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Abstract
According to Thomas Kuhn, the success of 'normal science,' the science we all practice on a daily basis, depends on the adherence to, and practice of, a paradigm accepted by the scientific community. When great scientific upheavals occur, they involve the rejection of the current paradigm in favor of a new paradigm that better integrates the facts available and better predicts the behavior of a particular scientific system. In the field of Alzheimer's disease, a recent example of such a paradigm shift has been the apparent rejection of the 'amyloid cascade hypothesis,' promulgated by Hardy and Higgins in 1992 to explain the etiology of Alzheimer's disease, in favor of what has been referred to as the 'oligomer cascade hypothesis'. This paradigm shift has been breathtaking in its rapidity, its pervasiveness in the Alzheimer's disease field, and its adoption in an increasing number of other fields, including those of Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and the prionoses. However, these facts do not mean, a priori, that the experiments extant, and any re-interpretation of them, should be accepted by rote as support for the new paradigm. In the discussion that follows, I consider the foundational studies leading to the oligomer cascade hypothesis and evaluate the current state of the paradigm. I argue here that, more often than not, insufficient rigor has been applied in studies upon which this new paradigm has been based. Confusion, rather than clarity, has resulted. If the field is to make progress forward using as its paradigmatic basis amyloid β-protein oligomerization, then an epistemological re-evaluation of the amyloid β-protein oligomer system is required.
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Affiliation(s)
- David B Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA, 635 Charles E. Young Dr. South, Room 445, Los Angeles, CA 90095, USA
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252
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Thakkar SV, Sahni N, Joshi SB, Kerwin BA, He F, Volkin DB, Middaugh CR. Understanding the relevance of local conformational stability and dynamics to the aggregation propensity of an IgG1 and IgG2 monoclonal antibodies. Protein Sci 2013; 22:1295-305. [PMID: 23893936 DOI: 10.1002/pro.2316] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/27/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022]
Abstract
Aggregation of monoclonal antibodies is often a multi-step process involving structural alterations in monomeric proteins and subsequent formation of soluble or insoluble oligomers. The role of local conformational stability and dynamics of native and/or partially altered structures in determining the aggregation propensity of monoclonal antibodies, however, is not well understood. Here, we investigate the role of conformational stability and dynamics of regions with distinct solvent exposure in determining the aggregation propensity of an IgG1 and IgG2 monoclonal antibody. The temperatures employed span the pre-unfolding range (10-40°C) and the onset temperatures (T onset ) for exposure of apolar residues (≈ 50°C), alterations in secondary structures (≈ 60°C) and initiation of visible aggregate formation (≈ 60°C). Solvent-exposed regions were found to precede solvent-shielded regions in an initiation of aggregation for both proteins. Such a process was observed upon alterations in overall tertiary structure while retaining the secondary structures in both the proteins. In addition, a greater dynamic nature of solvent-shielded regions in potential intermediates of IgG1 and the improved conformational stability increased its resistance to aggregation when compared to IgG2. These results suggest that local conformational stability and fluctuations of partially altered structures can influence the aggregation propensity of immunoglobulins.
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Affiliation(s)
- Santosh V Thakkar
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, USA
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253
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A Modified Lumry–Eyring Analysis for the Determination of the Predominant Mechanism Underlying the Diminution of Protein Aggregation by Glycerol. Cell Biochem Biophys 2013; 68:133-42. [DOI: 10.1007/s12013-013-9700-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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254
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Villar-Piqué A, Ventura S. Protein aggregation propensity is a crucial determinant of intracellular inclusion formation and quality control degradation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2714-2724. [PMID: 23856334 DOI: 10.1016/j.bbamcr.2013.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 01/13/2023]
Abstract
Protein aggregation is linked to many pathological conditions, including several neurodegenerative diseases. The aggregation propensities of proteins are thought to be controlled to a large extent by the physicochemical properties encoded in the primary sequence. We have previously exploited a set of amyloid β peptide (Aβ42) variants exhibiting a continuous gradient of intrinsic aggregation propensities to demonstrate that this rule applies in vivo in bacteria. In the present work we have characterized the behavior of these Aβ42 mutants when expressed in yeast. In contrast to bacteria, the intrinsic aggregation propensity is gated by yeast, in such a way that this property correlates with the formation of intracellular inclusions only above a specific aggregation threshold. Proteins displaying solubility levels above this threshold escape the inclusion formation pathway. In addition, the most aggregation-prone variants are selectively cleared by the yeast quality control degradation machinery. Thus, both inclusion formation and proteolysis target the same aggregation-prone variants and cooperate to minimize the presence of these potentially dangerous species in the cytosol. The demonstration that sorting to these pathways in eukaryotes is strongly influenced by protein primary sequence should facilitate the development of rational approaches to predict and hopefully prevent in vivo protein deposition.
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Affiliation(s)
- Anna Villar-Piqué
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain.
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255
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Misfolding and amyloid aggregation of apomyoglobin. Int J Mol Sci 2013; 14:14287-300. [PMID: 23839096 PMCID: PMC3742244 DOI: 10.3390/ijms140714287] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 01/03/2023] Open
Abstract
Apomyoglobin is an excellent example of a monomeric all α-helical globular protein whose folding pathway has been extensively studied and well characterized. Structural perturbation induced by denaturants or high temperature as well as amino acid substitution have been described to induce misfolding and, in some cases, aggregation. In this article, we review the molecular mechanism of the aggregation process through which a misfolded form of a mutated apomyoglobin aggregates at physiological pH and room temperature forming an amyloid fibril. The results are compared with data showing that either amyloid or aggregate formation occurs under particular denaturing conditions or upon cleavage of the residues corresponding to the C-terminal helix of apomyoglobin. The results are discussed in terms of the sequence regions that are more important than others in determining the amyloid aggregation process.
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256
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Amini R, Yazdanparast R, Bahramikia S. Apigenin reduces human insulin fibrillation in vitro and protects SK-N-MC cells against insulin amyloids. Int J Biol Macromol 2013; 60:334-40. [PMID: 23777711 DOI: 10.1016/j.ijbiomac.2013.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 06/10/2013] [Accepted: 06/13/2013] [Indexed: 01/21/2023]
Abstract
Deposition of proteins is a key pathogenic feature of more than 20 amyloid-related diseases. Inhibiting or reversing amyloid aggregation via the use of small molecules is proposed as two useful approaches in hampering the development of these diseases. In this research, we examined the inhibitory and disruptive effects of apigenin, a common dietary flavonoid with multiple pharmacological properties, against human insulin fibrillization. Besides, we investigated the potential cytotoxicity of insulin fibrils on SK-N-MC cells in the presence and absence of apigenin. The increase in Thioflavin T (ThT) and anilinonaphthalene-8-sulfonic acid (ANS) fluorescent intensities and Congo red absorbance were inhibited by simultaneous incubation of various concentrations of apigenin with insulin, in a dose-dependent manner. The spectroscopy results were confirmed by transmission electron microscopy, where lower extent of fibrillar structures was observed in the presence of apigenin. In addition, the cell exposure to the co-incubated insulin amyloids with apigenin led to the increased viability and decreased LDH release dose-dependently, compared to cells exposed to insulin fibrils alone. Co-incubation with apigenin also attenuated the extent of apoptotic cell death induced by insulin fibrils. It can be concluded that apigenin possess in vitro anti-amyloidogenic activities as well as protective effects against insulin amyloids cytotoxicity.
