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La Penna G, Morante S. Aggregates Sealed by Ions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2340:309-341. [PMID: 35167080 DOI: 10.1007/978-1-0716-1546-1_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The chapter draws a line connecting some recent results where the role of ions is found essential in sealing more or less pre-organized assemblies of macromolecules. We draw some dots along the line that starts from the effect of the ionic atmosphere and ends with the chemical bonds formed by multivalent ions acting as bridges between macromolecules. Many of these dots involve structurally disordered peptides and disordered regions of proteins. A broad perspective of the role of multivalent ions in assisting the assembly process, shifting population in polymorphic states, and sealing protein aggregates, is suggested.
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Affiliation(s)
- Giovanni La Penna
- Institute for Chemistry of Organo-Metallic Compounds, National Research Council of Italy, Florence, Italy.
| | - Silvia Morante
- Department of Physics, University of Roma Tor Vergata, Roma, Italy
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2
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Xu S, Wang W, Dong X, Sun Y. Molecular Insight into Cu 2+-Induced Conformational Transitions of Amyloid β-Protein from Fast Kinetic Analysis and Molecular Dynamics Simulations. ACS Chem Neurosci 2021; 12:300-310. [PMID: 33401892 DOI: 10.1021/acschemneuro.0c00502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cu2+-mediated amyloid β-protein (Aβ) aggregation is implicated in the pathogenesis of Alzheimer's disease, so it is of significance to understand Cu2+-mediated conformational transitions of Aβ. Herein, four Aβ mutants were created by using the environment-sensitive cyanophenylalanine to respectively substitute F4, Y10, F19, and F20 residues of Aβ40. By using stopped-flow fluorescence spectroscopy and molecular dynamics (MD) simulations, the early stage conformational transitions of the mutants mediated by Cu2+ binding were investigated. The fast kinetics unveils that Cu2+ has more significant influence on the conformational changes of N-terminal (F4 and Y10) than on the central hydrophobic core (CHC, F19, and F20) under different pH conditions (pH 6.6-8.0), especially Y10. Interestingly, lag periods of the conformational transitions are observed for the F19 and F20 mutants at pH 8.0, indicating the slow response of the two mutation sites on the conformational transitions. More importantly, significantly longer lag periods for F20 than for F19 indicate the conduction of the transition from F19 to F20. The conduction time (difference in lag period) decreases from 4.5 s at Cu2+ = 0 to undetectable (<1 ms) at Cu2+ = 10 μM. The significant difference in the response time of F19 and F20 and the fast local conformational changes of Y10 imply that the conformational transitions of Aβ start around Y10. MD simulations support the observation of hydrophobicity increase at N-terminal during the conformational transitions of Aβ-Cu2+. It also reveals that Y10 is immediately approached by Cu2+, supporting the speculation that the starting point of conformational transitions of Aβ is near Y10. The work has provided molecular insight into the early stage conformational transitions of Aβ40 mediated by Cu2+.
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Affiliation(s)
- Shaoying Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Wenjuan Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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3
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Coskuner O, Uversky VN. Intrinsically disordered proteins in various hypotheses on the pathogenesis of Alzheimer's and Parkinson's diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:145-223. [PMID: 31521231 DOI: 10.1016/bs.pmbts.2019.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amyloid-β (Aβ) and α-synuclein (αS) are two intrinsically disordered proteins (IDPs) at the centers of the pathogenesis of Alzheimer's and Parkinson's diseases, respectively. Different hypotheses have been proposed for explanation of the molecular mechanisms of the pathogenesis of these two diseases, with these two IDPs being involved in many of these hypotheses. Currently, we do not know, which of these hypothesis is more accurate. Experiments face challenges due to the rapid conformational changes, fast aggregation processes, solvent and paramagnetic effects in studying these two IDPs in detail. Furthermore, pathological modifications impact their structures and energetics. Theoretical studies using computational chemistry and computational biology have been utilized to understand the structures and energetics of Aβ and αS. In this chapter, we introduce Aβ and αS in light of various hypotheses, and discuss different experimental and theoretical techniques that are used to study these two proteins along with their weaknesses and strengths. We suggest that a promising solution for studying Aβ and αS at the center of varying hypotheses could be provided by developing new techniques that link quantum mechanics, statistical mechanics, thermodynamics, bioinformatics to machine learning. Such new developments could also lead to development in experimental techniques.
