggregation is challenging owing to the vast heterogeneity of the resulting soluble aggregates. To investigate the formation of these aggregates in solution, we designed an MS-based biophysical approach and applied it to the formation of soluble aggregates of the Aβ42 peptide, the proposed causative agent in Alzheimer's disease. The approach incorporates pulsed hydrogen-deuterium exchange coupled with MS analysis. The combined approach provides evidence for a self-catalyzed aggregation with a lag phase, as observed previously by fluorescence methods. Unlike those approaches, pulsed hydrogen-deuterium exchange does not require modified Aβ42 (e.g., labeling with a fluorophore). Furthermore, the approach reveals that the center region of Aβ42 is first to aggregate, followed by the C and N termini. We also found that the lag phase in the aggregation of soluble species is affected by temperature and Cu(2+) ions. This MS approach has sufficient structural resolution to allow interrogation of Aβ aggregation in physiologically relevant environments. This platform should be generally useful for investigating the aggregation of other amyloid-forming proteins and neurotoxic soluble peptide aggregates.
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62
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Meral D, Urbanc B. Discrete molecular dynamics study of oligomer formation by N-terminally truncated amyloid β-protein. J Mol Biol 2013; 425:2260-75. [PMID: 23500806 PMCID: PMC3665754 DOI: 10.1016/j.jmb.2013.03.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 03/05/2013] [Indexed: 01/09/2023]
Abstract
In Alzheimer's disease (AD), amyloid β-protein (Aβ) self-assembles into toxic oligomers. Of the two predominant Aβ alloforms, Aβ1-40 and Aβ1-42, the latter is particularly strongly linked to AD. N-terminally truncated and pyroglutamated Aβ peptides were recently shown to seed Aβ aggregation and contribute significantly to Aβ-mediated toxicity, yet their folding and assembly were not explored computationally. Discrete molecular dynamics approach previously captured in vitro-derived distinct Aβ1-40 and Aβ1-42 oligomer size distributions and predicted that the more toxic Aβ1-42 oligomers had more flexible and solvent-exposed N-termini than Aβ1-40 oligomers. Here, we examined oligomer formation of Aβ3-40, Aβ3-42, Aβ11-40, and Aβ11-42 by the discrete molecular dynamics approach. The four N-terminally truncated peptides showed increased oligomerization propensity relative to the full-length peptides, consistent with in vitro findings. Conformations formed by Aβ3-40/42 had significantly more flexible and solvent-exposed N-termini than Aβ1-40/42 conformations. In contrast, in Aβ11-40/42 conformations, the N-termini formed more contacts and were less accessible to the solvent. The compactness of the Aβ11-40/42 conformations was in part facilitated by Val12. Two single amino acid substitutions that reduced and abolished hydrophobicity at position 12, respectively, resulted in a proportionally increased structural variability. Our results suggest that Aβ11-40 and Aβ11-42 oligomers might be less toxic than Aβ1-40 and Aβ1-42 oligomers and offer a plausible explanation for the experimentally observed increased toxicity of Aβ3-40 and Aβ3-42 and their pyroglutamated forms.
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Affiliation(s)
- Derya Meral
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
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63
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Soper MT, DeToma AS, Hyung SJ, Lim MH, Ruotolo BT. Amyloid-β-neuropeptide interactions assessed by ion mobility-mass spectrometry. Phys Chem Chem Phys 2013; 15:8952-61. [PMID: 23612608 PMCID: PMC3664942 DOI: 10.1039/c3cp50721a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recently, small peptides have been shown to modulate aggregation and toxicity of the amyloid-β protein (Aβ). As such, these new scaffolds may help discover a new class of biotherapeutics useful in the treatment of Alzheimer's disease. Many of these inhibitory peptide sequences have been derived from natural sources or from Aβ itself (e.g., C-terminal Aβ fragments). In addition, much earlier work indicates that tachykinins, a broad class of neuropeptides, display neurotrophic properties, presumably through direct interactions with either Aβ or its receptors. Based on this work, we undertook a limited screen of neuropeptides using ion mobility-mass spectrometry to search for similar such peptides with direct Aβ binding properties. Our results reveal that the neuropeptides leucine enkephalin (LE) and galanin interact with both the monomeric and small oligomeric forms of Aβ(1-40) to create a range of complexes having diverse stoichiometries, while some tachyknins (i.e., substance P) do not. LE interacts with Aβ more strongly than galanin, and we utilized ion mobility-mass spectrometry, molecular dynamics simulations, gel electrophoresis/Western blot, and transmission electron microscopy to study the influence of this peptide on the structure of Aβ monomer, small Aβ oligomers, as well as the eventual formation of Aβ fibrils. We find that LE binds selectively within a region of Aβ between its N-terminal tail and hydrophobic core. Furthermore, our data indicate that LE modulates fibril generation, producing shorter fibrillar aggregates when added in stoichiometric excess relative to Aβ.
