1
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Klawa SJ, Lee M, Riker KD, Jian T, Wang Q, Gao Y, Daly ML, Bhonge S, Childers WS, Omosun TO, Mehta AK, Lynn DG, Freeman R. Uncovering supramolecular chirality codes for the design of tunable biomaterials. Nat Commun 2024; 15:788. [PMID: 38278785 PMCID: PMC10817930 DOI: 10.1038/s41467-024-45019-2] [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: 08/08/2023] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
In neurodegenerative diseases, polymorphism and supramolecular assembly of β-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-β 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.
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Affiliation(s)
- Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michelle Lee
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Kyle D Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Tengyue Jian
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Broad Pharm, San Diego, California, 92121, USA
| | - Qunzhao Wang
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yuan Gao
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Shreeya Bhonge
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - W Seth Childers
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- U.S. Department of Justice, Chicago, IL, 60603, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- The National High Magnetic Field Laboratory, University of Florida, Gainesville, FL, 32611, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA.
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.
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2
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Geng Y, Huang T, Zhou W, Shen L. Physical Mechanism of Amyloid-β Peptide Chain Aggregation on Fluidic Lipid Nanotubules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5752-5758. [PMID: 35476922 DOI: 10.1021/acs.langmuir.2c00357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The question of how peptide chain aggregation is influenced by lipid membranes with varying shapes and structures is crucial for a detailed understanding of the neurotoxicity effect of the peptide chains. Not like the more usual spherical liposomes and planar lipid membranes, herein, we use lipid nanotubules as a model of important neuron synapse nanowire structures and devote particular attention to the effect of nanotubule fluidity on amyloid-β peptide (Aβ) chain aggregation. We apply single-molecule tracking (SMT) to elucidate how Aβ chains diffuse and aggregate on lipid nanotubules with different fluidities. The physical mechanism implies that fluidic lipid nanotubules facilitate the super-diffusion of two-dimensional (2D)-mobile precursor Aβ chains and promote their aggregation. This aggregation mechanism is retarded on less fluidic lipid nanotubules where the super-diffusion of 2D-mobile precursor Aβ chains is restricted by "frozen" lipids with less mobility. This work provides a mechanistic explanation for Aβ chain aggregation on fluidic lipid nanotubules.
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3
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Misra S, Singh P, Mahata RN, Brandão P, Roy S, Mahapatra AK, Nanda J. Supramolecular Antiparallel β-Sheet Formation by Tetrapeptides Based on Amyloid Sequence. J Phys Chem B 2021; 125:4274-4285. [PMID: 33886330 DOI: 10.1021/acs.jpcb.0c10920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Self-assembly of short peptides has emerged as an interesting research field for a wide range of applications. Recently, several truncated fragments of long-chain peptides or proteins responsible for different neurodegenerative diseases were studied to understand whether they can mimic the property and function of native peptides or not. It was reported that such a kind of peptide adopts a β-sheet structure in the disease state. It was observed that aromatic amino acid-rich peptide fragments possess a high tendency to adopt a β-sheet conformation. In this article, we are first time reporting the crystal structure of two tetrapeptides: Boc-GAII-OMe (Peptide 1) and Boc-GGVV-OMe (Peptide 2), composed of aliphatic amino acids, and the sequences are similar to the Aβ-peptide fragments Aβ29-32 and Aβ37-40 , respectively. In the solid-state, they are self-assembled in an antiparallel β-sheet fashion. The peptide units are connected by the strong amide hydrogen-bonding (N-H···O) interactions. Apart from that, other noncovalent interactions are also present, which help to stabilize the cross-β-sheet arrangement. Interestingly, in the crystal structure of Peptide 1, noncovalent C···C interaction between the electron-deficient carbonyl carbon, and the electron-rich sp3-carbon atom is observed, which is quite rare in the literature. The calculated torsion angles for these peptides are lying in the β-sheet region of the Ramachandran plot. FT-IR studies also indicate the formation of an antiparallel β-sheet structure in the solid-state. Circular dichroism of the peptides in the aqueous solution also suggests the presence of predominantly β-sheet-like conformation in the aqueous solution. Under cross-polarized light, Congo Red stained both peptides showed green-gold color due to birefringence indicating their amyloidogenic nature. This result indicates that the short peptide composed of aliphatic amino acid is capable of forming a β-sheet structure in the absence of aromatic amino acid and also can mimic the function of the native amyloid peptide.
