101
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Majumder L, Chatterjee M, Bera K, Maiti NC, Banerji B. Solvent-Assisted Tyrosine-Based Dipeptide Forms Low-Molecular Weight Gel: Preparation and Its Potential Use in Dye Removal and Oil Spillage Separation from Water. ACS OMEGA 2019; 4:14411-14419. [PMID: 31528794 PMCID: PMC6739715 DOI: 10.1021/acsomega.9b01301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/27/2019] [Indexed: 06/10/2023]
Abstract
Low-molecular weight gelators (supramolecular, or simply molecular gels) are highly important molecular frameworks because of their potential application in drug delivery, catalysis, pollutant removal, sensing materials, and so forth. Herein, a small dipeptide composed of N-(tert-butoxycarbonyl)pentafluoro-l-phenylalanine and O-benzyl-l-tyrosine methyl ester was synthesized, and its gelation ability was investigated in different solvent systems. It was found that the dipeptide was unable to form gel with a single solvent, but a mixture of solvent systems was found to be suitable for the gelation of this dipeptide. Interestingly, water was found to be essential for gelation with the polar protic solvent, and long-chain hydrocarbon units such as, petroleum ether, kerosene, and diesel, were important for gelation with aromatic solvents. The structural insights of these gels were characterized by field-emission scanning electronic microscopy, atomic force microscopy, Fourier transform infrared analysis, and X-ray diffraction studies, and their mechanical strengths were characterized by rheological experiments. Both of the gels obtained from these two solvent systems were thermoreversible in nature, and these translucent gels had potential application for the treatment of waste water. The gel obtained from dipeptides with methanol-water was used to remove toxic dyes (crystal violet, Eriochrome Black T, and rhodamine B) from water. Furthermore, the gel obtained from dipeptide with assistance from toluene-petroleum ether was used as a phase-selective gelator for oil-spill recovery.
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Affiliation(s)
- Leena Majumder
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
| | - Moumita Chatterjee
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
| | - Kaushik Bera
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
| | - Nakul Chandra Maiti
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
| | - Biswadip Banerji
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
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102
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Zottig X, Al-Halifa S, Babych M, Quittot N, Archambault D, Bourgault S. Guiding the Morphology of Amyloid Assemblies by Electrostatic Capping: from Polymorphic Twisted Fibrils to Uniform Nanorods. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901806. [PMID: 31268238 DOI: 10.1002/smll.201901806] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Peptides that self-assemble into cross-β-sheet amyloid structures constitute promising building blocks to construct highly ordered proteinaceous materials and nanoparticles. Nevertheless, the intrinsic polymorphism of amyloids and the difficulty of controlling self-assembly currently limit their usage. In this study, the effect of electrostatic interactions on the supramolecular organization of peptide assemblies is investigated to gain insights into the structural basis of the morphological diversities of amyloids. Different charged capping units are introduced at the N-terminus of a potent β-sheet-forming sequence derived from the 20-29 segment of islet amyloid polypeptide, known to self-assemble into polymorphic fibrils. By tuning the charge and the electrostatic strength, different mesoscopic morphologies are obtained, including nanorods, rope-like fibrils, and twisted ribbons. Particularly, the addition of positive capping units leads to the formation of uniform rod-like assemblies, with lengths that can be modulated by the charge number. It is proposed that electrostatic repulsions between N-terminal positive charges hinder β-sheet tape twisting, leading to a unique control over the size of these cytocompatible nanorods by protofilament growth frustration. This study reveals the high susceptibility of amyloid formation to subtle chemical modifications and opens to promising strategies to control the final architecture of proteinaceous assemblies from the peptide sequence.
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Affiliation(s)
- Ximena Zottig
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
| | - Soultan Al-Halifa
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
| | - Margaryta Babych
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
| | - Noé Quittot
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
| | - Denis Archambault
- Department of Biological Sciences, Université du Québec à Montréal, Montreal, Québec, H2X 1Y4, Canada
- Swine and Poultry Infectious Diseases Research Center, CRIPA, Québec, J2S 2M2, Canada
| | - Steve Bourgault
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
- Swine and Poultry Infectious Diseases Research Center, CRIPA, Québec, J2S 2M2, Canada
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103
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Datta D, Kumar V, Kumar S, Nagaraj R, Chaudhary N. Limpid hydrogels from β-turn motif-connected tandem repeats of Aβ 16-22. SOFT MATTER 2019; 15:4827-4835. [PMID: 31180412 DOI: 10.1039/c9sm00343f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Self-assembling peptides constitute an important class of functional biomaterials. A number of short amyloidogenic stretches have been identified from amyloid proteins. Such peptides, as such or through subtle modifications, can turn out to be promising candidates for functional biomaterials. End-capped Aβ16-22, the well-studied amyloidogenic stretch from β-amyloid, is reported to be non-hydrogelating up to 20 mM concentration. Here we investigated the hydrogelation propensity of Aβ16-22 repeats connected through β-turn-supporting motifs. The peptide repeats connected through Asn-Gly, Aib-DPro, and DPro-Gly formed transparent hydrogels at concentrations ≥2 mM. The repeats of the aromatic analog Aβ16-22(F20Y) also resulted in similar hydrogels. Like other peptide-based gels reported earlier, these gels could trap the anticancer drug doxorubicin and displayed steady release in water. In addition, the gels supported the growth of mammalian cell lines, HEK-293 and RIN-5F. These data show that turn-inducing motifs can have marked effects on the hydrogelating propensity of self-assembling peptides.
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Affiliation(s)
- Debika Datta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India.
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104
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Zheng B, Zhou K, Zhang T, Lv C, Zhao G. Designed Two- and Three-Dimensional Protein Nanocage Networks Driven by Hydrophobic Interactions Contributed by Amyloidogenic Motifs. NANO LETTERS 2019; 19:4023-4028. [PMID: 31099248 DOI: 10.1021/acs.nanolett.9b01365] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Precise manipulation of protein self-assembly by noncovalent interactions into programmed networks to mimic naturally occurring nanoarchitectures in living organisms is a challenge due to its structural heterogeneity, flexibility, and complexity. Herein, by taking advantage of both the hydrophobic forces contributed by the "GLMVG" motif, a kind of amyloidogenic motif (AM), and the high symmetry of protein nanocages, we have built an effective protein self-assembly strategy for the construction of two-dimensional (2D) or three-dimensional (3D) protein nanocage arrays. According to this strategy, "GLMVG" AMs from β-amyloid 42 were grafted onto the outer surface of a 24-mer ferritin nanocage close to its C4 symmetry channels, initially resulting in the production of subgrade 2D nanocage arrays and ultimately generating 3D highly ordered arrays with a simple cubic packing pattern as the reaction time increases. More importantly, the reversibility and the formation rate of these protein arrays can be modulated by pH. This work provides a de novo design strategy for accurate control over 2D or 3D protein self-assemblies.
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Affiliation(s)
- Bowen Zheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources , Beijing 100083 , China
| | - Kai Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources , Beijing 100083 , China
| | - Tuo Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources , Beijing 100083 , China
| | - Chenyan Lv
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources , Beijing 100083 , China
| | - Guanghua Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources , Beijing 100083 , China
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105
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Bunce SJ, Wang Y, Stewart KL, Ashcroft AE, Radford SE, Hall CK, Wilson AJ. Molecular insights into the surface-catalyzed secondary nucleation of amyloid-β 40 (Aβ 40) by the peptide fragment Aβ 16-22. SCIENCE ADVANCES 2019; 5:eaav8216. [PMID: 31245536 PMCID: PMC6588359 DOI: 10.1126/sciadv.aav8216] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/15/2019] [Indexed: 05/15/2023]
Abstract
Understanding the structural mechanism by which proteins and peptides aggregate is crucial, given the role of fibrillar aggregates in debilitating amyloid diseases and bioinspired materials. Yet, this is a major challenge as the assembly involves multiple heterogeneous and transient intermediates. Here, we analyze the co-aggregation of Aβ40 and Aβ16-22, two widely studied peptide fragments of Aβ42 implicated in Alzheimer's disease. We demonstrate that Aβ16-22 increases the aggregation rate of Aβ40 through a surface-catalyzed secondary nucleation mechanism. Discontinuous molecular dynamics simulations allowed aggregation to be tracked from the initial random coil monomer to the catalysis of nucleation on the fibril surface. Together, the results provide insight into how dynamic interactions between Aβ40 monomers/oligomers on the surface of preformed Aβ16-22 fibrils nucleate Aβ40 amyloid assembly. This new understanding may facilitate development of surfaces designed to enhance or suppress secondary nucleation and hence to control the rates and products of fibril assembly.
