201
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Eugene C, Laghaei R, Mousseau N. Early oligomerization stages for the non-amyloid component of α-synuclein amyloid. J Chem Phys 2014; 141:135103. [DOI: 10.1063/1.4896381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Cindie Eugene
- Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Rozita Laghaei
- Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
- Department of Chemistry, University of Pittsburgh, 319 Eberly Hall, Pittsburgh, Pennsylvania 15260, USA
| | - Normand Mousseau
- Department of Chemistry, University of Pittsburgh, 319 Eberly Hall, Pittsburgh, Pennsylvania 15260, USA
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202
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Uversky VN. Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins. Biotechnol J 2014; 10:356-66. [PMID: 25287424 DOI: 10.1002/biot.201400374] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/23/2014] [Accepted: 08/27/2014] [Indexed: 11/09/2022]
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins or regions that do not have unique 3D structures under functional conditions. Therefore, from the viewpoint of their lack of stable 3D structure, IDPs/IDPRs are inherently unstable. As much as structure and function of normal ordered globular proteins are determined by their amino acid sequences, the lack of unique 3D structure in IDPs/IDPRs and their disorder-based functionality are also encoded in the amino acid sequences. Because of their specific sequence features and distinctive conformational behavior, these intrinsically unstable proteins or regions have several applications in biotechnology. This review introduces some of the most characteristic features of IDPs/IDPRs (such as peculiarities of amino acid sequences of these proteins and regions, their major structural features, and peculiar responses to changes in their environment) and describes how these features can be used in the biotechnology, for example for the proteome-wide analysis of the abundance of extended IDPs, for recombinant protein isolation and purification, as polypeptide nanoparticles for drug delivery, as solubilization tools, and as thermally sensitive carriers of active peptides and proteins.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Faculty of Science, Biology Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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203
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Sen S, Konar S, Pathak A, Dasgupta S, DasGupta S. Effect of Functionalized Magnetic MnFe2O4 Nanoparticles on Fibrillation of Human Serum Albumin. J Phys Chem B 2014; 118:11667-76. [DOI: 10.1021/jp507902y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shubhatam Sen
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Suraj Konar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Amita Pathak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sunando DasGupta
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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204
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Crowded milieu prevents fibrillation of hen egg white lysozyme with retention of enzymatic activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:8-16. [DOI: 10.1016/j.jphotobiol.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
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205
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Rajaram H, Palanivelu MK, Arumugam TV, Rao VM, Shaw PN, McGeary RP, Ross BP. ‘Click’ assembly of glycoclusters and discovery of a trehalose analogue that retards Aβ40 aggregation and inhibits Aβ40-induced neurotoxicity. Bioorg Med Chem Lett 2014; 24:4523-4528. [DOI: 10.1016/j.bmcl.2014.07.077] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/25/2014] [Accepted: 07/29/2014] [Indexed: 11/29/2022]
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206
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Han W, Schulten K. Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations. J Am Chem Soc 2014; 136:12450-60. [PMID: 25134066 PMCID: PMC4156860 DOI: 10.1021/ja507002p] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
A critical step of β-amyloid
fibril formation is fibril elongation
in which amyloid-β monomers undergo structural transitions to
fibrillar structures upon their binding to fibril tips. The atomic
detail of the structural transitions remains poorly understood. Computational
characterization of the structural transitions is limited so far to
short Aβ segments (5–10 aa) owing to the long time scale
of Aβ fibril elongation. To overcome the computational time
scale limit, we combined a hybrid-resolution model with umbrella sampling
and replica exchange molecular dynamics and performed altogether ∼1.3
ms of molecular dynamics simulations of fibril elongation for Aβ17–42. Kinetic network analysis of biased simulations
resulted in a kinetic model that encompasses all Aβ segments
essential for fibril formation. The model not only reproduces key
properties of fibril elongation measured in experiments, including
Aβ binding affinity, activation enthalpy of Aβ structural
transitions and a large time scale gap (τlock/τdock = 103–104) between Aβ
binding and its structural transitions, but also reveals detailed
pathways involving structural transitions not seen before, namely,
fibril formation both in hydrophobic regions L17-A21 and G37-A42 preceding
fibril formation in hydrophilic region E22-A30. Moreover, the model
identifies as important kinetic intermediates strand–loop–strand
(SLS) structures of Aβ monomers, long suspected to be related
to fibril elongation. The kinetic model suggests further that fibril
elongation arises faster at the fibril tip with exposed L17-A21, rather
than at the other tip, explaining thereby unidirectional fibril growth
observed previously in experiments.
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Affiliation(s)
- Wei Han
- Beckman Institute, ‡Center for Biophysics and Computational Biology, and §Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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207
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Sant'Anna R, Braga C, Varejão N, Pimenta KM, Graña-Montes R, Alves A, Cortines J, Cordeiro Y, Ventura S, Foguel D. The importance of a gatekeeper residue on the aggregation of transthyretin: implications for transthyretin-related amyloidoses. J Biol Chem 2014; 289:28324-37. [PMID: 25086037 PMCID: PMC4192486 DOI: 10.1074/jbc.m114.563981] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Protein aggregation into β-sheet-enriched amyloid fibrils is associated with an increasing number of human disorders. The adoption of such amyloid conformations seems to constitute a generic property of polypeptide chains. Therefore, during evolution, proteins have adopted negative design strategies to diminish their intrinsic propensity to aggregate, including enrichment of gatekeeper charged residues at the flanks of hydrophobic aggregation-prone segments. Wild type transthyretin (TTR) is responsible for senile systemic amyloidosis, and more than 100 mutations in the TTR gene are involved in familial amyloid polyneuropathy. The TTR 26–57 segment bears many of these aggressive amyloidogenic mutations as well as the binding site for heparin. We demonstrate here that Lys-35 acts as a gatekeeper residue in TTR, strongly decreasing its amyloidogenic potential. This protective effect is sequence-specific because Lys-48 does not affect TTR aggregation. Lys-35 is part of the TTR basic heparin-binding motif. This glycosaminoglycan blocks the protective effect of Lys-35, probably by neutralization of its side chain positive charge. A K35L mutation emulates this effect and results in the rapid self-assembly of the TTR 26–57 region into amyloid fibrils. This mutation does not affect the tetrameric protein stability, but it strongly increases its aggregation propensity. Overall, we illustrate how TTR is yet another amyloidogenic protein exploiting negative design to prevent its massive aggregation, and we show how blockage of conserved protective features by endogenous factors or mutations might result in increased disease susceptibility.