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Affiliation(s)
- Orkid Coskuner
- Turkish-German University, Molecular Biotechnology, Istanbul, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Moscow, Russia.
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Khatua P, Mondal S, Bandyopadhyay S. Effects of Metal Ions on Aβ 42 Peptide Conformations from Molecular Simulation Studies. J Chem Inf Model 2019; 59:2879-2893. [PMID: 31095382 DOI: 10.1021/acs.jcim.9b00098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this study, we investigate the conformational characteristics of full-length Aβ42 peptide monomers in the presence of Na+ and Zn2+ metal ions using atomistic molecular dynamics (MD) simulations with an aim to explore the possible driving forces behind enhanced aggregation rates of the peptides in the presence of salts. The calculations reveal that the presence of metal ions shifts the conformational equilibrium more toward the compact ordered Aβ structures. Such compact ordered structures stabilized by distant nonlocal contacts between two crucial hydrophobic segments, hp1 and hp2, primarily through two important hydrophobic aromatic residues, Phe-19 and Phe-20, are expected to trigger the aggregation process at a faster rate by populating and stabilizing the aggregation prone structures. Formation of a significant number of such distant contacts in the presence of Na+ ions has also been found to result in breaking of the N-terminal helix. On the contrary, binding of Zn2+ ion to Aβ peptide is highly specific, which stabilizes the N-terminal helix instead of breaking it. This explains why the aggregation rate of Aβ peptides is higher in the presence of divalent Zn2+ ions than monovalent Na+ ions. Relatively higher overall stability of the most populated Aβ peptide monomers in the presence of Zn2+ ions has been found to be associated with specific Zn2+-Aβ binding and significant free energy gain.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , India
| | - Souvik Mondal
- Molecular Modeling Laboratory, Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , India.,Centre for Computational and Data Sciences , Indian Institute of Technology , Kharagpur 721302 , India
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5
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Strodel B, Coskuner-Weber O. Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer's Disease: Insights from Computational Chemistry Studies. J Chem Inf Model 2019; 59:1782-1805. [PMID: 30933519 DOI: 10.1021/acs.jcim.8b00983] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Monomers and oligomers of the amyloid-β peptide aggregate to form the fibrils found in the brains of Alzheimer's disease patients. These monomers and oligomers are largely disordered and can interact with transition metal ions, affecting the mechanism and kinetics of amyloid-β aggregation. Due to the disordered nature of amyloid-β, its rapid aggregation, as well as solvent and paramagnetic effects, experimental studies face challenges in the characterization of transition metal ions bound to amyloid-β monomers and oligomers. The details of the coordination chemistry between transition metals and amyloid-β obtained from experiments remain debated. Furthermore, the impact of transition metal ion binding on the monomeric or oligomeric amyloid-β structures and dynamics are still poorly understood. Computational chemistry studies can serve as an important complement to experimental studies and can provide additional knowledge on the binding between amyloid-β and transition metal ions. Many research groups conducted first-principles calculations, ab initio molecular dynamics simulations, quantum mechanics/classical mechanics simulations, and classical molecular dynamics simulations for studying the interplay between transition metal ions and amyloid-β monomers and oligomers. This review summarizes the current understanding of transition metal interactions with amyloid-β obtained from computational chemistry studies. We also emphasize the current view of the coordination chemistry between transition metal ions and amyloid-β. This information represents an important foundation for future metal ion chelator and drug design studies aiming to combat Alzheimer's disease.