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Affiliation(s)
- Rahim Amini
- Institute of Biochemistry and Biophysics, P. O. Box 13145-1384, University of Tehran, Tehran, Iran
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257
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Cecchi C, Stefani M. The amyloid-cell membrane system. The interplay between the biophysical features of oligomers/fibrils and cell membrane defines amyloid toxicity. Biophys Chem 2013; 182:30-43. [PMID: 23820236 DOI: 10.1016/j.bpc.2013.06.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/03/2013] [Accepted: 06/03/2013] [Indexed: 12/14/2022]
Abstract
Amyloid cytotoxicity, structure and polymorphisms are themes of increasing importance. Present knowledge considers any peptide/protein able to undergo misfolding and aggregation generating intrinsically cytotoxic amyloids. It also describes growth and structure of amyloid fibrils and their possible disassembly, whereas reduced information is available on oligomer structure. Recent research has highlighted the importance of the environmental conditions as determinants of the amyloid polymorphisms and cytotoxicity. Another body of evidence describes chemical or biological surfaces as key sites of protein misfolding and aggregation or of interaction with amyloids and the resulting biochemical modifications inducing cell functional/viability impairment. In particular, the membrane lipid composition appears to modulate cell response to toxic amyloids, thus contributing to explain the variable vulnerability to the same amyloids of different cell types. Finally, a recent view describes amyloid toxicity as an emerging property dependent on a complex interplay between the biophysical features of early aggregates and the interacting cell membranes taken as a whole system.
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Affiliation(s)
- Cristina Cecchi
- Department of Biomedical Experimental and Clinical Sciences and Research Centre on the Molecular Basis of Neurodegeneration, University of Florence, Florence, Italy
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258
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Huang P, Lian F, Wen Y, Guo C, Lin D. Prion protein oligomer and its neurotoxicity. Acta Biochim Biophys Sin (Shanghai) 2013; 45:442-51. [PMID: 23557632 DOI: 10.1093/abbs/gmt037] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The prion diseases, also known as transmissible spongiform encephalopathies, are fatal neurodegenerative disorders. According to the 'protein only' hypothesis, the key molecular event in the pathogenesis of prion disease is the conformational conversion of the host-derived cellular prion protein (PrP(C)) into a misfolded form (scrapie PrP, PrP(Sc)). Increasing evidence has shown that the most infectious factor is the smaller subfibrillar oligomers formed by prion proteins. Both the prion oligomer and PrP(Sc) are rich in β-sheet structure and resistant to the proteolysis of proteinase K. The prion oligomer is soluble in physiologic environments whereas PrP(Sc) is insoluble. Various prion oligomers are formed in different conditions. Prion oligomers exhibited more neurotoxicity both in vitro and in vivo than the fibrillar forms of PrP(Sc), implying that prion oligomers could be potential drug targets for attacking prion diseases. In this article, we describe recent experimental evidence regarding prion oligomers, with a special focus on prion oligomer formation and its neurotoxicity.
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Affiliation(s)
- Pei Huang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 21009, China
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259
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Kim J, Park J, Lee T, Pak Y, Lim M. Dynamics of geminate rebinding of CO to cytochrome c in guanidine HCl probed by femtosecond vibrational spectroscopy. J Phys Chem B 2013; 117:4934-44. [PMID: 23590118 DOI: 10.1021/jp401481q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Femtosecond vibrational spectroscopy was used to probe the rebinding dynamics of CO to cytochrome c (Cytc) in 1.8 and 7 M guanidine HCl (GdnHCl) after photodeligation of the corresponding CO-bound protein in D2O buffer (pD = 7.4) at 283 K. Geminate rebinding (GR) dynamics of CO to the folded Cytc in 1.8 M GdnHCl (nCytc) is similar to that to chemically modified cytochrome c (cCytc), suggesting that the overall conformations of nCytcCO and cCytcCO are similar. About 86% of the dissociated CO molecules were geminately rebound to nCytc nonexponentially within 1 ns. The efficient GR of CO to the folded Cytc can be attributed to the organized protein matrix near the active site of nCytc that provides an efficient trap for the diffusing CO ligand after photodissociation. Although the concentration of nCytc did not affect its GR yield of CO, GR yield of CO to the unfolded Cytc in 7 M GdnHCl (uCytc) increased from 5 to 30% as the protein concentration increased from 0.3 to 9 mM. Time-resolved spectra of the (13)CO dissociated from both 9 mM nCytc(13)CO and 9 mM uCytc(13)CO showed a growing band with a peak at 2090 cm(-1) on the picosecond time scale, which was assigned to (13)CO in D2O solvent. At 1 ns, the fraction of the CO band in the solvent was about 10% of the nascent photodeligated protein in nCytc and more than 50% in the concentrated uCytc. Whereas a small opening in the active site of nCytc is responsible for the ultrafast escape of CO to solution in the folded protein, a large fraction of the CO escape to the solvent in uCytc results from the denatured structure of the active site in the unfolded protein. The spectrum of the CO dissociated from the concentrated uCytcCO contained a band that decayed as efficiently as that for the folded protein, suggesting that some fraction of uCytcCO might form aggregates even in 7 M denaturant, such that the aggregate acts as an efficient trap for the diffusing CO after deligation. No hint of precipitate in the concentrated uCytcCO and protein refolding upon dilution of the GdnHCl indicate that the aggregate does not grow continuously but remains as a soluble oligomer. The delayed appearance of the solvated CO and the inefficient GR of CO in uCytcCO suggest that the monomeric unfolded CytcCO so loosely arranged that the protein matrix cannot trap CO efficiently but the bound CO is still buried within hydrophobic residues even under the harsh denaturation condition.
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Affiliation(s)
- Jooyoung Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 609-735 Korea
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260
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Vilasi A, Vilasi S, Romano R, Acernese F, Barone F, Balestrieri ML, Maritato R, Irace G, Sirangelo I. Unraveling amyloid toxicity pathway in NIH3T3 cells by a combined proteomic and 1 H-NMR metabonomic approach. J Cell Physiol 2013. [PMID: 23192898 DOI: 10.1002/jcp.24294] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A range of debilitating human diseases is known to be associated with the formation of stable highly organized protein aggregates known as amyloid fibrils. The early prefibrillar aggregates behave as cytotoxic agents and their toxicity appears to result from an intrinsic ability to impair fundamental cellular processes by interacting with cellular membranes, causing oxidative stress and increase in free Ca(2+) that lead to apoptotic or necrotic cell death. However, specific signaling pathways that underlie amyloid pathogenicity remain still unclear. This work aimed to clarify cell impairment induced by amyloid aggregated. To this end, we used a combined proteomic and one-dimensional (1) H-NMR approach on NIH-3T3 cells exposed to prefibrillar aggregates from the amyloidogenic apomyoglobin mutant W7FW14F. The results indicated that cell exposure to prefibrillar aggregates induces changes of the expression level of proteins and metabolites involved in stress response. The majority of the proteins and metabolites detected are reported to be related to oxidative stress, perturbation of calcium homeostasis, apoptotic and survival pathways, and membrane damage. In conclusion, the combined proteomic and (1) H-NMR metabonomic approach, described in this study, contributes to unveil novel proteins and metabolites that could take part to the general framework of the toxicity induced by amyloid aggregates. These findings offer new insights in therapeutic and diagnostic opportunities.
