1
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Heerde T, Schütz D, Lin YJ, Münch J, Schmidt M, Fändrich M. Cryo-EM structure and polymorphic maturation of a viral transduction enhancing amyloid fibril. Nat Commun 2023; 14:4293. [PMID: 37464004 DOI: 10.1038/s41467-023-40042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Amyloid fibrils have emerged as innovative tools to enhance the transduction efficiency of retroviral vectors in gene therapy strategies. In this study, we used cryo-electron microscopy to analyze the structure of a biotechnologically engineered peptide fibril that enhances retroviral infectivity. Our findings show that the peptide undergoes a time-dependent morphological maturation into polymorphic amyloid fibril structures. The fibrils consist of mated cross-β sheets that interact by the hydrophobic residues of the amphipathic fibril-forming peptide. The now available structural data help to explain the mechanism of retroviral infectivity enhancement, provide insights into the molecular plasticity of amyloid structures and illuminate the thermodynamic basis of their morphological maturation.
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Affiliation(s)
- Thomas Heerde
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
| | - Desiree Schütz
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Yu-Jie Lin
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
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2
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Singh N, Patel K, Navalkar A, Kadu P, Datta D, Chatterjee D, Mukherjee S, Shaw R, Gahlot N, Shaw A, Jadhav S, Maji SK. Amyloid fibril-based thixotropic hydrogels for modeling of tumor spheroids in vitro. Biomaterials 2023; 295:122032. [PMID: 36791521 DOI: 10.1016/j.biomaterials.2023.122032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 12/28/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Biomaterials mimicking extracellular matrices (ECM) for three-dimensional (3D) cultures have gained immense interest in tumor modeling and in vitro organ development. Here, we introduce a new class of amyloid fibril-based peptide hydrogels as a versatile biomimetic ECM scaffold for 3D cell culture and homogenous tumor spheroid modeling. We show that these amyloid fibril-based hydrogels are thixotropic and allow cancer cell adhesion, proliferation, and migration. All seven designed hydrogels support 3D cell culture with five different cancer cell lines forming spheroid with necrotic core and upregulation of the cancer biomarkers. We further developed the homogenous, single spheroid using the drop cast method and the data suggest that all hydrogels support the tumor spheroid formation but with different necrotic core diameters. The detailed gene expression analysis of MCF7 spheroid by microarray suggested the involvement of pro-oncogenes and significant regulatory pathways responsible for tumor spheroid formation. Further, using breast tumor tissue from a mouse xenograft model, we show that selected amyloid hydrogels support the formation of tumor spheroids with a well-defined necrotic core, cancer-associated gene expression, higher drug resistance, and tumor heterogeneity reminiscent of the original tumor. Altogether, we have developed an easy-to-use, rapid, cost-effective, and scalable platform for generating in vitro cancer models for the screening of anti-cancer therapeutics and developing personalized medicine.
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Affiliation(s)
- Namrata Singh
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Debdeep Chatterjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ranjit Shaw
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Nitisha Gahlot
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Abhishek Shaw
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | | | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India.
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3
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Heerde T, Bansal A, Schmidt M, Fändrich M. Cryo-EM structure of a catalytic amyloid fibril. Sci Rep 2023; 13:4070. [PMID: 36906667 PMCID: PMC10008563 DOI: 10.1038/s41598-023-30711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/13/2023] Open
Abstract
Catalytic amyloid fibrils are novel types of bioinspired, functional materials that combine the chemical and mechanical robustness of amyloids with the ability to catalyze a certain chemical reaction. In this study we used cryo-electron microcopy to analyze the amyloid fibril structure and the catalytic center of amyloid fibrils that hydrolyze ester bonds. Our findings show that catalytic amyloid fibrils are polymorphic and consist of similarly structured, zipper-like building blocks that consist of mated cross-β sheets. These building blocks define the fibril core, which is decorated by a peripheral leaflet of peptide molecules. The observed structural arrangement differs from previously described catalytic amyloid fibrils and yielded a new model of the catalytic center.
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Affiliation(s)
- Thomas Heerde
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
| | - Akanksha Bansal
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
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4
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Protein Nanofibrils as Storage Forms of Peptide Drugs and Hormones. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:265-290. [PMID: 31713202 DOI: 10.1007/978-981-13-9791-2_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amyloids are highly organized cross β-sheet protein nanofibrils that are associated with both diseases and functions. Thermodynamically amyloids are stable structures as they represent the lowest free energy state that proteins can attain. However, recent studies suggest that amyloid fibrils can be dissociated by a change in environmental parameters such as pH and ionic strength. This reversibility of amyloids can not only be associated with disease, but function as well. In disease-associated amyloids, fibrils can act as reservoirs of cytotoxic oligomers. Recently, in higher organisms such as mammals, hormones were found to be stored in amyloid-like state, where these were reported to act as a reservoir of functional monomers. These hormone amyloids can dissociate to monomers upon release from the secretory granules, and subsequently bind to their respective receptors and perform their functions. In this book chapter, we describe in detail how these protein nanofibrils represent the densest possible peptide packing and are suitable for long-term storage. Thus, mimicking the feature of amyloids to release functional monomers, it is possible to formulate amyloid-based peptide/protein drugs, which can be used for sustained release.
