1
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Zheng X, Ni Z, Pei Q, Wang M, Tan J, Bai S, Shi F, Ye S. Probing the Molecular Structure and Dynamics of Membrane-Bound Proteins during Misfolding Processes by Sum-Frequency Generation Vibrational Spectroscopy. Chempluschem 2024; 89:e202300684. [PMID: 38380553 DOI: 10.1002/cplu.202300684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Protein misfolding and amyloid formation are implicated in the protein dysfunction, but the underlying mechanism remains to be clarified due to the lack of effective tools for detecting the transient intermediates. Sum frequency generation vibrational spectroscopy (SFG-VS) has emerged as a powerful tool for identifying the structure and dynamics of proteins at the interfaces. In this review, we summarize recent SFG-VS studies on the structure and dynamics of membrane-bound proteins during misfolding processes. This paper first introduces the methods for determining the secondary structure of interfacial proteins: combining chiral and achiral spectra of amide A and amide I bands and combining amide I, amide II, and amide III spectral features. To demonstrate the ability of SFG-VS in investigating the interfacial protein misfolding and amyloid formation, studies on the interactions between different peptides/proteins (islet amyloid polypeptide, amyloid β, prion protein, fused in sarcoma protein, hen egg-white lysozyme, fusing fusion peptide, class I hydrophobin SC3 and class II hydrophobin HFBI) and surfaces such as lipid membranes are discussed. These molecular-level studies revealed that SFG-VS can provide a unique understanding of the mechanism of interfacial protein misfolding and amyloid formation in real time, in situ and without any exogenous labeling.
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Affiliation(s)
- Xiaoxuan Zheng
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Zijian Ni
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Quanbing Pei
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Mengmeng Wang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Junjun Tan
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Shiyu Bai
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Fangwen Shi
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Shuji Ye
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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2
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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3
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Farrell KM, Fields CR, Dicke SS, Zanni MT. Simultaneously Measured Kinetics of Two Amyloid Polymorphs Using Cross Peak Specific 2D IR Spectroscopy. J Phys Chem Lett 2023; 14:11750-11757. [PMID: 38117179 PMCID: PMC11163371 DOI: 10.1021/acs.jpclett.3c02698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The origin of in vitro amyloid fibril polymorphs is debated, in part, because few techniques can simultaneously monitor the formation kinetics of multiple amyloid polymorphs. Using a cross-peak specific polarization scheme, ⟨0°,0°,60°,-60°⟩, we resolve 22 previously unseen cross peaks in the 2D IR spectra of amyloid fibrils formed by the human islet amyloid polypeptide (hIAPP). Those cross peaks include a subset assigned to a second fibril polymorph, which forms on a slower time scale. We simulated the data with three different kinetic models for polymorph formation. Only a model based on secondary nucleation reproduces the cross peak kinetics. These experiments are evidence that fibrils formed by secondary nucleation have a different polymorphic structure than the parent fibrils and illustrate the enhanced structural resolution of this new cross peak specific polarization scheme.
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Affiliation(s)
- Kieran M Farrell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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4
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Harper M, Nudurupati U, Workman RJ, Lakoba TI, Perez N, Nelson D, Ou Y, Punihaole D. Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy. J Chem Phys 2023; 159:225101. [PMID: 38078532 PMCID: PMC10720587 DOI: 10.1063/5.0177437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
We present structural models for three different amyloid fibril polymorphs prepared from amylin20-29 (sequence SNNFGAILSS) and amyloid-β25-35 (Aβ25-35) (sequence GSNKGAIIGLM) peptides. These models are based on the amide C=O bond and Ramachandran ψ-dihedral angle data from Raman spectroscopy, which were used as structural constraints to guide molecular dynamics (MD) simulations. The resulting structural models indicate that the basic structural motif of amylin20-29 and Aβ25-35 fibrils is extended β-strands. Our data indicate that amylin20-29 forms both antiparallel and parallel β-sheet fibril polymorphs, while Aβ25-35 forms a parallel β-sheet fibril structure. Overall, our work lays the foundation for using Raman spectroscopy in conjunction with MD simulations to determine detailed molecular-level structural models of amyloid fibrils in a manner that complements gold-standard techniques, such as solid-state nuclear magnetic resonance and cryogenic electron microscopy.
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Affiliation(s)
- Madeline Harper
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Uma Nudurupati
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Riley J. Workman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Taras I. Lakoba
- Department of Mathematics and Statistics, University of Vermont, Burlington, Vermont 05405, USA
| | - Nicholas Perez
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Delaney Nelson
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Yangguang Ou
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - David Punihaole
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
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5
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Khatri V, Jafari M, Gaudreault R, Beauregard M, Siaj M, Archambault D, Loranger É, Bourgault S. Bionanocomposites with Enhanced Physical Properties from Curli Amyloid Assemblies and Cellulose Nanofibrils. Biomacromolecules 2023; 24:5290-5302. [PMID: 37831506 DOI: 10.1021/acs.biomac.3c00786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Proteinaceous amyloid fibrils are one of the stiffest biopolymers due to their extensive cross-β-sheet quaternary structure, whereas cellulose nanofibrils (CNFs) exhibit interesting properties associated with their nanoscale size, morphology, large surface area, and biodegradability. Herein, CNFs were supplemented with amyloid fibrils assembled from the Curli-specific gene A (CsgA) protein, the main component of bacterial biofilms. The resulting composites showed superior mechanical properties, up to a 7-fold increase compared to unmodified CNF films. Wettability and thermogravimetric analyses demonstrated high surface hydrophobicity and robust thermal tolerance. Bulk spectroscopic characterization of CNF-CsgA films revealed key insights into the molecular organization within the bionanocomposites. Atomic force microscopy and photoinduced force microscopy revealed the high-resolution location of curli assemblies into the CNF films. This novel sustainable and cost-effective CNF-based bionanocomposites supplemented with intertwined bacterial amyloid fibrils opens novel directions for environmentally friendly applications demanding high mechanical, water-repelling properties, and thermal resistance.
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Affiliation(s)
- Vinay Khatri
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
- Department of Biological Sciences, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
- Québec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, Quebec H3C 3P8, Canada
| | - Maziar Jafari
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
| | - Roger Gaudreault
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
| | - Marc Beauregard
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 Des Forges, Trois-Rivières, Quebec G8Z 4M3, Canada
- Innovations Institute in Ecomatériaux, Ecoproduits et Ecoenergies (I2E3), Université du Québec à Trois-Rivières, 3351 Des Forges, Trois-Rivières, Québec G8Z 4M3, Canada
| | - Mohamed Siaj
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
| | - Denis Archambault
- Department of Biological Sciences, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
| | - Éric Loranger
- Innovations Institute in Ecomatériaux, Ecoproduits et Ecoenergies (I2E3), Université du Québec à Trois-Rivières, 3351 Des Forges, Trois-Rivières, Québec G8Z 4M3, Canada
- Department of Mechanical Engineering, Université du Québec à Trois-Rivières, 3351 Des Forges, Trois-Rivières, Quebec G8Z 4M3, Canada
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montreal, Quebec H3C 3P8, Canada
- Québec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, Quebec H3C 3P8, Canada
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6
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Sinha N, Zahra T, Gahane AY, Rout B, Bhattacharya A, Basu S, Chakrabarti A, Thakur AK. Protein reservoirs of seeds are amyloid composites employed differentially for germination and seedling emergence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:329-346. [PMID: 37675599 DOI: 10.1111/tpj.16429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/15/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Seed protein localization in seed storage protein bodies (SSPB) and their significance in germination are well recognized. SSPB are spherical and contain an assembly of water-soluble and salt-soluble proteins. Although the native structures of some SSPB proteins are explored, their structural arrangement to the functional correlation in SSPB remains unknown. SSPB are morphologically analogous to electron-dense amyloid-containing structures reported in other organisms. Here, we show that wheat, mungbean, barley, and chickpea SSPB exhibit a speckled pattern of amyloids interspersed in an amyloid-like matrix along with native structures, suggesting the composite nature of SSPB. This is confirmed by multispectral imaging methods, electron microscopy, infrared, and X-ray diffraction analysis, using in situ tissue sections, ex vivo protoplasts, and in vitro SSPB. Laser capture microdissection coupled with peptide fingerprinting has shown that globulin 1 and 3 in wheat, and 8S globulin and conglycinin in mungbean are the major amyloidogenic proteins. The amyloid composites undergo a sustained degradation during germination and seedling growth, facilitated by an intricate interplay of plant hormones and proteases. These results would lay down the foundation for understanding the amyloid composite structure during SSPB biogenesis and its evolution across the plant kingdom and have implications in both basic and applied plant biology.
