1
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Matsuda M, Ikeda K, Kameda T, Nakao H, Nakano M. Fine-Tuning and Enhancement of pH-Dependent Membrane Permeation of Cyclic Peptides by Utilizing Noncanonical Amino Acids with Extended Side Chains. J Med Chem 2023; 66:7054-7062. [PMID: 37186548 DOI: 10.1021/acs.jmedchem.3c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The development of cyclic peptides that exhibit pH-sensitive membrane permeation is a promising strategy for tissue-selective drug delivery. We investigated the pH-dependent interactions of designed cyclic peptides bearing noncanonical amino acids of long acidic side chains with lipid membranes, including surface binding, insertion, and translocation across the membrane. As the length of the side chain of acidic amino acid increased, the binding affinity of the peptides to phosphatidylcholine bilayer surfaces decreased, while the pH for the 50% insertion of the peptides into the bilayers increased. The pH for membrane permeation of the peptides increased with the side chain length, resulting in specific membrane permeation at pH ∼6.5. The longer side chain of acidic amino acids improved the maximum rate of membrane permeation at low pH, where both entropic and enthalpic contributions affected the permeation. Our peptide also showed intracellular delivery of cargo molecules into living cells in a pH-dependent manner.
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Affiliation(s)
- Motomi Matsuda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
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2
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Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
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Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
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3
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Howitz WJ, Guaglianone G, McKnelly KJ, Haduong K, Ashby SN, Laayouni M, Nowick JS. Macrocyclic Peptides Derived from Familial Alzheimer's Disease Mutants Show Charge-Dependent Oligomeric Assembly and Toxicity. ACS Chem Neurosci 2022; 13:714-720. [PMID: 35191689 PMCID: PMC9042422 DOI: 10.1021/acschemneuro.1c00833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This work probes the role of charge in the oligomeric assembly, toxicity, and membrane destabilization of a series of peptides derived from Aβ and the E22Q and E22K familial mutants. In the mutant Aβ peptides, an acidic residue (E) is replaced with either a neutral or basic residue (Q or K), thus altering the net charge of the peptide. Acetylation at peripheral positions permits modulation of charge of the peptides and allows investigation of the role of charge in their oligomeric assembly, cytotoxicity, and membrane disruption. Peptides with the same net charge generally behave similarly even if the amino acid residue at position 22 differs. As the net charge of the peptide decreases, so does the extent of assembly, cytotoxicity, and membrane destabilization, which were determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, lactate dehydrogenase (LDH)-release assays with SH-SY5Y cells, and dye leakage assays using liposomes. These findings suggest that the charge of the amino acid side chain, rather than its size or hydrophobicity, accounts for the differences in the oligomeric assembly and toxicity of the E22 familial mutants of Aβ.
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Affiliation(s)
- William J Howitz
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Gretchen Guaglianone
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Kate J McKnelly
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Katelyn Haduong
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Shareen N Ashby
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mohamed Laayouni
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
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4
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Warnock TMC, Rajkumar S, Fitzpatrick MP, Serpell CJ, Dingwall P, Knipe PC. Chiral, sequence-definable foldamer-derived macrocycles. Chem Sci 2021; 12:15632-15636. [PMID: 35003593 PMCID: PMC8654020 DOI: 10.1039/d1sc05021d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/03/2021] [Indexed: 12/22/2022] Open
Abstract
Nature's oligomeric macromolecules have been a long-standing source of inspiration for chemists producing foldamers. Natural systems are frequently conformationally stabilised by macrocyclisation, yet this approach has been rarely adopted in the field of foldamer chemistry. Here we present a new class of chiral cyclic trimers and tetramers formed by macrocyclisation of open-chain foldamer precursors. Symmetrical products are obtained via a [2 + 2] self-assembly approach, while full sequence control is demonstrated through linear synthesis and cyclisation of an unsymmetrical trimer. Structural characterisation is achieved through a combined X-ray and DFT approach, which indicates the tetramers adopt a near-planar conformation, while the trimers adopt a shallow bowl-like shape. Finally, a proof-of-concept experiment is conducted to demonstrate the macrocycles' capacity for cation binding. Dipole-controlled pre-organization enables the cyclization of sequence-defined foldamers into macrocycles. The structure and properties of trimeric and tetrameric macrocycles are explored, and their ability to bind cationic guests is demonstrated.![]()
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Affiliation(s)
- Toyah M C Warnock
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | | | - Matthew P Fitzpatrick
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | - Christopher J Serpell
- School of Physical Sciences, University of Kent Ingram Building Canterbury Kent CT2 7NH UK
| | - Paul Dingwall
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | - Peter C Knipe
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
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5
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Synthesis and study of macrocyclic β-hairpin peptides for investigating amyloid oligomers. Methods Enzymol 2021; 656:123-168. [PMID: 34325785 DOI: 10.1016/bs.mie.2021.04.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Chemically constrained peptides that self-assemble can be used to better understand the molecular basis of amyloid diseases. The formation of small assemblies of the amyloidogenic peptides and proteins, termed oligomers, is central to amyloid diseases. The use of chemical model systems can help provide insights into the structures and interactions of amyloid oligomers, which are otherwise difficult to study. This chapter describes the use of macrocyclic β-hairpin peptides as model systems to study amyloid oligomers. The first part of the chapter describes the chemical synthesis of the macrocyclic β-hairpin peptides and covalent assemblies thereof. The second part of the chapter describes the characterization of the oligomers formed by the macrocyclic β-hairpin peptides, focusing on SDS-PAGE, size-exclusion chromatography (SEC), and X-ray crystallography. The procedures provided focus on the β-amyloid peptide, but these strategies are applicable to a broad range of amyloid-derived peptides and proteins.