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Affiliation(s)
- Souvik Misra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.-Botanic Garden, Howrah-711103, West Bengal, India
| | - Pijush Singh
- Department of Biochemistry and Biophysics. University of Kalyani, Kalyani, Nadia, West Bengal, India
| | - Rabindra Nath Mahata
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.-Botanic Garden, Howrah-711103, West Bengal, India
| | - Paula Brandão
- Departamento de Química/CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Subhasish Roy
- Department of Chemistry, BITS-Pilani K. K. Birla Goa Campus, 433 Sancoale, Goa 403726, India
| | - Ajit K Mahapatra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.-Botanic Garden, Howrah-711103, West Bengal, India
| | - Jayanta Nanda
- Department of Chemistry, University of North Bengal, Raja Rammohunpur, P.O.-NBU campus, Darjeeling-734013, West Bengal, India
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4
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Bunce SJ, Wang Y, Radford SE, Wilson AJ, Hall CK. Structural insights into peptide self-assembly using photo-induced crosslinking experiments and discontinuous molecular dynamics. AIChE J 2021; 67:e17101. [PMID: 33776061 PMCID: PMC7988534 DOI: 10.1002/aic.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/07/2020] [Indexed: 11/09/2022]
Abstract
Determining the structure of the (oligomeric) intermediates that form during the self-assembly of amyloidogenic peptides is challenging because of their heterogeneous and dynamic nature. Thus, there is need for methodology to analyze the underlying molecular structure of these transient species. In this work, a combination of fluorescence quenching, photo-induced crosslinking (PIC) and molecular dynamics simulation was used to study the assembly of a synthetic amyloid-forming peptide, Aβ16-22. A PIC amino acid containing a trifluormethyldiazirine (TFMD) group-Fmoc(TFMD)Phe-was incorporated into the sequence (Aβ*16-22). Electrospray ionization ion-mobility spectrometry mass-spectrometry (ESI-IMS-MS) analysis of the PIC products confirmed that Aβ*16-22 forms assemblies with the monomers arranged as anti-parallel, in-register β-strands at all time points during the aggregation assay. The assembly process was also monitored separately using fluorescence quenching to profile the fibril assembly reaction. The molecular picture resulting from discontinuous molecule dynamics simulations showed that Aβ16-22 assembles through a single-step nucleation into a β-sheet fibril in agreement with these experimental observations. This study provides detailed structural insights into the Aβ16-22 self-assembly processes, paving the way to explore the self-assembly mechanism of larger, more complex peptides, including those whose aggregation is responsible for human disease.
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Affiliation(s)
- Samuel J. Bunce
- School of ChemistryUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Yiming Wang
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Department of Chemical and Biological EngineeringPrinceton UniversityPrincetonNew JerseyUSA
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Carol K. Hall
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
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5
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Gordon CK, Luu R, Lynn D. Capturing nested information from disordered peptide phases. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Regina Luu
- Departments of Chemistry and Biology Emory University Atlanta Georgia USA
| | - David Lynn
- Departments of Chemistry and Biology Emory University Atlanta Georgia USA
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6
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Lau CYJ, Fontana F, Mandemaker LDB, Wezendonk D, Vermeer B, Bonvin AMJJ, de Vries R, Zhang H, Remaut K, van den Dikkenberg J, Medeiros-Silva J, Hassan A, Perrone B, Kuemmerle R, Gelain F, Hennink WE, Weingarth M, Mastrobattista E. Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides. Commun Chem 2020; 3:164. [PMID: 36703336 PMCID: PMC9814929 DOI: 10.1038/s42004-020-00417-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/19/2020] [Indexed: 01/29/2023] Open
Abstract
Self-assembling peptides are an exemplary class of supramolecular biomaterials of broad biomedical utility. Mechanistic studies on the peptide self-assembly demonstrated the importance of the oligomeric intermediates towards the properties of the supramolecular biomaterials being formed. In this study, we demonstrate how the overall yield of the supramolecular assemblies are moderated through subtle molecular changes in the peptide monomers. This strategy is exemplified with a set of surfactant-like peptides (SLPs) with different β-sheet propensities and charged residues flanking the aggregation domains. By integrating different techniques, we show that these molecular changes can alter both the nucleation propensity of the oligomeric intermediates and the thermodynamic stability of the fibril structures. We demonstrate that the amount of assembled nanofibers are critically defined by the oligomeric nucleation propensities. Our findings offer guidance on designing self-assembling peptides for different biomedical applications, as well as insights into the role of protein gatekeeper sequences in preventing amyloidosis.