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Affiliation(s)
- Annalisa Vilasi
- Laboratory of Mass Spectrometry and Proteomics, Institute of Protein Biochemistry-CNR, Naples, Italy
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261
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Aquilina JA, Shrestha S, Morris AM, Ecroyd H. Structural and functional aspects of hetero-oligomers formed by the small heat shock proteins αB-crystallin and HSP27. J Biol Chem 2013; 288:13602-9. [PMID: 23532854 DOI: 10.1074/jbc.m112.443812] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND αB-crystallin and HSP27 are mammalian intracellular small heat shock proteins. RESULTS These proteins exchange subunits in a rapid and temperature-dependent manner. CONCLUSION This facile subunit exchange suggests that differential expression could be used by the cell to regulate the response to stress. SIGNIFICANCE A robust technique defines parameters for the dynamic interaction between the major mammalian small heat shock proteins. Small heat shock proteins (sHSPs) exist as large polydisperse species in which there is constant dynamic subunit exchange between oligomeric and dissociated forms. Their primary role in vivo is to bind destabilized proteins and prevent their misfolding and aggregation. αB-Crystallin (αB) and HSP27 are the two most widely distributed and most studied sHSPs in the human body. They are coexpressed in different tissues, where they are known to associate with each other to form hetero-oligomeric complexes. In this study, we aimed to determine how these two sHSPs interact to form hetero-oligomers in vitro and whether, by doing so, there is an increase in their chaperone activity and stability compared with their homo-oligomeric forms. Our results demonstrate that HSP27 and αB formed polydisperse hetero-oligomers in vitro, which had an average molecular mass that was intermediate of each of the homo-oligomers and which were more thermostable than αB, but less so than HSP27. The hetero-oligomer chaperone function was found to be equivalent to that of αB, with each being significantly better in preventing the amorphous aggregation of α-lactalbumin and the amyloid fibril formation of α-synuclein in comparison with HSP27. Using mass spectrometry to monitor subunit exchange over time, we found that HSP27 and αB exchanged subunits 23% faster than the reported rate for HSP27 and αA and almost twice that for αA and αB. This represents the first quantitative evaluation of αB/HSP27 subunit exchange, and the results are discussed in the broader context of regulation of function and cellular proteostasis.
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Affiliation(s)
- J Andrew Aquilina
- Illawarra Health and Medical Research Institute and School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia.
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262
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Bahramikia S, Yazdanparast R. Inhibition of human islet amyloid polypeptide or amylin aggregation by two manganese-salen derivatives. Eur J Pharmacol 2013; 707:17-25. [PMID: 23528352 DOI: 10.1016/j.ejphar.2013.03.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 03/09/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
Abstract
Aggregation of human islet amyloid polypeptide (IAPP) into pancreatic fibrillar deposits has been postulated to be one of the main contributors to impaired insulin secretion and pancreatic β-cell death in approximately 90% of type 2 diabetic patients. So, compounds that prevent cytotoxic protein/polypeptide self-assembly and amyloidogenesis are considered as novel therapeutic agents against this disease. In this study, using thioflavin-T (ThT) and Anilinonaphthalene-8-sulfonic acid (ANS) fluorescence assays, transmission electron microscopy (TEM) and docking studies, we investigated whether EUK-8 and EUK-134, two salen derivatives with proven antioxidants activities, could interfere with the conversion of synthetic human amylin to its insoluble amyloid form. Spectroscopy and electron microscopy data indicated that incubation of human amylin with either EUK-8 or EUK-134 significantly inhibited amyloid formation at two molar ratios of 1:1 and 5:1 (drugs to protein). In addition, [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] (MTT) assay showed that treatment of SK-N-MC cells with the pre-formed fibrils in the presence of compounds at drug-to-protein molar ratios of 1:1 and 5:1, dramatically increased the viability of cells compared to the only fibrils formed-treated SK-N-MC cells. Docking results also demonstrated that the aromatic rings of EUK-8 and EUK-134 interact with the hydrophobic region (23-25) of IAPP via Van der Waals interactions. Based on these results and the proven antioxidant properties of these compounds, it could be concluded that these compounds might provide a novel approach to prevent islet amyloid deposition in β-cells and provide useful information for developing other novel compounds for the treatment of type 2 diabetes.
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Affiliation(s)
- Seifollah Bahramikia
- Institute of Biochemistry and Biophysics, PO Box 13145-1384, University of Tehran, Enghelab Ave, Tehran, Iran
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263
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Yamashima T. Reconsider Alzheimer's disease by the 'calpain-cathepsin hypothesis'--a perspective review. Prog Neurobiol 2013; 105:1-23. [PMID: 23499711 DOI: 10.1016/j.pneurobio.2013.02.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/08/2013] [Accepted: 02/28/2013] [Indexed: 01/24/2023]
Abstract
Alzheimer's disease (AD) is characterized by slowly progressive neuronal death, but its molecular cascade remains elusive for over 100 years. Since accumulation of autophagic vacuoles (also called granulo-vacuolar degenerations) represents one of the pathologic hallmarks of degenerating neurons in AD, a causative connection between autophagy failure and neuronal death should be present. The aim of this perspective review is at considering such underlying mechanism of AD that age-dependent oxidative stresses may affect the autophagic-lysosomal system via carbonylation and cleavage of heat-shock protein 70.1 (Hsp70.1). AD brains exhibit gradual but continual ischemic insults that cause perturbed Ca(2+) homeostasis, calpain activation, amyloid β deposition, and oxidative stresses. Membrane lipids such as linoleic and arachidonic acids are vulnerable to the cumulative oxidative stresses, generating a toxic peroxidation product 'hydroxynonenal' that can carbonylate Hsp70.1. Recent data advocate for dual roles of Hsp70.1 as a molecular chaperone for damaged proteins and a guardian of lysosomal integrity. Accordingly, impairments of lysosomal autophagy and stabilization may be driven by the calpain-mediated cleavage of carbonylated Hsp70.1, and this causes lysosomal permeabilization and/or rupture with the resultant release of the cell degradation enzyme, cathepsins (calpain-cathepsin hypothesis). Here, the author discusses three topics; (1) how age-related decrease in lysosomal and autophagic activities has a causal connection to programmed neuronal necrosis in sporadic AD, (2) how genetic factors such as apolipoprotein E and presenilin 1 can facilitate lysosomal destabilization in the sequential molecular events, and (3) whether a single cascade can simultaneously account for implications of all players previously reported. In conclusion, Alzheimer neuronal death conceivably occurs by the similar 'calpain-hydroxynonenal-Hsp70.1-cathepsin cascade' with ischemic neuronal death. Blockade of calpain and/or extra-lysosomal cathepsins as well as scavenging of hydroxynonenal would become effective AD therapeutic approaches.
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Affiliation(s)
- Tetsumori Yamashima
- Department of Restorative Neurosurgery, Kanazawa University Graduate School of Medical Science, Takara-machi 13-1, Kanazawa 920-8641, Japan.
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264
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Iram A, Naeem A. Detection and analysis of protofibrils and fibrils of hemoglobin: implications for the pathogenesis and cure of heme loss related maladies. Arch Biochem Biophys 2013; 533:69-78. [PMID: 23500139 DOI: 10.1016/j.abb.2013.02.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 01/17/2023]
Abstract
TFE induces structural alterations of proteins similar to the lipid environment of biological membranes, implicating these studies worthy of analyzing protein conformation in membranes such as red blood cells (RBCs). Heme loss occurs on rupturing of RBCs as found in diseases namely haemophilia, haemolytic anaemia, diabetes mellitus. TFE can be implied in discovering therapeutic targets, as it mimics the biological membrane environment. A global transition of hemoglobin (Hb) in presence of TFE was studied by using multi-methodological approach. The presence of partially folded state of Hb at 15% v/v TFE was confirmed by altered tryptophan environment, and retention of native-like secondary and tertiary structure. Molten globule state was observed at 20% v/v TFE as detected by increase tryptophan and high ANS fluorescence, slight alterations in Soret band relative to native. TFE on increasing concentration induced protofibrils at 25% v/v and fibrils at 45% v/v as depicted by altered tryptophan environment, heme loss, increase in non-native β-sheet secondary and tertiary structure, large hydrodynamic radii of heme-protein, high ANS, thioflavin T fluorescence and shift in Congo Red absorbance. Comet assay showed that protofibrils are cytotoxic to lymphocytes. SEM and XRD confirmed these aggregates to be fibrillar in nature.
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Affiliation(s)
- Afshin Iram
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
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265
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Morris KL, Rodger A, Hicks MR, Debulpaep M, Schymkowitz J, Rousseau F, Serpell LC. Exploring the sequence-structure relationship for amyloid peptides. Biochem J 2013; 450:275-83. [PMID: 23252554 PMCID: PMC3573774 DOI: 10.1042/bj20121773] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 01/10/2023]
Abstract
Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with 'steric-zipper' features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.