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Affiliation(s)
- Samuel J. Bunce
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Katie L. Stewart
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
- Corresponding author. (S.E.R.); (C.K.H.); (A.J.W.)
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
- Corresponding author. (S.E.R.); (C.K.H.); (A.J.W.)
| | - Andrew J. Wilson
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Corresponding author. (S.E.R.); (C.K.H.); (A.J.W.)
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106
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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: 14] [Impact Index Per Article: 2.8] [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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107
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Urban JM, Ho J, Piester G, Fu R, Nilsson BL. Rippled β-Sheet Formation by an Amyloid-β Fragment Indicates Expanded Scope of Sequence Space for Enantiomeric β-Sheet Peptide Coassembly. Molecules 2019; 24:E1983. [PMID: 31126069 PMCID: PMC6571685 DOI: 10.3390/molecules24101983] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/10/2019] [Accepted: 05/22/2019] [Indexed: 11/30/2022] Open
Abstract
In 1953, Pauling and Corey predicted that enantiomeric β-sheet peptides would coassemble into so-called "rippled" β-sheets, in which the β-sheets would consist of alternating l- and d-peptides. To date, this phenomenon has been investigated primarily with amphipathic peptide sequences composed of alternating hydrophilic and hydrophobic amino acid residues. Here, we show that enantiomers of a fragment of the amyloid-β (Aβ) peptide that does not follow this sequence pattern, amyloid-β (16-22), readily coassembles into rippled β-sheets. Equimolar mixtures of enantiomeric amyloid-β (16-22) peptides assemble into supramolecular structures that exhibit distinct morphologies from those observed by self-assembly of the single enantiomer pleated β-sheet fibrils. Formation of rippled β-sheets composed of alternating l- and d-amyloid-β (16-22) is confirmed by isotope-edited infrared spectroscopy and solid-state NMR spectroscopy. Sedimentation analysis reveals that rippled β-sheet formation by l- and d-amyloid-β (16-22) is energetically favorable relative to self-assembly into corresponding pleated β-sheets. This work illustrates that coassembly of enantiomeric β-sheet peptides into rippled β-sheets is not limited to peptides with alternating hydrophobic/hydrophilic sequence patterns, but that a broader range of sequence space is available for the design and preparation of rippled β-sheet materials.
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Affiliation(s)
- Jennifer M Urban
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
| | - Janson Ho
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
| | - Gavin Piester
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
| | - Riqiang Fu
- The National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA.
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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108
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Chiricotto M, Melchionna S, Derreumaux P, Sterpone F. Multiscale Aggregation of the Amyloid Aβ 16-22 Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils. J Phys Chem Lett 2019; 10:1594-1599. [PMID: 30892042 DOI: 10.1021/acs.jpclett.9b00423] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work we investigate the multiscale dynamics of the aggregation process of an amyloid peptide, Aβ16-22. By performing massive coarse-grained simulations at the quasi-atomistic resolution and including hydrodynamic effects, we followed the formation and growth of a large elongated aggregate and its slow structuring. The elongation proceeds via a two-step nucleation mechanism with disordered aggregates formed initially and subsequently fusing to elongate the amorphous prefibril. A variety of coagulation events coexist, including lateral growth. The latter mechanism, sustained by long-range hydrodynamics correlations, actually can create a large branched structure spanning a few tens of nanometers. Our findings confirm the experimental hypothesis of a critical contribution of lateral growth to the amyloid aggregation kinetics and the capability of our model to sample critical structures like prefibril hosting annular pores.
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Affiliation(s)
- Mara Chiricotto
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080 , Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Simone Melchionna
- ISC-CNR, Dipartimento di Fisica , Universita Sapienza , P.le A. Moro 5 , 00185 Rome , Italy
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080 , Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080 , Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie , 75005 Paris , France
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109
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Paul S, Paul S. Inhibitory Effect of Choline-O-sulfate on Aβ16–22 Peptide Aggregation: A Molecular Dynamics Simulation Study. J Phys Chem B 2019; 123:3475-3489. [DOI: 10.1021/acs.jpcb.9b02727] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India 781039
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110
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Man VH, He X, Derreumaux P, Ji B, Xie XQ, Nguyen PH, Wang J. Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ 16-22 Dimer. J Chem Theory Comput 2019; 15:1440-1452. [PMID: 30633867 PMCID: PMC6745714 DOI: 10.1021/acs.jctc.8b01107] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We investigated the effects of 17 widely used atomistic molecular mechanics force fields (MMFFs) on the structures and kinetics of amyloid peptide assembly. To this end, we performed large-scale all-atom molecular dynamics simulations in explicit water on the dimer of the seven-residue fragment of the Alzheimer's amyloid-β peptide, Aβ16-22, for a total time of 0.34 ms. We compared the effects of these MMFFs by analyzing various global reaction coordinates, secondary structure contents, the fibril population, the in-register and out-of-register architectures, and the fibril formation time at 310 K. While the AMBER94, AMBER99, and AMBER12SB force fields do not predict any β-sheets, the seven force fields, AMBER96, GROMOS45a3, GROMOS53a5, GROMOS53a6, GROMOS43a1, GROMOS43a2, and GROMOS54a7, form β-sheets rapidly. In contrast, the following five force fields, AMBER99-ILDN, AMBER14SB, CHARMM22*, CHARMM36, and CHARMM36m, are the best candidates for studying amyloid peptide assembly, as they provide good balances in terms of structures and kinetics. We also investigated the assembly mechanisms of dimeric Aβ16-22 and found that the fibril formation rate is predominantly controlled by the total β-strand content.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xibing He
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Beihong Ji
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Corresponding Author:
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111
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Abstract
The aggregation of monomeric amyloid β protein (Aβ) peptide into oligomers and amyloid fibrils in the mammalian brain is associated with Alzheimer's disease. Insight into the thermodynamic stability of the Aβ peptide in different polymeric states is fundamental to defining and predicting the aggregation process. Experimental determination of Aβ thermodynamic behavior is challenging due to the transient nature of Aβ oligomers and the low peptide solubility. Furthermore, quantitative calculation of a thermodynamic phase diagram for a specific peptide requires extremely long computational times. Here, using a coarse-grained protein model, molecular dynamics (MD) simulations are performed to determine an equilibrium concentration and temperature phase diagram for the amyloidogenic peptide fragment Aβ16-22 Our results reveal that the only thermodynamically stable phases are the solution phase and the macroscopic fibrillar phase, and that there also exists a hierarchy of metastable phases. The boundary line between the solution phase and fibril phase is found by calculating the temperature-dependent solubility of a macroscopic Aβ16-22 fibril consisting of an infinite number of β-sheet layers. This in silico determination of an equilibrium (solubility) phase diagram for a real amyloid-forming peptide, Aβ16-22, over the temperature range of 277-330 K agrees well with fibrillation experiments and transmission electron microscopy (TEM) measurements of the fibril morphologies formed. This in silico approach of predicting peptide solubility is also potentially useful for optimizing biopharmaceutical production and manufacturing nanofiber scaffolds for tissue engineering.
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112
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Nishikawa N, Sakae Y, Gouda T, Tsujimura Y, Okamoto Y. Structural Analysis of a Trimer of β 2-Microgloblin Fragment by Molecular Dynamics Simulations. Biophys J 2019; 116:781-790. [PMID: 30771855 DOI: 10.1016/j.bpj.2018.11.3143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 06/08/2018] [Accepted: 11/06/2018] [Indexed: 01/22/2023] Open
Abstract
A peptide β2-m21-31, which is a fragment from residue 21 to residue 31 of β2-microgloblin, is experimentally known to self-assemble and form amyloid fibrils. In order to understand the mechanism of amyloid fibril formations, we applied the replica-exchange molecular dynamics method to the system consisting of three fragments of β2-m21-31. From the analyses on the temperature dependence, we found that there is a clear phase transition temperature in which the peptides aggregate with each other. Moreover, we found by the free energy analyses that there are two major stable states: One of them is like amyloid fibrils and the other is amorphous aggregates.