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Affiliation(s)
- Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , Jülich 52425 , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , Düsseldorf 40225 , Germany
| | - Orkid Coskuner-Weber
- Molecular Biotechnology , Turkish-German University , Sahinkaya Caddesi, No. 86, Beykoz , Istanbul 34820 , Turkey
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6
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Coskuner-Weber O. Revisiting Cu(II) Bound Amyloid-β40 and Amyloid-β42 Peptides: Varying Coordination Chemistries. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2018. [DOI: 10.18596/jotcsa.424144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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7
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Lee M, Kim JI, Na S, Eom K. Metal ions affect the formation and stability of amyloid β aggregates at multiple length scales. Phys Chem Chem Phys 2018; 20:8951-8961. [PMID: 29557445 DOI: 10.1039/c7cp05072k] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Amyloid β (Aβ) aggregates, which are a hallmark for neurodegenerative disease, are formed through a self-assembly process such as aggregation of Aβ peptide chains. This aggregation process depends on the solvent conditions under which the proteins are aggregated. Nevertheless, the underlying mechanism of the ionic effect on the formation and stability of amyloid aggregates has not been fully understood. Here, we report how metal ions play a role in the formation and stability of Aβ aggregates at different length scales, i.e. oligomers and fibrils. It is shown that the metal (i.e. zinc or copper) ion increases the stability of Aβ oligomers, whereas the metal ion reduces the stability of Aβ fibrils. In addition, we found that zinc ions are able to more effectively destabilize fibril structures than copper ions. Metal ion-mediated (de)stabilization of Aβ oligomers (or fibrils) is attributed to the critical effect of the metal ion on the β-sheet rich crystalline structure of the amyloid aggregate and the status of hydrogen bonds within the aggregate. Our study sheds light on the role of the metal ion in stabilizing the amyloid oligomers known as a toxic agent (to functional cells), which is consistent with clinical observation that high concentrations of metal ions are found in patients suffering from neurodegenerative diseases.
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Affiliation(s)
- Myeongsang Lee
- Institute of Advanced Machinery Design Technology, Korea University, Seoul 02481, Republic of Korea
| | - Jae In Kim
- Department of Mechanical Engineering, Korea University, Seoul 02481, Republic of Korea.
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul 02481, Republic of Korea.
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
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8
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Challenges in studying the structures of metal-amyloid oligomers related to type 2 diabetes, Parkinson's disease, and Alzheimer's disease. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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9
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Alí-Torres J, Mirats A, Maréchal JD, Rodríguez-Santiago L, Sodupe M. 3D structures and redox potentials of Cu2+-Aβ(1-16) complexes at different pH: a computational study. J Phys Chem B 2014; 118:4840-50. [PMID: 24738872 DOI: 10.1021/jp5019718] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Oxidative stress induced by redox-active metal cations such as Cu(2+) is a key event in the development of Alzheimer's disease. A detailed knowledge of the structure of Cu(2+)-Aβ complex is thus important to get a better understanding of this critical process. In the present study, we use a computational approach that combines homology modeling with quantum-mechanics-based methods to determine plausible 3D structures of Cu(2+)-Aβ(1-16) complexes that enclose the different metal coordination spheres proposed experimentally at different pH values. With these models in hand, we determine their standard reduction potential (SRP) with the aim of getting new insights into the relation between the structure of these complexes and their redox behavior. Results show that in all cases copper reduction induces CObackbone decoordination, which, for distorted square planar structures in the oxidized state (Ia_δδ, IIa_εδε, IIa_εεε, and IIc_ε), leads to tricoordinated species. For the pentacoordinated structural candidate Ib_δε with Glu11 at the apical position, the reduction leads to a distorted tetrahedral structure. The present results highlight the importance of the nature of the ligands on the SRP. The computed values (with respect to the standard hydrogen electrode) for complexes enclosing negatively charged ligands in the coordination sphere (from -0.81 to -0.12 V) are significantly lower than those computed for models involving neutral ligands (from 0.19 to 0.28 V). Major geometry changes induced by reduction, on both the metal site and the peptide configuration, are discussed as well as their possible influence in the formation of reactive oxygen species.