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Affiliation(s)
- Kyle L Morris
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
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266
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The how’s and why’s of protein folding intermediates. Arch Biochem Biophys 2013; 531:14-23. [DOI: 10.1016/j.abb.2012.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/05/2012] [Accepted: 10/11/2012] [Indexed: 12/13/2022]
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267
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Gazova Z, Siposova K, Kurin E, Mučaji P, Nagy M. Amyloid aggregation of lysozyme: the synergy study of red wine polyphenols. Proteins 2013; 81:994-1004. [PMID: 23280648 DOI: 10.1002/prot.24250] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 12/12/2012] [Indexed: 12/21/2022]
Abstract
The amyloidoses are diseases associated with nonnative folding of proteins and characterized by the presence of protein amyloid aggregates. The ability of quercetin, resveratrol, caffeic acid, and their equimolar mixtures to affect amyloid aggregation of hen egg white lysozyme in vitro was detected by Thioflavin T fluorescence assay. The anti-amyloid activities of tested polyphenols were evaluated by the median depolymerization concentrations DC50 and median inhibition concentrations IC50 . Single substances are more efficient (by at least one order) in the depolymerization of amyloid aggregates assay than in the inhibition of the amyloid formation with IC50 in 10(-4) to 10(-5) M range. Analyzed mixture samples showed synergic or antagonistic effects in both assays. DC50 values ranged from 10(-5) to 10(-8) M and IC50 from 10(-5) to 10(-9) M, respectively. We observed that certain mixtures of studied polyphenols can synergistically inhibit production of amyloids aggregates and are also effective in depolymerization of the aggregates. Synergic or antagonistic effects of studied mixtures were correlated with protein-small ligand docking studies and AFM results. Differences in these activities could be explained by binding of each polyphenol to a different amino acid sequence within the protein. Our results indicate that synergic/antagonistic anti-amyloid effects of studied mixtures depend on the selective binding of polyphenols to the known amyloidogenic sequences in the lysozyme chain. Our findings of the effective reduction of amyloid aggregation of lysozyme by polyphenol mixtures in vitro are of the utter physiological relevance considering the bioavailability and low toxicity of tested phenols.
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Affiliation(s)
- Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, Slovakia
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268
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Attanasio F, De Bona P, Cataldo S, Sciacca MFM, Milardi D, Pignataro B, Pappalardo G. Copper(ii) and zinc(ii) dependent effects on Aβ42 aggregation: a CD, Th-T and SFM study. NEW J CHEM 2013. [DOI: 10.1039/c3nj40999f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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269
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Giugliarelli A, Paolantoni M, Morresi A, Sassi P. Denaturation and Preservation of Globular Proteins: The Role of DMSO. J Phys Chem B 2012; 116:13361-7. [DOI: 10.1021/jp308655p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Marco Paolantoni
- Department of Chemistry, University of Perugia, Via Elce di sotto 8, 06100 Perugia, Italy
| | - Assunta Morresi
- Department of Chemistry, University of Perugia, Via Elce di sotto 8, 06100 Perugia, Italy
| | - Paola Sassi
- Department of Chemistry, University of Perugia, Via Elce di sotto 8, 06100 Perugia, Italy
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270
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Nelson AD, Hoffmann MM, Parks CA, Dasari S, Schrum AG, Gil D. IgG Fab fragments forming bivalent complexes by a conformational mechanism that is reversible by osmolytes. J Biol Chem 2012; 287:42936-50. [PMID: 23109335 DOI: 10.1074/jbc.m112.410217] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Generated by proteolytic cleavage of immunoglobulin, Fab fragments possess great promise as blocking reagents, able to bind receptors or other targets without inducing cross-linking. However, aggregation of Fab preparations is a common occurrence, which generates intrinsic stimulatory capacity and thwarts signal blockade strategies. Using a panel of biochemical approaches, including size exclusion chromatography, SDS-PAGE, mass spectrometry, and cell stimulation followed by flow cytometry, we have measured the oligomerization and acquisition of stimulatory capacity that occurs in four monoclonal IgG Fabs specific for TCR/CD3. Unexpectedly, we observed that all Fabs spontaneously formed complexes that were precisely bivalent, and these bivalent complexes possessed most of the stimulatory activity of each Fab preparation. Fabs composing bivalent complexes were more susceptible to proteolysis than monovalent Fabs, indicating a difference in conformation between the Fabs involved in these two different states of valency. Because osmolytes represent a class of compounds that stabilize protein folding and conformation, we sought to determine the extent to which the amino acid osmolyte l-proline might impact bivalent Fab complexation. We found that l-proline (i) inhibited the adoption of the conformation associated with bivalent complexation, (ii) preserved Fab monovalency, (iii) reversed the conformation of preformed bivalent Fabs to that of monovalent Fabs, and (iv) separated a significant percentage of preformed bivalent complexes into monovalent species. Thus, Fab fragments can adopt a conformation that is compatible with folding or packing of a bivalent complex in a process that can be inhibited by osmolytes.
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Affiliation(s)
- Alfreda D Nelson
- Department of Immunology, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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271
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Yousefi R, Jalili S, Alavi P, Moosavi-Movahedi AA. The enhancing effect of homocysteine thiolactone on insulin fibrillation and cytotoxicity of insulin fibril. Int J Biol Macromol 2012; 51:291-8. [DOI: 10.1016/j.ijbiomac.2012.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 05/14/2012] [Accepted: 05/15/2012] [Indexed: 10/28/2022]
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272
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Effects of oxidation of lysozyme by hypohalous acids and haloamines on enzymatic activity and aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1090-6. [DOI: 10.1016/j.bbapap.2012.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 06/14/2012] [Accepted: 06/19/2012] [Indexed: 12/18/2022]
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273
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Albrecht L, Hally D, Boyd RJ. Stabilizing effect of solvent and guest residue amino acids on a model alpha-helix peptide. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.06.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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274
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Hall D, Edskes H. Computational modeling of the relationship between amyloid and disease. Biophys Rev 2012; 4:205-222. [PMID: 23495357 PMCID: PMC3595053 DOI: 10.1007/s12551-012-0091-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 06/21/2012] [Indexed: 01/29/2023] Open
Abstract
Amyloid is a title conferred upon a special type of linear protein aggregate that exhibits a common set of structural features and dye binding capabilities. The formation of amyloid is associated with over twenty-seven distinct human diseases which are collectively referred to as the amyloidoses. Although there is great diversity amongst the amyloidoses with regard to the polypeptide monomeric precursor, targeted tissues and the nature and time course of disease development, the common underlying link of a structurally similar amyloid aggregate has prompted the search for a unified theory of disease progression in which amyloid production is the central element. Computational modeling has allowed the formulation and testing of scientific hypotheses for exploring this relationship. However, the majority of computational studies on amyloid aggregation are pitched at the atomistic level of description, in simple ideal solution environments, with simulation time scales of the order of microseconds and system sizes limited to a hundred monomers (or less). The experimental reality is that disease related amyloid aggregation processes occur in extremely complex reaction environments (i.e. the human body), over time-scales of months to years with monitoring of the reaction achieved using extremely coarse or indirect experimental markers that yield little or no atomistic insight. Clearly a substantial gap exists between computational and experimental communities with a deficit of 'useful' computational methodology that can be directly related to available markers of disease progression. This Review will place its focus on the development of these latter types of computational models and discuss them in relation to disease onset and progression.