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Affiliation(s)
- Nabodita Sinha
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
| | - Talat Zahra
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
| | - Avinash Yashwant Gahane
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
| | - Bandita Rout
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
| | | | | | | | - Ashwani Kumar Thakur
- Department of Biological Sciences and Bioengineering, The Mehta Family Centre For Engineering in Medicine, Indian Institute of Technology, Kanpur, Uttar Pradesh, 208016, India
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7
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Huang G, Tang H, Liu Y, Zhang C, Ke PC, Sun Y, Ding F. Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth. J Chem Inf Model 2023; 63:5863-5873. [PMID: 37651616 PMCID: PMC10529695 DOI: 10.1021/acs.jcim.3c00898] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Rapid growth of amyloid fibrils via a seeded conformational conversion of monomers is a critical step of fibrillization and important for disease transmission and progression. Amyloid fibrils often display diverse morphologies with distinct populations, and yet the molecular mechanisms of fibril elongation and their corresponding morphological dependence remain poorly understood. Here, we computationally investigated the single-molecular growth of two experimentally resolved human islet amyloid polypeptide fibrils of different morphologies. In both cases, the incorporation of monomers into preformed fibrils was observed. The conformational conversion dynamics was characterized by a small number of fibril growth intermediates. Fibril morphology affected monomer binding at fibril elongation and lateral surfaces as well as the seeded conformational conversion dynamics at the fibril ends, resulting in different fibril elongation rates and populations. We also observed an asymmetric fibril growth as in our prior experiments, attributing to differences of two fibril ends in terms of their local surface curvatures and exposed hydrogen-bond donors and acceptors. Together, our mechanistic findings afforded a theoretical basis for delineating different amyloid strains-entailed divergent disease progression.
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Affiliation(s)
- Gangtong Huang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Chi Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- The Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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8
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Unnikrishnan AC, Balamurugan K, Shanmugam G. Structural Insights into the Amyloid Fibril Polymorphism Using an Isotope-Edited Vibrational Circular Dichroism Study at the Amino Acid Residue Level. J Phys Chem B 2023; 127:7674-7684. [PMID: 37667494 DOI: 10.1021/acs.jpcb.3c03437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Polymorphism is common in both in vitro and in vivo amyloid fibrils formed by the same peptide/protein. However, the differences in their self-assembled structures at the amino acid level remain poorly understood. In this study, we utilized isotope-edited vibrational circular dichroism (VCD) on a well-known amyloidogenic peptide fragment (N22FGAIL27) of human islet amyloid polypeptide (IAPf) to investigate the structural polymorphism. Two individual isotope-labeled IAPf peptides were used, with a 13C label on the carbonyl group of phenylalanine (IAPf-F) and glycine (IAPf-G). We compared the amyloid-like nanofibril of IAPf induced by solvent casting (fibril B) with our previous report on the same IAPf peptide fibril but with a different fibril morphology (fibril A) formed in an aqueous buffer solution. Fibril B consisted of entangled, laterally fused amyloid-like nanofibrils with a relatively shorter diameter (15-50 nm) and longer length (several microns), while fibril A displayed nanofibrils with a higher diameter (30-60 nm) and shorter length (500 nm-2 μm). The isotope-edited VCD analysis indicated that fibrils B consisted of anti-parallel β-sheet arrangements with glycine residues in the registry and phenylalanine residues out of the registry, which was significantly different from fibrils A, where a mixture of parallel β-sheet and turn structure with the registry at phenylalanine and glycine residues was observed. The VCD analysis, therefore, suggests that polymorphism in amyloid-like fibrils can be attributed to the difference in the packing/arrangement of the individual β-strands in the β-sheet and the difference in the amino acid registry. Our findings provide insights into the structural aspects of fibril polymorphism related to various amyloid diseases and may aid in designing amyloid fibril inhibitors for therapeutic purposes.
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Affiliation(s)
- Anagha C Unnikrishnan
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research (CSIR)─Central Leather Research Institute (CLRI), Adyar, Chennai 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kanagasabai Balamurugan
- Centre for High Computing, Council of Scientific and Industrial Research (CSIR)─Central Leather Research Institute (CLRI), Adyar, Chennai 600020, India
| | - Ganesh Shanmugam
- Organic & Bioorganic Chemistry Laboratory, Council of Scientific and Industrial Research (CSIR)─Central Leather Research Institute (CLRI), Adyar, Chennai 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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9
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Muñoz-Gutiérrez C, Adasme-Carreño F, Alzate-Morales J, Ireta J. Effect of strand register in the stability and reactivity of crystals from peptides forming amyloid fibrils. Phys Chem Chem Phys 2023; 25:23885-23893. [PMID: 37642522 DOI: 10.1039/d3cp01762a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Amyloids are cytotoxic protein aggregates that deposit in human tissues, leading to several health disorders. Their aggregates can also exhibit catalytic properties, and they have been used as candidates for the development of functional biomaterials. Despite being polymorphic, amyloids often assemble as cross-β fibrils formed by in-register β sheet layers. Recent studies of some amyloidogenic protein segments revealed that they crystallize as antiparallel out-of-register β sheets. Such arrangement has been proposed to be responsible for the cytotoxicity in amyloid diseases, however, there is still no consensus on the molecular mechanism. Interestingly, two amyloidogenic peptide segments, NFGAILS and FGAILSS, arrange into out-of-register and in-register β sheets, respectively, even though they solely differ by one aminoacid residue at both termini. In this work, we used density functional theory (DFT) to address how the strand register contributes into the packing and molecular properties of the NFGAILS and FGAILSS crystals. Our results show that the out-of-register structure is substantially more stable, at 0 K, than the in-register one due to stronger inter-strand contacts. Based on an analysis of the electrostatic potential of the crystal slabs, it is suggested that the out-of-register may potentially interact with negatively charged groups, like those found in cell membranes. Moreover, calculated reactivity descriptors indicate a similar outcome, where only the out-of-register peptide exhibits intrinsic reactive surface sites at the exposed amine and carboxylic groups. It is therefore suggested that the out-of-register arrangement may indeed be crucial for amyloid cytotoxicity. The findings presented here could help to further our understanding of amyloid aggregation, function, and toxicity.
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Affiliation(s)
- Camila Muñoz-Gutiérrez
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Box 721, Talca, Chile
| | - Francisco Adasme-Carreño
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile
- Laboratorio de Bioinformática y Química Computacional (LBQC), Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480112, Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Box 721, Talca, Chile
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, Ciudad de México 09340, Mexico.
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10
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Horváth D, Dürvanger Z, K Menyhárd D, Sulyok-Eiler M, Bencs F, Gyulai G, Horváth P, Taricska N, Perczel A. Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation. Nat Commun 2023; 14:4621. [PMID: 37528104 PMCID: PMC10394066 DOI: 10.1038/s41467-023-40294-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/21/2023] [Indexed: 08/03/2023] Open
Abstract
A large group of hormones are stored as amyloid fibrils in acidic secretion vesicles before they are released into the bloodstream and readopt their functional state. Here, we identify an evolutionarily conserved hexapeptide sequence as the major aggregation-prone region (APR) of gastrointestinal peptides of the glucagon family: xFxxWL. We determine nine polymorphic crystal structures of the APR segments of glucagon-like peptides 1 and 2, and exendin and its derivatives. We follow amyloid formation by CD, FTIR, ThT assays, and AFM. We propose that the pH-dependent changes of the protonation states of glutamate/aspartate residues of APRs initiate switching between the amyloid and the folded, monomeric forms of the hormones. We find that pH sensitivity diminishes in the absence of acidic gatekeepers and amyloid formation progresses over a broad pH range. Our results highlight the dual role of short aggregation core motifs in reversible amyloid formation and receptor binding.
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Affiliation(s)
- Dániel Horváth
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Zsolt Dürvanger
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Dóra K Menyhárd
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Máté Sulyok-Eiler
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Fruzsina Bencs
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Gergő Gyulai
- Laboratory of Interfaces and Nanostructures, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre utca 9, Budapest, 1092, Hungary
| | - Nóra Taricska
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Perczel
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.
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11
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Pal I, Dey SG. The Role of Heme and Copper in Alzheimer's Disease and Type 2 Diabetes Mellitus. JACS AU 2023; 3:657-681. [PMID: 37006768 PMCID: PMC10052274 DOI: 10.1021/jacsau.2c00572] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/19/2023]
Abstract
Beyond the well-explored proposition of protein aggregation or amyloidosis as the central event in amyloidogenic diseases like Alzheimer's Disease (AD), and Type 2 Diabetes Mellitus (T2Dm); there are alternative hypotheses, now becoming increasingly evident, which suggest that the small biomolecules like redox noninnocent metals (Fe, Cu, Zn, etc.) and cofactors (Heme) have a definite influence in the onset and extent of such degenerative maladies. Dyshomeostasis of these components remains as one of the common features in both AD and T2Dm etiology. Recent advances in this course reveal that the metal/cofactor-peptide interactions and covalent binding can alarmingly enhance and modify the toxic reactivities, oxidize vital biomolecules, significantly contribute to the oxidative stress leading to cell apoptosis, and may precede the amyloid fibrils formation by altering their native folds. This perspective highlights this aspect of amyloidogenic pathology which revolves around the impact of the metals and cofactors in the pathogenic courses of AD and T2Dm including the active site environments, altered reactivities, and the probable mechanisms involving some highly reactive intermediates as well. It also discusses some in vitro metal chelation or heme sequestration strategies which might serve as a possible remedy. These findings might open up a new paradigm in our conventional understanding of amyloidogenic diseases. Moreover, the interaction of the active sites with small molecules elucidates potential biochemical reactivities that can inspire designing of drug candidates for such pathologies.