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Affiliation(s)
- Ricardo Sant'Anna
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Carolina Braga
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Nathalia Varejão
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Karinne M Pimenta
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Ricardo Graña-Montes
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Aline Alves
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Juliana Cortines
- the Instituto de Microbiologia Professor Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro CEP 21941-590, Brazil and
| | | | - Salvador Ventura
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Debora Foguel
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural,
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208
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Xu L, Chen Y, Wang X. Assembly of Amyloid β Peptides in the Presence of Fibril Seeds: One-Pot Coarse-Grained Molecular Dynamics Simulations. J Phys Chem B 2014; 118:9238-46. [DOI: 10.1021/jp505551m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Liang Xu
- School of Chemistry, ‡Network and Information Center, and §School of Chemical Machinery, Dalian University of Technology, Dalian, China
| | - Yonggang Chen
- School of Chemistry, ‡Network and Information Center, and §School of Chemical Machinery, Dalian University of Technology, Dalian, China
| | - Xiaojuan Wang
- School of Chemistry, ‡Network and Information Center, and §School of Chemical Machinery, Dalian University of Technology, Dalian, China
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209
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Truong PM, Viet MH, Nguyen PH, Hu CK, Li MS. Effect of Taiwan Mutation (D7H) on Structures of Amyloid-β Peptides: Replica Exchange Molecular Dynamics Study. J Phys Chem B 2014; 118:8972-81. [DOI: 10.1021/jp503652s] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Phan Minh Truong
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Man Hoang Viet
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13
rue Pierre et Marie Curie, 75005, Paris, France
| | - Chin-Kun Hu
- Institute
of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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210
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Goure WF, Krafft GA, Jerecic J, Hefti F. Targeting the proper amyloid-beta neuronal toxins: a path forward for Alzheimer's disease immunotherapeutics. ALZHEIMERS RESEARCH & THERAPY 2014; 6:42. [PMID: 25045405 PMCID: PMC4100318 DOI: 10.1186/alzrt272] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Levels of amyloid-beta monomer and deposited amyloid-beta in the Alzheimer’s
disease brain are orders of magnitude greater than soluble amyloid-beta oligomer
levels. Monomeric amyloid-beta has no known direct toxicity. Insoluble fibrillar
amyloid-beta has been proposed to be an in vivo mechanism for removal of
soluble amyloid-beta and exhibits relatively low toxicity. In contrast, soluble
amyloid-beta oligomers are widely reported to be the most toxic amyloid-beta form,
both causing acute synaptotoxicity and inducing neurodegenerative processes. None of
the amyloid-beta immunotherapies currently in clinical development selectively target
soluble amyloid-beta oligomers, and their lack of efficacy is not unexpected
considering their selectivity for monomeric or fibrillar amyloid-beta (or both)
rather than soluble amyloid-beta oligomers. Because they exhibit acute,
memory-compromising synaptic toxicity and induce chronic neurodegenerative toxicity
and because they exist at very low in vivo levels in the Alzheimer’s
disease brain, soluble amyloid-beta oligomers constitute an optimal immunotherapeutic
target that should be pursued more aggressively.
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Affiliation(s)
- William F Goure
- Acumen Pharmaceuticals, Inc., 4453 North First Street, #360, Livermore, CA 94551, USA
| | - Grant A Krafft
- Acumen Pharmaceuticals, Inc., 4453 North First Street, #360, Livermore, CA 94551, USA
| | - Jasna Jerecic
- Acumen Pharmaceuticals, Inc., 4453 North First Street, #360, Livermore, CA 94551, USA
| | - Franz Hefti
- Acumen Pharmaceuticals, Inc., 4453 North First Street, #360, Livermore, CA 94551, USA
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211
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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212
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Tarus B, Nguyen PH, Berthoumieu O, Faller P, Doig AJ, Derreumaux P. Molecular structure of the NQTrp inhibitor with the Alzheimer Aβ1-28 monomer. Eur J Med Chem 2014; 91:43-50. [PMID: 25011560 DOI: 10.1016/j.ejmech.2014.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/19/2014] [Accepted: 07/01/2014] [Indexed: 01/28/2023]
Abstract
The self-assembly of the amyloid-β (Aβ) peptide of various amino acid lengths into senile plaques is one hallmark of Alzheimer's disease pathology. In the past decade, many small molecules, including NQTrp, have been identified to reduce aggregation and toxicity. However, due to the heterogeneity of the conformational ensemble of Aβ with drugs, we lack detailed structures of the transient complexes. Following our previous simulation of the monomer of Aβ1-28, here we characterize the equilibrium ensemble of the Aβ1-28 monomer with NQTrp by means of extensive atomistic replica exchange molecular dynamics simulations using a force field known to fold diverse proteins correctly. While the secondary structure content and the intrinsic disorder of the whole peptides are very similar and the lifetimes of the salt-bridges remain constant, the population of β-hairpin is reduced by a factor of 1.5 and the population of α-helix in the region 17-24 is increased by a factor of two upon NQTrp binding. These two factors, which impact the free energy barrier for nucleation, provide a first explanation for the reported reduced Aβ1-40/1-42 aggregation kinetics in the presence of NQTrp. Backbone and side-chain interactions of Aβ with NQTrp may also inhibit Aβ-Aβ contacts. The fraction of free Aβ1-28 monomer is, however, on the order of 20-25% at 17.5 mM, and this shows that the affinity of NQTrp is low and hence its inhibitory activity is not very strong. This inhibitor can be improved to reduce the formation of dimer, a critical step in aggregation and toxicity.
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Affiliation(s)
- Bogdan Tarus
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Peter Faller
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Andrew J Doig
- Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France; Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France.
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213
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Pryor NE, Moss MA, Hestekin CN. Capillary electrophoresis for the analysis of the effect of sample preparation on early stages of Aβ1-40 aggregation. Electrophoresis 2014; 35:1814-20. [PMID: 24729203 DOI: 10.1002/elps.201400012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 11/05/2022]
Abstract
Aggregation of the amyloid-β protein (Aβ) contributes to the neurodegeneration characteristic of Alzheimer's disease. Of particular importance are the early stages of aggregation, which involve the formation of soluble oligomers and protofibrils. In these studies, we demonstrate the potential for CE with UV detection using a polyethylene oxide separation matrix to identify the evolution of various oligomeric species of Aβ1-40 . To demonstrate the efficacy of this technique, UV-CE was utilized to compare two methods commonly used to prepare Aβ for aggregation experiments and their effect on the formation of early aggregates. SEC-purified Aβ1-40 initially contained more small species, including monomer, than did freshly dissolved Aβ1-40 pretreated with hexafluoroisopropanol. Strikingly, the lag time to oligomer formation for SEC-isolated Aβ1-40 samples was ∼23 h shorter compared to freshly dissolved Aβ1-40 samples. Furthermore, oligomers formed from the aggregation of SEC-purified Aβ1-40 persisted within solution for a longer period of time. These results indicate that the initial sample preparation has a drastic influence on the early stages of Aβ1-40 aggregation. This is the first report of the use of UV-CE with a separation matrix to study the effect of sample preparation on early aggregation of Aβ1-40 . UV-CE was also used in parallel with dot blot analysis and inhibitory compounds to discern structural characteristics of individual oligomer peaks, demonstrating the capacity of UV-CE as a complimentary technique to further understand the aggregation process.