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Affiliation(s)
- Chun Yin Jerry Lau
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Federico Fontana
- grid.413503.00000 0004 1757 9135IRCCS Casa Sollievo della Sofferenza, Opera di San Pio da Pietralcina, Viale Capuccini 1, 71013 San Giovanni Rotondo, Italy
| | - Laurens D. B. Mandemaker
- grid.5477.10000000120346234Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Dennie Wezendonk
- grid.5477.10000000120346234Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Benjamin Vermeer
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre M. J. J. Bonvin
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Renko de Vries
- grid.4818.50000 0001 0791 5666Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Heyang Zhang
- grid.5342.00000 0001 2069 7798Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Katrien Remaut
- grid.5342.00000 0001 2069 7798Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Joep van den Dikkenberg
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - João Medeiros-Silva
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alia Hassan
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Barbara Perrone
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Fabrizio Gelain
- grid.413503.00000 0004 1757 9135IRCCS Casa Sollievo della Sofferenza, Opera di San Pio da Pietralcina, Viale Capuccini 1, 71013 San Giovanni Rotondo, Italy ,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell’Ospedale Maggiore 3, 20162 Milan, Italy
| | - Wim E. Hennink
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Markus Weingarth
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Enrico Mastrobattista
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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7
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Bal S, Ghosh C, Ghosh T, Vijayaraghavan RK, Das D. Non-Equilibrium Polymerization of Cross-β Amyloid Peptides for Temporal Control of Electronic Properties. Angew Chem Int Ed Engl 2020; 59:13506-13510. [PMID: 32348633 DOI: 10.1002/anie.202003721] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/13/2020] [Indexed: 11/09/2022]
Abstract
Hydrophobic collapse plays crucial roles in protein functions, from accessing the complex three-dimensional structures of native enzymes to the dynamic polymerization of non-equilibrium microtubules. However, hydrophobic collapse can also lead to the thermodynamically downhill aggregation of aberrant proteins, which has interestingly led to the development of a unique class of soft nanomaterials. There remain critical gaps in the understanding of the mechanisms of how hydrophobic collapse can regulate such aggregation. Demonstrated herein is a methodology for non-equilibrium amyloid polymerization through mutations of the core sequence of Aβ peptides by a thermodynamically activated moiety. An out of equilibrium state is realized because of the negative feedback from the transiently formed cross-β amyloid networks. Such non-equilibrium amyloid nanostructures were utilized to access temporal control over its electronic properties.