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Affiliation(s)
- Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick
Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick
Road, Jadavpur, Kolkata 700032, India
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12
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Understanding the mechanism of amylin aggregation: From identifying crucial segments to tracing dominant sequential events to modeling potential aggregation suppressors. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140866. [PMID: 36272537 DOI: 10.1016/j.bbapap.2022.140866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022]
Abstract
One of the most abundant, prevailing, and life-threatening human diseases that are currently baffling the scientific community is type 2 diabetes (T2D). The self-association of human amylin has been implicated in the pathogenesis of T2D, though with an inconclusive understanding of the mechanism. Hence, we focused on the characterization of the conformational ensembles of all the species that are believed to define the structural polymorphism of the aggregation process - the functional monomeric, the initially self-associated oligomeric, and the structured protofibril - by employing near-equilibrium, non-equilibrium, and equilibrium atomistic simulations on the sporadic, two familial variants (S20G and G33R), and their proline-substituted forms (S20P and G33P). The dynamic near-equilibrium assays hint toward - the abundance of helical conformation in the monomeric state, the retainment of the helicity in the initial self-associated oligomeric phase pointing toward the existence of the helix-helix association mechanism, the difference in preference of specific segments to have definite secondary structural features, the phase-dependent variability in the dominance of specific segments and mutation sites, and the simultaneous presence of generic and unique features among various sequences. Furthermore, the non-equilibrium pulling assays exemplify a generic sequential unzipping mechanism of the protofibrils, however, the sequence-dependent uniqueness comes from the difference in location and magnitude of the control of a specific terminus. Importantly, the equilibrium thermodynamic assays efficiently rank order the potential of aggregability among sequences and consequently suggests the probability of designing effective aggregation suppressors against sporadic and familial amylin variants incorporating proline as the mutation.
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13
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Das A, Shah M, Saraogi I. Molecular Aspects of Insulin Aggregation and Various Therapeutic Interventions. ACS BIO & MED CHEM AU 2022; 2:205-221. [PMID: 37101572 PMCID: PMC10114644 DOI: 10.1021/acsbiomedchemau.1c00054] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Protein aggregation leading to the formation of amyloid fibrils has various adverse effects on human health ranging from fatigue and numbness to organ failure and death in extreme cases. Insulin, a peptide hormone commonly used to treat diabetes, undergoes aggregation at the site of repeated injections in diabetic patients as well as during its industrial production and transport. The reduced bioavailability of insulin due to aggregation hinders the proper control of glucose levels in diabetic patients. Thus, it is necessary to develop rational approaches for inhibiting insulin aggregation, which in turn requires a detailed understanding of the mechanism of fibrillation. Given the relative simplicity of insulin and ease of access, insulin has also served as a model system for studying amyloids. Approaches to inhibit insulin aggregation have included the use of natural molecules, synthetic peptides or small molecules, and bacterial chaperone machinery. This review focuses on insulin aggregation with an emphasis on its mechanism, the structural features of insulin fibrils, and the reported inhibitors that act at different stages in the aggregation pathway. We discuss molecules that can serve as leads for improved inhibitors for use in commercial insulin formulations. We also discuss the aggregation propensity of fast- and slow-acting insulin biosimilars, commonly administered to diabetic patients. The development of better insulin aggregation inhibitors and insights into their mechanism of action will not only aid diabetic therapies, but also enhance our knowledge of protein amyloidosis.
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Affiliation(s)
- Anirban Das
- Department
of Chemistry and Department of Biological Sciences, Indian
Institute of Science Education and Research
Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Mosami Shah
- Department
of Chemistry and Department of Biological Sciences, Indian
Institute of Science Education and Research
Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department
of Chemistry and Department of Biological Sciences, Indian
Institute of Science Education and Research
Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
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14
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Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
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15
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Willbold D, Strodel B, Schröder GF, Hoyer W, Heise H. Amyloid-type Protein Aggregation and Prion-like Properties of Amyloids. Chem Rev 2021; 121:8285-8307. [PMID: 34137605 DOI: 10.1021/acs.chemrev.1c00196] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review will focus on the process of amyloid-type protein aggregation. Amyloid fibrils are an important hallmark of protein misfolding diseases and therefore have been investigated for decades. Only recently, however, atomic or near-atomic resolution structures have been elucidated from various in vitro and ex vivo obtained fibrils. In parallel, the process of fibril formation has been studied in vitro under highly artificial but comparatively reproducible conditions. The review starts with a summary of what is known and speculated from artificial in vitro amyloid-type protein aggregation experiments. A partially hypothetic fibril selection model will be described that may be suitable to explain why amyloid fibrils look the way they do, in particular, why at least all so far reported high resolution cryo-electron microscopy obtained fibril structures are in register, parallel, cross-β-sheet fibrils that mostly consist of two protofilaments twisted around each other. An intrinsic feature of the model is the prion-like nature of all amyloid assemblies. Transferring the model from the in vitro point of view to the in vivo situation is not straightforward, highly hypothetic, and leaves many open questions that need to be addressed in the future.
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Affiliation(s)
- Dieter Willbold
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.,Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia
| | - Birgit Strodel
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Henrike Heise
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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16
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Phyo P, Zhao X, Templeton AC, Xu W, Cheung JK, Su Y. Understanding molecular mechanisms of biologics drug delivery and stability from NMR spectroscopy. Adv Drug Deliv Rev 2021; 174:1-29. [PMID: 33609600 DOI: 10.1016/j.addr.2021.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/20/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
Protein therapeutics carry inherent limitations of membrane impermeability and structural instability, despite their predominant role in the modern pharmaceutical market. Effective formulations are needed to overcome physiological and physicochemical barriers, respectively, for improving bioavailability and stability. Knowledge of membrane affinity, cellular internalization, encapsulation, and release of drug-loaded carrier vehicles uncover the structural basis for designing and optimizing biopharmaceuticals with enhanced delivery efficiency and therapeutic efficacy. Understanding stabilizing and destabilizing interactions between protein drugs and formulation excipients provide fundamental mechanisms for ensuring the stability and quality of biological products. This article reviews the molecular studies of biologics using solution and solid-state NMR spectroscopy on structural attributes pivotal to drug delivery and stability. In-depth investigation of the structure-function relationship of drug delivery systems based on cell-penetrating peptides, lipid nanoparticles and polymeric colloidal, and biophysical and biochemical stability of peptide, protein, monoclonal antibody, and vaccine, as the integrative efforts on drug product design, will be elaborated.
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Affiliation(s)
- Pyae Phyo
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Xi Zhao
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Jason K Cheung
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States.
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17
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Fibrilar Polymorphism of the Bacterial Extracellular Matrix Protein TasA. Microorganisms 2021; 9:microorganisms9030529. [PMID: 33806534 PMCID: PMC8000256 DOI: 10.3390/microorganisms9030529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
Functional amyloid proteins often appear as fibers in extracellular matrices of microbial soft colonies. In contrast to disease-related amyloid structures, they serve a functional goal that benefits the organism that secretes them, which is the reason for the title “functional”. Biofilms are a specific example of a microbial community in which functional amyloid fibers play a role. Functional amyloid proteins contribute to the mechanical stability of biofilms and mediate the adhesion of the cells to themselves as well as to surfaces. Recently, it has been shown that functional amyloid proteins also play a regulatory role in biofilm development. TasA is the major proteinaceous fibrilar component of the extracellular matrix of biofilms made of the soil bacterium and Gram-positive Bacillus subtilis. We have previously shown, as later corroborated by others, that in acidic solutions, TasA forms compact aggregates that are composed of tangled fibers. Here, we show that in a neutral pH and above a certain TasA concentration, the fibers of TasA are elongated and straight and that they bundle up in highly concentrated salt solutions. TasA fibers resemble the canonic amyloid morphology; however, these fibers also bear an interesting nm-scale periodicity along the fiber axis. At the molecular level, TasA fibers contain a twisted β-sheet structure, as indicated by circular dichroism measurements. Our study shows that the morphology of TasA fibers depends on the environmental conditions. Different fibrilar morphologies may be related with different functional roles in biofilms, ranging from granting biofilms with a mechanical support to acting as antibiotic agents.