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6
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2021; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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7
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Haerianardakani S, Kreutzer AG, Salveson PJ, Samdin TD, Guaglianone GE, Nowick JS. Phenylalanine Mutation to Cyclohexylalanine Facilitates Triangular Trimer Formation by β-Hairpins Derived from Aβ. J Am Chem Soc 2020; 142:20708-20716. [PMID: 33237748 PMCID: PMC7821965 DOI: 10.1021/jacs.0c09281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oligomers of the β-amyloid peptide, Aβ, play a central role in the pathogenesis and progression of Alzheimer's disease. Trimers and higher-order oligomers composed of trimers are thought to be the most neurotoxic Aβ oligomers. To gain insights into the structure and assembly of Aβ oligomers, our laboratory has previously designed and synthesized macrocyclic peptides derived from Aβ17-23 and Aβ30-36 that fold to form β-hairpins and assemble to form trimers. In this study, we found that mutating Phe20 to cyclohexylalanine (Cha) in macrocyclic Aβ-derived peptides promotes crystallization of an Aβ-derived peptide containing the Aβ24-29 loop (peptide 3F20Cha) and permits elucidation of its structure and assembly by X-ray crystallography. X-ray crystallography shows that peptide 3F20Cha forms a hexamer. X-ray crystallography and SDS-PAGE further show that trimer 4F20Cha, a covalently stabilized trimer derived from peptide 3F20Cha, forms a dodecamer. Size exclusion chromatography shows that trimer 4F20Cha forms higher-order assemblies in solution. Trimer 4F20Cha exhibits cytotoxicity against the neuroblastoma cell line SH-SY5Y. These studies demonstrate the use of the F20Cha mutation to further stabilize oligomers of Aβ-derived peptides that contain more of the native sequence and thus better mimic the oligomers formed by full-length Aβ.
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Affiliation(s)
- Sepehr Haerianardakani
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Adam G Kreutzer
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Patrick J Salveson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Tuan D Samdin
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Gretchen E Guaglianone
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
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8
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Cao R, Rossdeutcher RB, Wu X, Gong B. Oligo(5-amino- N-acylanthranilic acids): Amide Bond Formation without Coupling Reagent and Folding upon Binding Anions. Org Lett 2020; 22:7496-7501. [PMID: 32959659 DOI: 10.1021/acs.orglett.0c02696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligomers of 5-amino-N-acylanthranilic acid, previously unknown aromatic oligoamides that cannot be obtained with known amide coupling methods, are synthesized based on a new, highly efficient amide-bond formation strategy that takes advantage of the ring-opening of benzoxazinone derivatives. These oligoamides offer multiple backbone NH groups as H-bond donors which, in the presence of iodide or chloride ion, are convergently arranged and H-bonded, which enforces a folded, crescent conformation. These aromatic oligoamides provide a versatile platform based on which anion-dependent foldamers, or anion binders with tunable affinity and specificity, are being constructed.