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Affiliation(s)
- Damien Hall
- Institute of Basic Medical Science, University of Tsukuba, Lab 225-B, Building D. 1-1-1 Tennodai, Tsukuba-shi, Ibaraki-ken 305-8577 Japan
| | - Herman Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830 USA
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275
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A zinc complex of heparan sulfate destabilises lysozyme and alters its conformation. Biochem Biophys Res Commun 2012; 425:794-9. [PMID: 22884801 DOI: 10.1016/j.bbrc.2012.07.154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 07/27/2012] [Indexed: 11/22/2022]
Abstract
The naturally occurring anionic cell surface polysaccharide heparan sulfate is involved in key biological activities and is implicated in amyloid formation. Following addition of Zn-heparan sulfate, hen lysozyme, a model amyloid forming protein, resembled β-rich amyloid by far UV circular dichroism (increased β-sheet: +25%), with a significantly reduced melting temperature (from 68 to 58 °C) by fluorescence shift assay. Secondary structure stability of the Zn-heparan sulfate complex with lysozyme was also distinct from that with heparan sulfate, under stronger denaturation conditions using synchrotron radiation circular dichroism. Changing the cation associated with heparan sulfate is sufficient to alter the conformation and stability of complexes formed between heparan sulfate and lysozyme, substantially reducing the stability of the protein. Complexes of heparan sulfate and cations, such as Zn, which are abundant in the brain, may provide alternative folding routes for proteins.
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276
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Trusova VM, Gorbenko GP. Fluorescence study on aggregated lysozyme and lipid bilayer interactions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2012; 113:51-5. [PMID: 22652331 DOI: 10.1016/j.jphotobiol.2012.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 04/20/2012] [Accepted: 05/01/2012] [Indexed: 11/25/2022]
Abstract
Fluorescent probes 1,6-diphenyl-1,3,5-hexatriene (DPH), pyrene, 4-dimethylaminochalcone (DMC) and 4-p-(dimethylaminostyryl)-1-dodecylpyridinium (DSP-12) have been utilized to monitor the impact of lysozyme (Lz) oligomers on physicochemical properties of phosphatidylcholine/cardiolipin (PC/CL) membranes. Analysis of spectral responses of the employed probes revealed the reduction of membrane free volume and dehydration of lipid bilayer surface upon incorporation of Lz self-assemblies. Hydrophobic interactions were found to control the binding of Lz oligomers to the lipid bilayer. Comparison of the effects of Lz monomers, oligomers and fibrils showed that soluble oligomeric intermediates exert the most destructive influence on membrane properties.
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Affiliation(s)
- Valeriya M Trusova
- Department of Biological and Medical Physics, V.N. Karazin Kharkov National University, 4 Svobody Sq., Kharkov 61022, Ukraine.
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277
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Oligomeric forms of insulin amyloid aggregation disrupt outgrowth and complexity of neuron-like PC12 cells. PLoS One 2012; 7:e41344. [PMID: 22848469 PMCID: PMC3407202 DOI: 10.1371/journal.pone.0041344] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 06/20/2012] [Indexed: 11/19/2022] Open
Abstract
Formation of protein amyloid fibrils consists of a series of intermediates including oligomeric aggregates, proto-fibrillar structures, and finally mature fibrils. Recent studies show higher toxicity for oligomeric and proto-fibrillar intermediates of protein relative to their mature fibrils. Here the kinetic of the insulin amyloid fibrillation was evaluated using a variety of techniques including ThT fluorescence, Congo red absorbance, circular dichroism, and atomic force microscopy (AFM). The solution surface tension changes were attributed to hydrophobic changes in insulin structure and were detected by Du Noüy Ring method. Determination of the surface tension of insulin oligomeric, proto-fibrillar and fibrillar forms indicated that the hydrophobicity of solution is enhanced by the formation of the oligomeric forms of insulin compared to other forms. In order to investigate the toxicity of the different forms of insulin we monitored morphological alterations of the differentiated neuron-like PC12 cells following incubation with native, oligomeric aggregates, proto-fibrillar, and fibrillar forms of insulin. The cell body area, average neurite length, neurite width, number of primary neurites, and percent of bipolar cells and node/primary neurite ratios were used to assess the growth and complexity of PC12 cells exposed to different forms of insulin. We observed that the oligomeric form of insulin impaired the growth and complexity of PC12 cells compared to other forms. Together our data suggest that the lower surface tension of oligomers and their perturbation affects the morphology of PC12 cells, mainly due to their enhanced hydrophobicity and detergent-like structures.
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278
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On the use of size exclusion chromatography for the resolution of mixed amyloid aggregate distributions: I. Equilibrium partition models. Anal Biochem 2012; 426:69-85. [DOI: 10.1016/j.ab.2012.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/30/2012] [Accepted: 04/01/2012] [Indexed: 11/24/2022]
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279
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Hu L, Cui W, He Z, Shi X, Feng K, Ma B, Cai YD. Cooperativity among short amyloid stretches in long amyloidogenic sequences. PLoS One 2012; 7:e39369. [PMID: 22761773 PMCID: PMC3382238 DOI: 10.1371/journal.pone.0039369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 05/18/2012] [Indexed: 12/29/2022] Open
Abstract
Amyloid fibrillar aggregates of polypeptides are associated with many neurodegenerative diseases. Short peptide segments in protein sequences may trigger aggregation. Identifying these stretches and examining their behavior in longer protein segments is critical for understanding these diseases and obtaining potential therapies. In this study, we combined machine learning and structure-based energy evaluation to examine and predict amyloidogenic segments. Our feature selection method discovered that windows consisting of long amino acid segments of ~30 residues, instead of the commonly used short hexapeptides, provided the highest accuracy. Weighted contributions of an amino acid at each position in a 27 residue window revealed three cooperative regions of short stretch, resemble the β-strand-turn-β-strand motif in A-βpeptide amyloid and β-solenoid structure of HET-s(218-289) prion (C). Using an in-house energy evaluation algorithm, the interaction energy between two short stretches in long segment is computed and incorporated as an additional feature. The algorithm successfully predicted and classified amyloid segments with an overall accuracy of 75%. Our study revealed that genome-wide amyloid segments are not only dependent on short high propensity stretches, but also on nearby residues.
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Affiliation(s)
- Lele Hu
- Institute of Systems Biology, Shanghai University, Shanghai, People’s Republic of China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - Weiren Cui
- CAS-MPG Partner Institute of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Zhisong He
- CAS-MPG Partner Institute of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Xiaohe Shi
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Kaiyan Feng
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Buyong Ma
- Basic Science Program, SAIC – Frederick, Center for Cancer Research Nanobiology Program, National Cancer Institute-Fredeick, National Institute of Health, Frederick, Maryland, United States of America
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai, People’s Republic of China
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280
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Xiong K, Asher SA. Impact of ion binding on poly-L-lysine (un)folding energy landscape and kinetics. J Phys Chem B 2012; 116:7102-12. [PMID: 22612556 PMCID: PMC3381074 DOI: 10.1021/jp302007g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We utilize T-jump UV resonance Raman spectroscopy (UVRR) to study the impact of ion binding on the equilibrium energy landscape and on (un)folding kinetics of poly-L-lysine (PLL). We observe that the relaxation rates of the folded conformations (including π-helix (bulge), pure α-helix, and turns) of PLL are slower than those of short alanine-based peptides. The PLL pure α-helix folding time is similar to that of short alanine-based peptides. We for the first time have directly observed that turn conformations are α-helix and π-helix (bulge) unfolding intermediates. ClO(4)(-) binding to the Lys side chain -NH(3)(+) groups and the peptide backbone slows the α-helix unfolding rate compared to that in pure water, but little impacts the folding rate, resulting in an increased α-helix stability. ClO(4)(-) binding significantly increases the PLL unfolding activation barrier but little impacts the folding barrier. Thus, the PLL folding coordinate(s) differs from the unfolding coordinate(s). The-π helix (bulge) unfolding and folding coordinates do not directly go through the α-helix energy well. Our results clearly demonstrate that PLL (un)folding is not a two-state process.