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Affiliation(s)
- N Elizabeth Pryor
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, Fayetteville, AR, USA
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214
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Ghosh S, Pandey NK, Banerjee P, Chaudhury K, Nagy NV, Dasgupta S. Copper(II) directs formation of toxic amorphous aggregates resulting in inhibition of hen egg white lysozyme fibrillation under alkaline salt-mediated conditions. J Biomol Struct Dyn 2014; 33:991-1007. [PMID: 24806136 DOI: 10.1080/07391102.2014.921864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Hen egg white lysozyme (HEWL) adopts a molten globule-like state at high pH (~12.75) and is found to form amyloid fibrils at alkaline pH. Here, we report that Cu(II) inhibits self-association of HEWL at pH 12.75 both at 37 and 65 °C. A significant reduction in Thioflavin T fluorescence intensity, attenuation in β-sheet content and reduction in hydrophobic exposure were observed with increasing Cu(II) stoichiometry. Electron paramagnetic resonance spectroscopy suggests a 4N type of coordination pattern around Cu(II) during fibrillation. Cu(II) is also capable of altering the cytotoxicity of the proteinaceous aggregates. Fibrillar species of diverse morphology were found in the absence of Cu(II) with the generation of amorphous aggregates in the presence of Cu(II), which are more toxic compared to the fibrils alone.
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Affiliation(s)
- Sudeshna Ghosh
- a Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , India
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215
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Sarkar B, Mithu VS, Chandra B, Mandal A, Chandrakesan M, Bhowmik D, Madhu PK, Maiti S. Significant Structural Differences between Transient Amyloid-β Oligomers and Less-Toxic Fibrils in Regions Known To Harbor Familial Alzheimer′s Mutations. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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216
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Sarkar B, Mithu VS, Chandra B, Mandal A, Chandrakesan M, Bhowmik D, Madhu PK, Maiti S. Significant structural differences between transient amyloid-β oligomers and less-toxic fibrils in regions known to harbor familial Alzheimer's mutations. Angew Chem Int Ed Engl 2014; 53:6888-92. [PMID: 24756858 DOI: 10.1002/anie.201402636] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 11/11/2022]
Abstract
Small oligomers of the amyloid β (Aβ) peptide, rather than the monomers or the fibrils, are suspected to initiate Alzheimer's disease (AD). However, their low concentration and transient nature under physiological conditions have made structural investigations difficult. A method for addressing such problems has been developed by combining rapid fluorescence techniques with slower two-dimensional solid-state NMR methods. The smallest Aβ40 oligomers that demonstrate a potential sign of toxicity, namely, an enhanced affinity for cell membranes, were thus probed. The two hydrophobic regions (residues 10-21 and 30-40) have already attained the conformation that is observed in the fibrils. However, the turn region (residues 22-29) and the N-terminal tail (residues 1-9) are strikingly different. Notably, ten of eleven known Aβ mutants that are linked to familial AD map to these two regions. Our results provide potential structural cues for AD therapeutics and also suggest a general method for determining transient protein structures.
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Affiliation(s)
- Bidyut Sarkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005 (India)
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217
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Simulated Interactions between Endothelin Converting Enzyme and Aβ Peptide: Insights into Subsite Recognition and Cleavage Mechanism. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9403-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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218
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Hunter S, Brayne C. Integrating the molecular and the population approaches to dementia research to help guide the future development of appropriate therapeutics. Biochem Pharmacol 2014; 88:652-60. [DOI: 10.1016/j.bcp.2013.12.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 12/13/2022]
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219
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Lan MY, Liu JS, Wu YS, Peng CH, Chang YY. A novel APP mutation (D678H) in a Taiwanese patient exhibiting dementia and cerebral microvasculopathy. J Clin Neurosci 2014; 21:513-5. [DOI: 10.1016/j.jocn.2013.03.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 03/24/2013] [Accepted: 03/30/2013] [Indexed: 10/26/2022]
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220
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Notarachille G, Arnesano F, Calò V, Meleleo D. Heavy metals toxicity: effect of cadmium ions on amyloid beta protein 1-42. Possible implications for Alzheimer's disease. Biometals 2014; 27:371-88. [PMID: 24557150 DOI: 10.1007/s10534-014-9719-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/12/2014] [Indexed: 02/02/2023]
Abstract
Cadmium (Cd) is an environmental contaminant, highly toxic to humans. This biologically non-essential element accumulates in the body, especially in the kidney, liver, lung and brain and can induce several toxic effects, depending on the concentration and the exposure time. Cd has been linked to Alzheimer's disease (AD) as a probable risk factor, as it shows higher concentrations in brain tissues of AD patients than in healthy people, its implication in the formation of neurofibrillary tangles and in the aggregation process of amyloid beta peptides (AβPs). AβPs seem to have toxic properties, particularly in their aggregated state; insoluble AβP forms, such as small and large aggregates, protofibrils and fibrils, appear to be implicated in the pathogenesis of AD. In our study, we have evaluated the effect of Cd, at different concentrations, both on the AβP1-42 ion channel incorporated in a planar lipid membrane made up of phosphatidylcholine containing 30 % cholesterol and on the secondary structure of AβP1-42 in aqueous environment. Cadmium is able to interact with the AβP1-42 peptide by acting on the channel incorporated into the membrane as well as on the peptide in solution, both decreasing AβP1-42 channel frequency and in solution forming large and amorphous aggregates prone to precipitate. These experimental observations suggesting a toxic role for Cd strengthen the hypothesis that Cd may interact directly with AβPs and may be a risk factor in AD.
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Affiliation(s)
- Gabriella Notarachille
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", via E. Orabona 4, 70126, Bari, Italy
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A hIAPP-derived all-d-amino-acid inhibits hIAPP fibrillation efficiently at membrane surface by targeting α-helical oligomeric intermediates. FEBS Lett 2014; 588:884-91. [DOI: 10.1016/j.febslet.2014.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 11/20/2022]
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222
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Clark TB, Ziółkowski M, Schatz GC, Goodson T. Two-Photon and Time-Resolved Fluorescence Spectroscopy as Probes for Structural Determination in Amyloid-β Peptides and Aggregates. J Phys Chem B 2014; 118:2351-9. [DOI: 10.1021/jp500883s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Travis B. Clark
- Department
of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Marcin Ziółkowski
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Theodore Goodson
- Department
of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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223
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Zhang T, Xu W, Mu Y, Derreumaux P. Atomic and dynamic insights into the beneficial effect of the 1,4-naphthoquinon-2-yl-L-tryptophan inhibitor on Alzheimer's Aβ1-42 dimer in terms of aggregation and toxicity. ACS Chem Neurosci 2014; 5:148-59. [PMID: 24246047 DOI: 10.1021/cn400197x] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer's disease (AD). The 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12-28 and 17-42, none of these studies were conducted on the full-length Aβ1-42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1-42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from in vitro and in silico experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1-42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1-42 dimer against AD.