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Affiliation(s)
- Ruikai Cao
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260, United States
| | - Robert B Rossdeutcher
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260, United States
| | - Xiangxiang Wu
- Academy of Chinese Medical Science, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou 450046, Henan, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260, United States
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9
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Zhong Y, Kauffmann B, Xu W, Lu ZL, Ferrand Y, Huc I, Zeng XC, Liu R, Gong B. Multiturn Hollow Helices: Synthesis and Folding of Long Aromatic Oligoamides. Org Lett 2020; 22:6938-6942. [PMID: 32794403 DOI: 10.1021/acs.orglett.0c02481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aromatic oligoamides adopting helical conformations are synthesized by coupling carboxyl-terminated basic units having two, four, and eight residues to amine-terminated oligomer precursors. Coupling yields show no noticeable reduction with the size of the basic units or the final product. One- and two-dimensional NMR spectroscopy and computational studies demonstrate the reliable helical folding of these oligomers. The X-ray structure of 16mer 7 reveals a compact, multiturn helix having a 9 Å inner pore.
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Affiliation(s)
- Yulong Zhong
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260, United States
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie, UMS3011/US001 CNRS, Inserm, Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Wenwu Xu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yann Ferrand
- Institut de Chimie et Biologie des Membranes et des Nano-objets, UMR 5248 CNRS, Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Ivan Huc
- Department Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, D-81377 Munich, Germany
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260, United States
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10
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Howitz WJ, Wierzbicki M, Cabanela RW, Saliba C, Motavalli A, Tran N, Nowick JS. Interpenetrating Cubes in the X-ray Crystallographic Structure of a Peptide Derived from Medin 19-36. J Am Chem Soc 2020; 142:15870-15875. [PMID: 32816461 DOI: 10.1021/jacs.0c06143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amyloidogenic peptides and proteins are rich sources of supramolecular assemblies. Sequences derived from well-known amyloids, including Aβ, human islet amyloid polypeptide, and tau have been found to assemble as fibrils, nanosheets, ribbons, and nanotubes. The supramolecular assembly of medin, a 50-amino acid peptide that forms fibrillary deposits in aging human vasculature, has not been heavily investigated. In this work, we present an X-ray crystallographic structure of a cyclic β-sheet peptide derived from the 19-36 region of medin that assembles to form interpenetrating cubes. The edge of each cube is composed of a single peptide, and each vertex is occupied by a divalent metal ion. This structure may be considered a metal-organic framework (MOF) containing a large peptide ligand. This work demonstrates that peptides containing Glu or Asp that are preorganized to adopt β-hairpin structures can serve as ligands and assemble with metal ions to form MOFs.
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Affiliation(s)
- William J Howitz
- Department of Chemistry and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Michał Wierzbicki
- Department of Chemistry and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rudy William Cabanela
- Department of Chemistry and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Cindy Saliba
- Department of Chemistry and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Ariana Motavalli
- Department of Chemistry and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Ngoctran Tran
- Department of Chemistry and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-2025, United States
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11
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Tang Q, Zhong Y, Miller DP, Liu R, Zurek E, Lu ZL, Gong B. Reverse Turn Foldamers: An Expanded β-Turn Motif Reinforced by Double Hydrogen Bonds. Org Lett 2020; 22:1003-1007. [DOI: 10.1021/acs.orglett.9b04547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quan Tang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel P. Miller
- Department of Chemistry, Hofstra University, Hempstead, New York 11549, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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12
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Zhang Y, Zhong Y, Connor AL, Miller DP, Cao R, Shen J, Song B, Baker ES, Tang Q, Pulavarti SVSRK, Liu R, Wang Q, Lu ZL, Szyperski T, Zeng H, Li X, Smith RD, Zurek E, Zhu J, Gong B. Folding and Assembly of Short α, β, γ-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures. J Am Chem Soc 2019; 141:14239-14248. [DOI: 10.1021/jacs.9b06094] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yukun Zhang
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Alan L. Connor
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel P. Miller
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Ruikai Cao
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jie Shen
- The NanoBio Lab, 31 Biopolis Way, The Nanos 138669, Singapore
| | - Bo Song
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Erin S. Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Quan Tang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Surya V. S. R. K. Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiwei Wang
