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Aguilar MI, Yarovsky I. Quest for New Generation Biocompatible Materials: Tailoring β-Peptide Structure and Interactions via Synergy of Experiments and Modelling. J Mol Biol 2024:168646. [PMID: 38848868 DOI: 10.1016/j.jmb.2024.168646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Peptide-based self-assembly has been used to produce a wide range of nanostructures. While most of these systems involve self-assembly of α-peptides, more recently β-peptides have also been shown to undergo supramolecular self-assembly, and have been used to produce materials for applications in tissue engineering, cell culture and drug delivery. In order to engineer new materials with specific structure and function, theoretical molecular modelling can provide significant insights into the collective balance of non-covalent interactions that drive the self-assembly and determine the structure of the resultant supramolecular materials under different conditions. However, this approach has only recently become feasible for peptide-based self-assembled nanomaterials, particularly those that incorporate non α-amino acids. This perspective provides an overview of the challenges associated with computational modelling of the self-assembly of β-peptides and the recent success using a combination of experimental and computational techniques to provide insights into the self-assembly mechanisms and fully atomistic models of these new biocompatible materials.
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Affiliation(s)
- Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia.
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2
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Pathak BK, Dey S, Mozumder S, Sengupta J. The role of membranes in function and dysfunction of intrinsically disordered amyloidogenic proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:397-434. [PMID: 35034725 DOI: 10.1016/bs.apcsb.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Membrane-protein interactions play a major role in human physiology as well as in diseases pathology. Interaction of a protein with the membrane was previously thought to be dependent on well-defined three-dimensional structure of the protein. In recent decades, however, it has become evident that a large fraction of the proteome, particularly in eukaryotes, stays disordered in solution and these proteins are termed as intrinsically disordered proteins (IDPs). Also, a vast majority of human proteomes have been reported to contain substantially long disordered regions, called intrinsically disordered regions (IDRs), in addition to the structurally ordered regions. IDPs exist in an ensemble of conformations and the conformational flexibility enables IDPs to achieve functional diversity. IDPs (and IDRs) are found to be important players in cell signaling, where biological membranes act as anchors for signaling cascades. Therefore, IDPs modulate the membrane architectures, at the same time membrane composition also affects the binding of IDPs. Because of intrinsic disorders, misfolding of IDPs often leads to formation of oligomers, protofibrils and mature fibrils through progressive self-association. Accumulation of amyloid-like aggregates of some of the IDPs is a known causative agent for numerous diseases. In this chapter we highlight recent advances in understanding membrane interactions of some of the intrinsically disordered proteins involved in the pathogenesis of human diseases.
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Affiliation(s)
- Bani Kumar Pathak
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sandip Dey
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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3
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Todorova N, Bentvelzen A, Yarovsky I. Electromagnetic field modulates aggregation propensity of amyloid peptides. J Chem Phys 2020; 152:035104. [DOI: 10.1063/1.5126367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- N. Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - A. Bentvelzen
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - I. Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
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4
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Zhang W, Christofferson AJ, Besford QA, Richardson JJ, Guo J, Ju Y, Kempe K, Yarovsky I, Caruso F. Metal-dependent inhibition of amyloid fibril formation: synergistic effects of cobalt-tannic acid networks. NANOSCALE 2019; 11:1921-1928. [PMID: 30644497 DOI: 10.1039/c8nr09221d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Metal-phenolic networks (MPNs) have received widespread interest owing to their modular incorporation of functional metal ions and phenolic ligands. However, the interaction between MPNs and biomolecules is still relatively unexplored. Herein, we studied the effects of MPN-coated gold nanoparticles on amyloid fibril formation (which is associated with Alzheimer's disease) as a function of the metal ion in the MPN systems. All coated particles examined inhibited amyloid formation, with cobalt(ii) MPN-coated particles exhibiting the highest inhibition activity (90%). Molecular dynamics simulations and quantum mechanics calculations suggested that the geometry of the exposed cobalt coordination site in the cobalt-tannic acid networks facilitates its interactions with histidine and methionine residues in the amyloid beta peptides. Furthermore, the unique structure of cobalt MPNs may enable a wider variety of biomedical applications.
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Affiliation(s)
- Wenjie Zhang
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
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5
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Todorova N, Yarovsky I. The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations. Aust J Chem 2019. [DOI: 10.1071/ch19059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insight into protein behaviour at spatial and temporal resolution still largely outside the reach of experiments. Herein we present an account of our theoretical modelling research conducted in collaboration with several experimental groups where we explored the effects of local environment on the structure and aggregation propensity of several types of amyloidogenic peptides and proteins, including apolipoprotein C-II, insulin, amylin, and amyloid-β using a variety of computational approaches.
