1
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Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ 42 Monomers. J Phys Chem B 2021; 125:1085-1097. [PMID: 33481611 DOI: 10.1021/acs.jpcb.0c09617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations sampled by Aβ monomers even before aggregation starts. Here, we perform extensive all-atom replica exchange molecular dynamics (REMD) simulations to provide a comparative study of the ensemble of conformations sampled by Aβ42 monomers in solutions that promote (i.e., aqueous solution containing NaCl) and inhibit (i.e., aqueous solutions containing scyllo-inositol or 4-aminophenol) aggregation. Simulations performed in pure water are used as our reference. We find that secondary-structure content is only affected in an antagonistic manner by promoters and inhibitors at the C-terminus and the central hydrophilic core. Moreover, the end of the C-terminus binds more favorably to the central hydrophobic core region of Aβ42 in NaCl adopting a type of strand-loop-strand structure that is disfavored by inhibitors. Nonpolar residues that form the dry core of larger aggregates of Aβ42 (e.g., PDB ID 2BEG) are found at close proximity in these strand-loop-strand structures, suggesting that their formation could play an important role in initiating nucleation. In the presence of inhibitors, the C-terminus binds the central hydrophilic core with a higher probability than in our reference simulation. This sensitivity of the C-terminus, which is affected in an antagonistic manner by inhibitors and promoters, provides evidence for its critical role in accounting for aggregation.
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Affiliation(s)
- Farbod Mahmoudinobar
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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2
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Deike S, Rothemund S, Voigt B, Samantray S, Strodel B, Binder WH. β-Turn mimetic synthetic peptides as amyloid-β aggregation inhibitors. Bioorg Chem 2020; 101:104012. [PMID: 32683138 DOI: 10.1016/j.bioorg.2020.104012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/28/2022]
Abstract
Aggregation of amyloid peptides results in severe neurodegenerative diseases. While the fibril structures of Aβ40 and Aβ42 have been described recently, resolution of the aggregation pathway and evaluation of potent inhibitors still remains elusive, in particular in view of the hairpin-region of Aβ40. We here report the preparation of beta-turn mimetic conjugates containing synthetic turn mimetic structures in the turn region of Aβ40 and Aβ16-35, replacing 2 amino acids in the turn-region G25 - K28. The structure of the turn mimic induces both, acceleration of fibrillation and the complete inhibition of fibrillation, confirming the importance of the turn region on the aggregation. Replacing position G25-S26 provided the best inhibition effect for both beta-turn mimetics, the bicyclic BTD 1 and the aromatic TAA 2, while positions N27-K28 and V24-G25 showed only weaker or no inhibitory effects. When comparing different turn mimetics at the same position (G25-S26), conjugate 1a bearing the BTD turn showed the best inhibition of Aβ40 aggregation, while 5-amino-valeric acid 4a showed the weakest effect. Thus there is a pronounced impact on fibrillation with the chemical nature of the embedded beta-turn-mimic: the conformationally constrained turns 1 and 2 lead to a significantly reduced fibrillation, even inhibiting fibrillation of native Aβ40 when added in amounts down to 1/10, whereas the more flexible beta-turn-mimics 4-amino-benzoic acid 3a and 5-amino-valeric acid 4a lead to enhanced fibrillation. Toxicity-testing of the most successful conjugate showed only minor toxicity in cell-viability assays using the N2a cell line. Structural downsizing lead to the short fragment BTD/peptide Aβ16-35 as inhibitor of the aggregation of Aβ40, opening large potential for further small peptide based inhibitors.
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Affiliation(s)
- Stefanie Deike
- Department of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Sven Rothemund
- Core Unit Peptid-Technologien, University Leipzig, Liebigstr. 21, 04103 Leipzig, Germany
| | - Bruno Voigt
- Department of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimannstrasse 7 4, 06120 Halle, Germany
| | - Suman Samantray
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang H Binder
- Department of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany.
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3
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Aβ(M1-40) and Wild-Type Aβ40 Self-Assemble into Oligomers with Distinct Quaternary Structures. Molecules 2019; 24:molecules24122242. [PMID: 31208071 PMCID: PMC6631858 DOI: 10.3390/molecules24122242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/12/2023] Open
Abstract
Amyloid-β oligomers (AβOs) self-assemble into polymorphic species with diverse biological activities that are implicated causally to Alzheimer’s disease (AD). Synaptotoxicity of AβO species is dependent on their quaternary structure, however, low-abundance and environmental sensitivity of AβOs in vivo have impeded a thorough assessment of structure–function relationships. We developed a simple biochemical assay to quantify the relative abundance and morphology of cross-linked AβOs. We compared oligomers derived from synthetic Aβ40 (wild-type (WT) Aβ40) and a recombinant source, called Aβ(M1–40). Both peptides assemble into oligomers with common sizes and morphology, however, the predominant quaternary structures of Aβ(M1–40) oligomeric states were more diverse in terms of dispersity and morphology. We identified self-assembly conditions that stabilize high-molecular weight oligomers of Aβ(M1–40) with apparent molecular weights greater than 36 kDa. Given that mixtures of AβOs derived from both peptides have been shown to be potent neurotoxins that disrupt long-term potentiation, we anticipate that the diverse quaternary structures reported for Aβ(M1–40) oligomers using the assays reported here will facilitate research efforts aimed at isolating and identifying common toxic species that contribute to synaptic dysfunction.