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhong-lin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Huaqiang Zeng
- The NanoBio Lab, 31 Biopolis Way, The Nanos 138669, Singapore
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jin Zhu
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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13
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Saavedra CJ, Carro C, Hernández D, Boto A. Conversion of “Customizable Units” into N-Alkyl Amino Acids and Generation of N-Alkyl Peptides. J Org Chem 2019; 84:8392-8410. [DOI: 10.1021/acs.joc.9b00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
- BIOSIGMA, Antonio Domı́nguez Alfonso 16, 38003-Sta. Cruz de Tenerife, Tenerife, Spain
| | - Carmen Carro
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
- BIOSIGMA, Antonio Domı́nguez Alfonso 16, 38003-Sta. Cruz de Tenerife, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
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14
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Olajos G, Hetényi A, Wéber E, Szögi T, Fülöp L, Martinek TA. Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches. Org Biomol Chem 2019; 16:5492-5499. [PMID: 30024580 DOI: 10.1039/c8ob01322e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Engineering water-soluble stand-alone β-sandwich mimetics is a current challenge because of the difficulties associated with tailoring long-range interactions. In this work, single cis-(1R,2S)-2-aminocyclohexanecarboxylic acid mutations were introduced into the edge strands of the eight-stranded β-sandwich mimetic structures from the betabellin family. Temperature-dependent NMR and CD measurements, together with thermodynamic analyses, demonstrated that the modified peripheral strands exhibited an irregular and partially disordered structure but were able to exert sufficient shielding on the hydrophobic core to retain the predominantly β-sandwich structure. Although the frustrated interactions decreased the free energy of unfolding, the temperature of the maximum stabilities increased to or remained at physiologically relevant temperatures. We found that the irregular peripheral strands were able to prevent edge-to-edge association and fibril formation in the aggregation-prone model. These findings establish a β-sandwich stabilization and aggregation inhibition approach, which does not interfere with the pillars of the peptide bond or change the net charge of the peptide.
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Affiliation(s)
- Gábor Olajos
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Edit Wéber
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary.
| | - Titanilla Szögi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Tamás A Martinek
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
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15
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Zhao Y, Connor AL, Sobiech TA, Gong B. Effects of Oligomer Length, Solvents, and Temperature on the Self-Association of Aromatic Oligoamide Foldamers. Org Lett 2018; 20:5486-5489. [DOI: 10.1021/acs.orglett.8b02438] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yongye Zhao
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Alan L. Connor
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Thomas A. Sobiech
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Bing Gong
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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16
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Salveson PJ, Haerianardakani S, Thuy-Boun A, Kreutzer AG, Nowick JS. Controlling the Oligomerization State of Aβ-Derived Peptides with Light. J Am Chem Soc 2018; 140:5842-5852. [PMID: 29627987 DOI: 10.1021/jacs.8b02658] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A key challenge in studying the biological and biophysical properties of amyloid-forming peptides is that they assemble to form heterogeneous mixtures of soluble oligomers and insoluble fibrils. Photolabile protecting groups have emerged as tools to control the properties of biomolecules with light. Blocking intermolecular hydrogen bonds that stabilize amyloid oligomers provides a general strategy to control the biological and biophysical properties of amyloid-forming peptides. In this paper we describe the design, synthesis, and characterization of macrocyclic β-hairpin peptides that are derived from amyloidogenic peptides and contain the N-2-nitrobenzyl photolabile protecting group. Each peptide contains two heptapeptide segments from Aβ16-36 or Aβ17-36 constrained into β-hairpins. The N-2-nitrobenzyl group is appended to the amide backbone of Gly33 to disrupt the oligomerization of the peptides by disrupting intermolecular hydrogen bonds. X-ray crystallography reveals that N-2-nitrobenzyl groups can either block assembly into discrete oligomers or permit formation of trimers, hexamers, and dodecamers. Photolysis of the N-2-nitrobenzyl groups with long-wave UV light unmasks the amide backbone and alters the assembly and the biological properties of the macrocyclic β-hairpin peptides. SDS-PAGE studies show that removing the N-2-nitrobenzyl groups alters the assembly of the peptides. MTT conversion and LDH release assays show that decaging the peptides induces cytotoxicity. Circular dichroism studies and dye leakage assays with liposomes reveal that decaging modulates interactions of the peptides with lipid bilayers. Collectively, these studies demonstrate that incorporating N-2-nitrobenzyl groups into macrocyclic β-hairpin peptides provides a new strategy to probe the structures and the biological properties of amyloid oligomers.