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18
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Adamcik J, Ruggeri FS, Berryman JT, Zhang A, Knowles TPJ, Mezzenga R. Evolution of Conformation, Nanomechanics, and Infrared Nanospectroscopy of Single Amyloid Fibrils Converting into Microcrystals. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002182. [PMID: 33511004 PMCID: PMC7816722 DOI: 10.1002/advs.202002182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/04/2020] [Indexed: 06/12/2023]
Abstract
Nanomechanical properties of amyloid fibrils and nanocrystals depend on their secondary and quaternary structure, and the geometry of intermolecular hydrogen bonds. Advanced imaging methods based on atomic force microscopy (AFM) have unravelled the morphological and mechanical heterogeneity of amyloids, however a full understanding has been hampered by the limited resolution of conventional spectroscopic methods. Here, it is shown that single molecule nanomechanical mapping and infrared nanospectroscopy (AFM-IR) in combination with atomistic modelling enable unravelling at the single aggregate scale of the morphological, nanomechanical, chemical, and structural transition from amyloid fibrils to amyloid microcrystals in the hexapeptides, ILQINS, IFQINS, and TFQINS. Different morphologies have different Young's moduli, within 2-6 GPa, with amyloid fibrils exhibiting lower Young's moduli compared to amyloid microcrystals. The origins of this stiffening are unravelled and related to the increased content of intermolecular β-sheet and the increased lengthscale of cooperativity following the transition from twisted fibril to flat nanocrystal. Increased stiffness in Young's moduli is correlated with increased density of intermolecular hydrogen bonding and parallel β-sheet structure, which energetically stabilize crystals over the other polymorphs. These results offer additional evidence for the position of amyloid crystals in the minimum of the protein folding and aggregation landscape.
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Affiliation(s)
- Jozef Adamcik
- Department of Health Sciences and TechnologyETH ZürichZürich8092Switzerland
| | | | - Joshua T. Berryman
- University of LuxembourgDepartment of Physics and Materials Science162a Avenue de la FaïencerieLuxembourgL‐1511Luxembourg
| | - Afang Zhang
- Shanghai University Department of Polymer MaterialsNanchen Street 333Shanghai200444China
| | - Tuomas P. J. Knowles
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cavendish LaboratoryUniversity of CambridgeJ. J. Thomson AvenueCambridgeCB3 0HEUK
| | - Raffaele Mezzenga
- Department of Health Sciences and TechnologyETH ZürichZürich8092Switzerland
- Department of MaterialsETH ZürichZürich8093Switzerland
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19
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Pal I, Roy M, Dey SG. Interaction of ApoMyoglobin with Heme-hIAPP complex. J Inorg Biochem 2020; 216:111348. [PMID: 33450674 DOI: 10.1016/j.jinorgbio.2020.111348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
Human Islet Amyloid Polypeptide (hIAPP) or amylin, can bind heme and the resultant complexes are prone to generate partially reduced oxygen species (PROS). The formation of PROS and the related oxidative stress highlight the importance of Heme-hIAPP in the onset and development of Type 2 Diabetes mellitus (T2Dm) in humans. In this study, the interaction of Heme-hIAPP with apomyoglobin (ApoMb) has been investigated using a combination of spectroscopic and electrophoresis techniques. Absorption, resonance Raman data and gel electrophoresis results confirm that ApoMb can uptake heme from Heme-hIAPP and constitute a six-coordinate high-spin ferric heme active site identical to that of myoglobin (Mb). The heme transfer reaction has two distinct kinetic steps. A possible mechanism of this reaction involves heme transfer to the apoprotein in the first step followed by a reorganisation of the protein chain to form the active site of native Mb. Increase in the pH of the reaction medium enhances the rate of the second step of heme transfer. This possibly corresponds to the deprotonation of a propionate side chain of the heme moiety at high pH which facilitates secondary interactions with the conserved distal Lys45 residue of horse heart Mb. Additionally, ApoMb sequesters ligand bound heme from Heme-hIAPP. After the heme transfer reaction, the amount of PROS formed by Heme-hIAPP complex diminishes significantly. This not only potentially diminishes heme-induced toxicity in the pancreatic β-cells but also produces Mb which has well-documented functions throughout the respiratory system and can thereby likely reduce the risks associated with T2Dm.
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Affiliation(s)
- Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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20
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Lao Z, Chen Y, Tang Y, Wei G. Molecular Dynamics Simulations Reveal the Inhibitory Mechanism of Dopamine against Human Islet Amyloid Polypeptide (hIAPP) Aggregation and Its Destabilization Effect on hIAPP Protofibrils. ACS Chem Neurosci 2019; 10:4151-4159. [PMID: 31436406 DOI: 10.1021/acschemneuro.9b00393] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The aberrant self-assembly of human islet amyloid polypeptide (hIAPP) into toxic oligomers, protofibrils, and mature fibrils is associated with the pathogenesis of type 2 diabetes (T2D). Inhibition of hIAPP aggregation and destabilization of preformed hIAPP fibrils are considered as two major therapeutic strategies for treating T2D. Previous experimental studies reported that dopamine prevented the formation of hIAPP oligomers and fibrils. However, the underlying inhibitory mechanism at the atomic level remains elusive. Herein we investigated the conformational ensembles of hIAPP dimer with and without dopamine using replica-exchange molecular dynamics simulations. The simulations demonstrated that dopamine preferentially bound to R11, L12, F15, H18, F23, I26, L27, and Y37 residues, inhibited the formation of β-sheets in the amyloidogenic regions spanning residues 11RLANFLVH18, 22NFGAIL27, and 30TNVGSNT36, and resulted in more disordered hIAPP dimers, thus hindering the amyloid formation of hIAPP. Protonated and deprotonated dopamine molecules displayed distinct binding capabilities but bound to similar residue sites on hIAPP. Additional microsecond molecular dynamics simulations showed that dopamine mainly bound to the β1 and turn regions of hIAPP protofibril and destabilized the protofibril structure. This study not only revealed the molecular mechanism of dopamine toward the inhibition of hIAPP aggregation but also demonstrated the protofibril-destabilizing effects of dopamine, which may be helpful for the design of drug candidates to treat T2D.
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Affiliation(s)
- Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
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21
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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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22
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Xu J, Zhang B, Gong G, Huang X, Du W. Inhibitory effects of oxidovanadium complexes on the aggregation of human islet amyloid polypeptide and its fragments. J Inorg Biochem 2019; 197:110721. [PMID: 31146152 DOI: 10.1016/j.jinorgbio.2019.110721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/26/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) is synthesized by pancreatic β-cells and co-secreted with insulin. Misfolding and amyloidosis of hIAPP induce β-cell dysfunction in type II diabetes mellitus. Numerous small organic molecules and metal complexes act as inhibitors against amyloid-related diseases, justifying the need to explore the inhibitory mechanism of these compounds. In this work, three oxidovanadium complexes, namely, (NH4)[VO(O2)2(bipy)]·4H2O (1) (bipy = 2,2' bipyridine), bis(ethyl-maltolato, O,O)oxido-vanadium(IV) (2), and (bipyH2)H2[O{VO(O2)(bipy)}2]·5H2O (3), were synthesized and used to inhibit the aggregation of hIAPP and its fragments, namely, hIAPP19-37 and hIAPP20-29. Results revealed that shortening the peptide sequence decreased the aggregation capability of hIAPP fragments, and the oxidovanadium complexes inhibited the fibrillization of hIAPP better than its fragments. Interestingly, the binding of oxidovanadium complexes to hIAPP and its fragments presented a distinct thermodynamic behavior. Oxidovanadium complexes featured the disaggregation capability against hIAPP, better than against its fragments. These complexes also decreased the cytotoxicity caused by hIAPP and its fragments by reducing the production of oligomers. 3 may be a good hIAPP inhibitor based on its inhibition, disaggregation capability, and regulatory effect on peptide-induced cytotoxicity. Oxidovanadium complexes exhibit potential as metallodrugs against amyloidosis-related diseases.
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Affiliation(s)
- Jufei Xu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Baohong Zhang
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Gehui Gong
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Xiangyi Huang
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Weihong Du
- Department of Chemistry, Renmin University of China, Beijing 100872, China.