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Affiliation(s)
- Naohiro Nishikawa
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
| | - Yoshitake Sakae
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Takuya Gouda
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yuichiro Tsujimura
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan; Information Technology Center, Nagoya University, Nagoya, Aichi, Japan; JST-CREST, Nagoya, Aichi, Japan.
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113
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Li X, Lei J, Qi R, Xie L, Wei G. Mechanistic insight into E22Q-mutation-induced antiparallel-to-parallel β-sheet transition of Aβ16−22fibrils: an all-atom simulation study. Phys Chem Chem Phys 2019; 21:15686-15694. [DOI: 10.1039/c9cp02561h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
E22Q mutation of Aβ16−22fibrils facilitates parallel β-sheet formation by enhancing Q22–Q22 hydrogen-bonding interaction and A21–A21, F20–F20, F19–F19 and V18–V18 hydrophobic interaction.
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Affiliation(s)
- Xuhua Li
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Jiangtao Lei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Ruxi Qi
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Luogang Xie
- College of Physics and Electronic Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 453002
- People's Republic of China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
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114
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Sahoo A, Xu H, Matysiak S. Pathways of amyloid-beta absorption and aggregation in a membranous environment. Phys Chem Chem Phys 2019; 21:8559-8568. [PMID: 30964132 DOI: 10.1039/c9cp00040b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aggregation of misfolded oligomeric amyloid-beta (Aβ) peptides on lipid membranes has been identified as a primary event in Alzheimer's pathogenesis. However, the structural and dynamical features of this membrane assisted Aβ aggregation have not been well characterized. The microscopic characterization of dynamic molecular-level interactions in peptide aggregation pathways has been challenging both computationally and experimentally. In this work, we explore differential patterns of membrane-induced Aβ 16-22 (K-L-V-F-F-A-E) aggregation from the microscopic perspective of molecular interactions. Physics-based coarse-grained molecular dynamics (CG-MD) simulations were employed to investigate the effect of lipid headgroup charge - zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: POPC) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine: POPS) - on Aβ 16-22 peptide aggregation. Our analyses present an extensive overview of multiple pathways for peptide absorption and biomechanical forces governing peptide folding and aggregation. In agreement with experimental observations, anionic POPS molecules promote extended configurations in Aβ peptides that contribute towards faster emergence of ordered β-sheet-rich peptide assemblies compared to POPC, suggesting faster fibrillation. In addition, lower cumulative rates of peptide aggregation in POPS due to higher peptide-lipid interactions and slower lipid diffusion result in multiple distinct ordered peptide aggregates that can serve as nucleation seeds for subsequent Aβ aggregation. This study provides an in-silico assessment of experimentally observed aggregation patterns, presents new morphological insights and highlights the importance of lipid headgroup chemistry in modulating the peptide absorption and aggregation process.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.
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115
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Morphological Transformation of Peptide Nanoassemblies through Conformational Transition of Core-forming Peptides. Polymers (Basel) 2018; 11:polym11010039. [PMID: 30960023 PMCID: PMC6401806 DOI: 10.3390/polym11010039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 12/25/2022] Open
Abstract
Morphological control of nanostructures that are composed of amphiphilic di- or tri-block molecules by external stimuli broadens their applications for molecular containers, nanoreactors, and controlled release materials. In this study, triblock amphiphiles comprising oligo(ethylene glycol), oligo(l-lysine), and tetra(l-phenylalanine) were prepared for the construction of nanostructures that can transform accompanying α-to-β transition of core-forming peptides. Circular dichroic (CD) measurements showed that the triblock amphiphiles adopted different secondary structures depending on the solvent environment: they adopt β-sheet structures in aqueous solution, while α-helix structures in 25% 2,2,2-trifluoroethanol (TFE) solution under basic pH conditions. Transmission electron microscopic (TEM) observation revealed that the triblock amphiphiles formed vesicle structures in 25% TFE aq. Solvent exchange from 25% TFE to water induced morphological transformation from vesicles to arc-shaped nanostructures accompanying α-β conformational transition. The transformable nanostructures may be useful as novel smart nanomaterials for molecular containers and micro reactors.
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116
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RETRACTED: Peptide-induced formation of protein aggregates and amyloid fibrils in human and guinea pig αA-crystallins under physiological conditions of temperature and pH. Exp Eye Res 2018; 179:193-205. [PMID: 30448341 DOI: 10.1016/j.exer.2018.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/17/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the request of the authors. The senior author contacted the journal in a forthright manner, in an effort to preserve the scientific integrity of the literature, after discovering a significant error in the results reported in the article. The authors were recently made aware of a paper by Kim et al. (Nature Commun. 2019) which shows a spirosome structure (the enzyme aldehyde-alcohol dehydrogenase) present in E. coli (Fig. 5a) that is very similar to the structure the authors thought formed when synthetic alpha A crystallin (66-80) peptide was incubated for 24 h with recombinant guinea pig alpha A insert crystallin (see Kumarasamy et al., Figs. 7C and F, and Fig. 9). Subsequent to publication of their report, the authors later found a number of images that showed what appeared to be the same structure present in samples of their presumably purified recombinant guinea pig alpha A insert crystallin which had been incubated without peptide for 24 h. Hence, the authors now conclude that the structures shown in Figs. 7C and F, and Fig. 9 of their article published in this journal are actually due to E. coli contaminant aldehyde-alcohol dehydrogenase. The authors deeply regret this error and any inconvenience it may have caused.
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117
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Carballo-Pacheco M, Ismail AE, Strodel B. On the Applicability of Force Fields To Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6063-6075. [PMID: 30336669 DOI: 10.1021/acs.jctc.8b00579] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations play an essential role in understanding biomolecular processes such as protein aggregation at temporal and spatial resolutions which are not attainable by experimental methods. For a correct modeling of protein aggregation, force fields must accurately represent molecular interactions. Here, we study the effect of five different force fields on the oligomer formation of Alzheimer's Aβ16-22 peptide and two of its mutants: Aβ16-22(F19V,F20V), which does not form fibrils, and Aβ16-22(F19L) which forms fibrils faster than the wild type. We observe that while oligomer formation kinetics depends strongly on the force field, structural properties, such as the most relevant protein-protein contacts, are similar between them. The oligomer formation kinetics obtained with different force fields differ more from each other than the kinetics between aggregating and nonaggregating peptides simulated with a single force field. We discuss the difficulties in comparing atomistic simulations of amyloid oligomer formation with experimental observables.
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Affiliation(s)
- Martín Carballo-Pacheco
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Ahmed E Ismail
- AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany.,Aachener Verfahrenstechnik, Faculty of Mechanical Engineering , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , 40225 Düsseldorf , Germany
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118
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Xu J, Wang K, Yuan Y, Li H, Zhang R, Guan S, Wang L. A Novel Peroxidase Mimics and Ameliorates Alzheimer's Disease-Related Pathology and Cognitive Decline in Mice. Int J Mol Sci 2018; 19:ijms19113304. [PMID: 30352982 PMCID: PMC6274722 DOI: 10.3390/ijms19113304] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 10/14/2018] [Accepted: 10/19/2018] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder in the elderly, which is characterized by the accumulation of amyloid β (Aβ) plaques, oxidative stress, and neuronal loss. Therefore, clearing Aβ aggregates and reducing oxidative stress could be an effective therapeutic strategy for AD. Deuterohemin-AlaHisThrValGluLys (DhHP-6), a novel deuterohemin-containing peptide mimetic of the natural microperoxidase-11 (MP-11), shows higher antioxidant activity and stability compared to the natural microperoxidases. DhHP-6 possesses the ability of extending lifespan and alleviating paralysis in the Aβ1-42 transgenic Caenorhabditis elegans CL4176 model of AD, as shown in our previous study. Therefore, this study was aimed at exploring the neuroprotective effect of DhHP-6 in the APPswe/PSEN1dE9 transgenic mouse model of AD. DhHP-6 reduced the diameter and fiber structure of Aβ1-42 aggregation in vitro, as shown by dynamic light scattering and transmission electron microscope. DhHP-6 exerted its neuroprotective effect by inhibiting Aβ aggregation and plaque formation, and by reducing Aβ1-42 oligomers-induced neurotoxicity on HT22 (mouse hippocampal neuronal) and SH-SY5Y (human neuroblastoma) cells. In the AD mouse model, DhHP-6 significantly ameliorated cognitive decline and improved spatial learning ability in behavioral tests including the Morris water maze, Y-maze, novel object recognition, open field, and nest-building test. Moreover, DhHP-6 reduced the deposition of Aβ plaques in the cerebral cortex and hippocampus. More importantly, DhHP-6 restored the morphology of astrocytes and microglia, and significantly reduced the levels of pro-inflammatory cytokines. Our findings provide a basis for considering the non-toxic, peroxidase mimetic DhHP-6 as a new candidate drug against AD.