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Affiliation(s)
- Patrick J Salveson
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
| | - Sepehr Haerianardakani
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
| | - Alexander Thuy-Boun
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
| | - Adam G Kreutzer
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
| | - James S Nowick
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
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17
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Chen L, Wang H, Zhang DW, Zhou Y, Li ZT. Pt⋯Pt and π–π interactions-induced pleated polymeric foldamers. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Connor AL, Hu T, Detchou CSF, Liu R, Pulavarti SVSRK, Szyperski T, Lu Z, Gong B. Aromatic oligureas as hosts for anions and cations. Chem Commun (Camb) 2018; 52:9905-8. [PMID: 27427283 DOI: 10.1039/c6cc03681c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Aromatic oligoureas 3 and 4 have urea moieties engaging in weak intramolecular H-bonding that constrains their backbones. The shorter 3a and 3b are able to bind chloride and acetate but not their corresponding counterion. The longer 4 binds both an anion and its counterion with the same affinity.
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Affiliation(s)
- Alan L Connor
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
| | - Ting Hu
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Cadnel S F Detchou
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
| | - Rui Liu
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA. and College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Surya V S R K Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
| | - Zhonglin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA. and College of Chemistry, Beijing Normal University, Beijing 100875, China.
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19
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Shi YD, Tang Q, Jiang YF, Pei Q, Tan HW, Lu ZL, Gong B. Effective formation of stable and versatile double-stranded β-sheets templated by a hydrogen-bonded duplex. Chem Commun (Camb) 2018; 54:3719-3722. [DOI: 10.1039/c8cc01564c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
An effective approach to construct stable and versatile double-stranded β-sheets composed of tetra- and penta-peptides through a hydrogen-bonded duplex template has been explored.
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Affiliation(s)
- You-Di Shi
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Quan Tang
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Ya-Fei Jiang
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Qiang Pei
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Hong-Wei Tan
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Zhong-Lin Lu
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Bing Gong
- Key Laboratory of Radiopharmaceuticals
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
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20
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Kreutzer AG, Spencer RK, McKnelly KJ, Yoo S, Hamza IL, Salveson PJ, Nowick JS. A Hexamer of a Peptide Derived from Aβ 16-36. Biochemistry 2017; 56:6061-6071. [PMID: 29028351 PMCID: PMC5689071 DOI: 10.1021/acs.biochem.7b00831] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/09/2017] [Indexed: 11/29/2022]
Abstract
The absence of high-resolution structures of amyloid oligomers constitutes a major gap in our understanding of amyloid diseases. A growing body of evidence indicates that oligomers of the β-amyloid peptide Aβ are especially important in the progression of Alzheimer's disease. In many Aβ oligomers, the Aβ monomer components are thought to adopt a β-hairpin conformation. This paper describes the design and study of a macrocyclic β-hairpin peptide derived from Aβ16-36. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and size exclusion chromatography studies show that the Aβ16-36 β-hairpin peptide assembles in solution to form hexamers, trimers, and dimers. X-ray crystallography reveals that the peptide assembles to form a hexamer in the crystal state and that the hexamer is composed of dimers and trimers. Lactate dehydrogenase release assays show that the oligomers formed by the Aβ16-36 β-hairpin peptide are toxic toward neuronally derived SH-SY5Y cells. Replica-exchange molecular dynamics demonstrates that the hexamer can accommodate full-length Aβ. These findings expand our understanding of the structure, solution-phase behavior, and biological activity of Aβ oligomers and may offer insights into the molecular basis of Alzheimer's disease.
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Affiliation(s)
- Adam G. Kreutzer
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Ryan K. Spencer
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Kate J. McKnelly
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Stan Yoo
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Imane L. Hamza
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Patrick J. Salveson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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21
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Chen KH, Corro KA, Le SP, Nowick JS. X-ray Crystallographic Structure of a Giant Double-Walled Peptide Nanotube Formed by a Macrocyclic β-Sheet Containing Aβ16–22. J Am Chem Soc 2017; 139:8102-8105. [DOI: 10.1021/jacs.7b03890] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin H. Chen
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Kelsey A. Corro
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Stephanie P. Le
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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22
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Hu T, Connor AL, Miller DP, Wang X, Pei Q, Liu R, He L, Zheng C, Zurek E, Lu ZL, Gong B. Helical Folding of Meta-Connected Aromatic Oligoureas. Org Lett 2017; 19:2666-2669. [DOI: 10.1021/acs.orglett.7b01005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ting Hu