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Affiliation(s)
- Molly T. Soper
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Alaina S. DeToma
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Suk-Joon Hyung
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Mi Hee Lim
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Life Science Institute, University of Michigan, Ann Arbor, MI 48109
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64
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Woods L, Radford S, Ashcroft A. Advances in ion mobility spectrometry-mass spectrometry reveal key insights into amyloid assembly. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1257-68. [PMID: 23063533 PMCID: PMC3787735 DOI: 10.1016/j.bbapap.2012.10.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/27/2012] [Accepted: 10/02/2012] [Indexed: 10/28/2022]
Abstract
Interfacing ion mobility spectrometry to mass spectrometry (IMS-MS) has enabled mass spectrometric analyses to extend into an extra dimension, providing unrivalled separation and structural characterization of lowly populated species in heterogeneous mixtures. One biological system that has benefitted significantly from such advances is that of amyloid formation. Using IMS-MS, progress has been made into identifying transiently populated monomeric and oligomeric species for a number of different amyloid systems and has led to an enhanced understanding of the mechanism by which small molecules modulate amyloid formation. This review highlights recent advances in this field, which have been accelerated by the commercial availability of IMS-MS instruments. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
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Affiliation(s)
| | - S.E. Radford
- Astbury Centre for Structural Molecular Biology & School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - A.E. Ashcroft
- Astbury Centre for Structural Molecular Biology & School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
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65
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Williams DM, Pukala TL. Novel insights into protein misfolding diseases revealed by ion mobility-mass spectrometry. MASS SPECTROMETRY REVIEWS 2013; 32:169-187. [PMID: 23345084 DOI: 10.1002/mas.21358] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 05/23/2012] [Accepted: 05/29/2012] [Indexed: 06/01/2023]
Abstract
Amyloid disorders incorporate a wide range of human diseases arising from the failure of a specific peptide or protein to adopt, or remain in, its native functional conformational state. These pathological conditions, such as Parkinson's disease, Alzheimer's disease and Huntington's disease are highly debilitating, exact enormous costs on both individuals and society, and are predicted to increase in prevalence. Consequently, they form the focus of a topical and rich area of current scientific research. A major goal in attempts to understand and treat protein misfolding diseases is to define the structures and interactions of protein species intermediate between fully folded and aggregated, and extract a description of the aggregation process. This has proven a difficult task due to the inability of traditional structural biology approaches to analyze structurally heterogeneous systems. Continued developments in instrumentation and analytical approaches have seen ion mobility-mass spectrometry (IM-MS) emerge as a complementary approach for protein structure determination, and in some cases, a structural biology tool in its own right. IM-MS is well suited to the study of protein misfolding, and has already yielded significant structural information for selected amyloidogenic systems during the aggregation process. This review describes IM-MS for protein structure investigation, and provides a summary of current research highlighting how this methodology has unequivocally and unprecedentedly provided structural and mechanistic detail pertaining to the oligomerization of a variety of disease related proteins.
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Affiliation(s)
- Danielle M Williams
- School of Chemistry and Physics, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
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66
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Pedersen JT, Heegaard NHH. Analysis of Protein Aggregation in Neurodegenerative Disease. Anal Chem 2013; 85:4215-27. [DOI: 10.1021/ac400023c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jeppe T. Pedersen
- Department of Chemistry, Faculty of Science, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen
Ø, Denmark
| | - Niels H. H. Heegaard
- Analytical Protein Chemistry, Department of Clinical Biochemistry, Immunology & Genetics, Statens Serum Institut, DK-2300 Copenhagen S, Denmark
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67
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Konijnenberg A, Butterer A, Sobott F. Native ion mobility-mass spectrometry and related methods in structural biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:1239-56. [PMID: 23246828 DOI: 10.1016/j.bbapap.2012.11.013] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 11/19/2012] [Accepted: 11/29/2012] [Indexed: 12/12/2022]
Abstract
Mass spectrometry-based methods have become increasingly important in structural biology - in particular for large and dynamic, even heterogeneous assemblies of biomolecules. Native electrospray ionization coupled to ion mobility-mass spectrometry provides access to stoichiometry, size and architecture of noncovalent assemblies; while non-native approaches such as covalent labeling and H/D exchange can highlight dynamic details of protein structures and capture intermediate states. In this overview article we will describe these methods and highlight some recent applications for proteins and protein complexes, with particular emphasis on native MS analysis. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
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68
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Liu T, Bitan G. Modulating self-assembly of amyloidogenic proteins as a therapeutic approach for neurodegenerative diseases: strategies and mechanisms. ChemMedChem 2012; 7:359-74. [PMID: 22323134 DOI: 10.1002/cmdc.201100585] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Indexed: 01/19/2023]
Abstract
Abnormal protein assembly causes multiple devastating disorders in the central nervous system (CNS), such as Alzheimer's, Parkinson's, Huntington's, and prion diseases. Due to the now extended human lifespan, these diseases have been increasing in prevalence, resulting in major public health problems and the associated financial difficulties worldwide. The wayward proteins that lead to disease self-associate into neurotoxic oligomers and go on to form fibrillar polymers through multiple pathways. Thus, a range of possible targets for pharmacotherapeutic intervention exists along these pathways. Many compounds have shown different levels of effectiveness in inhibiting aberrant self-assembly, dissociating existing aggregates, protecting cells against neurotoxic insults, and in some cases ameliorating disease symptoms in vivo, yet achieving efficient, disease-modifying therapy in humans remains a major unattained goal. To a large degree, this is because the mechanisms of action for these drugs are essentially unknown. For successful design of new effective drugs, it is crucial to elucidate the mechanistic details of their action, including the actual target(s) along the protein aggregation pathways, how the compounds modulate these pathways, and their effect at the cellular, tissue, organ, and organism level. Here, the current knowledge of major mechanisms by which some of the more extensively explored drug candidates work are discussed. In particular, we focus on three prominent strategies: 1) stabilizing the native fold of amyloidogenic proteins, 2) accelerating the aggregation pathways towards the fibrillar endpoint thereby reducing accumulation of toxic oligomers, and 3) modulating the assembly process towards nontoxic oligomers/aggregates. The merit of each strategy is assessed, and the key points to consider when analyzing the efficacy of possible drug candidates and their mechanism of action are discussed.
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Affiliation(s)
- Tingyu Liu
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 635 Charles E. Young Drive South/NRB 455, Los Angeles, CA 90095, USA
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