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4
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Liu Z, Jiang F, Wu YD. Significantly different contact patterns between Aβ40 and Aβ42 monomers involving the N-terminal region. Chem Biol Drug Des 2018; 94:1615-1625. [PMID: 30381893 DOI: 10.1111/cbdd.13431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/28/2018] [Accepted: 10/10/2018] [Indexed: 01/03/2023]
Abstract
Aβ42 peptide, with two additional residues at C-terminus, aggregates much faster than Aβ40. We performed equilibrium replica-exchange molecular dynamics simulations of their monomers using our residue-specific force field. Simulated 3 JHNH α -coupling constants agree excellently with experimental data. Aβ40 and Aβ42 have very similar local conformational features, with considerable β-strand structures in the segments: A2-H6 (A), L17-A21 (B), A30-V36 (C) of both peptides and V39-I41 (D) of Aβ42. Both peptides have abundant A-B and B-C contacts, but Aβ40 has much more contacts between A and C than Aβ42, which may retard its aggregation. Only Aβ42 has considerable A-B-C-D topology. Decreased probability of A-C contact in Aβ42 relates to the competition from C-D contact. Increased A-C contact probability may also explain the slower aggregation of A2T and A2V mutants of Aβ42.
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Affiliation(s)
- Ziye Liu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Fan Jiang
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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5
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Doran TM, Nilsson BL. Incorporation of an Azobenzene β-Turn Peptidomimetic into Amyloid-β to Probe Potential Structural Motifs Leading to β-Sheet Self-Assembly. Methods Mol Biol 2018; 1777:387-406. [PMID: 29744850 DOI: 10.1007/978-1-4939-7811-3_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Alzheimer's disease (AD) is characterized by chronic neurodegeneration and the insidious accumulation of senile plaques comprised of the amyloid-β (Aβ) peptide. An important goal in AD research is to characterize the structural basis for how Aβ aggregates exert their noxious effects on neurons. We describe herein synthetic steps to incorporate a light-controlled β-turn mimetic, 3-(3-aminomethylphenylazo)-phenylacetic acid (AMPP), into the backbone of a putative turn region within Aβ. AMPP adopts a rigid β-hairpin turn when azobenzene is in the cis conformation, and can adopt an extended "β-arc" turn in the trans-azobenzene conformation. The long lifetimes of these conformationally stable isomers permit detailed biochemical analyses that help to clarify the controversial role played by these two types of turns during the toxic misfolding pathway of Aβ. Methods to photo-nucleate the cis- or trans-AMPP isomeric turns in aqueous buffer are also described. Finally, we detail selected techniques to characterize the Aβ aggregates derived from these photoisomerized variants.
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Affiliation(s)
- Todd M Doran
- Department of Medicinal Chemistry, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
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6
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Zapadka KL, Becher FJ, Gomes Dos Santos AL, Jackson SE. Factors affecting the physical stability (aggregation) of peptide therapeutics. Interface Focus 2017; 7:20170030. [PMID: 29147559 DOI: 10.1098/rsfs.2017.0030] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The number of biological therapeutic agents in the clinic and development pipeline has increased dramatically over the last decade and the number will undoubtedly continue to increase in the coming years. Despite this fact, there are considerable challenges in the development, production and formulation of such biologics particularly with respect to their physical stabilities. There are many cases where self-association to form either amorphous aggregates or highly structured fibrillar species limits their use. Here, we review the numerous factors that influence the physical stability of peptides including both intrinsic and external factors, wherever possible illustrating these with examples that are of therapeutic interest. The effects of sequence, concentration, pH, net charge, excipients, chemical degradation and modification, surfaces and interfaces, and impurities are all discussed. In addition, the effects of physical parameters such as pressure, temperature, agitation and lyophilization are described. We provide an overview of the structures of aggregates formed, as well as our current knowledge of the mechanisms for their formation.
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Affiliation(s)
| | - Frederik J Becher
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Sophie E Jackson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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7
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Rajbhandary A, Nilsson BL. Investigating the effects of peptoid substitutions in self-assembly of Fmoc-diphenylalanine derivatives. Biopolymers 2017; 108. [PMID: 27696352 DOI: 10.1002/bip.22994] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/22/2016] [Indexed: 12/24/2022]
Abstract
Low molecular weight agents that undergo self-assembly into fibril networks with hydrogel properties are promising biomaterials. Most low molecular weight hydrogelators are discovered empirically or serendipitously due to imperfect understanding of the mechanisms of self-assembly, the packing structure of self-assembled materials, and how the self-assembly process corresponds to emergent hydrogelation. Herein, the mechanisms of self-assembly and hydrogelation of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-PhePhe), a well-studied low molecular weight hydrogelator, is probed by systematic comparison with derivatives in which Phe residues are replaced by corresponding N-benzyl glycine peptoid (Nphe) analogs. Peptoids are peptidomimetics that shift display of side chain functionality from the α-carbon to the terminal nitrogen. This alters the hydrogen bonding capacity, the side chain presentation geometry, amide cis/trans isomerization equilibrium, and β-sheet potential of the peptoid relative to the corresponding amino acid in the context of peptidic polymers. It was found that amino acid/peptoid hybrids Fmoc-Phe-Nphe and Fmoc-Nphe-Phe have altered fibril self-assembly propensity and reduced hydrogelation capacity relative to the parent dipeptide, and that fibril self-assembly of the dipeptoid, Fmoc-Nphe-Nphe, is completely curtailed. These findings provide insight into the potential of low molecular weight peptoids and peptide/peptoid hybrids as hydrogelation agents and illuminate the importance of hydrogen bonding and π-π interaction geometry in facilitating self-assembly of Fmoc-Phe-Phe.