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Alan L. Connor
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel P. Miller
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Xiao Wang
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Qiang Pei
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Rui Liu
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Lan He
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
- National Institute for Food and Drug Control, Institute of Chemical Drug Control, TianTanXiLi 2, Beijing, 100050, China
| | - Chong Zheng
- Department
of Chemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Eva Zurek
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Zhong-lin Lu
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
| | - Bing Gong
- College
of Chemistry, Beijing Normal University, 100875 Beijing, China
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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23
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Sarnowski MP, Kang CW, Elbatrawi YM, Wojtas L, Del Valle JR. Peptide N-Amination Supports β-Sheet Conformations. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Matthew P. Sarnowski
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Chang Won Kang
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Yassin M. Elbatrawi
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Juan R. Del Valle
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
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24
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Sarnowski MP, Kang CW, Elbatrawi YM, Wojtas L, Del Valle JR. Peptide N-Amination Supports β-Sheet Conformations. Angew Chem Int Ed Engl 2017; 56:2083-2086. [DOI: 10.1002/anie.201609395] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/12/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Matthew P. Sarnowski
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Chang Won Kang
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Yassin M. Elbatrawi
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Juan R. Del Valle
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
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25
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Kreutzer AG, Yoo S, Spencer RK, Nowick JS. Stabilization, Assembly, and Toxicity of Trimers Derived from Aβ. J Am Chem Soc 2017; 139:966-975. [PMID: 28001392 PMCID: PMC5256483 DOI: 10.1021/jacs.6b11748] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Oligomers
of the β-amyloid peptide Aβ have emerged
as important contributors to neurodegeneration in Alzheimer’s
disease. Mounting evidence suggests that Aβ trimers and higher-order
oligomers derived from trimers have special significance in the early
stages of Alzheimer’s disease. Elucidating the structures of
these trimers and higher-order oligomers is paramount for understanding
their role in neurodegeneration. This paper describes the design,
synthesis, X-ray crystallographic structures, and biophysical and
biological properties of two stabilized trimers derived from the central
and C-terminal regions of Aβ. These triangular
trimers are stabilized through three disulfide cross-links between
the monomer subunits. The X-ray crystallographic structures reveal
that the stabilized trimers assemble hierarchically to form hexamers,
dodecamers, and annular porelike structures. Solution-phase biophysical
studies reveal that the stabilized trimers assemble in solution to
form oligomers that recapitulate some of the higher-order assemblies
observed crystallographically. The stabilized trimers share many of
the biological characteristics of oligomers of full-length Aβ,
including toxicity toward a neuronally derived human cell line, activation
of caspase-3 mediated apoptosis, and reactivity with the oligomer-specific
antibody A11. These studies support the biological significance of
the triangular trimer assembly of Aβ β-hairpins and may
offer a deeper understanding of the molecular basis of Alzheimer’s
disease.
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Affiliation(s)
- Adam G Kreutzer
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Stan Yoo
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Ryan K Spencer
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
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26
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Yoo S, Kreutzer AG, Truex NL, Nowick JS. Square channels formed by a peptide derived from transthyretin. Chem Sci 2016; 7:6946-6951. [PMID: 28451128 PMCID: PMC5355858 DOI: 10.1039/c6sc01927g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/28/2016] [Indexed: 01/03/2023] Open
Abstract
High-resolution structures of peptide supramolecular assemblies are key to understanding amyloid diseases and designing peptide-based materials. This paper explores the supramolecular assembly of a macrocyclic β-sheet peptide derived from transthyretin (TTR). The peptide mimics the β-hairpin formed by the β-strands G and H of TTR, which form the interface of the TTR tetramer. X-ray crystallography reveals that the peptide does not form a tetramer, but rather assembles to form square channels. The square channels are formed by extended networks of β-sheets and pack in a "tilted windows" pattern. This unexpected structure represents an emergent property of the peptide and broadens the scope of known supramolecular assemblies of β-sheets.
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Affiliation(s)
- Stan Yoo
- Department of Chemistry , University of California , Irvine , California 92697-2025 , USA .
| | - Adam G Kreutzer
- Department of Chemistry , University of California , Irvine , California 92697-2025 , USA .
| | - Nicholas L Truex
- Department of Chemistry , University of California , Irvine , California 92697-2025 , USA .
| | - James S Nowick
- Department of Chemistry , University of California , Irvine , California 92697-2025 , USA .