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Affiliation(s)
- Kan Xiong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
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281
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Juritz E, Fornasari MS, Martelli PL, Fariselli P, Casadio R, Parisi G. On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. BMC Genomics 2012; 13 Suppl 4:S5. [PMID: 22759653 PMCID: PMC3303731 DOI: 10.1186/1471-2164-13-s4-s5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Non-synonymous coding SNPs (nsSNPs) that are associated to disease can also be related with alterations in protein stability. Computational methods are available to predict the effect of single amino acid substitutions (SASs) on protein stability based on a single folded structure. However, the native state of a protein is not unique and it is better represented by the ensemble of its conformers in dynamic equilibrium. The maintenance of the ensemble is essential for protein function. In this work we investigated how protein conformational diversity can affect the discrimination of neutral and disease related SASs based on protein stability estimations. For this purpose, we used 119 proteins with 803 associated SASs, 60% of which are disease related. Each protein was associated with its corresponding set of available conformers as found in the Protein Conformational Database (PCDB). Our dataset contains proteins with different extensions of conformational diversity summing up a total number of 1023 conformers. RESULTS The existence of different conformers for a given protein introduces great variability in the estimation of the protein stability (ΔΔG) after a single amino acid substitution (SAS) as computed with FoldX. Indeed, in 35% of our protein set at least one SAS can be described as stabilizing, destabilizing or neutral when a cutoff value of ±2 kcal/mol is adopted for discriminating neutral from perturbing SASs. However, when the ΔΔG variability among conformers is taken into account, the correlation among the perturbation of protein stability and the corresponding disease or neutral phenotype increases as compared with the same analysis on single protein structures. At the conformer level, we also found that the different conformers correlate in a different way to the corresponding phenotype. CONCLUSIONS Our results suggest that the consideration of conformational diversity can improve the discrimination of neutral and disease related protein SASs based on the evaluation of the corresponding Gibbs free energy change.
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Affiliation(s)
- Ezequiel Juritz
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | | | - Piero Fariselli
- Biocomputing Group, Department of Computer Science, University of Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Biology, University of Bologna, Italy
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
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282
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Beerten J, Jonckheere W, Rudyak S, Xu J, Wilkinson H, De Smet F, Schymkowitz J, Rousseau F. Aggregation gatekeepers modulate protein homeostasis of aggregating sequences and affect bacterial fitness. Protein Eng Des Sel 2012; 25:357-66. [PMID: 22706763 DOI: 10.1093/protein/gzs031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The most common mechanism by which proteins aggregate consists in the assembly of short hydrophobic primary sequence segments into extended β-structured agglomerates. A significant enrichment of charged residues is observed at the flank of these aggregation-prone sequence segments, suggesting selective pressure against aggregation. These so-called aggregation gatekeepers act by increasing the intrinsic solubility of aggregating sequences in vitro, but it has been suggested that they could also facilitate chaperone interactions. Here, we address whether aggregation gatekeepers affect bacterial fitness. In Escherichia coli MC4100 we overexpressed GFP fusions with an aggregation-prone segment of σ32 (further termed σ32β) flanked by gatekeeper and non-gatekeeper residues and measured pairwise competitive growth. We found that the identity of flanking residues had significant effect on bacterial growth. Overexpression of σ32β flanked by its natural gatekeepers displayed the greatest competitive fitness, followed by other combinations of gatekeepers, while absence of gatekeepers strongly affects bacterial fitness. Further analysis showed the diversity of effects of gatekeepers on the proteostasis of σ32β including synthesis and degradation rates, in vivo aggregation propensity and chaperone response. Our results suggest that gatekeeper residues affect bacterial fitness not only by modulating the intrinsic aggregation propensity of proteins but also by the manner in which they affect the processing of σ32β-GFP by the protein quality control machinery of the cell. In view of these observations, we hypothesize that variation at gatekeeper positions offers a flexible selective strategy to modulate the proteostatic regulation of proteins to the match intrinsic aggregation propensities of proteins with required expression levels.
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Affiliation(s)
- Jacinte Beerten
- Switch Laboratory, VIB, University of Leuven, Leuven, Belgium
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283
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Ghahghaei A, Bathaie SZ, Bahraminejad E. Mechanisms of the Effects of Crocin on Aggregation and Deposition of Aβ1–40 Fibrils in Alzheimer’s Disease. Int J Pept Res Ther 2012. [DOI: 10.1007/s10989-012-9308-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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284
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Healy J, Wong K, Sawyer EB, Roux C, Domigan L, Gras SL, Sunde M, Larsen NG, Gerrard J, Vasudevamurthy M. Polymorphism and higher order structures of protein nanofibers from crude mixtures of fish lens crystallins: Toward useful materials. Biopolymers 2012; 97:595-606. [DOI: 10.1002/bip.22045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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285
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Oladepo SA, Xiong K, Hong Z, Asher SA, Handen J, Lednev IK. UV resonance Raman investigations of peptide and protein structure and dynamics. Chem Rev 2012; 112:2604-28. [PMID: 22335827 PMCID: PMC3349015 DOI: 10.1021/cr200198a] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Kan Xiong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Zhenmin Hong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Joseph Handen
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222
| | - Igor K. Lednev
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222
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286
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Bahramikia S, Yazdanparast R, Gheysarzadeh A. Syntheses and structure-activity relationships of seven manganese-salen derivatives as anti-amyloidogenic and fibril-destabilizing agents against hen egg-white lysozyme aggregation. Chem Biol Drug Des 2012; 80:227-36. [PMID: 22530978 DOI: 10.1111/j.1747-0285.2012.01391.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Accumulation of intra- and/or extracellular misfolded proteins as amyloid fibrils is a key hallmark in more than 20 amyloid-related diseases. In that respect, blocking or reversing amyloid aggregation via the use of small compounds is considered as two useful approaches in hampering the development of these diseases. In this research, we have studied the ability of different manganese-salen derivatives to inhibit amyloid self-assembly as well as to dissolve amyloid aggregates of hen egg-white lysozyme, as an in vitro model system, with the aim of investigating their structure-activity relationships. By coupling several techniques such as thioflavin T and anilinonaphthalene-8-sulfonic acid fluorescence, congo red absorbance, far-UV circular dichroism, and transmission electron microscopy, we demonstrated that all compounds possessed anti-amyloidogenic activities and were capable of dispersing the fibrillar aggregates. In addition, MTT assay of the treated SK-N-MC cells with the preformed fibrils formed in the presence of compounds at a drug-to-protein molar ratio of 5:1, indicated a significant increase in the viability of cells, compared to the fibrils formed in the absence of each of the compounds. Our spectroscopy, electron microscopy, and cellular studies indicated that EUK-15, with a methoxy group at the para position (group R(5)), had higher activity to either inhibit or disrupt the β-sheet structures relative to other compounds. On the basis of these results, it can be concluded that in addition to aromatic rings of each of the derivatives, the type and position of the side group(s) contribute to lower lysozyme fibril accumulation.
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Affiliation(s)
- Seifollah Bahramikia
- Institute of Biochemistry and Biophysics, P. O. Box 13145-1384, University of Tehran, Tehran, Iran
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287
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Modulation of physiological and pathological activities of lysozyme by biological membranes. Cell Mol Biol Lett 2012; 17:349-75. [PMID: 22544762 PMCID: PMC6275811 DOI: 10.2478/s11658-012-0015-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/18/2012] [Indexed: 11/21/2022] Open
Abstract
The molecular details of interactions between lipid membranes and lysozyme (Lz), a small polycationic protein with a wide range of biological activities, have long been the focus of numerous studies. The biological consequences of this process are considered to embrace at least two aspects: i) correlation between antimicrobial and membranotropic properties of this protein, and ii) lipid-mediated Lz amyloidogenesis. The mechanisms underlying the lipid-assisted protein fibrillogenesis and membrane disruption exerted by Lz in bacterial cells are believed to be similar. The present investigation was undertaken to gain further insight into Lz-lipid interactions and explore the routes by which Lz exerts its antimicrobial and amyloidogenic actions. Binding and Förster resonance energy transfer studies revealed that upon increasing the content of anionic lipids in lipid vesicles, Lz forms aggregates in a membrane environment. Total internal reflection fluorescence microscopy and pyrene excimerization reaction were employed to study the effect of Lz on the structural and dynamic properties of lipid bilayers. It was found that Lz induces lipid demixing and reduction of bilayer free volume, the magnitude of this effect being much more pronounced for oligomeric protein.