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Affiliation(s)
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York
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8
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Lee NR, Bowerman CJ, Nilsson BL. Sequence length determinants for self-assembly of amphipathic β-sheet peptides. Biopolymers 2016; 100:738-50. [PMID: 23553562 DOI: 10.1002/bip.22248] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/18/2013] [Accepted: 03/22/2013] [Indexed: 12/29/2022]
Abstract
Amphipathic peptides composed of alternating hydrophobic and hydrophilic amino acids are a privileged class of peptide, which have a high propensity to self-assemble into β-sheet fibrils. The Ac-(FKFE)2-NH2 peptide has been extensively studied and forms putative β-sheet bilayer fibrils in which the hydrophobic Phe side chains are organized to a single face of each constituent sheet; upon bilayer formation, these hydrophobic benzyl groups are sequestered in the hydrophobic core of the resulting fibril. In order for the Phe side chains to be uniformly displayed on one face of Ac-(FKFE)2-NH2 β-sheets, an antiparallel packing orientation in which one amino acid residue is unpaired must be adopted. Based on molecular models, we hypothesized that truncated seven amino acid derivatives of Ac-(FKFE)2-NH2 in which either the N-terminal Phe residue (Ac-KFEFKFE-NH2) or the C-terminal Glu residue (Ac-FKFEFKF-NH2) is eliminated should readily self-assemble into β-sheet bilayers in which all hydrogen bond and hydrophobic/charge interactions are satisfied. We found, however, that these minute changes in peptide sequence have unanticipated and dramatic effects on the self-assembly of each peptide. Ac-FKFEFKF-NH2 self-assembled into fibrils with unique morphology relative to the parent peptide, whereas the Ac-KFEFKFE-NH2 peptide had a strongly reduced propensity to self-assemble, even failing to self-assemble altogether under some conditions. These findings provide significant insight into the effect of sequence length and strand registry as well as hydrophobicity and charge on the self-assembly of simple amphipathic peptides to illuminate the possibility of tuning self-assembly processes and the resulting structures with minute changes to peptide sequence.
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Affiliation(s)
- Naomi R Lee
- Department of Chemistry, University of Rochester, Rochester, NY, 14627-0216
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9
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Khan JM, Khan MS, Ali MS, Al-Shabib NA, Khan RH. Cetyltrimethylammonium bromide (CTAB) promote amyloid fibril formation in carbohydrate binding protein (concanavalin A) at physiological pH. RSC Adv 2016. [DOI: 10.1039/c6ra03707k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Low concentration of CTAB provoked cross β-sheet formation whereas high concentrations of CTAB direct to alpha helix induction in Con A.
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Affiliation(s)
- Javed Masood Khan
- Department of Food Science and Nutrition
- Faculty of Food and Agricultural Sciences
- King Saud University
- 2460 Riyadh 11451
- Saudi Arabia
| | - Mohd Shahnawaz Khan
- Protein Research Chair
- Department of Biochemistry
- College of Science
- King Saud University
- Riyadh
| | - Mohd Sajid Ali
- Department of Chemistry
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | - Nasser Abdulatif Al-Shabib
- Department of Food Science and Nutrition
- Faculty of Food and Agricultural Sciences
- King Saud University
- 2460 Riyadh 11451
- Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh
- India
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10
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Pallo SP, DiMaio J, Cook A, Nilsson B, Johnson GVW. Mechanisms of tau and Aβ-induced excitotoxicity. Brain Res 2015; 1634:119-131. [PMID: 26731336 DOI: 10.1016/j.brainres.2015.12.048] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/09/2015] [Accepted: 12/17/2015] [Indexed: 11/18/2022]
Abstract
Excitotoxicity was originally postulated to be a late stage side effect of Alzheimer׳s disease (AD)-related neurodegeneration, however more recent studies indicate that it may occur early in AD and contribute to the neurodegenerative process. Tau and amyloid beta (Aβ), the main components of neurofibrillary tangles (NFTs) and amyloid plaques, have been implicated in cooperatively and independently facilitating excitotoxicity. Our study investigated the roles of tau and Aβ in AD-related excitotoxicity. In vivo studies showed that tau knockout (tau(-/-)) mice were significantly protected from seizures and hippocampal superoxide production induced with the glutamate analog, kainic acid (KA). We hypothesized that tau accomplished this by facilitating KA-induced Ca(2+) influx into neurons, however lentiviral tau knockdown failed to ameliorate KA-induced Ca(2+) influx into primary rat cortical neurons. We further investigated if tau cooperated with Aβ to facilitate KA-induced Ca(2+) influx. While Aβ biphasically modulated the KA-induced Cacyt(2+) responses, tau knockdown continued to have no effect. Therefore, tau facilitates KA-induced seizures and superoxide production in a manner that does not involve facilitation of Ca(2+) influx through KA receptors (KAR). On the other hand, acute pretreatment with Aβ (10 min) enhanced KA-induced Ca(2+) influx, while chronic Aβ (24 h) significantly reduced it, regardless of tau knockdown. Given previously published connections between Aβ, group 1 metabotropic glutamate receptors (mGluRs), and KAR regulation, we hypothesized that Aβ modulates KAR via a G-protein coupled receptor pathway mediated by group 1 mGluRs. We found that Aβ did not activate group 1 mGluRs and inhibition of these receptors did not reverse Aβ modulation of KA-induced Ca(2+) influx. Therefore, Aβ biphasically regulates KAR via a mechanism that does not involve group 1mGluR activation.