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Affiliation(s)
- Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Chandranath Ghosh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Tapan Ghosh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Ratheesh K Vijayaraghavan
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
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8
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Bal S, Ghosh C, Ghosh T, Vijayaraghavan RK, Das D. Non‐Equilibrium Polymerization of Cross‐β Amyloid Peptides for Temporal Control of Electronic Properties. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Chandranath Ghosh
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Tapan Ghosh
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Ratheesh K. Vijayaraghavan
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
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9
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Rengifo RF, Sementilli A, Kim Y, Liang C, Li NX, Mehta AK, Lynn DG. Liquid‐Like Phases Preorder Peptides for Supramolecular Assembly. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Rolando F. Rengifo
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Anthony Sementilli
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Youngsun Kim
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Chen Liang
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Noel Xiang'An Li
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Anil K. Mehta
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - David G. Lynn
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
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10
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Sahoo A, Xu H, Matysiak S. Pathways of amyloid-beta absorption and aggregation in a membranous environment. Phys Chem Chem Phys 2019; 21:8559-8568. [PMID: 30964132 DOI: 10.1039/c9cp00040b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aggregation of misfolded oligomeric amyloid-beta (Aβ) peptides on lipid membranes has been identified as a primary event in Alzheimer's pathogenesis. However, the structural and dynamical features of this membrane assisted Aβ aggregation have not been well characterized. The microscopic characterization of dynamic molecular-level interactions in peptide aggregation pathways has been challenging both computationally and experimentally. In this work, we explore differential patterns of membrane-induced Aβ 16-22 (K-L-V-F-F-A-E) aggregation from the microscopic perspective of molecular interactions. Physics-based coarse-grained molecular dynamics (CG-MD) simulations were employed to investigate the effect of lipid headgroup charge - zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: POPC) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine: POPS) - on Aβ 16-22 peptide aggregation. Our analyses present an extensive overview of multiple pathways for peptide absorption and biomechanical forces governing peptide folding and aggregation. In agreement with experimental observations, anionic POPS molecules promote extended configurations in Aβ peptides that contribute towards faster emergence of ordered β-sheet-rich peptide assemblies compared to POPC, suggesting faster fibrillation. In addition, lower cumulative rates of peptide aggregation in POPS due to higher peptide-lipid interactions and slower lipid diffusion result in multiple distinct ordered peptide aggregates that can serve as nucleation seeds for subsequent Aβ aggregation. This study provides an in-silico assessment of experimentally observed aggregation patterns, presents new morphological insights and highlights the importance of lipid headgroup chemistry in modulating the peptide absorption and aggregation process.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.
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11
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Liang C, Hsieh MC, Li NX, Lynn DG. Conformational evolution of polymorphic amyloid assemblies. Curr Opin Struct Biol 2018; 51:135-140. [DOI: 10.1016/j.sbi.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
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12
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Taran O, Chen C, Omosun TO, Hsieh MC, Rha A, Goodwin JT, Mehta AK, Grover MA, Lynn DG. Expanding the informational chemistries of life: peptide/RNA networks. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0356. [PMID: 29133453 DOI: 10.1098/rsta.2016.0356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Olga Taran
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Chenrui Chen
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Ming-Chien Hsieh
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Allisandra Rha
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jay T Goodwin
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
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13
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Hsieh MC, Liang C, Mehta AK, Lynn DG, Grover MA. Multistep Conformation Selection in Amyloid Assembly. J Am Chem Soc 2017; 139:17007-17010. [PMID: 29111722 PMCID: PMC5709775 DOI: 10.1021/jacs.7b09362] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Defining pathways
for amyloid assembly could impact therapeutic
strategies for as many as 50 disease states. Here we show that amyloid
assembly is subject to different forces regulating nucleation and
propagation steps and provide evidence that the more global β-sheet/β-sheet
facial complementarity is a critical determinant for amyloid nucleation
and structural selection.
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Affiliation(s)
- Ming-Chien Hsieh
- Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Anil K Mehta
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - David G Lynn
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Martha A Grover
- Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
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14
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Abstract
Living systems contain remarkable functional capability built within sophisticated self-organizing frameworks. Defining the assembly codes that coordinate these systems could greatly extend nanobiotechnology. To that end, we have highlighted the self-assembling architecture of the chlorosome antenna arrays and report the emulation and extension of their features for the development of cell-compatible photoredox materials. We specifically review work on amyloid peptide scaffolds able to (1) organize light-harvesting chromophores, (2) break peptide bilayer symmetry for directional energy and electron transfer, and (3) incorporate redox active metal ions at high density for energy storage.
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Affiliation(s)
- Rolando F Rengifo
- Emory University, Departments of Biology and Chemistry, 1515 Dickey Dr. NE, Atlanta, GA 30322, USA.