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6
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Williamson NA. Operational Experience of an Open-Access, Subscription-Based Mass Spectrometry and Proteomics Facility. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:439-446. [PMID: 29299836 DOI: 10.1007/s13361-017-1862-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 06/07/2023]
Abstract
This paper discusses the successful adoption of a subscription-based, open-access model of service delivery for a mass spectrometry and proteomics facility. In 2009, the Mass Spectrometry and Proteomics Facility at the University of Melbourne (Australia) moved away from the standard fee for service model of service provision. Instead, the facility adopted a subscription- or membership-based, open-access model of service delivery. For a low fixed yearly cost, users could directly operate the instrumentation but, more importantly, there were no limits on usage other than the necessity to share available instrument time with all other users. All necessary training from platform staff and many of the base reagents were also provided as part of the membership cost. These changes proved to be very successful in terms of financial outcomes for the facility, instrument access and usage, and overall research output. This article describes the systems put in place as well as the overall successes and challenges associated with the operation of a mass spectrometry/proteomics core in this manner. Graphical abstract ᅟ.
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Affiliation(s)
- Nicholas A Williamson
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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7
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Amdursky N, Rashid MH, Stevens MM, Yarovsky I. Exploring the binding sites and proton diffusion on insulin amyloid fibril surfaces by naphthol-based photoacid fluorescence and molecular simulations. Sci Rep 2017; 7:6245. [PMID: 28740173 PMCID: PMC5524688 DOI: 10.1038/s41598-017-06030-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/09/2017] [Indexed: 11/18/2022] Open
Abstract
The diffusion of protons along biological surfaces and the interaction of biological structures with water are fundamental areas of interest in biology and chemistry. Here, we examine the surface of insulin amyloid fibrils and follow the binding of small molecules (photoacids) that differ according to the number and location of their sulfonic groups. We use transient fluorescence combined with a spherically-symmetric diffusion theory to show that the binding mode of different photoacids determines the efficiency of proton dissociation from the photoacid and the dimensionality of the proton’s diffusion. We use molecular dynamics simulations to examine the binding mode and mechanism of the photoacids and its influence on the unique kinetic rates and diffusion properties of the photoacid’s dissociated proton, where we also suggest a proton transfer process between one of the photoacids to proximal histidine residues. We show that the photoacids can be used as fluorescent markers for following the progression of amyloidogenic processes. The detailed characterisation of different binding modes to the surface of amyloid fibrils paves the way for better understanding of the binding mechanism of small molecules to amyloid fibrils.
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Affiliation(s)
- Nadav Amdursky
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom. .,Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel.
| | - M Harunur Rashid
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
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8
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Todorova N, Bentvelzen A, English NJ, Yarovsky I. Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides. J Chem Phys 2016; 144:085101. [PMID: 26931725 DOI: 10.1063/1.4941108] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (<0.004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.
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Affiliation(s)
- Nevena Todorova
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
| | - Alan Bentvelzen
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
| | - Niall J English
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Irene Yarovsky
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
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9
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Thapa A, Jett SD, Chi EY. Curcumin Attenuates Amyloid-β Aggregate Toxicity and Modulates Amyloid-β Aggregation Pathway. ACS Chem Neurosci 2016; 7:56-68. [PMID: 26529184 DOI: 10.1021/acschemneuro.5b00214] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The abnormal misfolding and aggregation of amyloid-β (Aβ) peptides into β-sheet enriched insoluble deposits initiates a cascade of events leading to pathological processes and culminating in cognitive decline in Alzheimer's disease (AD). In particular, soluble oligomeric/prefibrillar Aβ have been shown to be potent neurotoxins. The naturally occurring polyphenol curcumin has been shown to exert a neuroprotective effect against age-related neurodegenerative diseases such as AD. However, its protective mechanism remains unclear. In this study, we investigated the effects of curcumin on the aggregation of Aβ40 as well as Aβ40 aggregate induced neurotoxicity. Our results show that the curcumin does not inhibit Aβ fibril formation, but rather enriches the population of "off-pathway" soluble oligomers and prefibrillar aggregates that were nontoxic. Curcumin also exerted a nonspecific neuroprotective effect, reducing toxicities induced by a range of Aβ conformers, including monomeric, oligomeric, prefibrillar, and fibrillar Aβ. The neuroprotective effect is possibly membrane-mediated, as curcumin reduced the extent of cell membrane permeabilization induced by Aβ aggregates. Taken together, our study shows that curcumin exerts its neuroprotective effect against Aβ induced toxicity through at least two concerted pathways, modifying the Aβ aggregation pathway toward the formation of nontoxic aggregates and ameliorating Aβ-induced toxicity possibly through a nonspecific pathway.