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Affiliation(s)
- Susanne P Pallo
- Department of Anesthesiology, University of Rochester Medical Center, Rochester, NY, USA.
| | - John DiMaio
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
| | - Alexis Cook
- Department of Anesthesiology, University of Rochester Medical Center, Rochester, NY, USA.
| | - Bradley Nilsson
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
| | - Gail V W Johnson
- Department of Anesthesiology, University of Rochester Medical Center, Rochester, NY, USA.
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11
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Poloni C, Stuart MCA, van der Meulen P, Szymanski W, Feringa BL. Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper. Chem Sci 2015; 6:7311-7318. [PMID: 28757990 PMCID: PMC5512536 DOI: 10.1039/c5sc02735g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/18/2015] [Indexed: 12/14/2022] Open
Abstract
The external photocontrol over peptide folding, by the incorporation of molecular photoswitches into their structure, provides a powerful tool to study biological processes. However, it is limited so far to switches that exhibit only a rather limited geometrical change upon photoisomerization and that show thermal instability of the photoisomer. Here we describe the use of an overcrowded alkene photoswitch to control a model β-hairpin peptide. This photoresponsive unit undergoes a large conformational change and has two thermally stable isomers which has major influence on the secondary structure and the aggregation of the peptide, permitting the phototriggered formation of amyloid-like fibrils.
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Affiliation(s)
- Claudia Poloni
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Marc C A Stuart
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Pieter van der Meulen
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Wiktor Szymanski
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
- Department of Radiology , University of Groningen , University Medical Center Groningen , Hanzeplein 1 , 9713 GZ , Groningen , The Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
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12
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Akter R, Cao P, Noor H, Ridgway Z, Tu LH, Wang H, Wong AG, Zhang X, Abedini A, Schmidt AM, Raleigh DP. Islet Amyloid Polypeptide: Structure, Function, and Pathophysiology. J Diabetes Res 2015; 2016:2798269. [PMID: 26649319 PMCID: PMC4662979 DOI: 10.1155/2016/2798269] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/24/2015] [Indexed: 01/29/2023] Open
Abstract
The hormone islet amyloid polypeptide (IAPP, or amylin) plays a role in glucose homeostasis but aggregates to form islet amyloid in type-2 diabetes. Islet amyloid formation contributes to β-cell dysfunction and death in the disease and to the failure of islet transplants. Recent work suggests a role for IAPP aggregation in cardiovascular complications of type-2 diabetes and hints at a possible role in type-1 diabetes. The mechanisms of IAPP amyloid formation in vivo or in vitro are not understood and the mechanisms of IAPP induced β-cell death are not fully defined. Activation of the inflammasome, defects in autophagy, ER stress, generation of reactive oxygen species, membrane disruption, and receptor mediated mechanisms have all been proposed to play a role. Open questions in the field include the relative importance of the various mechanisms of β-cell death, the relevance of reductionist biophysical studies to the situation in vivo, the molecular mechanism of amyloid formation in vitro and in vivo, the factors which trigger amyloid formation in type-2 diabetes, the potential role of IAPP in type-1 diabetes, the development of clinically relevant inhibitors of islet amyloidosis toxicity, and the design of soluble, bioactive variants of IAPP for use as adjuncts to insulin therapy.