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5
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Tufail S, Sherwani MA, Shoaib S, Azmi S, Owais M, Islam N. Ovalbumin self-assembles into amyloid nanosheets that elicit immune responses and facilitate sustained drug release. J Biol Chem 2018; 293:11310-11324. [PMID: 29853634 PMCID: PMC6065171 DOI: 10.1074/jbc.ra118.002550] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/14/2018] [Indexed: 11/06/2022] Open
Abstract
Amyloids are associated with many neurodegenerative diseases, motivating investigations into their structure and function. Although not linked to a specific disease, albumins have been reported to form many structural aggregates. We were interested in investigating host immune responses to amyloid fibrils assembled from the model protein ovalbumin. Surprisingly, upon subjecting ovalbumin to standard denaturing conditions, we encountered giant protein nanosheets harboring amyloid-like features and hypothesized that these nanosheets might have potential in clinical or therapeutic applications. We found that the nanosheets, without the administration of any additional adjuvant, evoked a strong antibody response in mice that was higher than that observed for native ovalbumin. This suggests that amyloid nanosheets have a self-adjuvanting property. The nanosheet-induced immune response was helper T cell 2 (Th2) biased and negligibly inflammatory. While testing whether the nanosheets might form depots for the sustained release of precursor proteins, we did observe release of ovalbumin that mimicked the conformation of native protein. Moreover, the nanosheets could load the anticancer drug doxorubicin and release it in a slow and sustained manner. Taken together, our results suggest that amyloid nanosheets should be further investigated as either an antigen delivery vehicle or a multifunctional antigen and drug co-delivery system, with potential applications in simultaneous immunotherapy and chemotherapy.
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Affiliation(s)
- Saba Tufail
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India; Biochemistry Section, Women's College, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India.
| | - Mohd Asif Sherwani
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Shoaib Shoaib
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Sarfuddin Azmi
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Najmul Islam
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India.
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6
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Das S, Jacob RS, Patel K, Singh N, Maji SK. Amyloid Fibrils: Versatile Biomaterials for Cell Adhesion and Tissue Engineering Applications. Biomacromolecules 2018; 19:1826-1839. [DOI: 10.1021/acs.biomac.8b00279] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Subhadeep Das
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076 Maharashtra, India
| | - Reeba S. Jacob
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076 Maharashtra, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076 Maharashtra, India
| | - Namrata Singh
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076 Maharashtra, India
| | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076 Maharashtra, India
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7
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Jacob RS, Das S, Singh N, Patel K, Datta D, Sen S, Maji SK. Amyloids Are Novel Cell-Adhesive Matrices. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1112:79-97. [PMID: 30637692 DOI: 10.1007/978-981-13-3065-0_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Amyloids are highly ordered peptide/protein aggregates traditionally associated with multiple human diseases including neurodegenerative disorders. However, recent studies suggest that amyloids can also perform several biological functions in organisms varying from bacteria to mammals. In many lower organisms, amyloid fibrils function as adhesives due to their unique surface topography. Recently, amyloid fibrils have been shown to support attachment and spreading of mammalian cells by interacting with the cell membrane and by cell adhesion machinery activation. Moreover, similar to cellular responses on natural extracellular matrices (ECMs), mammalian cells on amyloid surfaces also use integrin machinery for spreading, migration, and differentiation. This has led to the development of biocompatible and implantable amyloid-based hydrogels that could induce lineage-specific differentiation of stem cells. In this chapter, based on adhesion of both lower organisms and mammalian cells on amyloid nanofibrils, we posit that amyloids could have functioned as a primitive extracellular matrix in primordial earth.