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Affiliation(s)
- Jorge Alí-Torres
- Departament de Química, Universitat Autònoma de Barcelona , 08193 Bellaterra, Barcelona, Spain
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10
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Parthasarathy S, Yoo B, McElheny D, Tay W, Ishii Y. Capturing a reactive state of amyloid aggregates: NMR-based characterization of copper-bound Alzheimer disease amyloid β-fibrils in a redox cycle. J Biol Chem 2014; 289:9998-10010. [PMID: 24523414 DOI: 10.1074/jbc.m113.511345] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The interaction of redox-active copper ions with misfolded amyloid β (Aβ) is linked to production of reactive oxygen species (ROS), which has been associated with oxidative stress and neuronal damages in Alzheimer disease. Despite intensive studies, it is still not conclusive how the interaction of Cu(+)/Cu(2+) with Aβ aggregates leads to ROS production even at the in vitro level. In this study, we examined the interaction between Cu(+)/Cu(2+) and Aβ fibrils by solid-state NMR (SSNMR) and other spectroscopic methods. Our photometric studies confirmed the production of ~60 μM hydrogen peroxide (H2O2) from a solution of 20 μM Cu(2+) ions in complex with Aβ(1-40) in fibrils ([Cu(2+)]/[Aβ] = 0.4) within 2 h of incubation after addition of biological reducing agent ascorbate at the physiological concentration (~1 mM). Furthermore, SSNMR (1)H T1 measurements demonstrated that during ROS production the conversion of paramagnetic Cu(2+) into diamagnetic Cu(+) occurs while the reactive Cu(+) ions remain bound to the amyloid fibrils. The results also suggest that O2 is required for rapid recycling of Cu(+) bound to Aβ back to Cu(2+), which allows for continuous production of H2O2. Both (13)C and (15)N SSNMR results show that Cu(+) coordinates to Aβ(1-40) fibrils primarily through the side chain Nδ of both His-13 and His-14, suggesting major rearrangements from the Cu(2+) coordination via Nε in the redox cycle. (13)C SSNMR chemical shift analysis suggests that the overall Aβ conformations are largely unaffected by Cu(+) binding. These results present crucial site-specific evidence of how the full-length Aβ in amyloid fibrils offers catalytic Cu(+) centers.
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11
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Maiorana A, Marino T, Minicozzi V, Morante S, Russo N. A micro-environmental study of the Zn+2–Aβ1–16 structural properties. Biophys Chem 2013; 182:86-93. [DOI: 10.1016/j.bpc.2013.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/14/2013] [Accepted: 07/07/2013] [Indexed: 11/29/2022]
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12
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Singharoy A, Polavarapu A, Joshi H, Baik MH, Ortoleva P. Epitope fluctuations in the human papillomavirus are under dynamic allosteric control: a computational evaluation of a new vaccine design strategy. J Am Chem Soc 2013; 135:18458-68. [PMID: 24199651 DOI: 10.1021/ja407489r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The dynamic properties of the capsid of the human papillomavirus (HPV) type 16 were examined using classical molecular dynamics simulations. By systematically comparing the structural fluctuations of the capsid protein, a strong dynamic allosteric connection between the epitope containing loops and the h4 helix located more than 50 Å away is identified, which was not recognized thus far. Computer simulations show that restricting the structural fluctuations of the h4 helix is key to rigidifying the epitopes, which is thought to be required for eliciting a proper immune response. The allostery identified in the components of the HPV is nonclassical because the mean structure of the epitope carrying loops remains unchanged, but as a result of allosteric effect the structural fluctuations are altered significantly, which in turn changes the biochemical reactivity profile of the epitopes. Exploiting this novel insight, a new vaccine design strategy is proposed wherein a relatively small virus capsid fragment is deposited on a silica nanoparticle in such a way that the fluctuations of the h4 helix are suppressed. The structural and dynamic properties of the epitope carrying loops on this hybrid nanoparticle match the characteristics of epitopes found on the full virus-like particle precisely, suggesting that these nanoparticles may serve as potent, cost-effective, and safe alternatives to traditionally developed vaccines. The structural and dynamic properties of the hybrid nanoparticle are examined in detail to establish the general concepts of the proposed new design.