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Affiliation(s)
- Rehana Akter
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Ping Cao
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Harris Noor
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Zachary Ridgway
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Ling-Hsien Tu
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Hui Wang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Amy G. Wong
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Xiaoxue Zhang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Andisheh Abedini
- Diabetes Research Program, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Ann Marie Schmidt
- Diabetes Research Program, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Research Department of Structural and Molecule Biology, University College London, Gower Street, London WC1E 6BT, UK
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13
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Hong L, Huang YJ, Yong WA. A Kinetic Model for Cell Damage Caused by Oligomer Formation. Biophys J 2015; 109:1338-46. [PMID: 26445435 DOI: 10.1016/j.bpj.2015.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 07/27/2015] [Accepted: 08/11/2015] [Indexed: 11/25/2022] Open
Abstract
It is well known that the formation of amyloid fiber may cause invertible damage to cells, although the underlying mechanism has not been fully understood. In this article, a microscopic model considering the detailed processes of amyloid formation and cell damage is constructed based on four simple assumptions, one of which is that cell damage is raised by oligomers rather than mature fibrils. By taking the maximum entropy principle, this microscopic model in the form of infinite mass-action equations together with two reaction-convection partial differential equations (PDEs) has been greatly coarse-grained into a macroscopic system consisting of only five ordinary differential equations (ODEs). With this simple model, the effects of primary nucleation, elongation, fragmentation, and protein and seeds concentration on amyloid formation and cell damage have been extensively explored and compared with experiments. We hope that our results will provide new insights into the quantitative linkage between amyloid formation and cell damage.
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Affiliation(s)
- Liu Hong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Peking, P.R. China.
| | - Ya-Jing Huang
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Peking, P.R. China
| | - Wen-An Yong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Peking, P.R. China
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14
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Pietropaolo A, Satriano C, Strano G, La Mendola D, Rizzarelli E. Different zinc(II) complex species and binding modes at Aβ N-terminus drive distinct long range cross-talks in the Aβ monomers. J Inorg Biochem 2015; 153:367-376. [PMID: 26298865 DOI: 10.1016/j.jinorgbio.2015.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 07/24/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
The present study addresses the reconstruction of the free-energy landscapes of amyloid-beta1-42 (Aβ42) coordinated respectively with one and two zinc ions, to scrutinize whether different Aβ-zinc complex species, i.e., mononuclear and dinuclear metal complexes, induce different Aβ conformation features. We found a subtle switch of intramolecular interactions, depending both on the zinc coordination environment and on the peptide to zinc stoichiometric ratio. On the one side, hairpin-like structures are predominant in mononuclear complexes, where a salt-bridge that involves Lys28-Glu22 and Lys16-Asp23 is stabilized. On the other side, elongated conformations are instead stabilized in the dinuclear zinc complexes. Experimental studies of atomic force microscopy as well as of zinc-Aβ complex species distribution diagrams provide evidence that the theoretical calculations can be rationalized in terms of the correlation between the increased amount of amorphous aggregates and the Aβ/Zn(2+) ratio.
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Affiliation(s)
- Adriana Pietropaolo
- Dipartimento di Scienze della Salute, Università di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Cristina Satriano
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, viale Andrea Doria, 6, 95125 Catania, Italy
| | - Gaetano Strano
- Fondazione RI.MED, Via Bandiera 11, 90133 Palermo, Italy
| | - Diego La Mendola
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano, 6, 56126 Pisa, Italy
| | - Enrico Rizzarelli
- Istituto di Biostrutture e Bioimagini-Consiglio Nazionale delle Ricerche (IBB-CNR), Via Paolo Gaifami, 18, 95126 Catania, Italy.
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15
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Hubin E, Deroo S, Schierle GK, Kaminski C, Serpell L, Subramaniam V, van Nuland N, Broersen K, Raussens V, Sarroukh R. Two distinct β-sheet structures in Italian-mutant amyloid-beta fibrils: a potential link to different clinical phenotypes. Cell Mol Life Sci 2015; 72:4899-913. [PMID: 26190022 PMCID: PMC4648968 DOI: 10.1007/s00018-015-1983-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 06/06/2015] [Accepted: 07/02/2015] [Indexed: 12/22/2022]
Abstract
Most Alzheimer’s disease (AD) cases are late-onset and characterized by the aggregation and deposition of the amyloid-beta (Aβ) peptide in extracellular plaques in the brain. However, a few rare and hereditary Aβ mutations, such as the Italian Glu22-to-Lys (E22K) mutation, guarantee the development of early-onset familial AD. This type of AD is associated with a younger age at disease onset, increased β-amyloid accumulation, and Aβ deposition in cerebral blood vessel walls, giving rise to cerebral amyloid angiopathy (CAA). It remains largely unknown how the Italian mutation results in the clinical phenotype that is characteristic of CAA. We therefore investigated how this single point mutation may affect the aggregation of Aβ1–42 in vitro and structurally characterized the resulting fibrils using a biophysical approach. This paper reports that wild-type and Italian-mutant Aβ both form fibrils characterized by the cross-β architecture, but with distinct β-sheet organizations, resulting in differences in thioflavin T fluorescence and solvent accessibility. E22K Aβ1–42 oligomers and fibrils both display an antiparallel β-sheet structure, in comparison with the parallel β-sheet structure of wild-type fibrils, characteristic of most amyloid fibrils described in the literature. Moreover, we demonstrate structural plasticity for Italian-mutant Aβ fibrils in a pH-dependent manner, in terms of their underlying β-sheet arrangement. These findings are of interest in the ongoing debate that (1) antiparallel β-sheet structure might represent a signature for toxicity, which could explain the higher toxicity reported for the Italian mutant, and that (2) fibril polymorphism might underlie differences in disease pathology and clinical manifestation.