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288
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Göransson AL, Nilsson KPR, Kågedal K, Brorsson AC. Identification of distinct physiochemical properties of toxic prefibrillar species formed by Aβ peptide variants. Biochem Biophys Res Commun 2012; 420:895-900. [PMID: 22475489 DOI: 10.1016/j.bbrc.2012.03.097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 03/20/2012] [Indexed: 11/28/2022]
Abstract
The formation of amyloid-β peptide (Aβ) aggregates at an early stage during the self-assembly process is an important factor in the development of Alzheimer's disease. The toxic effect is believed to be exerted by prefibrillar species of Aβ. It is therefore important to identify which prefibrillar species are toxic and characterize their distinct properties. In the present study, we investigated the in vitro aggregation behavior of Aβ-derived peptides possessing different levels of neurotoxic activity, using fluorescence spectroscopy in combination with transmission electron microscopy. The toxicity of various Aβ aggregates was assessed by using cultures of human neuroblastoma cells. Through combined use of the fluorescence probe 8-anilino-1-napthalenesulfonate (ANS) and the novel luminescent probe pentamer formyl thiophene acetic acid (p-FTAA), we were able to identify those Aβ peptide-derived prefibrillar species which exhibited cellular toxicity. In particular, species, which formed early during the aggregation process and showed strong p-FTAA and ANS fluorescence, were the species that possessed toxic activities. Moreover, by manipulating the aggregation conditions, it was possible to change the capacity of the Aβ peptide to form nontoxic versus toxic species.
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Affiliation(s)
- Anna-Lena Göransson
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, Sweden.
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289
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Ranganathan S, Singh PK, Singh U, Singru PS, Padinhateeri R, Maji SK. Molecular interpretation of ACTH-β-endorphin coaggregation: relevance to secretory granule biogenesis. PLoS One 2012; 7:e31924. [PMID: 22403619 PMCID: PMC3293876 DOI: 10.1371/journal.pone.0031924] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 01/20/2012] [Indexed: 01/07/2023] Open
Abstract
Peptide/protein hormones could be stored as non-toxic amyloid-like structures in pituitary secretory granules. ACTH and β-endorphin are two of the important peptide hormones that get co-stored in the pituitary secretory granules. Here, we study molecular interactions between ACTH and β-endorphin and their colocalization in the form of amyloid aggregates. Although ACTH is known to be a part of ACTH-β-endorphin aggregate, ACTH alone cannot aggregate into amyloid under various plausible conditions. Using all atom molecular dynamics simulation we investigate the early molecular interaction events in the ACTH-β-endorphin system, β-endorphin-only system and ACTH-only system. We find that β-endorphin and ACTH formed an interacting unit, whereas negligible interactions were observed between ACTH molecules in ACTH-only system. Our data suggest that ACTH is not only involved in interaction with β-endorphin but also enhances the stability of mixed oligomers of the entire system.
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Affiliation(s)
- Srivastav Ranganathan
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pradeep K. Singh
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Uday Singh
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, India
| | - Praful S. Singru
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail: (SKM); (RP)
| | - Samir K. Maji
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail: (SKM); (RP)
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290
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Naeem A, Fazili NA. Defective protein folding and aggregation as the basis of neurodegenerative diseases: the darker aspect of proteins. Cell Biochem Biophys 2012; 61:237-50. [PMID: 21573992 DOI: 10.1007/s12013-011-9200-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability of a polypeptide to fold into a unique, functional, and three-dimensional structure depends on the intrinsic properties of the amino acid sequence, function of the molecular chaperones, proteins, and enzymes. Every polypeptide has a finite tendency to misfold and this forms the darker side of the protein world. Partially folded and misfolded proteins that escape the cellular quality control mechanism have the high tendency to form inter-molecular hydrogen bonding between the same protein molecules resulting in aggregation. This review summarizes the underlying and universal mechanism of protein folding. It also deals with the factors responsible for protein misfolding and aggregation. This article describes some of the consequences of such behavior particularly in the context of neurodegenerative conformational diseases such as Alzheimer's, Parkinson's, Huntington's, amyotrophic lateral sclerosis and other non-neurodegenerative conformational diseases such as cancer and cystic fibrosis etc. This will encourage a more proactive approach to the early diagnosis of conformational diseases and nutritional counseling for patients.
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Affiliation(s)
- Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India.
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291
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Singh JP, Whitford PC, Hayre NR, Onuchic J, Cox DL. Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways. Proteins 2012; 80:1299-307. [PMID: 22274922 DOI: 10.1002/prot.24026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 10/19/2011] [Accepted: 11/18/2011] [Indexed: 11/11/2022]
Abstract
We employ all-atom structure-based models with a force field with multiple energetic basins for the C-terminal (residues 166-226) of the mammalian prion protein. One basin represents the known alpha-helical (αH) structure while the other represents the same residues in a left-handed beta-helical (LHBH) conformation. The LHBH structure has been proposed to help describe one class of in vitro grown fibrils, as well as possibly self-templating the conversion of normal cellular prion protein to the infectious form. Yet, it is unclear how the protein may make this global rearrangement. Our results demonstrate that the conformation changes are not strongly limited by large-scale geometry modification and that there may exist an overall preference for the LHBH conformation. Furthermore, our model presents novel intermediate trapping conformations with twisted LHBH structure.
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Affiliation(s)
- Jesse P Singh
- Department of Physics and the Institute for Complex Adaptive Matter, University of California at Davis, Davis, California 95616, USA.
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292
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Siposova K, Kubovcikova M, Bednarikova Z, Koneracka M, Zavisova V, Antosova A, Kopcansky P, Daxnerova Z, Gazova Z. Depolymerization of insulin amyloid fibrils by albumin-modified magnetic fluid. NANOTECHNOLOGY 2012; 23:055101. [PMID: 22238252 DOI: 10.1088/0957-4484/23/5/055101] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Pathogenesis of amyloid-related diseases is associated with the presence of protein amyloid deposits. Insulin amyloids have been reported in a patient with diabetes undergoing treatment by injection of insulin and causes problems in the production and storage of this drug and in pplication of insulin pumps. We have studied the interference of insulin amyloid fibrils with a series of 18 albumin magnetic fluids (MFBSAs) consisting of magnetite nanoparticles modified by different amounts of bovine serum albumin (w/w BSA/Fe₃O₄ from 0.005 up to 15). We have found that MFBSAs are able to destroy amyloid fibrils in vitro. The extent of fibril depolymerization was affected by nanoparticle physical-chemical properties (hydrodynamic diameter, zeta potential and isoelectric point) determined by the BSA amount present in MFBSAs. The most effective were MFBSAs with lower BSA/Fe₃O₄ ratios (from 0.005 to 0.1) characteristic of about 90% depolymerizing activity. For the most active magnetic fluids (ratios 0.01 and 0.02) the DC50 values were determined in the range of low concentrations, indicating their ability to interfere with insulin fibrils at stoichiometric concentrations. We assume that the present findings represent a starting point for the application of the active MFBSAs as therapeutic agents targeting insulin amyloidosis.