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Affiliation(s)
- Reeba S Jacob
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Subhadeep Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Namrata Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Shamik Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
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8
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Ranganathan S, Maji SK, Padinhateeri R. Defining a Physical Basis for Diversity in Protein Self-Assemblies Using a Minimal Model. J Am Chem Soc 2016; 138:13911-13922. [DOI: 10.1021/jacs.6b06433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Srivastav Ranganathan
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Samir K. Maji
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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9
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Friedmann MP, Torbeev V, Zelenay V, Sobol A, Greenwald J, Riek R. Towards Prebiotic Catalytic Amyloids Using High Throughput Screening. PLoS One 2015; 10:e0143948. [PMID: 26650386 PMCID: PMC4674085 DOI: 10.1371/journal.pone.0143948] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023] Open
Abstract
Enzymes are capable of directing complex stereospecific transformations and of accelerating reaction rates many orders of magnitude. As even the simplest known enzymes comprise thousands of atoms, the question arises as to how such exquisite catalysts evolved. A logical predecessor would be shorter peptides, but they lack the defined structure and size that are apparently necessary for enzyme functions. However, some very short peptides are able to assemble into amyloids, thereby forming a well-defined tertiary structure called the cross-β-sheet, which bestows unique properties upon the peptides. We have hypothesized that amyloids could have been the catalytically active precursor to modern enzymes. To test this hypothesis, we designed an amyloid peptide library that could be screened for catalytic activity. Our approach, amenable to high-throughput methodologies, allowed us to find several peptides and peptide mixtures that form amyloids with esterase activity. These results indicate that amyloids, with their stability in a wide range of conditions and their potential as catalysts with low sequence specificity, would indeed be fitting precursors to modern enzymes. Furthermore, our approach can be efficiently expanded upon in library size, screening conditions, and target activity to yield novel amyloid catalysts with potential applications in aqueous-organic mixtures, at high temperature and in other extreme conditions that could be advantageous for industrial applications.
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Affiliation(s)
- Michael P. Friedmann
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Vladimir Torbeev
- Laboratory of Organic Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Viviane Zelenay
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Alexander Sobol
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
- * E-mail: (JG); (RR)
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
- * E-mail: (JG); (RR)
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10
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Maury CPJ. Origin of life. Primordial genetics: Information transfer in a pre-RNA world based on self-replicating beta-sheet amyloid conformers. J Theor Biol 2015. [DOI: 10.1016/j.jtbi.2015.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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11
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Udomprasert A, Bongiovanni MN, Sha R, Sherman WB, Wang T, Arora PS, Canary JW, Gras SL, Seeman NC. Amyloid fibrils nucleated and organized by DNA origami constructions. NATURE NANOTECHNOLOGY 2014; 9:537-41. [PMID: 24880222 PMCID: PMC4082467 DOI: 10.1038/nnano.2014.102] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/23/2014] [Indexed: 05/24/2023]
Abstract
Amyloid fibrils are ordered, insoluble protein aggregates that are associated with neurodegenerative conditions such as Alzheimer's disease. The fibrils have a common rod-like core structure, formed from an elongated stack of β-strands, and have a rigidity similar to that of silk (Young's modulus of 0.2-14 GPa). They also exhibit high thermal and chemical stability and can be assembled in vitro from short synthetic non-disease-related peptides. As a result, they are of significant interest in the development of self-assembled materials for bionanotechnology applications. Synthetic DNA molecules have previously been used to form intricate structures and organize other materials such as metal nanoparticles and could in principle be used to nucleate and organize amyloid fibrils. Here, we show that DNA origami nanotubes can sheathe amyloid fibrils formed within them. The fibrils are built by modifying the synthetic peptide fragment corresponding to residues 105-115 of the amyloidogenic protein transthyretin and a DNA origami construct is used to form 20-helix DNA nanotubes with sufficient space for the fibrils inside. Once formed, the fibril-filled nanotubes can be organized onto predefined two-dimensional platforms via DNA-DNA hybridization interactions.
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Affiliation(s)
| | - Marie N. Bongiovanni
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - William B. Sherman
- Bard High School Early College - Queens, 30-20 Thomson Ave., Queens, NY 11101, USA
| | - Tong Wang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sally L. Gras
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
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12
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Bongiovanni MN, Puri D, Goldie KN, Gras SL. Noncore Residues Influence the Kinetics of Functional TTR105–115-Based Amyloid Fibril Assembly. J Mol Biol 2012; 421:256-69. [DOI: 10.1016/j.jmb.2011.12.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 12/07/2011] [Accepted: 12/08/2011] [Indexed: 11/25/2022]
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13
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Liang Y, Ore MO, Morin S, Wilson DJ. Specific disruption of transthyretin(105-115) fibrilization using "stabilizing" inhibitors of transthyretin amyloidogenesis. Biochemistry 2012; 51:3523-30. [PMID: 22482799 DOI: 10.1021/bi3002727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transthyretin (TTR) is a cerebrospinal fluid and serum protein that undergoes ordered aggregation (amyloidogenesis) in familial amyloidotic polyneuropathy (FAP) and senile systemic amyloidosis (SSA). It is now widely accepted that dissociation of the native TTR tetramer is a precondition for amyloidogenesis; thus, molecules that stabilize the tetramer have received much attention as potential TTR amyloidosis inhibitors. Many of these inhibitors bind to the thyroxine (T(4)) binding pocket and interact specifically with a section of the TTR sequence, corresponding to residues 105-115, that is implicated in amyloidogenic propensity. In this work, we study the effects of "stabilizing" inhibitors on ordered aggregation of TTR(105-115) peptide. We show that molecules known to bind full-length TTR at the T(4) site are potent, specific inhibitors of ordered aggregation, while molecules that do not interact with TTR exhibit milder, nonspecific disruption through a "hyperbundling" effect. Our results suggest that, in addition to annealing the native tetramer, "stabilizing" inhibitors may also directly disrupt amyloidogenic aggregation of TTR monomers through specific interactions with the exposed TTR(105-115) sequence.