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Affiliation(s)
- Abhishek Singharoy
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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13
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Xu L, Wang X, Wang X. Effects of Zn2+ binding on the structural and dynamic properties of amyloid β peptide associated with Alzheimer's disease: Asp1 or Glu11? ACS Chem Neurosci 2013; 4:1458-68. [PMID: 23947440 DOI: 10.1021/cn4001445] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Extensive experimental and computational studies have suggested that multiple Zn(2+) binding modes in amyloid β (Aβ) peptides could exist simultaneously. However, consistent results have not been obtained for the effects of Zn(2+) binding on Aβ structure, dynamics, and kinetics in particular. Some key questions such as why it is so difficult to distinguish the polymorphic states of metal ions binding to Aβ and what the underlying rationale is, necessitate elucidation. In this work, two 3N1O Zn(2+) binding modes were constructed with three histidines (His(6), His(13), and His(14)), and Asp(1)/Glu(11) of Aβ40 coordinated to Zn(2+). Results from molecular dynamics simulations reveal that the conformational ensembles of different Zn(2+)-Aβ40 complexes are nonoverlapping. The formation of turn structure and, especially, the salt bridge between Glu(22)/Asp(23) and Lys(28) is dependent on specific Zn(2+) binding mode. Agreement with available NMR observations of secondary and tertiary structures could be better achieved if the two simulation results are considered together. The free energy landscape constructed by combining both conformations of Aβ40 indicates that transitions between distinct Aβ40 conformations thar are ready for Zn(2+) binding could be possible in aqueous solution. Markov state model analyses reveal the complex network of conformational space of Aβ40 modeulated by Zn(2+) binding, suggesting various misfolding pathways. The binding free energies evaluated using a combination of quantum mechanics calculations and the MM/3D-RISM method suggest that Glu(11) is the preferred oxygen ligand of Zn(2+). However, such preference is dependent on the relative populations of different conformations with specific Zn(2+) binding modes, and therefore could be shifted when experimental or simulation conditions are altered.
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Affiliation(s)
- Liang Xu
- School of
Chemistry, ‡State Key Laboratory of Fine Chemicals, §School of
Chemical Machinery, ∥Department of Engineering Mechanics, ⊥State
Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
| | - Xiaojuan Wang
- School of
Chemistry, ‡State Key Laboratory of Fine Chemicals, §School of
Chemical Machinery, ∥Department of Engineering Mechanics, ⊥State
Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
| | - Xicheng Wang
- School of
Chemistry, ‡State Key Laboratory of Fine Chemicals, §School of
Chemical Machinery, ∥Department of Engineering Mechanics, ⊥State
Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
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14
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Characterization of the polymorphic states of copper(II)-bound Aβ(1-16) peptides by computational simulations. J Comput Chem 2013; 34:2524-36. [DOI: 10.1002/jcc.23416] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/23/2013] [Accepted: 08/01/2013] [Indexed: 01/07/2023]
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15
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Hernández-Rodríguez M, Correa-Basurto J, Benitez-Cardoza CG, Resendiz-Albor AA, Rosales-Hernández MC. In silico and in vitro studies to elucidate the role of Cu2+ and galanthamine as the limiting step in the amyloid beta (1-42) fibrillation process. Protein Sci 2013; 22:1320-35. [PMID: 23904252 DOI: 10.1002/pro.2319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/03/2013] [Accepted: 07/12/2013] [Indexed: 11/06/2022]
Abstract
The formation of fibrils and oligomers of amyloid beta (Aβ) with 42 amino acid residues (Aβ 1-42 ) is the most important pathophysiological event associated with Alzheimer's disease (AD). The formation of Aβ fibrils and oligomers requires a conformational change from an α-helix to a β-sheet conformation, which is encouraged by the formation of a salt bridge between Asp 23 or Glu 22 and Lys 28. Recently, Cu(2+) and various drugs used for AD treatment, such as galanthamine (Reminyl(®) ), have been reported to inhibit the formation of Aβ fibrils. However, the mechanism of this inhibition remains unclear. Therefore, the aim of this work was to explore how Cu(2+) and galanthamine prevent the formation of Aβ1-42 fibrils using molecular dynamics (MD) simulations (20 ns) and in vitro studies using fluorescence and circular dichroism (CD) spectroscopies. The MD simulations revealed that Aβ1-42 acquires a characteristic U-shape before the α-helix to β-sheet conformational change. The formation of a salt bridge between Asp 23 and Lys 28 was also observed beginning at 5 ns. However, the MD simulations of Aβ 1-42 in the presence of Cu(2+) or galanthamine demonstrated that both ligands prevent the formation of the salt bridge by either binding to Glu 22 and Asp 23 (Cu(2+) ) or to Lys 28 (galanthamine), which prevents Aβ 1-42 from adopting the U-characteristic conformation that allows the amino acids to transition to a β-sheet conformation. The docking results revealed that the conformation obtained by the MD simulation of a monomer from the 1Z0Q structure can form similar interactions to those obtained from the 2BGE structure in the oligomers. The in vitro studies demonstrated that Aβ remains in an unfolded conformation when Cu(2+) and galanthamine are used. Then, ligands that bind Asp 23 or Glu 22 and Lys 28 could therefore be used to prevent β turn formation and, consequently, the formation of Aβ fibrils.