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15
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Hsieh MC, Lynn DG, Grover MA. Kinetic Model for Two-Step Nucleation of Peptide Assembly. J Phys Chem B 2017; 121:7401-7411. [DOI: 10.1021/acs.jpcb.7b03085] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ming-Chien Hsieh
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David G. Lynn
- Departments
of Chemistry and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Martha A. Grover
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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16
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Omosun TO, Hsieh MC, Childers WS, Das D, Mehta AK, Anthony NR, Pan T, Grover MA, Berland KM, Lynn DG. Catalytic diversity in self-propagating peptide assemblies. Nat Chem 2017; 9:805-809. [DOI: 10.1038/nchem.2738] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/19/2017] [Indexed: 01/03/2023]
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17
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Cinar G, Orujalipoor I, Su CJ, Jeng US, Ide S, Guler MO. Supramolecular Nanostructure Formation of Coassembled Amyloid Inspired Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6506-6514. [PMID: 27267733 DOI: 10.1021/acs.langmuir.6b00704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Characterization of amyloid-like aggregates through converging approaches can yield deeper understanding of their complex self-assembly mechanisms and the nature of their strong mechanical stability, which may in turn contribute to the design of novel supramolecular peptide nanostructures as functional materials. In this study, we investigated the coassembly kinetics of oppositely charged short amyloid-inspired peptides (AIPs) into supramolecular nanostructures by using confocal fluorescence imaging of thioflavin T binding, turbidity assay and in situ small-angle X-ray scattering (SAXS) analysis. We showed that coassembly kinetics of the AIP nanostructures were consistent with nucleation-dependent amyloid-like aggregation, and aggregation behavior of the AIPs was affected by the initial monomer concentration and sonication. Moreover, SAXS analysis was performed to gain structural information on the size, shape, electron density, and internal organization of the coassembled AIP nanostructures. The scattering data of the coassembled AIP nanostructures were best fitted into to a combination of polydisperse core-shell cylinder (PCSC) and decoupling flexible cylinder (FCPR) models, and the structural parameters were estimated based on the fitting results of the scattering data. The stability of the coassembled AIP nanostructures in both fiber organization and bulk viscoelastic properties was also revealed via temperature-dependent SAXS analysis and oscillatory rheology measurements, respectively.
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Affiliation(s)
- Goksu Cinar
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University , 06800 Ankara, Turkey
| | - Ilghar Orujalipoor
- Department of Nanotechnology and Nanoscience, Hacettepe University , 06800 Beytepe, Ankara, Turkey
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center , 101 Hsin-Ann Road, Hsinchu Park, Hsinchu, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center , 101 Hsin-Ann Road, Hsinchu Park, Hsinchu, Taiwan
| | - Semra Ide
- Department of Nanotechnology and Nanoscience, Hacettepe University , 06800 Beytepe, Ankara, Turkey
- Department of Physics Engineering, Hacettepe University , 06800 Beytepe, Ankara, Turkey
| | - Mustafa O Guler
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University , 06800 Ankara, Turkey
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18
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Li S, Mehta AK, Sidorov AN, Orlando TM, Jiang Z, Anthony NR, Lynn DG. Design of Asymmetric Peptide Bilayer Membranes. J Am Chem Soc 2016; 138:3579-86. [DOI: 10.1021/jacs.6b00977] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sha Li
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anil K. Mehta
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton N. Sidorov
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Thomas M. Orlando
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhigang Jiang
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Neil R. Anthony
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David G. Lynn
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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19
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Tiiman A, Jarvet J, Gräslund A, Vukojević V. Heterogeneity and Turnover of Intermediates during Amyloid-β (Aβ) Peptide Aggregation Studied by Fluorescence Correlation Spectroscopy. Biochemistry 2015; 54:7203-11. [PMID: 26574169 DOI: 10.1021/acs.biochem.5b00976] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-assembly of amyloid β (Aβ) peptide molecules into large aggregates is a naturally occurring process driven in aqueous solution by a dynamic interplay between hydrophobic interactions among Aβ molecules, which promote aggregation, and steric and overall electrostatic hindrance, which stifles it. Aβ self-association is entropically unfavorable, as it implies order increase in the system, but under favorable kinetic conditions, the process proceeds at appreciable rates, yielding Aβ aggregates of different sizes and structures. Despite the great relevance and extensive research efforts, detailed kinetic mechanisms underlying Aβ aggregation remain only partially understood. In this study, fluorescence correlation spectroscopy (FCS) and Thioflavin T (ThT) were used to monitor the time dependent growth of structured aggregates and characterize multiple components during the aggregation of Aβ peptides in a heterogeneous aqueous solution. To this aim, we collected data during a relatively large number of observation periods, 30 consecutive measurements lasting 10 s each, at what we consider to be a constant time point in the slow aggregation process. This approach enabled monitoring the formation of nanomolar concentrations of structured amyloid aggregates and demonstrated the changing distribution of amyloid aggregate sizes throughout the aggregation process. We identified aggregates of different sizes with molecular weight from 260 to more than 1 × 10(6) kDa and revealed the hitherto unobserved kinetic turnover of intermediates during Aβ aggregation. The effect of different Aβ concentrations, Aβ:ThT ratios, differences between the 40 (Aβ40) and 42 (Aβ42) residue long variants of Aβ, and the effect of stirring were also examined.