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27
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Kreutzer AG, Hamza IL, Spencer RK, Nowick JS. X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an Aβ17-36 β-Hairpin. J Am Chem Soc 2016; 138:4634-42. [PMID: 26967810 PMCID: PMC4831588 DOI: 10.1021/jacs.6b01332] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
High-resolution structures of oligomers
formed by the β-amyloid
peptide Aβ are needed to understand the molecular basis of Alzheimer’s
disease and develop therapies. This paper presents the X-ray crystallographic
structures of oligomers formed by a 20-residue peptide segment derived
from Aβ. The development of a peptide in which Aβ17–36 is stabilized as a β-hairpin is described,
and the X-ray crystallographic structures of oligomers it forms are
reported. Two covalent constraints act in tandem to stabilize the
Aβ17–36 peptide in a hairpin conformation:
a δ-linked ornithine turn connecting positions 17 and 36 to
create a macrocycle and an intramolecular disulfide linkage between
positions 24 and 29. An N-methyl group at position
33 blocks uncontrolled aggregation. The peptide readily crystallizes
as a folded β-hairpin, which assembles hierarchically in the
crystal lattice. Three β-hairpin monomers assemble to form a
triangular trimer, four trimers assemble in a tetrahedral arrangement
to form a dodecamer, and five dodecamers pack together to form an
annular pore. This hierarchical assembly provides a model, in which
full-length Aβ transitions from an unfolded monomer to a folded
β-hairpin, which assembles to form oligomers that further pack
to form an annular pore. This model may provide a better understanding
of the molecular basis of Alzheimer’s disease at atomic resolution.
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Affiliation(s)
- Adam G Kreutzer
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Imane L Hamza
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Ryan K Spencer
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
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28
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Salveson PJ, Spencer RK, Nowick JS. X-ray Crystallographic Structure of Oligomers Formed by a Toxic β-Hairpin Derived from α-Synuclein: Trimers and Higher-Order Oligomers. J Am Chem Soc 2016; 138:4458-67. [PMID: 26926877 PMCID: PMC4825732 DOI: 10.1021/jacs.5b13261] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Oligomeric
assemblies of the protein α-synuclein are thought
to cause neurodegeneration in Parkinson’s disease and related
synucleinopathies. Characterization of α-synuclein oligomers
at high resolution is an outstanding challenge in the field of structural
biology. The absence of high-resolution structures of oligomers formed
by α-synuclein impedes understanding the synucleinopathies at
the molecular level. This paper reports the X-ray crystallographic
structure of oligomers formed by a peptide derived from residues 36–55
of α-synuclein. The peptide 1a adopts a β-hairpin
structure, which assembles in a hierarchical fashion. Three β-hairpins
assemble to form a triangular trimer. Three copies of the triangular
trimer assemble to form a basket-shaped nonamer. Two nonamers pack
to form an octadecamer. Molecular modeling suggests that full-length
α-synuclein may also be able to assemble in this fashion. Circular
dichroism spectroscopy demonstrates that peptide 1a interacts
with anionic lipid bilayer membranes, like oligomers of full-length
α-synuclein. LDH and MTT assays demonstrate that peptide 1a is toxic toward SH-SY5Y cells. Comparison of peptide 1a to homologues suggests that this toxicity results from
nonspecific interactions with the cell membrane. The oligomers formed
by peptide 1a are fundamentally different than the proposed
models of the fibrils formed by α-synuclein and suggest that
α-Syn36–55, rather than the NAC, may nucleate
oligomer formation.
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Affiliation(s)
- Patrick J Salveson
- Department of Chemistry, University of California Irvine , Irvine, California 92697-2025, United States
| | - Ryan K Spencer
- Department of Chemistry, University of California Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California Irvine , Irvine, California 92697-2025, United States
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29
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Liu R, Chen S, Cheng S, Baker ES, Smith RD, Zeng XC, Gong B. Surprising impact of remote groups on the folding--unfolding and dimer-chain equilibria of bifunctional H-bonding unimers. Chem Commun (Camb) 2016; 52:3773-6. [PMID: 26830456 PMCID: PMC5168931 DOI: 10.1039/c6cc00224b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligoamide 1, consisting of two H-bonding units linked by a trimethylene linker, was previously found to form a very stable, folded dimer. In this work, replacing the side chains and end groups of 1 led to derivatives that show the surprising impact of end groups on the folding and dimer-chain equilibria of the resultant molecules.