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Affiliation(s)
- Maricarmen Hernández-Rodríguez
- Laboratorio de Modelado Molecular y Bioinformatica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 México City, D.F., México; Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 México City, D.F., México
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16
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Mold M, Ouro-Gnao L, Wieckowski BM, Exley C. Copper prevents amyloid-β(1-42) from forming amyloid fibrils under near-physiological conditions in vitro. Sci Rep 2013; 3:1256. [PMID: 23409247 PMCID: PMC3570782 DOI: 10.1038/srep01256] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 01/24/2013] [Indexed: 11/30/2022] Open
Abstract
The aggregation and deposition of amyloid-β((1-42) )(Aβ(42)) in the brain is implicated in the aetiology of Alzheimer's disease (AD). While the mechanism underlying its deposition in vivo is unknown its precipitation in vitro is influenced by metal ions. For example, Aβ(42) is known to bind copper, Cu(II), in vitro and binding results in aggregation of the peptide. The biophysical properties of Cu(II)-Aβ(42) aggregates are of significant importance to their putative involvement in the amyloid cascade hypothesis of AD and are currently the subject of strong debate. In particular the question has been raised if sub- and super-stoichiometric concentrations of Cu(II) act in opposing ways in respectively accelerating and preventing amyloid fibril formation by Aβ(42). Herein we have used fluorimetry and transmission electron microscopy to provide unequivocal evidence that under near-physiological conditions both sub- and super-stoichiometric concentrations of Cu(II) prevented the assembly of Aβ(42) into ThT-positive β-sheet rich amyloid fibrils.
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Affiliation(s)
- Matthew Mold
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Staffordshire, ST5 5BG, UK
| | | | - Beata M Wieckowski
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Staffordshire, ST5 5BG, UK
| | - Christopher Exley
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Staffordshire, ST5 5BG, UK
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17
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Miller Y, Ma B, Nussinov R. Metal binding sites in amyloid oligomers: Complexes and mechanisms. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.12.022] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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18
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Giannozzi P, Jansen K, Penna GL, Minicozzi V, Morante S, Rossi G, Stellato F. Zn induced structural aggregation patterns of β-amyloid peptides by first-principle simulations and XAS measurements. Metallomics 2012; 4:156-65. [DOI: 10.1039/c2mt00148a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Pramanik D, Ghosh C, Dey SG. Heme–Cu Bound Aβ Peptides: Spectroscopic Characterization, Reactivity, and Relevance to Alzheimer’s Disease. J Am Chem Soc 2011; 133:15545-52. [DOI: 10.1021/ja204628b] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Debajyoti Pramanik
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India 700032
| | - Chandradeep Ghosh
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India 700032
| | - Somdatta Ghosh Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India 700032
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Alí-Torres J, Maréchal JD, Rodríguez-Santiago L, Sodupe M. Three dimensional models of Cu(2+)-Aβ(1-16) complexes from computational approaches. J Am Chem Soc 2011; 133:15008-14. [PMID: 21846101 DOI: 10.1021/ja203407v] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Elucidation of the coordination of metal ions to Aβ is essential to understand their role in its aggregation and to rationally design new chelators with potential therapeutic applications in Alzheimer disease. Because of that, in the last 10 years several studies have focused their attention in determining the coordination properties of Cu(2+) interacting with Aβ. However, more important than characterizing the first coordination sphere of the metal is the determination of the whole Cu(2+)-Aβ structure. In this study, we combine homology modeling (HM) techniques with quantum mechanics based approaches (QM) to determine plausible three-dimensional models for Cu(2+)-Aβ(1-16) with three histidines in their coordination sphere. We considered both ε and δ coordination of histidines 6, 13, and 14 as well as the coordination of different possible candidates containing oxygen as fourth ligand (Asp1, Glu3, Asp7, Glu11, and CO(Ala2)). Among the 32 models that enclose COO(-), the lowest energy structures correspond to [O(E3),N(δ)(H6),N(ε)(H13),N(ε)(H14)] (1), [O(E3),N(δ)(H6),N(δ)(H13),N(δ)(H14)] (2), and [O(D7),N(ε)(H6),N(δ)(H13),N(δ)(H14)] (3). The most stable model containing CO(Ala2) as fourth ligand in the Cu(2+) coordination sphere is [O(c)(A2),N(ε)(H6),N(δ)(H13),N(ε)(H14)] (4). An estimation of the relative stability between Glu3 (1) and CO(Ala2) (4) coordinated complexes seems to indicate that the preference for the latter coordination may be due to solvent effects. The present results also show the relationship between the peptidic and metallic moieties in defining the overall geometry of the complex and illustrate that the final stability of the complexes results from a balance between the metal coordination site and amyloid folding upon complexation.