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Affiliation(s)
- Tong Zhang
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Weixin Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- State Key Laboratory of Precision Spectroscopy, Department
of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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224
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Nguyen P, Derreumaux P. Understanding amyloid fibril nucleation and aβ oligomer/drug interactions from computer simulations. Acc Chem Res 2014; 47:603-11. [PMID: 24368046 DOI: 10.1021/ar4002075] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Evolution has fine-tuned proteins to accomplish a variety of tasks. Yet, with aging, some proteins assemble into harmful amyloid aggregates associated with neurodegenerative diseases, such as Alzheimer's disease (AD), which presents a complex and costly challenge to our society. Thus, far, drug after drug has failed to slow the progression of AD, characterized by the self-assembly of the 39-43 amino acid β-amyloid (Aβ) protein into extracellular senile plaques that form a cross-β structure. While there is experimental evidence that the Aβ small oligomers are the primary toxic species, standard tools of biology have failed to provide structures of these transient, inhomogeneous assemblies. Despite extensive experimental studies, researchers have not successfully characterized the nucleus ensemble, the starting point for rapid fibril formation. Similarly scientists do not have atomic data to show how the compounds that reduce both fibril formation and toxicity in cells bind to Aβ42 oligomers. In this context, computer simulations are important tools for gaining insights into the self-assembly of amyloid peptides and the molecular mechanism of inhibitors. This Account reviews what analytical models and simulations at different time and length scales tell us about the dynamics, kinetics, and thermodynamics of amyloid fibril formation and, notably, the nucleation process. Though coarse-grained and mesoscopic protein models approximate atomistic details by averaging out unimportant degrees of freedom, they provide generic features of amyloid formation and insights into mechanistic details of the self-assembly process. The thermodynamics and kinetics vary from linear peptides adopting straight β-strands in fibrils to longer peptides adopting in parallel U shaped conformations in fibrils. In addition, these properties change with the balance between electrostatic and hydrophobic interactions and the intrinsic disorder of the system. However, simulations suggest that the critical nucleus size might be on the order of 20 chains under physiological conditions. The transition state might be characterized by a simultaneous change from mixed antiparallel/parallel β-strands with random side-chain packing to the final antiparallel or parallel states with the steric zipper packing of the side chains. Second, we review our current computer-based knowledge of the 3D structures of inhibitors with Aβ42 monomer and oligomers, a prerequisite for developing new drugs against AD. Recent extensive all-atom simulations of Aβ42 dimers with known inhibitors such as the green tea compound epigallocatechin-3-gallate and 1,4-naphthoquinon-2-yl-l-tryptophan provide a spectrum of initial Aβ42/inhibitor structures useful for screening and drug design. We conclude by discussing future directions that may offer opportunities to fully understand nucleation and further AD drug development.
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Affiliation(s)
- Phuong Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France
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225
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Qi R, Luo Y, Ma B, Nussinov R, Wei G. Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer. Biomacromolecules 2014; 15:122-31. [PMID: 24313776 PMCID: PMC6429924 DOI: 10.1021/bm401406e] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Experiments suggested that the fibrillation of the 11-25 fragment (hIAPP(11-25)) of human islet amyloid polypeptide (hIAPP or amylin) involves the formation of transient α-helical intermediates, followed by conversion to β-sheet-rich structure. However, atomic details of α-helical intermediates and the transition mechanism are mostly unknown. We investigated the structural properties of the monomer and dimer in atomistic detail by replica exchange molecular dynamics (REMD) simulations. Transient α-helical monomers and dimers were both observed in the REMD trajectories. Our calculated H(α) chemical shifts based on the monomer REMD run are in agreement with the solution-state NMR experimental observations. Multiple 300 ns MD simulations at 310 K show that α-helix-to-β-sheet transition follows two mechanisms: the first involved direct transition of the random coil part of the helical conformation into antiparallel β-sheet, and in the second, the α-helical conformation unfolded and converted into antiparallel β-sheet. In both mechanisms, the α-helix-to-β-sheet transition occurred via random coil, and the transition was accompanied by an increase of interpeptide contacts. In addition, our REMD simulations revealed different temperature dependencies of helical and β-structures. Comparison with experimental data suggests that the propensity for hIAPP(11-25) to form α-helices and amyloid structures is concentration- and temperature-dependent.
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Affiliation(s)
- Ruxi Qi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , Shanghai, China
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226
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Lasmézas C, Zhou M. Newly defined toxic α-helical prion protein monomer: implications for other neurodegenerative diseases? Expert Rev Proteomics 2014; 9:233-5. [DOI: 10.1586/epr.12.26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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227
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Nguyen PH, Tarus B, Derreumaux P. Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer. J Phys Chem B 2014; 118:501-10. [DOI: 10.1021/jp4115404] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Phuong H. Nguyen
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Bogdan Tarus
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France
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228
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229
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Viet MH, Nguyen PH, Ngo ST, Li MS, Derreumaux P. Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci 2013; 4:1446-57. [PMID: 24041307 DOI: 10.1021/cn400110d] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent experiments have shown that the mutation Tottori (D7N) alters the toxicity, assembly and rate of fibril formation of the wild type (WT) amyloid beta (Aβ) Aβ40 and Aβ42 peptides. We used all-atom molecular dynamics simulations in explicit solvent of the monomer and dimer of both alloforms with their WT and D7N sequences. The monomer simulations starting from a random coil and totaling 3 μs show that the D7N mutation changes the fold and the network of salt bridges in both alloforms. The dimer simulations starting from the amyloid fibrillar states and totaling 4.4 μs also reveal noticeable changes in terms of secondary structure, salt bridge, and topology. Overall, this study provides physical insights into the enhanced rate of fibril formation upon D7N mutation and an atomic picture of the D7N-mediated conformational change on Aβ40 and Aβ42 peptides.
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Affiliation(s)
- Man Hoang Viet
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Son Tung Ngo
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc
District, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theorique, UPR
9080 CNRS, IBPC, Universite Denis Diderot, Paris Sorbonne Cité 13 rue Pierre et Marie Curie, 75005, Paris, France
- Institut Universitaire de France, Bvd
Saint Michel, 75005, Paris, France
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230
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Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet. Proc Natl Acad Sci U S A 2013; 110:19285-90. [PMID: 24218609 DOI: 10.1073/pnas.1314481110] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid formation is implicated in more than 20 human diseases, yet the mechanism by which fibrils form is not well understood. We use 2D infrared spectroscopy and isotope labeling to monitor the kinetics of fibril formation by human islet amyloid polypeptide (hIAPP or amylin) that is associated with type 2 diabetes. We find that an oligomeric intermediate forms during the lag phase with parallel β-sheet structure in a region that is ultimately a partially disordered loop in the fibril. We confirm the presence of this intermediate, using a set of homologous macrocyclic peptides designed to recognize β-sheets. Mutations and molecular dynamics simulations indicate that the intermediate is on pathway. Disrupting the oligomeric β-sheet to form the partially disordered loop of the fibrils creates a free energy barrier that is the origin of the lag phase during aggregation. These results help rationalize a wide range of previous fragment and mutation studies including mutations in other species that prevent the formation of amyloid plaques.