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Affiliation(s)
- Jia Xu
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Kai Wang
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Ye Yuan
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Hui Li
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Ruining Zhang
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Shuwen Guan
- School of Life Sciences, Jilin University, Changchun 130012, China.
- Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun 130012, China.
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin Universtiy, Changchun 130012, China.
| | - Liping Wang
- School of Life Sciences, Jilin University, Changchun 130012, China.
- Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun 130012, China.
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin Universtiy, Changchun 130012, China.
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119
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Datta D, Harikrishna A, Nagaraj R, Chaudhary N. Self-assembly of β-turn motif-connected tandem repeats of Aβ16-22
and its aromatic analogs. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Debika Datta
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Guwahati India
| | | | | | - Nitin Chaudhary
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Guwahati India
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120
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Sankar K, Krystek SR, Carl SM, Day T, Maier JKX. AggScore: Prediction of aggregation-prone regions in proteins based on the distribution of surface patches. Proteins 2018; 86:1147-1156. [PMID: 30168197 DOI: 10.1002/prot.25594] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/12/2018] [Accepted: 08/24/2018] [Indexed: 02/02/2023]
Abstract
Protein aggregation is a phenomenon that has attracted considerable attention within the pharmaceutical industry from both a developability standpoint (to ensure stability of protein formulations) and from a research perspective for neurodegenerative diseases. Experimental identification of aggregation behavior in proteins can be expensive; and hence, the development of accurate computational approaches is crucial. The existing methods for predicting protein aggregation rely mostly on the primary sequence and are typically trained on amyloid-like proteins. However, the training bias toward beta amyloid peptides may worsen prediction accuracy of such models when applied to larger protein systems. Here, we present a novel algorithm to identify aggregation-prone regions in proteins termed "AggScore" that is based entirely on three-dimensional structure input. The method uses the distribution of hydrophobic and electrostatic patches on the surface of the protein, factoring in the intensity and relative orientation of the respective surface patches into an aggregation propensity function that has been trained on a benchmark set of 31 adnectin proteins. AggScore can accurately identify aggregation-prone regions in several well-studied proteins and also reliably predict changes in aggregation behavior upon residue mutation. The method is agnostic to an amyloid-specific aggregation context and thus may be applied to globular proteins, small peptides and antibodies.
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Affiliation(s)
| | - Stanley R Krystek
- Molecular Discovery Technologies, Bristol-Myers Squibb, Princeton, New Jersey
| | - Stephen M Carl
- Discovery Pharmaceutics and Analytical Sciences and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey
| | - Tyler Day
- Schrödinger Inc., New York, New York
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121
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Etersalate prevents the formations of 6Aβ16-22 oligomer: An in silico study. PLoS One 2018; 13:e0204026. [PMID: 30226897 PMCID: PMC6143259 DOI: 10.1371/journal.pone.0204026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/01/2018] [Indexed: 11/19/2022] Open
Abstract
Oligomerization of amyloid beta (Aβ) peptides has been considered as the crucially causative agent in the development of Alzheimer's disease. Etersalate, a nonsteroidal anti-inflammatory oral drug (United State Food and Drug Administration—Unique Ingredient Identifier: 653GN04T2G) was previously suggested to bind well to proto-fibrils of Aβ peptides in silico. Here, the effect of etersalate on the oligomerization of soluble Aβ16–22 hexamer (6Aβ16–22) were extensively investigated using temperature replica exchange molecular dynamics (REMD) simulations over ~16.8 μs in total for 48 replicas (350 ns per replica). The results reveal that etersalate can enter the inner space or bind on the surface of 6Aβ16–22 conformations, which destabilizes the hexamer. Etersalate was predicted to able to cross the blood brain barrier using prediction of absorption, distribution, metabolism, and excretion—toxicity (preADMET) tools. Overall, although the investigation was performed with the low concentration of trial inhibitor, the obtained results indicate that etersalate is a potential drug candidate for AD through inhibiting formation of Aβ oligomers with the average binding free energy of -11.7 kcal/mol.
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122
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Martial B, Lefèvre T, Auger M. Understanding amyloid fibril formation using protein fragments: structural investigations via vibrational spectroscopy and solid-state NMR. Biophys Rev 2018; 10:1133-1149. [PMID: 29855812 PMCID: PMC6082320 DOI: 10.1007/s12551-018-0427-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022] Open
Abstract
It is well established that amyloid proteins play a primary role in neurodegenerative diseases. Alzheimer's, Parkinson's, type II diabetes, and Creutzfeldt-Jakob's diseases are part of a wider family encompassing more than 50 human pathologies related to aggregation of proteins. Although this field of research is thoroughly investigated, several aspects of fibrillization remain misunderstood, which in turn slows down, or even impedes, advances in treating and curing amyloidoses. To solve this problem, several research groups have chosen to focus on short fragments of amyloid proteins, sequences that have been found to be of great importance for the amyloid formation process. Studying short peptides allows bypassing the complexity of working with full-length proteins and may provide important information relative to critical segments of amyloid proteins. To this end, efficient biophysical tools are required. In this review, we focus on two essential types of spectroscopic techniques, i.e., vibrational spectroscopy and its derivatives (conventional Raman scattering, deep-UV resonance Raman (DUVRR), Raman optical activity (ROA), surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), infrared (IR) absorption spectroscopy, vibrational circular dichroism (VCD)) and solid-state nuclear magnetic resonance (ssNMR). These techniques revealed powerful to provide a better atomic and molecular comprehension of the amyloidogenic process and fibril structure. This review aims at underlining the information that these techniques can provide and at highlighting their strengths and weaknesses when studying amyloid fragments. Meaningful examples from the literature are provided for each technique, and their complementarity is stressed for the kinetic and structural characterization of amyloid fibril formation.
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Affiliation(s)
- Benjamin Martial
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Thierry Lefèvre
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada.
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123
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Nieuwendaal RC, DeLongchamp DM, Richter LJ, Snyder CR, Jones RL, Engmann S, Herzing A, Heeney M, Fei Z, Sieval AB, Hummelen JC. Characterization of Interfacial Structure in Polymer-Fullerene Bulk Heterojunctions via ^{13}C {^{2}H} Rotational Echo Double Resonance NMR. PHYSICAL REVIEW LETTERS 2018; 121:026101. [PMID: 30085721 PMCID: PMC6207377 DOI: 10.1103/physrevlett.121.026101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 06/08/2023]
Abstract
We introduce a new application of solid state NMR measurements towards characterizing the donor-acceptor interfaces within bulk heterojunction (BHJ) films. Rotational echo double resonance (REDOR) is used to measure dipolar couplings between ^{13}C nuclei on the acceptor phenyl-C_{61}-butyric acid methyl ester (PCBM) fullerene cage, which is ≈18% isotopically enriched with ^{13}C, and beta hydrogens on the donor poly(3-hexyl thiophene) (P3HT) main chain, which are >95% isotopically enriched with ^{2}H. The ^{13}C-^{2}H dipolar couplings are used for constraining possible models of molecular packing in the amorphous mixed phase of a P3HT/PCBM BHJ. The films studied are highly mixed (>80%) and have a maximum length scale of composition nonuniformity of ≈6 nm in the mixed phase, as demonstrated by ^{1}H spin diffusion NMR and supported by TEM. The REDOR results show that despite the lack of phase separation at length scales greater than ≈6 nm, neat P3HT and PCBM clusters exist on ≈3 nm size scales, and, for the average PCBM molecule, the number of nearest neighbors P3HTs is two.