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23
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Yin X, Liu S, Perez-Aguilar JM, Zhou H, Shao Q, Yang Z, Zhou R. Different protonated states at the C-terminal of the amyloid-β peptide modulate the stability of S-shaped protofibril. J Chem Phys 2019; 150:185102. [DOI: 10.1063/1.5081948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Xiuhua Yin
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | | | - Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Qiwen Shao
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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24
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Sun Y, Kakinen A, Xing Y, Faridi P, Nandakumar A, Purcell AW, Davis TP, Ke PC, Ding F. Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805166. [PMID: 30908844 PMCID: PMC6499678 DOI: 10.1002/smll.201805166] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/21/2019] [Indexed: 05/19/2023]
Abstract
The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet-rich nanofibrils is associated with the pathogeny of type 2 diabetes. Soluble hIAPP is intrinsically disordered with N-terminal residues 8-17 as α-helices. To understand the contribution of the N-terminal helix to the aggregation of full-length hIAPP, here the oligomerization dynamics of the hIAPP fragment 8-20 (hIAPP8-20) are investigated with combined computational and experimental approaches. hIAPP8-20 forms cross-β nanofibrils in silico from isolated helical monomers via the helical oligomers and α-helices to β-sheets transition, as confirmed by transmission electron microscopy, atomic force microscopy, circular dichroism spectroscopy, Fourier transform infrared spectroscopy, and reversed-phase high performance liquid chromatography. The computational results also suggest that the critical nucleus of aggregation corresponds to hexamers, consistent with a recent mass-spectroscopy study of hIAPP8-20 aggregation. hIAPP8-20 oligomers smaller than hexamers are helical and unstable, while the α-to-β transition starts from the hexamers. Converted β-sheet-rich oligomers first form β-barrel structures as intermediates before aggregating into cross-β nanofibrils. This study uncovers a complete picture of hIAPP8-20 peptide oligomerization, aggregation nucleation via conformational conversion, formation of β-barrel intermediates, and assembly of cross-β protofibrils, thereby shedding light on the aggregation of full-length hIAPP, a hallmark of pancreatic beta-cell degeneration.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics, Faculty of Science, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pouya Faridi
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Corresponding authors ,
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Corresponding authors ,
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25
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Khatun S, Singh A, Pawar N, Gupta AN. Aggregation of amylin: Spectroscopic investigation. Int J Biol Macromol 2019; 133:1242-1248. [PMID: 31028814 DOI: 10.1016/j.ijbiomac.2019.04.167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 12/17/2022]
Abstract
Apart from its relevance to pathology, protein misfolding disease like Type-II Diabetes Mellitus, caused by amyloids of amylin protein has attracted more attention due to structural changes occurring during the aggregation process. We report extensive spectroscopy data of amylin during fibril formation through Raman, FTIR, CD, UV-vis absorption and photoluminescence (PL) spectroscopy. UV-vis and PL spectrum showed the sigmoidal growth of fibril with a lag time of ~2 days, which is consistent with earlier reported work using dynamic light scattering (DLS). Raman spectra revealed the formation of parallel and anti-parallel β-sheet from 0% to 20% with ageing (1st day to 21st day) at pH 6.5 ± 0.1. The results are corroborated by CD and FTIR data. These show the change in β-sheet by 23% at pH 6.5 ± 0.1, 26% at pH = 1.0 ± 0.1 and 30% at pH = 12 ± 0.1. It is also shown that the formation and conversion of other secondary structures into β-sheet is very sensitive towards the pH and ageing. The study may be used for the development of therapeutic strategies that could inhibit or even reverse the process of aggregation.
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Affiliation(s)
- Suparna Khatun
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Anurag Singh
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Nisha Pawar
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Amar Nath Gupta
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India.
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26
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Hajiraissi R, Hanke M, Gonzalez Orive A, Duderija B, Hofmann U, Zhang Y, Grundmeier G, Keller A. Effect of Terminal Modifications on the Adsorption and Assembly of hIAPP(20-29). ACS OMEGA 2019; 4:2649-2660. [PMID: 31459500 PMCID: PMC6649277 DOI: 10.1021/acsomega.8b03028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/22/2019] [Indexed: 06/10/2023]
Abstract
The assembly of peptides and proteins into nanoscale amyloid fibrils via formation of intermolecular β-sheets not only plays an important role in the development of degenerative diseases but also represents a promising approach for the synthesis of functional nanomaterials. In many biological and technological settings, peptide assembly occurs in the presence of organic and inorganic interfaces with different physicochemical properties. In an attempt to dissect the relative contributions of the different molecular interactions governing amyloid assembly at interfaces, we here present a systematic study of the effects of terminal modifications on the adsorption and assembly of the human islet amyloid polypeptide fragment hIAPP(20-29) at organic self-assembled monolayers (SAMs) presenting different functional groups (cationic, anionic, polar, or hydrophobic). Using a selection of complementary in situ and ex situ analytical techniques, we find that even this well-defined and comparatively simple model system is governed by a rather complex interplay of electrostatic interactions, hydrophobic interactions, and hydrogen bonding, resulting in a plethora of observations and dependencies, some of which are rather counterintuitive. In particular, our results demonstrate that terminal modifications can have tremendous effects on peptide adsorption and assembly dynamics, as well as aggregate morphology and molecular structure. The effects exerted by the terminal modifications can furthermore be modulated in nontrivial ways by the physicochemical properties of the SAM surface. Therefore, terminal modifications are an important factor to consider when conducting and comparing peptide adsorption and aggregation studies and may represent an additional parameter for guiding the assembly of peptide-based nanomaterials.
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Affiliation(s)
- Roozbeh Hajiraissi
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Marcel Hanke
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Alejandro Gonzalez Orive
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Belma Duderija
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Ulrike Hofmann
- B
CUBE—Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Yixin Zhang
- B
CUBE—Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Guido Grundmeier
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Adrian Keller
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
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27
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Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity. Sci Rep 2019; 9:2530. [PMID: 30792475 PMCID: PMC6384915 DOI: 10.1038/s41598-018-38401-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022] Open
Abstract
In order to investigate the early phase of the amyloid formation by the short amyloidogenic octapeptide sequence (‘NFGAILSS’) derived from IAPP, we carried out a 100ns all-atom molecular dynamics (MD) simulations of systems that contain 27 peptides and over 30,000 water molecules. The large-scale calculations were performed for the wild type sequence and seven alanine-scanned sequences using AMBER 8.0 on RIKEN’s special purpose MD-GRAPE3 supercomputer, using the all-atom point charge force field ff99, which do not favor β-structures. Large peptide clusters (size 18–26 mers) were observed for all simulations, and our calculations indicated that isoleucine at position 5 played important role in the formation of β-rich clusters. In the oligomeric state, the wild type and the S7A sequences had the highest β-structure content (~14%), as calculated by DSSP, in line with experimental observations, whereas I5A and G3A had the highest helical content (~20%). Importantly, the β-structure preferences of wild type IAPP originate from its association into clusters and are not intrinsic to its sequence. Altogether, the results of this first large-scale, multi-peptide all-atom molecular dynamics simulation appear to provide insights into the mechanism of amyloidogenic and non-amyloidogenic oligomers that mainly corroborate previous experimental observations.
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28
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Sun Y, Kakinen A, Xing Y, Pilkington EH, Davis TP, Ke PC, Ding F. Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide. Biochim Biophys Acta Mol Basis Dis 2018; 1865:434-444. [PMID: 30502402 DOI: 10.1016/j.bbadis.2018.11.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/10/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet rich amyloid aggregates is associated with pancreatic β-cell death in type 2 diabetes (T2D). Prior experimental studies of hIAPP aggregation reported the early accumulation of α-helical intermediates before the rapid conversion into β-sheet rich amyloid fibrils, as also corroborated by our experimental characterizations with transmission electron microscopy and Fourier transform infrared spectroscopy. Although increasing evidence suggests that small oligomers populating early hIAPP aggregation play crucial roles in cytotoxicity, structures of these oligomer intermediates and their conformational conversions remain unknown, hindering our understanding of T2D disease mechanism and therapeutic design targeting these early aggregation species. We further applied large-scale discrete molecule dynamics simulations to investigate the oligomerization of full-length hIAPP, employing multiple molecular systems of increasing number of peptides. We found that the oligomerization process was dynamic, involving frequent inter-oligomeric exchanges. On average, oligomers had more α-helices than β-sheets, consistent with ensemble-based experimental measurements. However, in ~4-6% independent simulations, β-rich oligomers expected as the fibrillization intermediates were observed, especially in the pentamer and hexamer simulations. These β-rich oligomers could adopt β-barrel conformations, recently postulated to be the toxic oligomer species but only observed computationally in the aggregates of short amyloid protein fragments. Free-energy analysis revealed high energies of these β-rich oligomers, supporting the nucleated conformational changes of oligomers in amyloid aggregation. β-barrel oligomers of full-length hIAPP with well-defined three-dimensional structures may play an important pathological role in T2D etiology and may be a therapeutic target for the disease.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Emily H Pilkington
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Thomas P Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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29
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Babych M, Bertheau-Mailhot G, Zottig X, Dion J, Gauthier L, Archambault D, Bourgault S. Engineering and evaluation of amyloid assemblies as a nanovaccine against the Chikungunya virus. NANOSCALE 2018; 10:19547-19556. [PMID: 30324958 DOI: 10.1039/c8nr05948a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The design of nanoparticles exposing a high density of antigens constitutes a promising strategy to address safety concerns of conventional life-attenuated vaccines as well as to increase the immunogenicity of subunit vaccines. In this study, we developed a fully synthetic nanovaccine based on an amyloid peptide sequence with high self-assembling properties. The immunogenic epitope E2EP3 from the E2 glycoprotein of the Chikungunya virus was used to evaluate the potential of a 10-mer peptide derived from an endogenous amyloidogenic polypeptide as a novel vaccine platform. Chimeric peptides, comprising the peptide antigen attached to the amyloid core by a short flexible linker, were prepared by solid phase synthesis. As observed using atomic force microscopy, these polypeptides self-assembled into linear and unbranched fibrils with a diameter ranging from 6 to 8 nm. A quaternary conformation rich in cross-β-sheets characterized these assemblies, as demonstrated by circular dichroism spectroscopy and thioflavin T fluorescence. ELISA assays and transmission electronic microscopy of immunogold labeled-fibrils revealed a high density of the Chikungunya virus E2 glycoprotein derived epitope exposed on the fibril surface. These amyloid fibrils were cytocompatible and were efficiently uptaken by macrophages. Mice immunization revealed a robust IgG response against the E2EP3 epitope, which was dependent on self-assembly and did not require co-injection of the Alhydrogel adjuvant. These results indicate that cross-β-sheet amyloid assemblies constitute suitable synthetic self-adjuvanted assemblies to anchor antigenic determinants and to increase the immunogenicity of peptide epitopes.