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231
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Qiao Q, Bowman GR, Huang X. Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. J Am Chem Soc 2013; 135:16092-101. [PMID: 24021023 DOI: 10.1021/ja403147m] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Amyloid fibril deposits of the intrinsically disordered hIAPP peptide are found in 95% of type II diabetes patients, and the aggregation of this peptide is suggested to induce apoptotic cell-death in insulin-producing β-cells. Understanding the structure and dynamics of the hIAPP monomer in solution is thus important for understanding the nucleation of aggregation and the formation of oligomers. In this study, we identify the metastable conformational states of the hIAPP monomer and the dynamics of transitioning between them using Markov state models constructed from extensive molecular dynamics simulations. We show that the overall structure of the hIAPP peptide is random coil-like and lacks a dominant folded structure. Despite this fact, our model reveals a large number of reasonably well-populated metastable conformational states (or local free energy minima) having populations of a few percent or less. The time scales for transitioning between these states range from several microseconds to milliseconds. In contrast to folded proteins, there is no kinetic hub. More strikingly, a few states contain significant amounts of β-hairpin secondary structure and extended hydrophobic surfaces that are exposed to the solvent. We propose that these states may facilitate the nucleation of hIAPP aggregation through a significant component of the conformational selection mechanism, because they may increase their populations upon aggregation by promoting hydrophobic interactions and at the same time provide a flat geometry to seed the ordered β-strand packing of the fibrils.
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Affiliation(s)
- Qin Qiao
- Bioengineering Graduate Program, Division of Biomedical Engineering, ‡Department of Chemistry, §Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong
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232
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233
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Kang L, Janowska MK, Moriarty GM, Baum J. Mechanistic insight into the relationship between N-terminal acetylation of α-synuclein and fibril formation rates by NMR and fluorescence. PLoS One 2013; 8:e75018. [PMID: 24058647 PMCID: PMC3776725 DOI: 10.1371/journal.pone.0075018] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/09/2013] [Indexed: 11/20/2022] Open
Abstract
Aggregation of α-synuclein (αSyn), the primary protein component in Lewy body inclusions of patients with Parkinson’s disease, arises when the normally soluble intrinsically disordered protein converts to amyloid fibrils. In this work, we provide a mechanistic view of the role of N-terminal acetylation on fibrillation by first establishing a quantitative relationship between monomer secondary structural propensity and fibril assembly kinetics, and secondly by demonstrating in the N-terminal acetylated form of the early onset A53T mutation, that N-terminal transient helices formed and/or inhibited by N-terminal acetylation modulate the fibril assembly rates. Using NMR chemical shifts and fluorescence experiments, we report that secondary structural propensity in residues 5–8, 14–31, and 50–57 are highly correlated to fibril growth rate. A four-way comparison of secondary structure propensity and fibril growth rates of N-terminally acetylated A53T and WT αSyn with non-acetylated A53T and WT αSyn present novel mechanistic insight into the role of N-terminal acetylation in amyloid fibril formation. We show that N-terminal acetylation inhibits the formation of the “fibrillation promoting” transient helix at residues 14–31 resulting from the A53T mutation in the non-acetylated variant and supports the formation of the “fibrillation inhibiting” transient helix in residues 1–12 thereby resulting in slower fibrillation rates relative to the previously studied non-acetylated A53T variant. Our results highlight the critical interplay of the region-specific transient secondary structure of the N-terminal region with fibrillation, and the inhibitory role of the N-terminal acetyl group in fibril formation.
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Affiliation(s)
- Lijuan Kang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Maria K. Janowska
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Gina M. Moriarty
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey, United States of America
- * E-mail:
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234
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Ghosh S, Pandey NK, Singha Roy A, Tripathy DR, Dinda AK, Dasgupta S. Prolonged glycation of hen egg white lysozyme generates non amyloidal structures. PLoS One 2013; 8:e74336. [PMID: 24066139 PMCID: PMC3774808 DOI: 10.1371/journal.pone.0074336] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/02/2013] [Indexed: 11/18/2022] Open
Abstract
Glycation causes severe damage to protein structure that could lead to amyloid formation in special cases. Here in this report, we have shown for the first time that hen egg white lysozyme (HEWL) does not undergo amyloid formation even after prolonged glycation in the presence of D-glucose, D-fructose and D-ribose. Cross-linked oligomers were formed in all the cases and ribose was found to be the most potent among the three sugars. Ribose mediated oligomers, however, exhibit Thioflavin T binding properties although microscopic images clearly show amorphous and globular morphology of the aggregates. Our study demonstrates that the structural damage of hen egg white lysozyme due to glycation generates unstructured aggregates.
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Affiliation(s)
- Sudeshna Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Nitin Kumar Pandey
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Atanu Singha Roy
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Debi Ranjan Tripathy
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Dinda
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
- * E-mail:
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235
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Gerben SR, Lemkul JA, Brown AM, Bevan DR. Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer’s amyloid β-peptide. J Biomol Struct Dyn 2013; 32:1817-32. [DOI: 10.1080/07391102.2013.838518] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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236
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Mazumder P, Suk JE, Ulmer TS. Insight into α-synuclein plasticity and misfolding from differential micelle binding. J Phys Chem B 2013; 117:11448-59. [PMID: 23978162 DOI: 10.1021/jp402589x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Misfolded species of the 140-residue protein α-synuclein (αS) are implicated in the demise of dopaminergic neurons, resulting in fatal neurodegeneration. The intrinsically unstructured protein binds curved synaptic vesicle membranes in helical conformations but misfolds into amyloid fibrils via β-sheet interactions. Breaks in helical αS conformation may offer a pathway to transition from helical to sheet conformation. Here, we explore the evolution of broken αS helix conformations formed in complex with SDS and SLAS micelles by molecular dynamics simulations. The population distribution of experimentally observed αS conformations is related to the spatial concentration of intrinsic micelle shape perturbations. For the success of micelle-induced αS folding, we posit the length of the first helical segment formed, which controls micelle ellipticity, to be a key determinant. The degree of micelle curvature relates to the arrangement and segmental motions of helical secondary structure elements. A criterion for assessing the reproduction of such intermediate time scale protein dynamics is introduced by comparing the sampling of experimental and simulated spin label distributions. Finally, at the sites of breaks in the elongated, marginally stable αS helix, vulnerability to forming a transient, intramolecular β-sheet is identified. Upon subsequent intermolecular β-sheet pairing, pathological αS amyloid formation from initial helical conformation is thus achievable.
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Affiliation(s)
- Parichita Mazumder
- Department of Biochemistry & Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , 1501 San Pablo Street, Los Angeles, California 90033, United States
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237
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Bossis F, Palese LL. Amyloid beta(1-42) in aqueous environments: effects of ionic strength and E22Q (Dutch) mutation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2486-93. [PMID: 24016775 DOI: 10.1016/j.bbapap.2013.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 01/15/2023]
Abstract
Development of extracellular plaques characteristic of Alzheimer's disease is related to aggregation of amyloid peptides. The Aβ-42 peptide is the most aggregation prone species, and some missense mutant forms increase this aggregation ability. Due to its poor solubility as monomer in aqueous solutions, Aβ-42 conformational transitions in water have been largely investigated by molecular dynamics. Here we report an all-atom molecular dynamics analysis of the Aβ-42 peptide in aqueous environment using as starting conformation a structure obtained in an isotropic, low-polarity medium, representing a plausible model for the membrane-bound species. While previous studies commonly show that Aβ-42 is largely unstructured in aqueous solution, here we report that this peptide can adopt partially folded structures. Importance of ionic strength has been also investigated, showing that at physiological ionic strength condition a loop stabilizing electrostatic interaction involving Lys28 builds up. In addition, besides stable α-helix structures, we observe the appearance of 310 helix, similar to what was reported experimentally for the Aβ-40 species. The effect of E22Q (Dutch) mutation in high ionic strength condition has been explored. We show that this mutation has a dramatic impact on the Aβ-42 structure. Instead of a partially folded, but extended, conformation obtained with the wild type, the E22Q assumes a two-helix collapsed one due to the clustering of hydrophobic residues.