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Affiliation(s)
- Jorge Alí-Torres
- Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
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Parthasarathy S, Long F, Miller Y, Xiao Y, McElheny D, Thurber K, Ma B, Nussinov R, Ishii Y. Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy. J Am Chem Soc 2011; 133:3390-400. [PMID: 21341665 PMCID: PMC3074258 DOI: 10.1021/ja1072178] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cu(2+) binding to Alzheimer's β (Aβ) peptides in amyloid fibrils has attracted broad attention, as it was shown that Cu ion concentration elevates in Alzheimer's senile plaque and such association of Aβ with Cu(2+) triggers the production of neurotoxic reactive oxygen species (ROS) such as H(2)O(2). However, detailed binding sites and binding structures of Cu(2+) to Aβ are still largely unknown for Aβ fibrils or other aggregates of Aβ. In this work, we examined molecular details of Cu(2+) binding to amyloid fibrils by detecting paramagnetic signal quenching in 1D and 2D high-resolution (13)C solid-state NMR (SSNMR) for full-length 40-residue Aβ(1-40). Selective quenching observed in (13)C SSNMR of Cu(2+)-bound Aβ(1-40) suggested that primary Cu(2+) binding sites in Aβ(1-40) fibrils include N(ε) in His-13 and His-14 and carboxyl groups in Val-40 as well as in Glu sidechains (Glu-3, Glu-11, and/or Glu-22). (13)C chemical shift analysis demonstrated no major structural changes upon Cu(2+) binding in the hydrophobic core regions (residues 18-25 and 30-36). Although the ROS production via oxidization of Met-35 in the presence of Cu(2+) has been long suspected, our SSNMR analysis of (13)C(ε)H(3)-S- in M35 showed little changes after Cu(2+) binding, excluding the possibility of Met-35 oxidization by Cu(2+) alone. Preliminary molecular dynamics (MD) simulations on Cu(2+)-Aβ complex in amyloid fibrils confirmed binding sites suggested by the SSNMR results and the stabilities of such bindings. The MD simulations also indicate the coexistence of a variety of Cu(2+)-binding modes unique in Aβ fibril, which are realized by both intra- and intermolecular contacts and highly concentrated coordination sites due to the in-register parallel β-sheet arrangements.