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Affiliation(s)
- Ann Tiiman
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University , 10691 Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University , 10691 Stockholm, Sweden.,The National Institute of Chemical Physics and Biophysics , Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University , 10691 Stockholm, Sweden
| | - Vladana Vukojević
- Department of Clinical Neuroscience, Center for Molecular Medicine CMM L8:01, Karolinska Institutet , 17176 Stockholm, Sweden
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20
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Smith JE, Liang C, Tseng M, Li N, Li S, Mowles AK, Mehta AK, Lynn DG. Defining the Dynamic Conformational Networks of Cross-β Peptide Assembly. Isr J Chem 2015. [DOI: 10.1002/ijch.201500012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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21
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Smith JE, Mowles AK, Mehta AK, Lynn DG. Looked at life from both sides now. Life (Basel) 2014; 4:887-902. [PMID: 25513758 PMCID: PMC4284472 DOI: 10.3390/life4040887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/25/2023] Open
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.
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Affiliation(s)
- Jillian E Smith
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Allisandra K Mowles
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Anil K Mehta
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - David G Lynn
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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22
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Liang C, Ni R, Smith JE, Childers WS, Mehta AK, Lynn DG. Kinetic Intermediates in Amyloid Assembly. J Am Chem Soc 2014; 136:15146-9. [DOI: 10.1021/ja508621b] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Chen Liang
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Rong Ni
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Jillian E. Smith
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - W. Seth Childers
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
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23
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Xie L, Lin D, Luo Y, Li H, Yang X, Wei G. Effects of hydroxylated carbon nanotubes on the aggregation of Aβ16-22 peptides: a combined simulation and experimental study. Biophys J 2014; 107:1930-1938. [PMID: 25418174 PMCID: PMC4213673 DOI: 10.1016/j.bpj.2014.08.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/27/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
The pathogenesis of Alzheimer's disease (AD) is associated with the aggregation of amyloid-β (Aβ) peptides into toxic aggregates with ?-sheet character. In a previous computational study, we showed that pristine single-walled carbon nanotubes (SWCNTs) can inhibit the formation of β-sheet-rich oligomers in the central hydrophobic core fragment of Aβ (Aβ16-22). However, the poor solubility of SWCNTs in water hinders their use in biomedical applications and nanomedicine. Here, we investigate the influence of hydroxylated SWCNT, a water-soluble SWCNT derivative, on the aggregation of Aβ16-22 peptides using all-atom explicit-water replica exchange molecular dynamics simulations. Our results show that hydroxylated SWCNTs can significantly inhibit β-sheet formation and shift the conformations of Aβ16-22 oligomers from ordered β-sheet-rich structures toward disordered coil aggregates. Detailed analyses of the SWCNT-Aβ interaction reveal that the inhibition of β-sheet formation by hydroxylated SWCNTs mainly results from strong electrostatic interactions between the hydroxyl groups of SWCNTs and the positively charged residue K16 of Aβ16-22 and hydrophobic and aromatic stacking interactions between SWCNTs and F19 and F20. In addition, our atomic force microscopy and thioflavin T fluorescence experiments confirm the inhibitory effect of both pristine and hydroxylated SWCNTs on Aβ16-22 fibrillization, in support of our previous and present replica exchange molecular dynamics simulation results. These results demonstrate that hydroxylated SWCNTs efficiently inhibit the aggregation of Aβ16-22; in addition, they offer molecular insight into the inhibition mechanism, thus providing new clues for the design of therapeutic drugs against amyloidosis.
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Affiliation(s)
- Luogang Xie
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Dongdong Lin
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Yin Luo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Huiyu Li
- Department of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, China
| | - Xinju Yang
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China.
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