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Affiliation(s)
- Ellen Hubin
- Nanobiophysics Group, Faculty of Science and Technology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE, Enschede, The Netherlands.,Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Stéphanie Deroo
- Laboratory of Structure and Function of Biological Membrane, Faculté des Sciences, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Campus de la Plaine CP 206/02, Boulevard du Triomphe, 1050, Brussels, Belgium
| | - Gabriele Kaminksi Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Clemens Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Louise Serpell
- School of Life Sciences, University of Sussex, Falmer, East Sussex, BN1 9QG, UK
| | - Vinod Subramaniam
- Nanobiophysics Group, Faculty of Science and Technology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE, Enschede, The Netherlands.,FOM Institute AMOLF, Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Nico van Nuland
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Kerensa Broersen
- Nanobiophysics Group, Faculty of Science and Technology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE, Enschede, The Netherlands.
| | - Vincent Raussens
- Laboratory of Structure and Function of Biological Membrane, Faculté des Sciences, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Campus de la Plaine CP 206/02, Boulevard du Triomphe, 1050, Brussels, Belgium
| | - Rabia Sarroukh
- Laboratory of Structure and Function of Biological Membrane, Faculté des Sciences, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Campus de la Plaine CP 206/02, Boulevard du Triomphe, 1050, Brussels, Belgium.
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16
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Xu L, Shan S, Chen Y, Wang X, Nussinov R, Ma B. Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization. J Chem Inf Model 2015; 55:1218-30. [PMID: 26017140 PMCID: PMC6407634 DOI: 10.1021/acs.jcim.5b00063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nonfibrillar neurotoxic amyloid β (Aβ) oligomer structures are typically rich in β-sheets, which could be promoted by metal ions like Zn(2+). Here, using molecular dynamics (MD) simulations, we systematically examined combinations of Aβ40 peptide conformations and Zn(2+) binding modes to probe the effects of secondary structure on Aβ dimerization energies and kinetics. We found that random conformations do not contribute to dimerization either thermodynamically or kinetically. Zn(2+) couples with preformed secondary structures (α-helix and β-hairpin) to speed dimerization and stabilize the resulting dimer. Partial α-helices increase the dimerization speed, and dimers with α-helix rich conformations have the lowest energy. When Zn(2+) coordinates with residues D1, H6, H13, and H14, Aβ40 β-hairpin monomers have the fastest dimerization speed. Dimers with experimentally observed zinc coordination (E11, H6, H13, and H14) form with slower rate but have lower energy. Zn(2+) cannot stabilize fibril-like β-arch dimers. However, Zn(2+)-bound β-arch tetramers have the lowest energy. Collectively, zinc-stabilized β-hairpin oligomers could be important in the nucleation-polymerization of cross-β structures. Our results are consistent with experimental findings that α-helix to β-structural transition should accompany Aβ aggregation in the presence of zinc ions and that Zn(2+) stabilizes nonfibrillar Aβ oligomers and, thus, inhibits formation of less toxic Aβ fibrils.
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Affiliation(s)
- Liang Xu
- School of Chemistry, Dalian University of Technology, Dalian, China
| | - Shengsheng Shan
- School of Chemistry, Dalian University of Technology, Dalian, China
| | - Yonggang Chen
- Network and Information Center, Dalian University of Technology, Dalian, China
| | - Xiaojuan Wang
- School of Chemical Machinery, Dalian University of Technology, Dalian, China
| | - Ruth Nussinov
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702
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17
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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18
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Li X, Wang Y, Yang C, Shi S, Jin L, Luo Z, Yu J, Zhang Z, Yang Z, Chen H. Supramolecular nanofibers of triamcinolone acetonide for uveitis therapy. NANOSCALE 2014; 6:14488-94. [PMID: 25341704 DOI: 10.1039/c4nr04761c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Supramolecular nanofibers of prodrugs hold advantages for drug release due to their high drug payload, sustained and constant drug release behavior, and stimuli responsiveness. In this study, we report on a supramolecular hydrogel mainly formed by a clinically used drug triamcinolone acetonide (TA). Such a hydrogel could only be prepared via an ester bond hydrolysis process from its prodrug of succinated triamcinolone acetonide (STA). The resulting hydrogel could constantly release TA in the in vitro release experiment. The TA hydrogel possessed an excellent transscleral penetration ability, as evaluated by the in vitro transscleral transport study. The developed TA hydrogel also exhibited a great ocular compatibility in rats, as indicated by the optical coherence tomography (OCT) images, HE observation, and glial fibrillary acidic protein (GFAP) and vimentin immuno-staining assays of the retinas. Our TA hydrogel showed a decreased efficacy to inhibit ocular inflammation in the rat's experiment autoimmune uveitis (EAU) model compared to the commercial TA suspension (Transton), but without causing complications such as high intraocular pressure and cataracts. These promising properties of the hydrogel indicated its great potential for the treatment of eye diseases.
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Affiliation(s)
- Xingyi Li
- Institute of Biomedical Engineering, School of Ophthalmology & Optometry and Eye hospital, Wenzhou Medical University, 270 Xueyuan Road, Wenzhou 325027, P.R. China.