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238
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Sharoar MG, Shahnawaz M, Islam MI, Ramasamy VS, Shin SY, Park IS. The inhibitory effects of Escherichia coli maltose binding protein on β-amyloid aggregation and cytotoxicity. Arch Biochem Biophys 2013; 538:41-8. [PMID: 23948569 DOI: 10.1016/j.abb.2013.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 07/29/2013] [Accepted: 08/02/2013] [Indexed: 01/14/2023]
Abstract
The aggregation of β-amyloid (Aβ) peptide from its monomeric to its fibrillar form importantly contributes to the development of Alzheimer's disease. Here, we investigated the effects of Escherichia coli maltose binding protein (MBP), which has been previously used as a fusion protein, on Aβ42 fibrillization, in order to improve understanding of the self-assembly process and the cytotoxic mechanism of Aβ42. MBP, at a sub-stoichiometric ratio with respect to Aβ42, was found to have chaperone-like inhibitory effects on β-sheet fibril formation, due to the accumulation of Aβ42 aggregates by sequestration of active Aβ42 species as Aβ42-MBP complexes. Furthermore, MBP increased the lag time of Aβ42 polymerization, decreased the growth rate of fibril extension, and suppressed Aβ42 mediated toxicity in human neuroblastoma SH-SY5Y cells. It appears that MBP decreases the active concentration of Aβ42 by sequestering it as Aβ42-MBP complex, and that this sequestration suppresses ongoing nucleation and retards the growth rate of Aβ42 species required for fibril formation. We speculate that inhibition of the growth rate of potent Aβ42 species by MBP suppresses Aβ42-mediated toxicity in SH-SY5Y cells.
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Affiliation(s)
- Md Golam Sharoar
- Department of Bio-Materials Engineering, Chosun University, Gwanju 501-759, Republic of Korea; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
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Binding, conformational transition and dimerization of amyloid-β peptide on GM1-containing ternary membrane: insights from molecular dynamics simulation. PLoS One 2013; 8:e71308. [PMID: 23951128 PMCID: PMC3739818 DOI: 10.1371/journal.pone.0071308] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/27/2013] [Indexed: 12/16/2022] Open
Abstract
Interactions of amyloid-β (Aβ) with neuronal membrane are associated with the progression of Alzheimer's disease (AD). Ganglioside GM1 has been shown to promote the structural conversion of Aβ and increase the rate of peptide aggregation; but the exact nature of interaction driving theses processes remains to be explored. In this work, we have carried out atomistic-scale computer simulations (totaling 2.65 µs) to investigate the behavior of Aβ monomer and dimers in GM1-containing raft-like membrane. The oligosaccharide head-group of GM1 was observed to act as scaffold for Aβ-binding through sugar-specific interactions. Starting from the initial helical peptide conformation, a β-hairpin motif was formed at the C-terminus of the GM1-bound Aβ-monomer; that didn't appear in absence of GM1 (both in fluid POPC and liquid-ordered cholesterol/POPC bilayers and also in aqueous medium) within the simulation time span. For Aβ-dimers, the β-structure was further enhanced by peptide-peptide interactions, which might influence the propensity of Aβ to aggregate into higher-ordered structures. The salt-bridges and inter-peptide hydrogen bonds were found to account for dimer stability. We observed spontaneous formation of intra-peptide D(23)-K(28) salt-bridge and a turn at V(24)GSN(27) region - long been accepted as characteristic structural-motifs for amyloid self-assembly. Altogether, our results provide atomistic details of Aβ-GM1 and Aβ-Aβ interactions and demonstrate their importance in the early-stages of GM1-mediated Aβ-oligomerisation on membrane surface.
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240
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Chong SH, Ham S. Assessing the influence of solvation models on structural characteristics of intrinsically disordered protein. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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241
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Silva KI, Saxena S. Zn(II) ions substantially perturb Cu(II) ion coordination in amyloid-β at physiological pH. J Phys Chem B 2013; 117:9386-94. [PMID: 23841511 DOI: 10.1021/jp406067n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction of Cu(II) and Zn(II) ions with amyloid-β (Aβ) plays an important role in the etiology of Alzheimer's disease. We describe the use of electron spin resonance (ESR) to measure metal-binding competition between Cu(II) and Zn(II) in amyloid-β at physiological pH. Continuous wave ESR measurements show that the affinity of Cu(II) toward Aβ(1-16) is significantly higher than that of Zn(II) at physiological pH. Importantly, of the two known Cu(II) coordination modes in Aβ, component I and component II, Zn(II) displaces Cu(II) only from component I. Our results indicate that at excess amounts of Zn(II) component II becomes the most dominant coordination mode. This observation is important as Aβ aggregates in the brain contain a high Zn(II) ion concentration. In order to determine details of the metal ion competition, electron spin echo envelope modulation experiments were carried out on Aβ variants that were systematically (15)N labeled. In the presence of Zn(II), most peptides use His 14 as an equatorial ligand to bind Cu(II) ions. Interestingly, Zn(II) ions completely substitute Cu(II) ions that are simultaneously coordinated to His 6 and His 13. Furthermore, in the presence of Zn(II), the proportion of Cu(II) ions that are simultaneously coordinated to His 13 and His 14 is increased. On the basis of our results we suggest that His 13 plays a critical role in modulating the morphology of Aβ aggregates.
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Affiliation(s)
- K Ishara Silva
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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242
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Inhibiting toxic aggregation of amyloidogenic proteins: a therapeutic strategy for protein misfolding diseases. Biochim Biophys Acta Gen Subj 2013; 1830:4860-71. [PMID: 23820032 DOI: 10.1016/j.bbagen.2013.06.029] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND The deposition of self-assembled amyloidogenic proteins is associated with multiple diseases, including Alzheimer's disease, Parkinson's disease and type 2 diabetes mellitus. The toxic misfolding and self-assembling of amyloidogenic proteins are believed to underlie protein misfolding diseases. Novel drug candidates targeting self-assembled amyloidogenic proteins represent a potential therapeutic approach for protein misfolding diseases. SCOPE OF REVIEW In this perspective review, we provide an overview of the recent progress in identifying inhibitors that block the aggregation of amyloidogenic proteins and the clinical applications thereof. MAJOR CONCLUSIONS Compounds such as polyphenols, certain short peptides, and monomer- or oligomer-specific antibodies, can interfere with the self-assembly of amyloidogenic proteins, prevent the formation of oligomers, amyloid fibrils and the consequent cytotoxicity. GENERAL SIGNIFICANCE Some inhibitors have been tested in clinical trials for treating protein misfolding diseases. Inhibitors that target the aggregation of amyloidogenic proteins bring new hope to therapy for protein misfolding diseases.