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Affiliation(s)
- R. C. Nieuwendaal
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA
| | - D. M. DeLongchamp
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA
| | - L. J. Richter
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA
| | - C. R. Snyder
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA
| | - R. L. Jones
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA
| | - S. Engmann
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA
| | - A. Herzing
- Surface and Microanalysis Science Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA
| | - M Heeney
- Department of Chemistry, Imperial College, London SW7 2AZ, United Kingdom
| | - Z. Fei
- Department of Chemistry, Imperial College, London SW7 2AZ, United Kingdom
| | - A. B. Sieval
- Solenne BV, Zernikepark 6-8, 9747AN Groningen, Netherlands
| | - J. C. Hummelen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
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124
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Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys 2018; 148:215106. [PMID: 29884031 DOI: 10.1063/1.5028575] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite much progress in the understanding of the protein aggregation process, the factors governing fibril formation rates and fibril stability have not been fully understood. Using lattice models, we have shown that the fibril formation time is controlled by the kinetic stability of the fibril state but not by its energy. Having performed all-atom explicit solvent molecular dynamics simulations with the GROMOS43a1 force field for full-length amyloid beta peptides Aβ40 and Aβ42 and truncated peptides, we demonstrated that kinetic stability can be accessed via mechanical stability in such a way that the higher the mechanical stability or the kinetic stability, the faster the fibril formation. This result opens up a new way for predicting fibril formation rates based on mechanical stability that may be easily estimated by steered molecular dynamics.
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Affiliation(s)
- Maksim Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, The Research Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, Ohio 43215, USA
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125
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Pazos IM, Ma J, Mukherjee D, Gai F. Ultrafast Hydrogen-Bonding Dynamics in Amyloid Fibrils. J Phys Chem B 2018; 122:11023-11029. [PMID: 29883122 DOI: 10.1021/acs.jpcb.8b04642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While there are many studies on the subject of hydrogen-bonding dynamics in biological systems, few, if any, have investigated this fundamental process in amyloid fibrils. Herein, we seek to add insight into this topic by assessing the dynamics of a hydrogen bond buried in the dry interface of amyloid fibrils. To prepare a suitable model peptide system for this purpose, we introduce two mutations into the amyloid-forming Aβ16-22 peptide. The first one is a lysine analogue at position 19, which is used to help form structurally homogeneous fibrils, and the second one is an aspartic acid derivative (DM) at position 17, which is intended (1) to be used as a site-specific infrared probe and (2) to serve as a hydrogen-bond acceptor to lysine so that an inter-β-sheet hydrogen bond can be formed in the fibrils. Using both infrared spectroscopy and atomic force microscopy, we show that (1) this mutant peptide indeed forms well-defined fibrils, (2) when bulk solvent is removed, there is no detectable water present in the fibrils, (3) infrared results obtained with the DM probe are consistent with a protofibril structure that is composed of two antiparallel β-sheets stacked in a parallel fashion, leading to formation of the expected hydrogen bond. Using two-dimensional infrared spectroscopy, we further show that the dynamics of this hydrogen bond occur on a time scale of ∼2.3 ps, which is attributed to the rapid rotation of the -NH3+ group of lysine around its Cε-Nζ bond. Taken together, these results suggest that (1) DM is a useful infrared marker in facilitating structure determination of amyloid fibrils and (2) even in the tightly packed core of amyloid fibrils certain amino acid side chains can undergo ultrafast motions, hence contributing to the thermodynamic stability of the system.
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126
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Song M, Sun Y, Luo Y, Zhu Y, Liu Y, Li H. Exploring the Mechanism of Inhibition of Au Nanoparticles on the Aggregation of Amyloid-β(16-22) Peptides at the Atom Level by All-Atom Molecular Dynamics. Int J Mol Sci 2018; 19:ijms19061815. [PMID: 29925792 PMCID: PMC6032210 DOI: 10.3390/ijms19061815] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 01/01/2023] Open
Abstract
The abnormal self-assembly of the amyloid-β peptide into toxic β-rich aggregates can cause Alzheimer’s disease. Recently, it has been shown that small gold nanoparticles (AuNPs) inhibit Aβ aggregation and fibrillation by slowing down the nucleation process in experimental studies. However, the effects of AuNPs on Aβ oligomeric structures are still unclear. In this study, we investigate the conformation of Aβ(16-22) tetramers/octamers in the absence and presence of AuNPs using extensive all-atom molecular-dynamics simulations in explicit solvent. Our studies demonstrate that the addition of AuNPs into Aβ(16-22) solution prevents β-sheet formation, and the inhibition depends on the concentration of Aβ(16-22) peptides. A detailed analysis of the Aβ(16-22)/Aβ(16-22)/water/AuNPs interactions reveals that AuNPs inhibit the β-sheet formation resulting from the same physical forces: hydrophobic interactions. Overall, our computational study provides evidence that AuNPs are likely to inhibit Aβ(16-22) and full-length Aβ fibrillation. Thus, this work provides theoretical insights into the development of inorganic nanoparticles as drug candidates for treatment of AD.
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Affiliation(s)
- Menghua Song
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China.
- College of Energy and Mechanical Engineering, Shanghai University of Electric Power, Shanghai 200090, China.
| | - Yunxiang Sun
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Yin Luo
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Yanyan Zhu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China.
| | - Yongsheng Liu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China.
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China.
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
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127
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Lampel A, Ulijn RV, Tuttle T. Guiding principles for peptide nanotechnology through directed discovery. Chem Soc Rev 2018; 47:3737-3758. [PMID: 29748676 DOI: 10.1039/c8cs00177d] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.
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Affiliation(s)
- A Lampel
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), New York, NY, USA.
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128
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Zhang SM, Liao Y, Neo TL, Lu Y, Liu DX, Vahlne A, Tam JP. Identification and application of self-binding zipper-like sequences in SARS-CoV spike protein. Int J Biochem Cell Biol 2018; 101:103-112. [PMID: 29800727 PMCID: PMC7108413 DOI: 10.1016/j.biocel.2018.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 05/03/2018] [Accepted: 05/21/2018] [Indexed: 12/15/2022]
Abstract
Self-binding peptides containing zipper-like sequences, such as the Leu/Ile zipper sequence within the coiled coil regions of proteins and the cross-β spine steric zippers within the amyloid-like fibrils, could bind to the protein-of-origin through homophilic sequence-specific zipper motifs. These self-binding sequences represent opportunities for the development of biochemical tools and/or therapeutics. Here, we report on the identification of a putative self-binding β-zipper-forming peptide within the severe acute respiratory syndrome-associated coronavirus spike (S) protein and its application in viral detection. Peptide array scanning of overlapping peptides covering the entire length of S protein identified 34 putative self-binding peptides of six clusters, five of which contained octapeptide core consensus sequences. The Cluster I consensus octapeptide sequence GINITNFR was predicted by the Eisenberg’s 3D profile method to have high amyloid-like fibrillation potential through steric β-zipper formation. Peptide C6 containing the Cluster I consensus sequence was shown to oligomerize and form amyloid-like fibrils. Taking advantage of this, C6 was further applied to detect the S protein expression in vitro by fluorescence staining. Meanwhile, the coiled-coil-forming Leu/Ile heptad repeat sequences within the S protein were under-represented during peptide array scanning, in agreement with that long peptide lengths were required to attain high helix-mediated interaction avidity. The data suggest that short β-zipper-like self-binding peptides within the S protein could be identified through combining the peptide scanning and predictive methods, and could be exploited as biochemical detection reagents for viral infection.
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Affiliation(s)
- Si Min Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Sweden
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Tuan Ling Neo
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Yanning Lu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Ding Xiang Liu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Anders Vahlne
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Sweden
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore.
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129
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Xu QX, Hu Y, Li GY, Xu W, Zhang YT, Yang XW. Multi-Target Anti-Alzheimer Activities of Four Prenylated Compounds from Psoralea Fructus. Molecules 2018. [PMID: 29518051 PMCID: PMC6017461 DOI: 10.3390/molecules23030614] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Alzheimer’s disease (AD) is an age-related neurodegenerative disease that is mediated by multiple signaling pathways. In recent years, the components of Psoralea Fructus (PF) have demonstrated some anti-Alzheimer effects both in vitro and in vivo. To further reveal the active compounds of PF and their mechanisms regulating key targets of AD, in this study, we identified four prenylated compounds from the 70% ethanolic aqueous extract of PF, namely bavachin, bavachinin, bavachalcone, and isobavachalcone. Multi-target bioactivity analysis showed that these compounds could differentially inhibit neuroinflammation, oxidative damage, and key AD-related protein targets, such as amyloid β-peptide 42, β-secretase, glycogen synthase kinase 3β, and acetylcholinesterase. These compounds may generate beneficial effects in AD prevention and treatment.