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Affiliation(s)
| | - Fei Long
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Yifat Miller
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
| | - Yiling Xiao
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Kent Thurber
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda MD 20892
| | - Buyong Ma
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
- Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
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Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev 2010; 110:4820-38. [PMID: 20402519 PMCID: PMC2920034 DOI: 10.1021/cr900377t] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Indexed: 01/13/2023]
Affiliation(s)
| | | | - Ruth Nussinov
- To whom correspondence should be addressed. Tel.: (301) 846-5579. Fax: (301) 846-5598. E-mail:
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Lin CJ, Huang HC, Jiang ZF. Cu(II) interaction with amyloid-beta peptide: a review of neuroactive mechanisms in AD brains. Brain Res Bull 2010; 82:235-42. [PMID: 20598459 DOI: 10.1016/j.brainresbull.2010.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 05/27/2010] [Accepted: 06/07/2010] [Indexed: 12/28/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by the dys-homeostasis of biometal metabolism, the extracellular accumulation of neurotoxic amyloid-beta (Abeta) peptide, the intracellular accumulation of hyperphosphorylated tau and the loss of synapses. Copper plays a key role in AD development. The Abeta peptide and amyloid precursor protein (APP), the parental molecule of Abeta, are modulated by copper in the brain. Increased copper concentration has been found in the AD brain that implies that copper may participate in the pathophysiology of AD. Copper can bind to APP and Abeta, then affects the structure and toxic of APP and Abeta. Some researchers have reported that copper could affect the formation of beta-sheet structure that is widely accepted as toxic secondary structure of Abeta. This review explores the role of copper on the conformation and aggregation of Abeta, and the copper-induced neuroactive mechanisms. Copper may be involved in the following pathways to affect the neuroactivation of Abeta: (1) change of the secondary structure of Abeta; (2) induction of oxidative stress in AD brains, and (3) regulation of cellular signal pathway. Thus, correcting brain copper imbalance may represent a relevant therapeutic target for Alzheimer's disease.
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Affiliation(s)
- Chang-Jun Lin
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing, China
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On the metal ion (Zn2+, Cu2+) coordination with beta-amyloid peptide: DFT computational study. Interdiscip Sci 2010; 2:57-69. [DOI: 10.1007/s12539-010-0086-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 11/10/2009] [Accepted: 11/11/2009] [Indexed: 01/02/2023]
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Shearer J, Szalai VA. The amyloid-beta peptide of Alzheimer's disease binds Cu(I) in a linear bis-his coordination environment: insight into a possible neuroprotective mechanism for the amyloid-beta peptide. J Am Chem Soc 2008; 130:17826-35. [PMID: 19035781 PMCID: PMC2935688 DOI: 10.1021/ja805940m] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oxidative stress has been suggested to contribute to neuronal apoptosis associated with Alzheimer's disease (AD). Copper may participate in oxidative stress through redox-cycling between its +2 and +1 oxidation states to generate reactive oxygen species (ROS). In vitro, copper binds to the amyloid-beta peptide of AD, and in vivo, copper is associated with amyloid plaques characteristic of AD. As a result, the AbetaCu(I) complex may be a critical reactant involved in ROS associated with AD etiology. To characterize the AbetaCu(I) complex, we have pursued X-ray absorption (XAS) and electron paramagnetic resonance (EPR) spectroscopy of AbetaCu(II) and AbetaCu(I) (produced by ascorbate reduction of AbetaCu(II)). The AbetaCu(II) complex Cu K-edge XAS spectrum is indicative of a square-planar Cu(II) center with mixed N/O ligation. Multiple scattering analysis of the extended X-ray absorption fine structure (EXAFS) data for AbetaCu(II) indicates that two of the ligands are imidazole groups of histidine ligands, indicating a (N(Im))(2)(N/O)(2) Cu(II) ligation sphere for AbetaCu(II). After reduction of the AbetaCu(II) complex with ascorbate, the edge region decreases in energy by approximately 4 eV. The X-ray absorption near-edge spectrum region of AbetaCu(I) displays an intense pre-edge feature at 8984.1(2) eV. EXAFS data fitting yielded a two-coordinate geometry, with two imidazole ligands coordinated to Cu(I) at 1.877(2) A in a linear geometry. Ascorbate reduction of AbetaCu(II) under inert atmosphere and subsequent air oxidation of AbetaCu(I) to regenerate AbetaCu(II) was monitored by low-temperature EPR spectroscopy. Slow reappearance of the AbetaCu(II) EPR signal indicates that O(2) oxidation of the AbetaCu(I) complex is kinetically sluggish and Abeta damage is occurring following reoxidation of AbetaCu(I) by O(2). Together, these results lead us to hypothesize that Cu(I) is ligated by His13 and His14 in a linear coordination environment in Alphabeta, that Abeta may be playing a neuroprotective role, and that metal-mediated oxidative damage of Abeta occurs over multiple redox cycles.
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Affiliation(s)
- Jason Shearer
- Department of Chemistry/216, University of Nevada-Reno, 1664 N. Virginia St, Reno, NV 89557
| | - Veronika A. Szalai
- Department of Chemistry & Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
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