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243
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Caillon L, Lequin O, Khemtémourian L. Evaluation of membrane models and their composition for islet amyloid polypeptide-membrane aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2091-8. [PMID: 23707907 DOI: 10.1016/j.bbamem.2013.05.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 04/26/2013] [Accepted: 05/13/2013] [Indexed: 01/01/2023]
Abstract
Human islet amyloid polypeptide (IAPP) forms amyloid fibrils in the pancreatic islets of patients suffering from type 2 diabetes mellitus (T2DM). The formation of IAPP fibrils has been shown to cause membrane damage which most likely is responsible for the death of pancreatic islet β-cells during the pathogenesis of T2DM. Several studies have demonstrated a clear interaction between IAPP and lipid membranes. However the effect of different lipid compositions and of various membrane mimetics (including micelles, bicelles, SUV and LUV) on fibril formation kinetics and fibril morphology has not yet systematically been analysed. Here we report that the interaction of IAPP with various membrane models promoted different processes of fibril formation. Our data reveal that in SDS and DPC micelles, IAPP adopts a stable α-helical structure for several days, suggesting that the micelle models may stabilize monomeric or small oligomeric species of IAPP. In contrast, zwitterionic DMPC/DHPC bicelles and DOPC SUV accelerate the fibril formation compared to zwitterionic DOPC LUV, indicating that the size of the membrane model and its curvature influence the fibrillation process. Negatively charged membranes decrease the lag-time of the fibril formation kinetics while phosphatidylethanolamine and cholesterol have an opposite effect, probably due to the modulation of the physical properties of the membrane and/or due to direct interactions with IAPP within the membrane core. Finally, our results show that the modulation of lipid composition influences not only the growth of fibrils at the membrane surface but also the interactions of β-sheet oligomers with membranes.
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Key Words
- 1,1,1,3,3,3-hexafluoro-2-propanol
- 1,2-dihexanoyl-sn-glycero-3-phosphocholine
- 1,2-dimyristoyl-sn-glycero-3-phosphocholine
- 1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol)
- 1,2-dioleoyl-sn-glycero-3-phospho-L-serine
- 1,2-dioleoyl-sn-glycero-3-phosphocholine
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
- 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- Aggregation kinetics
- Amyloid
- CD
- Chol
- DHPC
- DMPC
- DMSO
- DOPC
- DOPE
- DOPG
- DOPS
- DPC
- DPPC
- Fibril morphology
- HFIP
- IAPP
- LUV
- Model membranes (LUV SUV, bicelles, micelles)
- POPC
- Phospholipid
- SDS
- SM
- ThT
- Thioflavin T
- cholesterol
- circular dichroism
- dimethyl sulfoxide
- dodecyl phosphocholine
- human Islet Amyloid Polypeptide
- large unilamellar vesicle
- sodium dodecyl sulphate
- sphingomyelin
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Affiliation(s)
- Lucie Caillon
- UPMC Univ Paris 06, UMR 7203 CNRS-UPMC-ENS, Laboratoire des Biomolécules, 4 place Jussieu, 75005 Paris, France
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244
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Xu L, Shan S, Wang X. Single Point Mutation Alters the Microstate Dynamics of Amyloid β-Protein Aβ42 as Revealed by Dihedral Dynamics Analyses. J Phys Chem B 2013; 117:6206-16. [DOI: 10.1021/jp403288b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Liang Xu
- School of Chemistry, Dalian University of Technology, Dalian 116023, China
| | - Shengsheng Shan
- School of Chemistry, Dalian University of Technology, Dalian 116023, China
| | - Xicheng Wang
- Department of Engineering Mechanics,
State Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
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245
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Hefti F, Goure WF, Jerecic J, Iverson KS, Walicke PA, Krafft GA. The case for soluble Aβ oligomers as a drug target in Alzheimer's disease. Trends Pharmacol Sci 2013; 34:261-6. [DOI: 10.1016/j.tips.2013.03.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 10/27/2022]
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246
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Chen YR, Huang HB, Lo CJ, Wang CC, Ho LK, Liu HT, Shiao MS, Lin TH, Chen YC. Effect of alanine replacement of l17 and f19 on the aggregation and neurotoxicity of arctic-type aβ40. PLoS One 2013; 8:e61874. [PMID: 23634215 PMCID: PMC3636269 DOI: 10.1371/journal.pone.0061874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 03/15/2013] [Indexed: 01/18/2023] Open
Abstract
Alzheimer’s disease is the most common form of neurodegenerative disease. Beta-amyloid peptides (Aβ) are responsible for neuronal death both in vitro and in vivo. Previously, L17 and F19 residues were identified as playing key roles in the stabilization of the Aβ40 conformation and in the reduction of its neurotoxicity. In this study, the effects of L17A/F19A mutations on the neurotoxicity of Aβ genetic mutant Arctic-type Aβ40(E22G) were tested. The results showed that compared to Aβ40(E22G), Aβ40(L17A/F19A/E22G) reduced the rate of conformation conversion, aggregation, and cytotoxicity, suggesting that L17 and F19 are critical residues responsible for conformational changes which may trigger the neurotoxic cascade of Aβ. Aβ40(L17A/F19A/E22G) also had decreased damage due to reactive oxygen species. The results are consistent with the discordant helix hypothesis, and confirm that residues 17–25 are in the discordant helix region. Compared to Aβ40(L17A/F19A), reduction in aggregation of Aβ40(L17A/F19A/E22G) was less significantly decreased. This observation provides an explanation based on the discordant helix hypothesis that the mutation of E22 to G22 of Aβ40(E22G) alters the propensity of the discordant helix. Arctic-type Aβ40(E22G) aggregates more severely than wild-type Aβ40, with a consequential increase in toxicity.