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Affiliation(s)
- Qing-Xia Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, No. 38, Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Ying Hu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, No. 38, Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Gui-Yang Li
- Department of Pharmacology, State Province Key Laboratories of Biomedicine and Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, No. 157, Baojian Road, Nangang District, Harbin 150086, China.
| | - Wei Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, No. 38, Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Ying-Tao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, No. 38, Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Xiu-Wei Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, No. 38, Xueyuan Road, Haidian District, Beijing 100191, China.
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130
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Huang D, Hudson BC, Gao Y, Roberts EK, Paravastu AK. Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels. Methods Mol Biol 2018; 1777:23-68. [PMID: 29744827 PMCID: PMC7490753 DOI: 10.1007/978-1-4939-7811-3_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
For the structural characterization methods discussed here, information on molecular conformation and intermolecular organization within nanostructured peptide assemblies is discerned through analysis of solid-state NMR spectral features. This chapter reviews general NMR methodologies, requirements for sample preparation, and specific descriptions of key experiments. An attempt is made to explain choices of solid-state NMR experiments and interpretation of results in a way that is approachable to a nonspecialist. Measurements are designed to determine precise NMR peak positions and line widths, which are correlated with secondary structures, and probe nuclear spin-spin interactions that report on three-dimensional organization of atoms. The formulation of molecular structural models requires rationalization of data sets obtained from multiple NMR experiments on samples with carefully chosen 13C and 15N isotopic labels. The information content of solid-state NMR data has been illustrated mostly through the use of simulated data sets and references to recent structural work on amyloid fibril-forming peptides and designer self-assembling peptides.
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Affiliation(s)
- Danting Huang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Benjamin C Hudson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Evan K Roberts
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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131
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Methods to Characterize the Nanostructure and Molecular Organization of Amphiphilic Peptide Assemblies. Methods Mol Biol 2018; 1777:3-21. [PMID: 29744826 DOI: 10.1007/978-1-4939-7811-3_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods to characterize the nanostructure and molecular organization of aggregates of peptides such as amyloid or amphiphilic peptide assemblies are reviewed. We discuss techniques to characterize conformation and secondary structure including circular and linear dichroism and FTIR and Raman spectroscopies, as well as fluorescence methods to detect aggregation. NMR spectroscopy methods, especially solid-state NMR measurements to probe beta-sheet packing motifs, are also briefly outlined. Also discussed are scattering methods including X-ray diffraction and small-angle scattering techniques including SAXS (small-angle X-ray scattering) and SANS (small-angle neutron scattering) and dynamic light scattering. Imaging methods are direct methods to uncover features of peptide nanostructures, and we provide a summary of electron microscopy and atomic force microscopy techniques. Selected examples are highlighted showing data obtained using these techniques, which provide a powerful suite of methods to probe ordering from the molecular scale to the aggregate superstructure.
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132
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Giri RS, Mandal B. Boc-Val-Val-OMe (Aβ39–40) and Boc-Ile-Ala-OMe (Aβ41–42) crystallize in a parallel β-sheet arrangement but generate a different morphology. CrystEngComm 2018. [DOI: 10.1039/c8ce00097b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structures and morphologies of Boc-Val-Val-OMe (Aβ39–40) and Boc-Ile-Ala-OMe (Aβ41–42), the two consecutive dipeptides of the C-terminus of Aβ, are reported.
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Affiliation(s)
- Rajat Subhra Giri
- Department of Chemistry
- Laboratory of Peptide and Amyloid Research
- Indian Institute of Technology Guwahati
- India
| | - Bhubaneswar Mandal
- Department of Chemistry
- Laboratory of Peptide and Amyloid Research
- Indian Institute of Technology Guwahati
- India
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133
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Qiu F, Tang C, Chen Y. Amyloid-like aggregation of designer bolaamphiphilic peptides: Effect of hydrophobic section and hydrophilic heads. J Pept Sci 2017; 24. [PMID: 29239498 DOI: 10.1002/psc.3062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 02/05/2023]
Abstract
Amyloid-like aggregation of natural proteins or polypeptides is an important process involved in many human diseases as well as some normal biological functions. Plenty of works have been done on this ubiquitous phenomenon, but the molecular mechanism of amyloid-like aggregation has not been fully understood yet. In this study, we showed that a series of designer bolaamphiphilic peptides could undergo amyloid-like aggregation even though they didn't possess typical β-sheet secondary structure. Through systematic amino acid substitution, we found that for the self-assembling ability, the number and species of amino acid in hydrophobic section could be variable as long as enough hydrophobic interaction is provided, while different polar amino acids as the hydrophilic heads could change the self-assembling nanostructures with their aggregating behaviors affected by pH value change. Based on these results, novel self-assembling models and aggregating mechanisms were proposed, which might provide new insight into the molecular basis of amyloid-like aggregation.
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Affiliation(s)
- Feng Qiu
- Laboratory of Anaesthesia and Critical Care Medicine, Translational Neuroscience Centre, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chengkang Tang
- Core Facility of West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yongzhu Chen
- Periodical Press of West China Hospital, Sichuan University, Chengdu, 610041, China
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134
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Hu Y, Kienlen-Campard P, Tang TC, Perrin F, Opsomer R, Decock M, Pan X, Octave JN, Constantinescu SN, Smith SO. β-Sheet Structure within the Extracellular Domain of C99 Regulates Amyloidogenic Processing. Sci Rep 2017; 7:17159. [PMID: 29215043 PMCID: PMC5719365 DOI: 10.1038/s41598-017-17144-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/20/2017] [Indexed: 11/15/2022] Open
Abstract
Familial mutations in C99 can increase the total level of the soluble Aβ peptides produced by proteolysis, as well as the Aβ42/Aβ40 ratio, both of which are linked to the progression of Alzheimer’s disease. We show that the extracellular sequence of C99 forms β-sheet structure upon interaction with membrane bilayers. Mutations that disrupt this structure result in a significant increase in Aβ production and, in specific cases, result in an increase in the amount of Aβ42 relative to Aβ40. Fourier transform infrared and solid-state NMR spectroscopic studies reveal a central β-hairpin within the extracellular sequence comprising Y10-E11-V12 and L17-V18-F19 connected by a loop involving H13-H14-Q15. These results suggest how familial mutations in the extracellular sequence influence C99 processing and provide a structural basis for the development of small molecule modulators that would reduce Aβ production.
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Affiliation(s)
- Yi Hu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | | | - Tzu-Chun Tang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Florian Perrin
- Institute of Neuroscience, Université catholique de Louvain, Brussels, 1200, Belgium.,Ludwig Institute for Cancer Research and de Duve Institute, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Rémi Opsomer
- Institute of Neuroscience, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Marie Decock
- Institute of Neuroscience, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Xiaoshu Pan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jean-Noel Octave
- Institute of Neuroscience, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research and de Duve Institute, Université catholique de Louvain, Brussels, 1200, Belgium.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
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135
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Qian Z, Zhang Q, Liu Y, Chen P. Assemblies of amyloid-β30-36 hexamer and its G33V/L34T mutants by replica-exchange molecular dynamics simulation. PLoS One 2017; 12:e0188794. [PMID: 29186195 PMCID: PMC5706729 DOI: 10.1371/journal.pone.0188794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/13/2017] [Indexed: 02/02/2023] Open
Abstract
The aggregation of amyloid-β peptides is associated with the pathogenesis of Alzheimer’s disease, in which the 30–36 fragments play an important part as a fiber-forming hydrophobic region. The fibrillar structure of Aβ30–36 has been detected by means of X-ray diffraction, but its oligomeric structural determination, biophysical characterization, and pathological mechanism remain elusive. In this study, we have investigated the structures of Aβ30–36 hexamer as well as its G33V and L34T mutants in explicit water environment using replica-exchange molecular dynamics (REMD) simulations. Our results show that the wild-type (WT) Aβ30–36 hexamer has a preference to form β-barrel and bilayer β-sheet conformations, while the G33V or L34T mutation disrupts the β-barrel structures: the G33V mutant is homogenized to adopt β-sheet-rich bilayers, and the structures of L34T mutant on the contrary get more diverse. The hydrophobic interaction plays a critical role in the formation and stability of oligomeric assemblies among all the three systems. In addition, the substitution of G33 by V reduces the β-sheet content in the most populated conformations of Aβ30–36 oligomers through a steric effect. The L34T mutation disturbs the interpeptide hydrogen bonding network, and results in the increased coil content and morphological diversity. Our REMD runs provide structural details of WT and G33V/L34T mutant Aβ30–36 oligomers, and molecular insight into the aggregation mechanism, which will be helpful for designing novel inhibitors or amyloid-based materials.