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Affiliation(s)
- Margaryta Babych
- Department of Chemistry, Université du Québec à Montréal, Montréal, QC, Canada.
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30
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Buchanan LE, Maj M, Dunkelberger EB, Cheng PN, Nowick JS, Zanni MT. Structural Polymorphs Suggest Competing Pathways for the Formation of Amyloid Fibrils That Diverge from a Common Intermediate Species. Biochemistry 2018; 57:6470-6478. [PMID: 30375231 DOI: 10.1021/acs.biochem.8b00997] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It is now recognized that many amyloid-forming proteins can associate into multiple fibril structures. Here, we use two-dimensional infrared spectroscopy to study two fibril polymorphs formed by human islet amyloid polypeptide (hIAPP or amylin), which is associated with type 2 diabetes. The polymorphs exhibit different degrees of structural organization near the loop region of hIAPP fibrils. The relative populations of these polymorphs are systematically altered by the presence of macrocyclic peptides which template β-sheet formation at specific sections of the hIAPP sequence. These experiments are consistent with polymorphs that result from competing pathways for fibril formation and that the macrocycles bias hIAPP aggregation toward one pathway or the other. Another macrocyclic peptide that matches the loop region but extends the lag time leaves the relative populations of the polymorphs unaltered, suggesting that the branching point for structural divergence occurs after the lag phase, when the oligomers convert into seeds that template fibril formation. Thus, we conclude that the structures of the polymorphs stem from restricting oligomers along diverging folding pathways, which has implications for drug inhibition, cytotoxicity, and the free energy landscape of hIAPP aggregation.
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Affiliation(s)
- Lauren E Buchanan
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Michał Maj
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Emily B Dunkelberger
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
| | - Pin-Nan Cheng
- 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
| | - Martin T Zanni
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , United States
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31
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Bhasne K, Mukhopadhyay S. Formation of Heterotypic Amyloids: α-Synuclein in Co-Aggregation. Proteomics 2018; 18:e1800059. [PMID: 30216674 DOI: 10.1002/pmic.201800059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/28/2018] [Indexed: 12/13/2022]
Abstract
Protein misfolding resulting in the formation of ordered amyloid aggregates is associated with a number of devastating human diseases. Intrinsically disordered proteins (IDPs) do not autonomously fold up into a unique stable conformation and remain as an ensemble of rapidly fluctuating conformers. Many IDPs are prone to convert into the β-rich amyloid state. One such amyloidogenic IDP is α-synuclein that is involved in Parkinson's disease. Recent studies have indicated that other neuronal proteins, especially IDPs, can co-aggregate with α-synuclein in many pathological ailments. This article describes several such observations highlighting the role of heterotypic protein-protein interactions in the formation of hetero-amyloids. It is believed that the characterizations of molecular cross talks between amyloidogenic proteins as well as the mechanistic studies of heterotypic protein aggregation will allow us to decipher the role of the interacting proteins in amyloid proteomics.
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Affiliation(s)
- Karishma Bhasne
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India
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32
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Qian Z, Zou Y, Zhang Q, Chen P, Ma B, Wei G, Nussinov R. Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1818-1825. [PMID: 29428499 PMCID: PMC6408309 DOI: 10.1016/j.bbamem.2018.02.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/01/2018] [Accepted: 02/03/2018] [Indexed: 01/25/2023]
Abstract
The pathology of type 2 diabetes mellitus is associated with the aggregation of human islet amyloid polypeptide (hIAPP) and aggregation-mediated membrane disruption. The interactions of hIAPP aggregates with lipid membrane, as well as the effects of pH and lipid composition at the atomic level, remain elusive. Herein, using molecular dynamics simulations, we investigate the interactions of hIAPP protofibrillar oligomers with lipids, and the membrane perturbation that they induce, when they are partially inserted in an anionic dipalmitoyl-phosphatidylglycerol (DPPG) membrane or a mixed dipalmitoyl-phosphatidylcholine (DPPC)/DPPG (7:3) lipid bilayer under acidic/neutral pH conditions. We observed that the tilt angles and insertion depths of the hIAPP protofibril are strongly correlated with the pH and lipid composition. At neutral pH, the tilt angle and insertion depth of hIAPP protofibrils at a DPPG bilayer reach ~52° and ~1.62 nm with respect to the membrane surface, while they become ~77° and ~1.75 nm at a mixed DPPC/DPPG membrane. The calculated tilt angle of hIAPP at DPPG membrane is consistent with a recent chiral sum frequency generation spectroscopic study. The acidic pH induces a smaller tilt angle of ~40° and a shallower insertion depth (~1.24 nm) of hIAPP at the DPPG membrane surface, mainly due to protonation of His18 near the turn region. These differences mainly result from a combination of distinct electrostatic, van der Waals, hydrogen bonding and salt-bridge interactions between hIAPP and lipid bilayers. The hIAPP-membrane interaction energy analysis reveals that besides charged residues K1, R11 and H18, aromatic residues Phe15 and Phe23 also exhibit strong interactions with lipid bilayers, revealing the crucial role of aromatic residues in stabilizing the membrane-bound hIAPP protofibrils. hIAPP-membrane interactions disturb the lipid ordering and the local bilayer thickness around the peptides. Our results provide atomic-level information of membrane interaction of hIAPP protofibrils, revealing pH-dependent and membrane-modulated hIAPP aggregation at the early stage.
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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 200438, China; Department of Physics, State Key Laboratory of Surface physics, Key Laboratory for Computational Physical Science (Ministry of Education), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, China
| | - Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, Shanghai 200438, China
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, Shanghai 200438, China
| | - Peijie Chen
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface physics, Key Laboratory for Computational Physical Science (Ministry of Education), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, China.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States; Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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33
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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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34
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Adamcik J, Mezzenga R. Amyloid Polymorphism in the Protein Folding and Aggregation Energy Landscape. Angew Chem Int Ed Engl 2018; 57:8370-8382. [DOI: 10.1002/anie.201713416] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Jozef Adamcik
- Department of Health Sciences & Technology ETH Zurich Schmelzbergstrasse 9 8092 Zurich Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology ETH Zurich Schmelzbergstrasse 9 8092 Zurich Switzerland
- Department of Materials ETH Zurich Wolfgang-Pauli-Strasse 10 8093 Zurich Switzerland
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35
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Adamcik J, Mezzenga R. Amyloid‐Polymorphie in der Energielandschaft der Faltung und Aggregation von Proteinen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713416] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jozef Adamcik
- Departement Gesundheitswissenschaften und Technologie ETH Zürich Schmelzbergstrasse 9 8092 Zürich Schweiz
| | - Raffaele Mezzenga
- Departement Gesundheitswissenschaften und Technologie ETH Zürich Schmelzbergstrasse 9 8092 Zürich Schweiz
- Departement Materialwissenschaft ETH Zürich Wolfgang-Pauli-Strasse 10 8093 Zürich Schweiz
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36
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Affiliation(s)
- I. W. Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
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37
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Reynolds NP, Adamcik J, Berryman JT, Handschin S, Zanjani AAH, Li W, Liu K, Zhang A, Mezzenga R. Competition between crystal and fibril formation in molecular mutations of amyloidogenic peptides. Nat Commun 2017; 8:1338. [PMID: 29109399 PMCID: PMC5673901 DOI: 10.1038/s41467-017-01424-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022] Open
Abstract
Amyloidogenic model peptides are invaluable for investigating assembly mechanisms in disease related amyloids and in protein folding. During aggregation, such peptides can undergo bifurcation leading to fibrils or crystals, however the mechanisms of fibril-to-crystal conversion are unclear. We navigate herein the energy landscape of amyloidogenic peptides by studying a homologous series of hexapeptides found in animal, human and disease related proteins. We observe fibril-to-crystal conversion occurring within single aggregates via untwisting of twisted ribbon fibrils possessing saddle-like curvature and cross-sectional aspect ratios approaching unity. Changing sequence, pH or concentration shifts the growth towards larger aspect ratio species assembling into stable helical ribbons possessing mean-curvature. By comparing atomistic calculations of desolvation energies for association of peptides we parameterise a kinetic model, providing a physical explanation of fibril-to-crystal interconversion. These results shed light on the self-assembly of amyloidogenic peptides, suggesting amyloid crystals, not fibrils, represent the ground state of the protein folding energy landscape. Aggregation of amyloidogenic peptides into fibrils and crystals has incidence in several amyloid-related diseases. Here, the authors investigate the origins of the fibril-to-crystal conversion in amyloidogenic hexapeptides pointing to the amyloid crystals as the ground state in the protein folding energy landscape.