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19
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Spirig T, Ovchinnikova O, Vagt T, Glockshuber R. Direct evidence for self-propagation of different amyloid-β fibril conformations. NEURODEGENER DIS 2014; 14:151-9. [PMID: 25300967 DOI: 10.1159/000363623] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Amyloid fibrils formed by amyloid-β (Aβ) peptides are associated with Alzheimer's disease and can occur in a range of distinct morphologies that are not uniquely determined by the Aβ sequence. Whether distinct conformations of Aβ fibrils can be stably propagated over multiple cycles of seeding and fibril growth has not been established experimentally. OBJECTIVE The ability of the 40-residue peptide Aβ1-40 to assemble into fibrils with the conformation of the mutant Aβ1-40 peptide containing the 'Osaka' mutation E22Δ was investigated. METHODS Fibril formation of highly pure, recombinant Aβ1-40 in the presence of distinct, preformed seeds in vitro was recorded with thioflavin T fluorescence, and distinct fibrillar structures were identified and distinguished by fluorescence spectroscopy and electron microscopy. RESULTS We propagated the specific quaternary structure of Aβ1-40 E22Δ fibrils with wild-type Aβ1-40 over up to seven cycles of seeding and fibril elongation. As a result of a 10(7)-fold dilution of the initially present Aβ1-40 E22Δ seeds, the vast majority of fibrils formed after the seventh propagation cycle with Aβ1-40 did not contain a single molecule of Aβ1-40 E22Δ, but still retained the conformation of the initial Aβ1-40 E22Δ seeds. Increased critical concentrations of Aβ1-40 fibrils formed in the presence of Aβ1-40 E22Δ nuclei suggest that these fibrils are less stable than homologously seeded Aβ1-40 fibrils, consistent with a kinetically controlled mechanism of fibril formation. CONCLUSION The propagation of a distinct Aβ fibril conformation over multiple cycles of seeded fibril growth demonstrates the basic ability of the Aβ peptide to form amyloid strains that in turn may cause phenotypes in Alzheimer's disease.
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Affiliation(s)
- Thomas Spirig
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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20
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Fanghänel S, Wadhwani P, Strandberg E, Verdurmen WPR, Bürck J, Ehni S, Mykhailiuk PK, Afonin S, Gerthsen D, Komarov IV, Brock R, Ulrich AS. Structure analysis and conformational transitions of the cell penetrating peptide transportan 10 in the membrane-bound state. PLoS One 2014; 9:e99653. [PMID: 24937132 PMCID: PMC4061077 DOI: 10.1371/journal.pone.0099653] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/18/2014] [Indexed: 11/18/2022] Open
Abstract
Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic α-helices, (ii) intrinsically disordered peptides, as well as (iii) β-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state (19)F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg) as a reporter group for (19)F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal α-helix is embedded in the membrane with an oblique tilt angle of ∼ 55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile β-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the α-helix counteracts the tendency of the unfolded N-terminus to self-assemble into β-pleated fibrils.
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Affiliation(s)
- Susanne Fanghänel
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
| | - Parvesh Wadhwani
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Erik Strandberg
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Wouter P. R. Verdurmen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jochen Bürck
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | - Sebastian Ehni
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
| | - Pavel K. Mykhailiuk
- Taras Shevchenko National University of Kyiv, Chemistry Department, Kyiv, Ukraine and Enamine Ltd., Kyiv, Ukraine
| | - Sergii Afonin
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
| | | | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv, Institute of High Technologies, Kyiv, Ukraine
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry and DFG-Center for Functional Nanostructures (CFN), Karlsruhe, Germany
- KIT, Institute of Biological Interfaces (IBG2), Karlsruhe, Germany
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21
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The characterization and comparison of amyloidogenic segments and non-amyloidogenic segments shed light on amyloid formation. Biochem Biophys Res Commun 2014; 447:255-62. [DOI: 10.1016/j.bbrc.2014.03.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 11/30/2022]
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22
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Doran TM, Ryan DM, Nilsson BL. Reversible photocontrol of self-assembled peptide hydrogel viscoelasticity. Polym Chem 2014. [DOI: 10.1039/c3py00903c] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide hydrogels are promising biomaterials for applications ranging from drug delivery to tissue engineering.
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Affiliation(s)
- Todd M. Doran
- Department of Chemistry
- University of Rochester
- Rochester
- USA
| | - Derek M. Ryan
- Department of Chemistry
- University of Rochester
- Rochester
- USA
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23
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Biswas A, Kurkute P, Jana B, Laskar A, Ghosh S. An amyloid inhibitor octapeptide forms amyloid type fibrous aggregates and affects microtubule motility. Chem Commun (Camb) 2014; 50:2604-7. [DOI: 10.1039/c3cc49396b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide in dual action: an amyloid inhibitor octapeptide spontaneously forms amyloid like fibrillar aggregates in solution and slows down the microtubule gliding speed through strong peptide–tubulin interaction.