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Affiliation(s)
- Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai, China
- * E-mail: (ZQ); (PC)
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, Shanghai, China
| | - Yu Liu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Peijie Chen
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai, China
- * E-mail: (ZQ); (PC)
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136
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Hsieh MC, Liang C, Mehta AK, Lynn DG, Grover MA. Multistep Conformation Selection in Amyloid Assembly. J Am Chem Soc 2017; 139:17007-17010. [PMID: 29111722 PMCID: PMC5709775 DOI: 10.1021/jacs.7b09362] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Defining pathways
for amyloid assembly could impact therapeutic
strategies for as many as 50 disease states. Here we show that amyloid
assembly is subject to different forces regulating nucleation and
propagation steps and provide evidence that the more global β-sheet/β-sheet
facial complementarity is a critical determinant for amyloid nucleation
and structural selection.
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Affiliation(s)
- Ming-Chien Hsieh
- Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Anil K Mehta
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - David G Lynn
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Martha A Grover
- Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
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137
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Aliyan A, Paul TJ, Jiang B, Pennington C, Sharma G, Prabhakar R, Martí AA. Photochemical Identification of Molecular Binding Sites on the Surface of Amyloid-β Fibrillar Aggregates. Chem 2017. [DOI: 10.1016/j.chempr.2017.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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138
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Sun Y, Wang B, Ge X, Ding F. Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide. Phys Chem Chem Phys 2017; 19:28414-28423. [PMID: 29038815 PMCID: PMC5657190 DOI: 10.1039/c7cp05695h] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A direct observation of amyloid aggregation from isolated peptides to cross-β fibrils is crucial for understanding the nucleation-dependence process, but the corresponding macroscopic timescales impose a major computational challenge. Using rapid all-atom discrete molecular dynamics simulations, we capture the oligomerization and fibrillization dynamics of the amyloid core sequences of amyloid-β (Aβ) in Alzheimer's disease and islet amyloid polypeptide (IAPP) in type-2 diabetes, namely Aβ16-22 and IAPP22-28. Both peptides and their mixture spontaneously assemble into cross-β aggregates in silico, but follow distinct pathways. Aβ16-22 is highly aggregation-prone with a funneled free energy basin toward multi-layer β-sheet aggregates. IAPP22-28, on the other hand, features the accumulation of unstructured oligomers before the nucleation of β-sheets and growth into double-layer β-sheet aggregates. In the presence of Aβ16-22, the aggregation of IAPP22-28 is promoted by forming co-aggregated multi-layer β-sheets. Our study offers a detailed molecular insight to the long-postulated oligomerization-nucleation process in the amyloid aggregations.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC, USA.
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139
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de Almeida NEC, Do TD, LaPointe NE, Tro M, Feinstein SC, Shea JE, Bowers MT. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose Binds to the N-terminal Metal Binding Region to Inhibit Amyloid β-protein Oligomer and Fibril Formation. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 420:24-34. [PMID: 29056865 PMCID: PMC5644501 DOI: 10.1016/j.ijms.2016.09.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The early oligomerization of amyloid β-protein (Aβ) is a crucial step in the etiology of Alzheimer's disease (AD), in which soluble and highly neurotoxic oligomers are produced and accumulated inside neurons. In search of therapeutic solutions for AD treatment and prevention, potent inhibitors that remodel Aβ assembly and prevent neurotoxic oligomer formation offer a promising approach. In particular, several polyphenolic compounds have shown anti-aggregation properties and good efficacy on inhibiting oligomeric amyloid formation. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose is a large polyphenol that has been shown to be effective at inhibiting aggregation of full-length Aβ1-40 and Aβ1-42, but has the opposite effect on the C-terminal fragment Aβ25-35. Here, we use a combination of ion mobility coupled to mass spectrometry (IMS-MS), transmission electron microscopy (TEM) and molecular dynamics (MD) simulations to elucidate the inhibitory effect of PGG on aggregation of full-length Aβ1-40 and Aβ1-42. We show that PGG interacts strongly with these two peptides, especially in their N-terminal metal binding regions, and suppresses the formation of Aβ1-40 tetramer and Aβ1-42 dodecamer. By exploring multiple facets of polyphenol-amyloid interactions, we provide a molecular basis for the opposing effects of PGG on full-length Aβ and its C-terminal fragments.
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Affiliation(s)
- Natália E. C. de Almeida
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Thanh D. Do
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nichole E. LaPointe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Michael Tro
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Stuart C. Feinstein
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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140
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Abstract
Living systems contain remarkable functional capability built within sophisticated self-organizing frameworks. Defining the assembly codes that coordinate these systems could greatly extend nanobiotechnology. To that end, we have highlighted the self-assembling architecture of the chlorosome antenna arrays and report the emulation and extension of their features for the development of cell-compatible photoredox materials. We specifically review work on amyloid peptide scaffolds able to (1) organize light-harvesting chromophores, (2) break peptide bilayer symmetry for directional energy and electron transfer, and (3) incorporate redox active metal ions at high density for energy storage.
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Affiliation(s)
- Rolando F Rengifo
- Emory University, Departments of Biology and Chemistry, 1515 Dickey Dr. NE, Atlanta, GA 30322, USA.
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141
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Nishikawa N, Sakae Y, Gouda T, Tsujimura Y, Okamoto Y. Two major stable structures of amyloid-forming peptides: amorphous aggregates and amyloid fibrils. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1359746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Naohiro Nishikawa
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Japan
| | - Yoshitake Sakae
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takuya Gouda
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuichiro Tsujimura
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Japan
- Information Technology Center, Nagoya University, Nagoya, Japan
- JST-CREST, Nagoya, Japan
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142
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Frederix PWJM, Idé J, Altay Y, Schaeffer G, Surin M, Beljonne D, Bondarenko AS, Jansen TLC, Otto S, Marrink SJ. Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles. ACS NANO 2017; 11:7858-7868. [PMID: 28723067 PMCID: PMC5616102 DOI: 10.1021/acsnano.7b02211] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.
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Affiliation(s)
- Pim W. J. M. Frederix
- University
of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747AG Groningen, The Netherlands
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
- E-mail:
| | - Julien Idé
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - Yigit Altay
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
| | - Gaël Schaeffer
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
| | - Mathieu Surin
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - David Beljonne
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - Anna S. Bondarenko
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Sijbren Otto
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
- E-mail:
| | - Siewert J. Marrink
- University
of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747AG Groningen, The Netherlands
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
- E-mail:
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143
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Abstract
We present a theoretical model for the nucleation of amyloid fibrils. In our model we use helix-coil theory to describe the equilibrium between a soluble native state and an aggregation-prone unfolded state. We then extend the theory to include oligomers with β-sheet cores and calculate the free energy of these states using estimates for the energies of H-bonds, steric zipper interactions, and the conformational entropy cost of forming secondary structure. We find that states with fewer than ~10 β-strands are unstable relative to the dissociated state and three β-strands is the highest free energy state. We then use a modified version of Classical Nucleation Theory to compute the nucleation rate of fibrils from a supersaturated solution of monomers, dimers, and trimers. The nucleation rate has a non-monotonic dependence on denaturant concentration reflecting the competing effects of destabilizing the fibril and increasing the concentration of unfolded monomers. We estimate heterogeneous nucleation rates and discuss the application of our model to secondary nucleation.