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Affiliation(s)
- Rui Liu
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA. and College of Chemistry, Beijing Normal University, Beijing 100875, China
| | | | - Shuang Cheng
- Kuang Yaming Honors School, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Erin S Baker
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Richard D Smith
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA. and College of Chemistry, Beijing Normal University, Beijing 100875, China
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30
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Lengyel GA, Reinert ZE, Griffith BD, Horne WS. Comparison of backbone modification in protein β-sheets by α→γ residue replacement and α-residue methylation. Org Biomol Chem 2015; 12:5375-81. [PMID: 24909436 DOI: 10.1039/c4ob00886c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The mimicry of protein tertiary structure by oligomers with unnatural backbones is a significant contemporary research challenge. Among common elements of secondary structure found in natural proteins, sheets have proven the most difficult to address. Here, we report the systematic comparison of different strategies for peptide backbone modification in β-sheets with the goal of identifying the best method for replacing a multi-stranded sheet in a protein tertiary fold. The most effective sheet modifications examined led to native-like tertiary folding behavior with a thermodynamic folded stability comparable to the prototype protein on which the modified backbones are based.
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Affiliation(s)
- George A Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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31
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Spencer RK, Kreutzer AG, Salveson PJ, Li H, Nowick JS. X-ray Crystallographic Structures of Oligomers of Peptides Derived from β2-Microglobulin. J Am Chem Soc 2015; 137:6304-11. [PMID: 25915729 DOI: 10.1021/jacs.5b01673] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid diseases such as Alzheimer's disease, Parkinson's disease, and type II diabetes share common features of toxic soluble protein oligomers. There are no structures at atomic resolution of oligomers formed by full-length amyloidogenic peptides and proteins, and only a few structures of oligomers formed by peptide fragments. The paucity of structural information provides a fundamental roadblock to understanding the pathology of amyloid diseases and developing preventions or therapies. Here, we present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of β2-microglobulin (β2m). Each macrocyclic peptide contains the heptapeptide sequence β2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form β-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of β-sheets. These structures illustrate a common theme in which dimer and trimer subunits further associate to form a hydrophobic core. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers. A cocrystallization experiment in which a dodecamer-forming peptide recruits a hexamer-forming peptide to form mixed dodecamers demonstrates that one species can dictate the oligomerization of another. These findings should also be relevant to the formation of oligomers of full-length peptides and proteins in amyloid diseases.
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Affiliation(s)
- Ryan K Spencer
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Adam G Kreutzer
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Patrick J Salveson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Hao Li
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
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Liu R, Connor AL, Al-mkhaizim FY, Gong B. Aromatic oligoamides with increased backbone flexibility: improved synthetic efficiencies, solvent-dependent folding and cooperative conformational transitions. NEW J CHEM 2015. [DOI: 10.1039/c4nj01820f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 15-residue aromatic oligoamide with a backbone of increased flexibility exhibits solvent- and temperature-dependent folding and highly cooperative conformational transition.
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Affiliation(s)
- Rui Liu
- Department of Chemistry
- the State University of New York at Buffalo
- Buffalo
- USA
- College of Chemistry
| | - Alan L. Connor
- Department of Chemistry
- the State University of New York at Buffalo
- Buffalo
- USA
| | | | - Bing Gong
- Department of Chemistry
- the State University of New York at Buffalo
- Buffalo
- USA
- College of Chemistry
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33
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Mout R, Tonga GY, Ray M, Moyano DF, Xing Y, Rotello VM. Environmentally responsive histidine-carboxylate zipper formation between proteins and nanoparticles. NANOSCALE 2014; 6:8873-7. [PMID: 24960536 PMCID: PMC4113908 DOI: 10.1039/c4nr02097a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Interfacing synthetic materials with biomacromolecules provides new systems for biological applications. We report the creation of a reversible multivalent supramolecular "zipper" recognition motif between gold nanoparticles and proteins. In this assembly, carboxylate-functionalized nanoparticles interact strongly with oligohistidine tags. This interaction can be tuned through His-tag length, and offers unique binding profiles based on the pH and electrolyte concentration of the medium.
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Affiliation(s)
- Rubul Mout
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA.
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Spencer RK, Li H, Nowick JS. X-ray crystallographic structures of trimers and higher-order oligomeric assemblies of a peptide derived from Aβ(17-36). J Am Chem Soc 2014; 136:5595-8. [PMID: 24669800 PMCID: PMC4004244 DOI: 10.1021/ja5017409] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A peptide derived
from Aβ17–36 crystallizes
to form trimers that further associate to form higher-order oligomers.
The trimers consist of three highly twisted β-hairpins in a
triangular arrangement. Two trimers associate face-to-face in the
crystal lattice to form a hexamer; four trimers in a tetrahedral arrangement
about a central cavity form a dodecamer. These structures provide
a working model for the structures of oligomers associated with neurodegeneration
in Alzheimer’s disease.
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Affiliation(s)
- Ryan K Spencer
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
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