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Affiliation(s)
- Nicholas P Reynolds
- Swinburne University of Technology, ARC Training Centre for Biodevices, Faculty of Science, Engineering and Technology, John Street, Melbourne, VIC, 3122, Australia
| | - Jozef Adamcik
- ETH Zurich, Department of Health Sciences & Technology, Schmelzbergstrasse 9, LFO, E23, 8092, Zürich, Switzerland
| | - Joshua T Berryman
- University of Luxembourg, Department of Physics and Materials Science, 162a Avenue de la Faïencerie, Luxembourg City, L-1511, Luxembourg
| | - Stephan Handschin
- ETH Zurich, Department of Health Sciences & Technology, Schmelzbergstrasse 9, LFO, E23, 8092, Zürich, Switzerland
| | - Ali Asghar Hakami Zanjani
- University of Luxembourg, Department of Physics and Materials Science, 162a Avenue de la Faïencerie, Luxembourg City, L-1511, Luxembourg
| | - Wen Li
- Shanghai University, Department of Polymer Materials, Nanchen Street 333, Shanghai, 200444, China
| | - Kun Liu
- Shanghai University, Department of Polymer Materials, Nanchen Street 333, Shanghai, 200444, China
| | - Afang Zhang
- Shanghai University, Department of Polymer Materials, Nanchen Street 333, Shanghai, 200444, China
| | - Raffaele Mezzenga
- ETH Zurich, Department of Health Sciences & Technology, Schmelzbergstrasse 9, LFO, E23, 8092, Zürich, Switzerland. .,ETH Zurich, Department of Materials, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland.
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38
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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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39
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Wang ST, Lin Y, Spencer RK, Thomas MR, Nguyen AI, Amdursky N, Pashuck ET, Skaalure SC, Song CY, Parmar PA, Morgan RM, Ercius P, Aloni S, Zuckermann RN, Stevens MM. Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils. ACS NANO 2017; 11:8579-8589. [PMID: 28771324 PMCID: PMC5618150 DOI: 10.1021/acsnano.7b02325] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/28/2017] [Indexed: 05/18/2023]
Abstract
Determining the structural origins of amyloid fibrillation is essential for understanding both the pathology of amyloidosis and the rational design of inhibitors to prevent or reverse amyloid formation. In this work, the decisive roles of peptide structures on amyloid self-assembly and morphological diversity were investigated by the design of eight amyloidogenic peptides derived from islet amyloid polypeptide. Among the segments, two distinct morphologies were highlighted in the form of twisted and planar (untwisted) ribbons with varied diameters, thicknesses, and lengths. In particular, transformation of amyloid fibrils from twisted ribbons into untwisted structures was triggered by substitution of the C-terminal serine with threonine, where the side chain methyl group was responsible for the distinct morphological change. This effect was confirmed following serine substitution with alanine and valine and was ascribed to the restriction of intersheet torsional strain through the increased hydrophobic interactions and hydrogen bonding. We also studied the variation of fibril morphology (i.e., association and helicity) and peptide aggregation propensity by increasing the hydrophobicity of the peptide side group, capping the N-terminus, and extending sequence length. We anticipate that our insights into sequence-dependent fibrillation and morphological diversity will shed light on the structural interpretation of amyloidogenesis and development of structure-specific imaging agents and aggregation inhibitors.
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Affiliation(s)
- Shih-Ting Wang
- Department
of Materials and Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Yiyang Lin
- Department
of Materials and Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Ryan K. Spencer
- Molecular
Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Michael R. Thomas
- Department
of Materials and Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Andy I. Nguyen
- Molecular
Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Nadav Amdursky
- Department
of Materials and Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - E. Thomas Pashuck
- Department
of Materials and Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Stacey C. Skaalure
- Department
of Materials and Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Cheng Yu Song
- Molecular
Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Paresh A. Parmar
- Department
of Materials and Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Rhodri M. Morgan
- Department
of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Peter Ercius
- Molecular
Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Shaul Aloni
- Molecular
Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Molecular
Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Molly M. Stevens
- Department
of Materials and Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
- E-mail:
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40
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Tracking the amyloidogenic core of IAPP amyloid fibrils: Insights from micro-Raman spectroscopy. J Struct Biol 2017; 199:140-152. [PMID: 28602716 DOI: 10.1016/j.jsb.2017.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/19/2017] [Accepted: 06/03/2017] [Indexed: 12/14/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) is the major protein component of extracellular amyloid deposits, located in the islets of Langerhans, a hallmark of type II diabetes. The underlying mechanisms of IAPP aggregation have not yet been clearly defined, although the highly amyloidogenic sequence of the protein has been extensively studied. Several segments have been highlighted as aggregation-prone regions (APRs), with much attention focused on the central 8-17 and 20-29 stretches. In this work, we employ micro-Raman spectroscopy to identify specific regions that are contributing to or are excluded from the amyloidogenic core of IAPP amyloid fibrils. Our results demonstrate that both the N-terminal region containing a conserved disulfide bond between Cys residues at positions 2 and 7, and the C-terminal region containing the only Tyr residue are excluded from the amyloid core. Finally, by performing detailed aggregation assays and molecular dynamics simulations on a number of IAPP variants, we demonstrate that point mutations within the central APRs contribute to the reduction of the overall amyloidogenic potential of the protein but do not completely abolish the formation of IAPP amyloid fibrils.
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41
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Choi H, Chang HJ, Lee M, Na S. Characterizing Structural Stability of Amyloid Motif Fibrils Mediated by Water Molecules. Chemphyschem 2017; 18:817-827. [PMID: 28160391 DOI: 10.1002/cphc.201601327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/12/2017] [Indexed: 11/12/2022]
Abstract
In biological systems, structural confinements of amyloid fibrils can be mediated by the role of water molecules. However, the underlying effect of the dynamic behavior of water molecules on structural stabilities of amyloid fibrils is still unclear. By performing molecular dynamics simulations, we investigate the dynamic features and the effect of interior water molecules on conformations and mechanical characteristics of various amyloid fibrils. We find that a specific mechanism induced by the dynamic properties of interior water molecules can affect diffusion of water molecules inside amyloid fibrils, inducing their different structural stabilities. The conformation of amyloid fibrils induced by interior water molecules show the fibrils' different mechanical features. We elucidate the role of confined and movable interior water molecules in structural stabilities of various amyloid fibrils. Our results offer insights not only in further understanding of mechanical features of amyloids as mediated by water molecules, but also in the fine-tuning of the functional abilities of amyloid fibrils for applications.
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Affiliation(s)
- Hyunsung Choi
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hyun Joon Chang
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Myeongsang Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
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42
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Hajiraissi R, Giner I, Grundmeier G, Keller A. Self-Assembly, Dynamics, and Polymorphism of hIAPP(20-29) Aggregates at Solid-Liquid Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:372-381. [PMID: 27935715 DOI: 10.1021/acs.langmuir.6b03288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The misfolding and subsequent assembly of proteins and peptides into insoluble amyloid structures play important roles in the development of numerous diseases. The dynamics of self-assembly and the morphology of the resulting aggregates critically depend on various environmental factors and especially on the presence of interfaces. Here, we show in detail how the presence of surfaces with different physicochemical properties influences the assembly dynamics and especially the aggregate morphology of hIAPP(20-29), an amyloidogenic fragment of the peptide hormone human islet amyloid polypeptide (hIAPP), which is involved in the development of type 2 diabetes. Time-lapse atomic force microscopy is employed to study the assembly dynamics of hIAPP(20-29) and the morphology of the resulting aggregates in bulk solution as well as at hydrophilic and hydrophobic model surfaces. We find that the presence of hydrophilic mica surfaces promotes fibrillation when compared with the assembly in bulk solution and results in a more pronounced polymorphism. Three fibrillar species are found to coexist on the mica surface, that is, straight, coiled, and ribbon-like fibrils, whereas only the straight and coiled fibrils are observed in bulk solution after comparable incubation times. In addition, the straight and coiled fibrils assembled at the mica surface have significantly different dimensions compared with those assembled in bulk solution. The three fibrillar species found on the mica surface most likely form independently by lateral association of arbitrary numbers of protofibrils with about 2 nm height. On hydrophobic hydrocarbon surfaces, fibrillation is retarded but not completely suppressed, in contrast to previous observations for full-length hIAPP(1-37). Our results show that peptide-surface interactions may induce diverse, peptide-specific alterations of amyloid assembly dynamics and fibrillar polymorphism. They may therefore contribute to a deeper understanding of the molecular processes that govern amyloid aggregation at different surfaces.