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Affiliation(s)
- Atanu Biswas
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Prashant Kurkute
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Batakrishna Jana
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Aparna Laskar
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
| | - Surajit Ghosh
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032, India
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24
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ATR-FTIR: A “rejuvenated” tool to investigate amyloid proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2328-38. [DOI: 10.1016/j.bbamem.2013.04.012] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/20/2013] [Accepted: 04/02/2013] [Indexed: 12/24/2022]
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25
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Lee NR, Bowerman CJ, Nilsson BL. Effects of Varied Sequence Pattern on the Self-Assembly of Amphipathic Peptides. Biomacromolecules 2013; 14:3267-77. [DOI: 10.1021/bm400876s] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Naomi R. Lee
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Charles J. Bowerman
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Bradley L. Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
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26
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Rosenman DJ, Connors CR, Chen W, Wang C, García AE. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. J Mol Biol 2013; 425:3338-59. [PMID: 23811057 DOI: 10.1016/j.jmb.2013.06.021] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/15/2013] [Accepted: 06/12/2013] [Indexed: 12/24/2022]
Abstract
Amyloid β (Aβ) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer's disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Aβ monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Aβ aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the microseconds-per-replica timescale are used to characterize the structural ensembles of Aβ42, Aβ40, and M35-oxidized Aβ42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of nanoseconds-per-replica toward ensembles that yield good agreement with experiment. Though all three Aβ species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel β-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Aβ42, the absence of a second β-hairpin in Aβ40 and the sampling of alternate β topologies by M35-oxidized Aβ42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side-chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Aβ monomer folding. These characterizations help illustrate the conformational landscapes of Aβ monomers at atomic resolution and provide insight into the early stages of Aβ aggregation pathways.
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Affiliation(s)
- David J Rosenman
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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27
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Kar K, Hoop CL, Drombosky KW, Baker MA, Kodali R, Arduini I, van der Wel PCA, Horne WS, Wetzel R. β-hairpin-mediated nucleation of polyglutamine amyloid formation. J Mol Biol 2013; 425:1183-97. [PMID: 23353826 PMCID: PMC3602386 DOI: 10.1016/j.jmb.2013.01.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/15/2013] [Accepted: 01/15/2013] [Indexed: 12/01/2022]
Abstract
The conformational preferences of polyglutamine (polyQ) sequences are of major interest because of their central importance in the expanded CAG repeat diseases that include Huntington's disease. Here, we explore the response of various biophysical parameters to the introduction of β-hairpin motifs within polyQ sequences. These motifs (tryptophan zipper, disulfide, d-Pro-Gly, Coulombic attraction, l-Pro-Gly) enhance formation rates and stabilities of amyloid fibrils with degrees of effectiveness well correlated with their known abilities to enhance β-hairpin formation in other peptides. These changes led to decreases in the critical nucleus for amyloid formation from a value of n=4 for a simple, unbroken Q23 sequence to approximate unitary n values for similar length polyQs containing β-hairpin motifs. At the same time, the morphologies, secondary structures, and bioactivities of the resulting fibrils were essentially unchanged from simple polyQ aggregates. In particular, the signature pattern of solid-state NMR (13)C Gln resonances that appears to be unique to polyQ amyloid is replicated exactly in fibrils from a β-hairpin polyQ. Importantly, while β-hairpin motifs do produce enhancements in the equilibrium constant for nucleation in aggregation reactions, these Kn values remain quite low (~10(-)(10)) and there is no evidence for significant enhancement of β-structure within the monomer ensemble. The results indicate an important role for β-turns in the nucleation mechanism and structure of polyQ amyloid and have implications for the nature of the toxic species in expanded CAG repeat diseases.
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Affiliation(s)
- Karunakar Kar
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Cao P, Marek P, Noor H, Patsalo V, Tu LH, Wang H, Abedini A, Raleigh DP. Islet amyloid: from fundamental biophysics to mechanisms of cytotoxicity. FEBS Lett 2013; 587:1106-18. [PMID: 23380070 DOI: 10.1016/j.febslet.2013.01.046] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 12/21/2022]
Abstract
Pancreatic islet amyloid is a characteristic feature of type 2 diabetes. The major protein component of islet amyloid is the polypeptide hormone known as islet amyloid polypeptide (IAPP, or amylin). IAPP is stored with insulin in the β-cell secretory granules and is released in response to the stimuli that lead to insulin secretion. IAPP is normally soluble and is natively unfolded in its monomeric state, but forms islet amyloid in type 2 diabetes. Islet amyloid is not the cause of type 2 diabetes, but it leads to β-cell dysfunction and cell death, and contributes to the failure of islet cell transplantation. The mechanism of IAPP amyloid formation is not understood and the mechanisms of cytotoxicity are not fully defined.
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Affiliation(s)
- Ping Cao
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
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Abstract
In this chapter we provided the overall background to the subject of protein aggregation and fibrillogenesis in amyloidogenesis, with introduction and brief discussion of the various topics that are included with the coming chapters. The division of the book into basic science and clinical science sections enables correlation of the topics to be made. The many proteins and peptides that have currently been found to undergo fibrillogenesis are tabulated. A broad technical survey is made, to indicate the vast array of techniques currently available to study aspects of protein oligomerization, aggregation and fibrillogenesis. These are split into three groups and tabulated, as the microscopical techniques, the analytical and biophysical methods, and the biochemical and cellular techniques. A few techniques are discussed, but in most cases only a link to relevant recent literature is provided.
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