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Affiliation(s)
- Lingyun Zhang
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
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144
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Su T, Hong KH, Zhang W, Li F, Li Q, Yu F, Luo G, Gao H, He YP. Scaleable two-component gelator from phthalic acid derivatives and primary alkyl amines: acid-base interaction in the cooperative assembly. SOFT MATTER 2017; 13:4066-4073. [PMID: 28536712 DOI: 10.1039/c7sm00797c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A series of phthalic acid derivatives (P) with a carbon-chain tail was designed and synthesized as single-component gelators. A combination of the single-component gelator P and a non-gelling additive n-alkylamine A through acid-base interaction brought about a series of novel phase-selective two-component gelators PA. The gelation capabilities of P and PA, and the structural, morphological, thermo-dynamic and rheological properties of the corresponding gels were investigated. A molecular dynamics simulation showed that the H-bonding network in PA formed between the NH of A and the carbonyl oxygen of P altered the assembly process of gelator P. Crude PA could be synthesized through a one-step process without any purification and could selectively gel the oil phase without a typical heating-cooling process. Moreover, such a crude PA and its gelation process could be amplified to the kilogram scale with high efficiency, which offers a practical economically viable solution to marine oil-spill recovery.
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Affiliation(s)
- Ting Su
- College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Dandong Lu West 1, Fushun 113001, Liaoning, P. R. China.
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145
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Wu R, Liu J, Qiu X, Deng M. Molecular dynamics simulation of the nanofibrils formed by amyloid-based peptide amphiphiles. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1321758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rongliang Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Jun Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Xinlong Qiu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Manli Deng
- Key Laboratory of Colloid and Interface Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, P.R. China
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146
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Tran TT, Nguyen PH, Derreumaux P. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides. J Chem Phys 2017; 144:205103. [PMID: 27250331 DOI: 10.1063/1.4951739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.
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Affiliation(s)
- Thanh Thuy Tran
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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147
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Eschmann NA, Georgieva ER, Ganguly P, Borbat PP, Rappaport MD, Akdogan Y, Freed JH, Shea JE, Han S. Signature of an aggregation-prone conformation of tau. Sci Rep 2017; 7:44739. [PMID: 28303942 PMCID: PMC5356194 DOI: 10.1038/srep44739] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/13/2017] [Indexed: 11/09/2022] Open
Abstract
The self-assembly of the microtubule associated tau protein into fibrillar cell inclusions is linked to a number of devastating neurodegenerative disorders collectively known as tauopathies. The mechanism by which tau self-assembles into pathological entities is a matter of much debate, largely due to the lack of direct experimental insights into the earliest stages of aggregation. We present pulsed double electron-electron resonance measurements of two key fibril-forming regions of tau, PHF6 and PHF6*, in transient as aggregation happens. By monitoring the end-to-end distance distribution of these segments as a function of aggregation time, we show that the PHF6(*) regions dramatically extend to distances commensurate with extended β-strand structures within the earliest stages of aggregation, well before fibril formation. Combined with simulations, our experiments show that the extended β-strand conformational state of PHF6(*) is readily populated under aggregating conditions, constituting a defining signature of aggregation-prone tau, and as such, a possible target for therapeutic interventions.
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Affiliation(s)
- Neil A Eschmann
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, 93106, USA
| | - Elka R Georgieva
- National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York, 14853, USA.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, 93106, USA
| | - Peter P Borbat
- National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York, 14853, USA.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Maxime D Rappaport
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, 93106, USA
| | - Yasar Akdogan
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, 93106, USA
| | - Jack H Freed
- National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York, 14853, USA.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, 93106, USA
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, 93106, USA
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148
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Castelletto V, Ryumin P, Cramer R, Hamley IW, Taylor M, Allsop D, Reza M, Ruokolainen J, Arnold T, Hermida-Merino D, Garcia CI, Leal MC, Castaño E. Self-Assembly and Anti-Amyloid Cytotoxicity Activity of Amyloid beta Peptide Derivatives. Sci Rep 2017; 7:43637. [PMID: 28272542 PMCID: PMC5341572 DOI: 10.1038/srep43637] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/26/2017] [Indexed: 12/11/2022] Open
Abstract
The self-assembly of two derivatives of KLVFF, a fragment Aβ(16-20) of the amyloid beta (Aβ) peptide, is investigated and recovery of viability of neuroblastoma cells exposed to Aβ (1-42) is observed at sub-stoichiometric peptide concentrations. Fluorescence assays show that NH2-KLVFF-CONH2 undergoes hydrophobic collapse and amyloid formation at the same critical aggregation concentration (cac). In contrast, NH2-K(Boc)LVFF-CONH2 undergoes hydrophobic collapse at a low concentration, followed by amyloid formation at a higher cac. These findings are supported by the β-sheet features observed by FTIR. Electrospray ionization mass spectrometry indicates that NH2-K(Boc)LVFF-CONH2 forms a significant population of oligomeric species above the cac. Cryo-TEM, used together with SAXS to determine fibril dimensions, shows that the length and degree of twisting of peptide fibrils seem to be influenced by the net peptide charge. Grazing incidence X-ray scattering from thin peptide films shows features of β-sheet ordering for both peptides, along with evidence for lamellar ordering of NH2-KLVFF-CONH2. This work provides a comprehensive picture of the aggregation properties of these two KLVFF derivatives and shows their utility, in unaggregated form, in restoring the viability of neuroblastoma cells against Aβ-induced toxicity.
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Affiliation(s)
- V. Castelletto
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - P. Ryumin
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - R. Cramer
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - I. W. Hamley
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - M. Taylor
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - D. Allsop
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - M. Reza
- Department of Applied Physics, Aalto University School of Science, Aalto FI-00076, Finland
| | - J. Ruokolainen
- Department of Applied Physics, Aalto University School of Science, Aalto FI-00076, Finland
| | - T. Arnold
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - D. Hermida-Merino
- European Synchrotron Radiation Facility, ESRF, 71 avenue des Martyrs, 38000 Grenoble, France
| | - C. I. Garcia
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - M. C. Leal
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - E. Castaño
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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149
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Omosun TO, Hsieh MC, Childers WS, Das D, Mehta AK, Anthony NR, Pan T, Grover MA, Berland KM, Lynn DG. Catalytic diversity in self-propagating peptide assemblies. Nat Chem 2017; 9:805-809. [DOI: 10.1038/nchem.2738] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/19/2017] [Indexed: 01/03/2023]
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150
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Jia Z, Beugelsdijk A, Chen J, Schmit JD. The Levinthal Problem in Amyloid Aggregation: Sampling of a Flat Reaction Space. J Phys Chem B 2017; 121:1576-1586. [PMID: 28129689 DOI: 10.1021/acs.jpcb.7b00253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The formation of amyloid fibrils has been associated with many neurodegenerative disorders, yet the mechanism of aggregation remains elusive, partly because aggregation time scales are too long to probe with atomistic simulations. A microscopic theory of fibril elongation was recently developed that could recapitulate experimental results with respect to the effects of temperature, denaturants, and protein concentration on fibril growth kinetics (Schmit, J. D. J. Chem. Phys. 2013, 138 (18), 185102). The theory identifies the conformational search over H-bonding states as the slowest step in the aggregation process and suggests that this search can be efficiently modeled as a random walk on a rugged one-dimensional energy landscape. This insight motivated the multiscale computational algorithm for simulating fibril growth presented in this paper. Briefly, a large number of short atomistic simulations are performed to compute the system diffusion tensor in the reaction coordinate space predicted by the analytic theory. Ensemble aggregation pathways and growth kinetics are then computed from Markov state model (MSM) trajectories. The algorithm is deployed here to understand the fibril growth mechanism and kinetics of Aβ16-22 and three of its mutants. The order of growth rates of the wild-type and two single mutation peptides (CHA19 and CHA20) predicted by the MSM trajectories is consistent with experimental results. The simulation also correctly predicts that the double mutation (CHA19/CHA20) would reduce the fibril growth rate, even though the degree of rate reduction with respect to either single mutation is overestimated. This artifact may be attributed to the simplistic implicit solvent model. These trends in the growth rate are not apparent from inspection of the rate constants of individual bonds or the lifetimes of the mis-registered states that are the primary kinetic traps but only emerge in the ensemble of trajectories generated by the MSM.
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Affiliation(s)
- Zhiguang Jia
- Department of Biochemistry and Molecular Biophysics and ‡Department of Physics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Alex Beugelsdijk
- Department of Biochemistry and Molecular Biophysics and ‡Department of Physics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics and ‡Department of Physics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Jeremy D Schmit
- Department of Biochemistry and Molecular Biophysics and ‡Department of Physics, Kansas State University , Manhattan, Kansas 66506, United States
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