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Affiliation(s)
- Katarina Siposova
- Department of Biophysics, Department of Magnetism, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001 Kosice, Slovakia
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293
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Ryan SJ, Brashares JS, Walsh C, Milbers K, Kilroy C, Chapman CA. A survey of gastrointestinal parasites of olive baboons (Papio anubis) in human settlement areas of Mole National Park, Ghana. J Parasitol 2012; 98:885-8. [PMID: 22300265 DOI: 10.1645/ge-2976.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Fecal samples from 55 free-ranging olive baboons (Papio anubis) in Mole National Park, Ghana, were collected 22 June-7 July 2008 and analyzed for gastrointestinal parasites. This is the first survey of baboon gastrointestinal parasites in Ghana and provides baseline data for this area. Ninety-three percent of samples were infected, leaving 7% with no parasites observed. Of those infected, there was a 76% prevalence of strongyles, 53% Strongyloides spp., 11% Abbreviata caucasica , 62% prevalence of Balantidium coli (trophozoites and cysts identified), 4% Entomeba hystolytica/dispar, and 47% unidentified protozoan parasites. Of the strongyle infections, 9% were identified as Oesophagostamum sp. One sample contained an unidentified spirurid nematode that resembled Gongylonema sp. Mole has a mixed forest-savanna habitat, and baboons frequently range into human areas, which makes them subject to parasites from each habitat and multiple sources of exposure. We found a high prevalence of nematode parasites, consistent with a wet or cooler forest environment, or high rates of fecal contamination. The presence of Strongyloides sp., E. hystolitica/dispar, and B. coli suggest potential public health risk from baboons, but molecular identification of these parasites, and documentation of their presence in local human populations, would be necessary to confirm zoonotic transmission.
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Affiliation(s)
- Sadie J Ryan
- Department ofEnvironmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA.
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294
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Wasiak T, Ionov M, Nieznanski K, Nieznanska H, Klementieva O, Granell M, Cladera J, Majoral JP, Caminade AM, Klajnert B. Phosphorus Dendrimers Affect Alzheimer’s (Aβ1–28) Peptide and MAP-Tau Protein Aggregation. Mol Pharm 2012; 9:458-69. [DOI: 10.1021/mp2005627] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomasz Wasiak
- Department of General Biophysics, University of Lodz, Poland
| | - Maksim Ionov
- Department of General Biophysics, University of Lodz, Poland
| | - Krzysztof Nieznanski
- Department of Biochemistry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Hanna Nieznanska
- Department of Biochemistry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Oxana Klementieva
- Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona, Spain
| | - Maritxell Granell
- Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona, Spain
| | - Josep Cladera
- Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona, Spain
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295
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Ghodke S, Nielsen SB, Christiansen G, Hjuler HA, Flink J, Otzen D. Mapping out the multistage fibrillation of glucagon. FEBS J 2012; 279:752-65. [PMID: 22212535 DOI: 10.1111/j.1742-4658.2011.08465.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 29-residue peptide hormone glucagon forms many different morphological types of amyloid-like fibrils, depending on solvent conditions. Here, we combine time-series far-UV CD with singular value decomposition analysis to reveal six different conformational states populated during fibrillation at 25 °C and pH 2.5. The existence of these states is supported by complementary fluorescence and electron microscopy data. This highlights a multitude of structural transitions of glucagon from unordered structure to β sheets, β turns and further tertiary-level changes. We attribute the observed unusual far-UV CD spectra to tertiary-level structural changes during the formation and maturation of fibrils. The fibrillation model for the whole process involves the formation of three oligomeric species and two different morphologies of fibrils in the same solution. The visualization of annular pore-like species in the early stages of glucagon fibrillation and the prevalence of such species in the amyloidogenesis of several proteins indicates that they may be a common feature of the fibrillation process. This study gives significant insights into the stepwise conversion of soluble glucagon to its fibrillar state and identifies the importance of fibril twisting for its thermodynamic stabilization.
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Affiliation(s)
- Shirin Ghodke
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark
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296
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Es-Haghi A, Shariatizi S, Ebrahim-Habibi A, Nemat-Gorgani M. Amyloid fibrillation in native and chemically-modified forms of carbonic anhydrase II: role of surface hydrophobicity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:468-77. [PMID: 22251892 DOI: 10.1016/j.bbapap.2011.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 12/02/2011] [Accepted: 12/25/2011] [Indexed: 10/14/2022]
Abstract
Chemical modification or mutation of proteins may bring about significant changes in the net charge or surface hydrophobicity of a protein structure. Such events may be of major physiological significance and may provide important insights into the genetics of amyloid diseases. In the present study, fibrillation potential of native and chemically-modified forms of bovine carbonic anhydrase II (BCA II) were investigated. Initially, various denaturing conditions including low pH and high temperatures were tested to induce fibrillation. At a low pH of around 2.4, where the protein is totally dissociated, the apo form was found to take up a pre-molten globular (PMG) conformation with the capacity for fibril formation. Upon increasing the pH to around 3.6, a molten globular (MG) form became abundant, forming amorphous aggregates. Charge neutralization and enhancement of hydrophobicity by methylation, acetylation and propionylation of lysine residues appeared very effective in promoting fibrillation of both the apo and holo forms under native conditions, the rates and extents of which were directly proportional to surface hydrophobicity, and influenced by salt concentration and temperature. These modified structures underwent more pronounced fibrillation under native conditions, than the PMG intermediate form, observed under denaturing conditions. The nature of the fibrillation products obtained from intermediate and modified structures were characterized and compared and their possible cytotoxicity determined. Results are discussed in terms of the importance of surface net charge and hydrophobicity in controlling protein aggregation. A discussion on the physiological significance of the observations is also presented.
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Affiliation(s)
- Ali Es-Haghi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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297
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Murugan NA, Kongsted J, Rinkevicius Z, Ågren H. Color modeling of protein optical probes. Phys Chem Chem Phys 2012; 14:1107-12. [DOI: 10.1039/c1cp23060c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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298
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Abstract
Amyloid fibrils are polymeric assemblies of normally soluble proteins or peptides. To investigate their structure, it is generally not possible to use conventional methods of crystallography and solution nuclear magnetic resonance. To examine the repeating crystalline structure along the fibre axis, X-ray fibre diffraction has been a useful tool. Here we discuss the methods by which amyloid-like fibrils may be prepared to form a sample suitable for structural analysis and describe how data may be collected and then analysed to arrive at a potential model structure.
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299
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Bahramikia S, Yazdanparast R. Anti-amyloidogenic and fibril-destabilizing effects of two manganese–salen derivatives against hen egg-white lysozyme aggregation. Int J Biol Macromol 2012; 50:187-97. [DOI: 10.1016/j.ijbiomac.2011.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/09/2011] [Accepted: 10/20/2011] [Indexed: 10/16/2022]
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300
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Fibrillization propensity for short designed hexapeptides predicted by computer simulation. J Mol Biol 2011; 416:598-609. [PMID: 22227390 DOI: 10.1016/j.jmb.2011.12.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/30/2011] [Accepted: 12/17/2011] [Indexed: 12/16/2022]
Abstract
Assembly of normally soluble proteins into ordered aggregates, known as amyloid fibrils, is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. Here, we test the ability of discontinuous molecular dynamics (DMD) simulations based on PRIME20, a new intermediate-resolution protein force field, to predict which designed hexapeptide sequences will form fibrils, which will not, and how this depends on temperature and concentration. Simulations were performed on 48-peptide systems containing STVIIE, STVIFE, STVIVE, STAIIE, STVIAE, STVIGE, and STVIEE starting from random-coil configurations. By the end of the simulations, STVIIE and STVIFE (which form fibrils in vitro) form fibrils over a range of temperatures, STVIEE (which does not form fibrils in vitro) does not form fibrils, and STVIVE, STAIIE, STVIAE, and STVIGE (which do not form fibrils in vitro) form fibrils at lower temperatures but stop forming fibrils at higher temperatures. At the highest temperatures simulated, the results on the fibrillization propensity of the seven short de novo designed peptides all agree with the experiments of López de la Paz and Serrano. Our results suggest that the fibrillization temperature (temperature above which fibrils cease to form) is a measure of fibril stability and that by rank ordering the fibrillization temperatures of various sequences, PRIME20/DMD simulations could be used to ascertain their relative fibrillization propensities. A phase diagram showing regions in the temperature-concentration plane where fibrils are formed in our simulations is presented.
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