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Affiliation(s)
- Yi-Ru Chen
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Department and Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Hsien-bin Huang
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan, R.O.C
| | - Chi-Jen Lo
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Chih-Ching Wang
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Li-Kang Ho
- Department and Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Hsin-Tzu Liu
- Voiding Dysfunction Therapeutic Center in the Research Department, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, R.O.C
| | - Ming-Shi Shiao
- Department of Life Science, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, R.O.C
| | - Ta-Hsien Lin
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
- * E-mail: (YCC); (THL)
| | - Yi-Cheng Chen
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan, R.O.C
- * E-mail: (YCC); (THL)
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247
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Faller P, Hureau C, Berthoumieu O. Role of metal ions in the self-assembly of the Alzheimer's amyloid-β peptide. Inorg Chem 2013; 52:12193-206. [PMID: 23607830 DOI: 10.1021/ic4003059] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Aggregation of amyloid-β (Aβ) by self-assembly into oligomers or amyloids is a central event in Alzheimer's disease. Coordination of transition-metal ions, mainly copper and zinc, to Aβ occurs in vivo and modulates the aggregation process. A survey of the impact of Cu(II) and Zn(II) on the aggregation of Aβ reveals some general trends: (i) Zn(II) and Cu(II) at high micromolar concentrations and/or in a large superstoichiometric ratio compared to Aβ have a tendency to promote amorphous aggregations (precipitation) over the ordered formation of fibrillar amyloids by self-assembly; (ii) metal ions affect the kinetics of Aβ aggregations, with the most significant impact on the nucleation phase; (iii) the impact is metal-specific; (iv) Cu(II) and Zn(II) affect the concentrations and/or the types of aggregation intermediates formed; (v) the binding of metal ions changes both the structure and the charge of Aβ. The decrease in the overall charge at physiological pH increases the overall driving force for aggregation but may favor more precipitation over fibrillation, whereas the induced structural changes seem more relevant for the amyloid formation.
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Affiliation(s)
- Peter Faller
- CNRS, LCC (Laboratoire de Chimie de Coordination) , 205 route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France
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248
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Zhang T, Zhang J, Derreumaux P, Mu Y. Molecular mechanism of the inhibition of EGCG on the Alzheimer Aβ(1-42) dimer. J Phys Chem B 2013; 117:3993-4002. [PMID: 23537203 DOI: 10.1021/jp312573y] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Growing evidence supports that amyloid β (Aβ) oligomers are the major causative agents leading to neural cell death in Alzheimer's disease. The polyphenol (-)-epigallocatechin gallate (EGCG) was recently reported to inhibit Aβ fibrillization and redirect Aβ aggregation into unstructured, off-pathway oligomers. Given the experimental challenge to characterize the structures of Aβ/EGCG complexes, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer in the present and absence of EGCG in explicit solvent. Our equilibrium Aβ dimeric structures free of EGCG are consistent with the collision cross section from ion-mobility mass spectrometry and the secondary structure composition from circular dichroism experiment. In the presence of EGCG, the Aβ structures are characterized by increased inter-center-of-mass distances, reduced interchain and intrachain contacts, reduced β-sheet content, and increased coil and α-helix contents. Analysis of the free energy surfaces reveals that the Aβ dimer with EGCG adopts new conformations, affecting therefore its propensity to adopt fibril-prone states. Overall, this study provides, for the first time, insights on the equilibrium structures of Aβ1-42 dimer in explicit aqueous solution and an atomic picture of the EGCG-mediated conformational change on Aβ dimer.
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Affiliation(s)
- Tong Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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249
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Lv Z, Condron MM, Teplow DB, Lyubchenko YL. Nanoprobing of the effect of Cu(2+) cations on misfolding, interaction and aggregation of amyloid β peptide. J Neuroimmune Pharmacol 2013; 8:262-73. [PMID: 23143330 PMCID: PMC3586772 DOI: 10.1007/s11481-012-9416-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 10/29/2012] [Indexed: 12/15/2022]
Abstract
Misfolding and aggregation of the amyloid β-protein (Aβ) are hallmarks of Alzheimer's disease. Both processes are dependent on the environmental conditions, including the presence of divalent cations, such as Cu(2+). Cu(2+) cations regulate early stages of Aβ aggregation, but the molecular mechanism of Cu(2+) regulation is unknown. In this study we applied single molecule AFM force spectroscopy to elucidate the role of Cu(2+) cations on interpeptide interactions. By immobilizing one of two interacting Aβ42 molecules on a mica surface and tethering the counterpart molecule onto the tip, we were able to probe the interpeptide interactions in the presence and absence of Cu(2+) cations at pH 7.4, 6.8, 6.0, 5.0, and 4.0. The results show that the presence of Cu(2+) cations change the pattern of Aβ interactions for pH values between pH 7.4 and pH 5.0. Under these conditions, Cu(2+) cations induce Aβ42 peptide structural changes resulting in N-termini interactions within the dimers. Cu(2+) cations also stabilize the dimers. No effects of Cu(2+) cations on Aβ-Aβ interactions were observed at pH 4.0, suggesting that peptide protonation changes the peptide-cation interaction. The effect of Cu(2+) cations on later stages of Aβ aggregation was studied by AFM topographic images. The results demonstrate that substoichiometric Cu(2+) cations accelerate the formation of fibrils at pH 7.4 and 5.0, whereas no effect of Cu(2+) cations was observed at pH 4.0. Taken together, the combined AFM force spectroscopy and imaging analyses demonstrate that Cu(2+) cations promote both the initial and the elongation stages of Aβ aggregation, but protein protonation diminishes the effect of Cu(2+).
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Affiliation(s)
- Zhengjian Lv
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198
| | | | - David B. Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA
- Molecular Biology and Brain Research Institutes, and Mary S. Easton Center for Alzheimer’s Disease Research at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198
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250
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Richman M, Wilk S, Chemerovski M, Wärmländer SKTS, Wahlström A, Gräslund A, Rahimipour S. In vitro and mechanistic studies of an antiamyloidogenic self-assembled cyclic D,L-α-peptide architecture. J Am Chem Soc 2013; 135:3474-84. [PMID: 23360549 DOI: 10.1021/ja310064v] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Misfolding of the Aβ protein and its subsequent aggregation into toxic oligomers are related to Alzheimer's disease. Although peptides of various sequences can self-assemble into amyloid structures, these structures share common three-dimensional features that may promote their cross-reaction. Given the significant similarities between amyloids and the architecture of self-assembled cyclic D,L-α-peptide, we hypothesized that the latter may bind and stabilize a nontoxic form of Aβ, thereby preventing its aggregation into toxic forms. By screening a focused library of six-residue cyclic D,L-α-peptides and optimizing the activity of a lead peptide, we found one cyclic D,L-α-peptide (CP-2) that interacts strongly with Aβ and inhibits its aggregation. In transmission electron microscopy, optimized thioflavin T and cell survival assays, CP-2 inhibits the formation of Aβ aggregates, entirely disassembles preformed aggregated and fibrillar Aβ, and protects rat pheochromocytoma PC12 cells from Aβ toxicity, without inducing any toxicity by itself. Using various immunoassays, circular dichroism spectroscopy, photoinduced cross-linking of unmodified proteins (PICUP) combined with SDS/PAGE, and NMR, we probed the mechanisms underlying CP-2's antiamyloidogenic activity. NMR spectroscopy indicates that CP-2 interacts with Aβ through its self-assembled conformation and induces weak secondary structure in Aβ. Upon coincubation, CP-2 changes the aggregation pathway of Aβ and alters its oligomer distribution by stabilizing small oligomers (1-3 mers). Our results support studies suggesting that toxic early oligomeric states of Aβ may be composed of antiparallel β-peptide structures and that the interaction of Aβ with CP-2 promotes formation of more benign parallel β-structures. Further studies will show whether these kinds of abiotic cyclic D,L-α-peptides are also beneficial as an intervention in related in vivo models.
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Affiliation(s)
- Michal Richman
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290, Israel
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