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Affiliation(s)
- Roozbeh Hajiraissi
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
| | - Ignacio Giner
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
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43
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Krotee P, Rodriguez JA, Sawaya MR, Cascio D, Reyes FE, Shi D, Hattne J, Nannenga BL, Oskarsson ME, Philipp S, Griner S, Jiang L, Glabe CG, Westermark GT, Gonen T, Eisenberg DS. Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity. eLife 2017; 6. [PMID: 28045370 PMCID: PMC5207774 DOI: 10.7554/elife.19273] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/01/2016] [Indexed: 01/09/2023] Open
Abstract
hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15-25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19-29 S20G may serve as a model for the toxic spine of hIAPP.
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Affiliation(s)
- Pascal Krotee
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Jose A Rodriguez
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Michael R Sawaya
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Duilio Cascio
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Brent L Nannenga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Marie E Oskarsson
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Stephan Philipp
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States
| | - Sarah Griner
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Lin Jiang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Brain Research Institute (BRI), University of California, Los Angeles, Los Angeles, United States
| | - Charles G Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States.,Biochemistry Department, Faculty of Science and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - David S Eisenberg
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
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44
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Das A, Makarov DE. Effect of Mutation on an Aggregation-Prone Segment of p53: From Monomer to Dimer to Multimer. J Phys Chem B 2016; 120:11665-11673. [DOI: 10.1021/acs.jpcb.6b07457] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Atanu Das
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dmitrii E. Makarov
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Institute
for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
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45
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Conformational Ensemble of hIAPP Dimer: Insight into the Molecular Mechanism by which a Green Tea Extract inhibits hIAPP Aggregation. Sci Rep 2016; 6:33076. [PMID: 27620620 PMCID: PMC5020610 DOI: 10.1038/srep33076] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/18/2016] [Indexed: 12/20/2022] Open
Abstract
Small oligomers formed early along human islet amyloid polypeptide (hIAPP) aggregation is responsible for the cell death in Type II diabetes. The epigallocatechin gallate (EGCG), a green tea extract, was found to inhibit hIAPP fibrillation. However, the inhibition mechanism and the conformational distribution of the smallest hIAPP oligomer – dimer are mostly unknown. Herein, we performed extensive replica exchange molecular dynamic simulations on hIAPP dimer with and without EGCG molecules. Extended hIAPP dimer conformations, with a collision cross section value similar to that observed by ion mobility-mass spectrometry, were observed in our simulations. Notably, these dimers adopt a three-stranded antiparallel β-sheet and contain the previously reported β-hairpin amyloidogenic precursor. We find that EGCG binding strongly blocks both the inter-peptide hydrophobic and aromatic-stacking interactions responsible for inter-peptide β-sheet formation and intra-peptide interaction crucial for β-hairpin formation, thus abolishes the three-stranded β-sheet structures and leads to the formation of coil-rich conformations. Hydrophobic, aromatic-stacking, cation-π and hydrogen-bonding interactions jointly contribute to the EGCG-induced conformational shift. This study provides, on atomic level, the conformational ensemble of hIAPP dimer and the molecular mechanism by which EGCG inhibits hIAPP aggregation.
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46
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Structural Characterization of Fibrils from Recombinant Human Islet Amyloid Polypeptide by Solid-State NMR: The Central FGAILS Segment Is Part of the β-Sheet Core. PLoS One 2016; 11:e0161243. [PMID: 27607147 PMCID: PMC5015977 DOI: 10.1371/journal.pone.0161243] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/02/2016] [Indexed: 11/19/2022] Open
Abstract
Amyloid deposits formed from islet amyloid polypeptide (IAPP) are a hallmark of type 2 diabetes mellitus and are known to be cytotoxic to pancreatic β-cells. The molecular structure of the fibrillar form of IAPP is subject of intense research, and to date, different models exist. We present results of solid-state NMR experiments on fibrils of recombinantly expressed and uniformly 13C, 15N-labeled human IAPP in the non-amidated, free acid form. Complete sequential resonance assignments and resulting constraints on secondary structure are shown. A single set of chemical shifts is found for most residues, which is indicative of a high degree of homogeneity. The core region comprises three to four β-sheets. We find that the central 23-FGAILS-28 segment, which is of critical importance for amyloid formation, is part of the core region and forms a β-strand in our sample preparation. The eight N-terminal amino acid residues of IAPP, forming a ring-like structure due to a disulfide bridge between residues C2 and C7, appear to be well defined but with an increased degree of flexibility. This study supports the elucidation of the structural basis of IAPP amyloid formation and highlights the extent of amyloid fibril polymorphism.
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47
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Habenstein B, Loquet A. Solid-state NMR: An emerging technique in structural biology of self-assemblies. Biophys Chem 2016; 210:14-26. [DOI: 10.1016/j.bpc.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022]
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48
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Soriaga AB, Sangwan S, Macdonald R, Sawaya MR, Eisenberg D. Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets. J Phys Chem B 2016; 120:5810-6. [PMID: 26629790 DOI: 10.1021/acs.jpcb.5b09981] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structural studies of amyloidogenic segments by X-ray crystallography have revealed a novel packing motif, consisting of out-of-register β sheets, which may constitute one of the toxic species in aggregation related diseases. Here we sought to determine the presence of such a motif in islet amyloid polypeptide (IAPP), whose amyloidogenic properties are associated with type 2 diabetes. We determined four new crystal structures of segments within IAPP, all forming steric zippers. Most interestingly, one of the segments in the fibril core of IAPP forms an out-of-register steric zipper. Analysis of this structure reveals several commonalities with previously solved out-of-register fibrils. Our results provide additional evidence of out-of-register β sheets as a common structural motif in amyloid aggregates.
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Affiliation(s)
- Angela B Soriaga
- Howard Hughes Medical Institute, ‡UCLA-DOE Institute of Genomics and Proteomics, §Department of Biological Chemistry, and ∥Department of Chemistry & Biochemistry, UCLA , Los Angeles, California 90095, United States
| | - Smriti Sangwan
- Howard Hughes Medical Institute, ‡UCLA-DOE Institute of Genomics and Proteomics, §Department of Biological Chemistry, and ∥Department of Chemistry & Biochemistry, UCLA , Los Angeles, California 90095, United States
| | - Ramsay Macdonald
- Howard Hughes Medical Institute, ‡UCLA-DOE Institute of Genomics and Proteomics, §Department of Biological Chemistry, and ∥Department of Chemistry & Biochemistry, UCLA , Los Angeles, California 90095, United States
| | - Michael R Sawaya
- Howard Hughes Medical Institute, ‡UCLA-DOE Institute of Genomics and Proteomics, §Department of Biological Chemistry, and ∥Department of Chemistry & Biochemistry, UCLA , Los Angeles, California 90095, United States
| | - David Eisenberg
- Howard Hughes Medical Institute, ‡UCLA-DOE Institute of Genomics and Proteomics, §Department of Biological Chemistry, and ∥Department of Chemistry & Biochemistry, UCLA , Los Angeles, California 90095, United States
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49
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Choi H, Lee M, Park HS, Na S. The effect of structural heterogeneity on the conformation and stability of Aβ–tau mixtures. RSC Adv 2016. [DOI: 10.1039/c6ra09467h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Oligomeric and fibrillar amyloids, which cause neurodegenerative diseases, are typically formed through repetitive fracture and elongation processes involving single homogeneous amyloid monomers.
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Affiliation(s)
- Hyunsung Choi
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Myeongsang Lee
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Harold S. Park
- Department of Mechanical Engineering
- Boston University
- Boston
- USA
| | - Sungsoo Na
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
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Baek I, Lee M, Na S. Understanding structural characteristics of out-of-register hIAPP amyloid proteins via molecular dynamics. RSC Adv 2016. [DOI: 10.1039/c6ra19100b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We investigated characteristics of out-of-register (OOR) hIAPP amyloids. By varying the length size of OOR hIAPP, we found 8 layers is most stable. In addition, OOR hIAPP has relative structural instability than in-register hAIPP.
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Affiliation(s)
- Inchul Baek
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Myeongsang Lee
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| |
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