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Affiliation(s)
- Arjun Thapa
- Department
of Chemical and Biological Engineering
and the Center for Biomedical Engineering, and ‡Department of Cell Biology
and Physiology, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Stephen D. Jett
- Department
of Chemical and Biological Engineering
and the Center for Biomedical Engineering, and ‡Department of Cell Biology
and Physiology, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Eva Y. Chi
- Department
of Chemical and Biological Engineering
and the Center for Biomedical Engineering, and ‡Department of Cell Biology
and Physiology, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico 87131, United States
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The Role of Lipid in Misfolding and Amyloid Fibril Formation by Apolipoprotein C-II. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:157-74. [DOI: 10.1007/978-3-319-17344-3_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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11
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Luo J, Abrahams JP. Cyclic Peptides as Inhibitors of Amyloid Fibrillation. Chemistry 2014; 20:2410-9. [DOI: 10.1002/chem.201304253] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Indexed: 11/06/2022]
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12
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Todorova N, Makarucha AJ, Hine NDM, Mostofi AA, Yarovsky I. Dimensionality of carbon nanomaterials determines the binding and dynamics of amyloidogenic peptides: multiscale theoretical simulations. PLoS Comput Biol 2013; 9:e1003360. [PMID: 24339760 PMCID: PMC3854483 DOI: 10.1371/journal.pcbi.1003360] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/09/2013] [Indexed: 12/22/2022] Open
Abstract
Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth.
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Affiliation(s)
| | | | - Nicholas D. M. Hine
- Department of Materials and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London, United Kingdom
| | - Arash A. Mostofi
- Department of Materials and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London, United Kingdom
| | - Irene Yarovsky
- Health Innovations Research Institute, Melbourne, Australia
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Stefani M, Rigacci S. Protein folding and aggregation into amyloid: the interference by natural phenolic compounds. Int J Mol Sci 2013; 14:12411-57. [PMID: 23765219 PMCID: PMC3709793 DOI: 10.3390/ijms140612411] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/29/2013] [Accepted: 06/04/2013] [Indexed: 01/17/2023] Open
Abstract
Amyloid aggregation is a hallmark of several degenerative diseases affecting the brain or peripheral tissues, whose intermediates (oligomers, protofibrils) and final mature fibrils display different toxicity. Consequently, compounds counteracting amyloid aggregation have been investigated for their ability (i) to stabilize toxic amyloid precursors; (ii) to prevent the growth of toxic oligomers or speed that of fibrils; (iii) to inhibit fibril growth and deposition; (iv) to disassemble preformed fibrils; and (v) to favor amyloid clearance. Natural phenols, a wide panel of plant molecules, are one of the most actively investigated categories of potential amyloid inhibitors. They are considered responsible for the beneficial effects of several traditional diets being present in green tea, extra virgin olive oil, red wine, spices, berries and aromatic herbs. Accordingly, it has been proposed that some natural phenols could be exploited to prevent and to treat amyloid diseases, and recent studies have provided significant information on their ability to inhibit peptide/protein aggregation in various ways and to stimulate cell defenses, leading to identify shared or specific mechanisms. In the first part of this review, we will overview the significance and mechanisms of amyloid aggregation and aggregate toxicity; then, we will summarize the recent achievements on protection against amyloid diseases by many natural phenols.
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Affiliation(s)
- Massimo Stefani
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, Florence 50134, Italy; E-Mail:
- Research Centre on the Molecular Basis of Neurodegeneration, Viale Morgagni 50, Florence 50134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-55-275-8307; Fax: +39-55-275-8905
| | - Stefania Rigacci
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, Florence 50134, Italy; E-Mail:
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"Janus" cyclic peptides: a new approach to amyloid fibril inhibition? PLoS One 2013; 8:e57437. [PMID: 23437387 PMCID: PMC3577749 DOI: 10.1371/journal.pone.0057437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/22/2013] [Indexed: 11/19/2022] Open
Abstract
Cyclic peptides are increasingly being shown as powerful inhibitors of fibril formation, and have the potential to be therapeutic agents for combating many debilitating amyloid-related diseases. One such example is a cyclic peptide derivative from the human apolipoprotein C-II, which has the ability to inhibit fibril formation by the fibrillogenic peptide apoC-II(60–70). Using classical molecular dynamics and electronic structure calculations, we were able to provide insight into the interaction between the amyloidogenic peptide apoC-II(60–70) and its cyclic derivative, cyc(60–70). Our results showed that cyc(60–70) induced increased flexibility in apoC-II(60–70), suggesting that one mechanism by which cyc(60–70) inhibits fibrillisation is by destabilising apoC-II(60–70) structure, rendering it incapable of adopting fibril favouring conformations. In contrast, cyc(60–70) shows less flexibility upon binding to apoC-II(60–70), which is predominantly mediated by hydrophobic interactions between the aromatic rings of the peptides. This effectively creates a cap around the fibril-forming region of apoC-II(60–70) and generates an outer hydrophilic shell that discourages further apoC-II(60–70) peptide self-association. We showed that apoC-II(60–70) exhibited stronger binding affinity for the hydrophobic face of cyc(60–70) and weakest binding affinity for the hydrophilic side. This suggests that cyc(60–70) can be an effective fibril inhibitor due to its amphipathic character, like that of the "Janus"-type particles. This property can be exploited in the design of specific inhibitors of amyloid fibril formation.
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