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Affiliation(s)
- Yanfang Liang
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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14
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Functional fibrils derived from the peptide TTR1-cycloRGDfK that target cell adhesion and spreading. Biomaterials 2011; 32:6099-110. [DOI: 10.1016/j.biomaterials.2011.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 05/05/2011] [Indexed: 11/19/2022]
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15
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Mankar S, Anoop A, Sen S, Maji SK. Nanomaterials: amyloids reflect their brighter side. NANO REVIEWS 2011; 2:NANO-2-6032. [PMID: 22110868 PMCID: PMC3215191 DOI: 10.3402/nano.v2i0.6032] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 04/20/2011] [Accepted: 04/26/2011] [Indexed: 12/31/2022]
Abstract
Amyloid fibrils belong to the group of ordered nanostructures that are self-assembled from a wide range of polypeptides/proteins. Amyloids are highly rigid structures possessing a high mechanical strength. Although amyloids have been implicated in the pathogenesis of several human diseases, growing evidence indicates that amyloids may also perform native functions in host organisms. Discovery of such amyloids, referred to as functional amyloids, highlight their possible use in designing novel nanostructure materials. This review summarizes recent advances in the application of amyloids for the development of nanomaterials and prospective applications of such materials in nanotechnology and biomedicine.
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Affiliation(s)
- Shruti Mankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay
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16
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Deciphering the structure, growth and assembly of amyloid-like fibrils using high-speed atomic force microscopy. PLoS One 2010; 5:e13240. [PMID: 20949034 PMCID: PMC2951901 DOI: 10.1371/journal.pone.0013240] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 09/15/2010] [Indexed: 11/19/2022] Open
Abstract
Formation of fibrillar structures of proteins that deposit into aggregates has been suggested to play a key role in various neurodegenerative diseases. However mechanisms and dynamics of fibrillization remains to be elucidated. We have previously established that lithostathine, a protein overexpressed in the pre-clinical stages of Alzheimer's disease and present in the pathognomonic lesions associated with this disease, form fibrillar aggregates after its N-terminal truncation. In this paper we visualized, using high-speed atomic force microscopy (HS-AFM), growth and assembly of lithostathine protofibrils under physiological conditions with a time resolution of one image/s. Real-time imaging highlighted a very high velocity of elongation. Formation of fibrils via protofibril lateral association and stacking was also monitored revealing a zipper-like mechanism of association. We also demonstrate that, like other amyloid ß peptides, two lithostathine protofibrils can associate to form helical fibrils. Another striking finding is the propensity of the end of a growing protofibril or fibril to associate with the edge of a second fibril, forming false branching point. Taken together this study provides new clues about fibrillization mechanism of amyloid proteins.
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17
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Tamamis P, Kasotakis E, Mitraki A, Archontis G. Amyloid-Like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations. J Phys Chem B 2009; 113:15639-47. [DOI: 10.1021/jp9066718] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Phanourios Tamamis
- Department of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus, and Department of Materials Science and Technology, University of Crete, and Institute for Electronic Structure and Laser, FORTH, Heraklion, Crete, Greece
| | - Emmanouil Kasotakis
- Department of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus, and Department of Materials Science and Technology, University of Crete, and Institute for Electronic Structure and Laser, FORTH, Heraklion, Crete, Greece
| | - Anna Mitraki
- Department of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus, and Department of Materials Science and Technology, University of Crete, and Institute for Electronic Structure and Laser, FORTH, Heraklion, Crete, Greece
| | - Georgios Archontis
- Department of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus, and Department of Materials Science and Technology, University of Crete, and Institute for Electronic Structure and Laser, FORTH, Heraklion, Crete, Greece
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18
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Liang Y, Jasbi SZ, Haftchenary S, Morin S, Wilson DJ. Binding interactions in early- and late-stage amyloid aggregates of TTR(105–115). Biophys Chem 2009; 144:1-8. [DOI: 10.1016/j.bpc.2009.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 05/13/2009] [Accepted: 05/18/2009] [Indexed: 11/15/2022]
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19
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Maurstad G, Prass M, Serpell LC, Sikorski P. Dehydration stability of amyloid fibrils studied by AFM. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:1135-40. [DOI: 10.1007/s00249-009-0526-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 07/11/2009] [Accepted: 07/22/2009] [Indexed: 10/20/2022]
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Buehler MJ, Yung YC. Deformation and failure of protein materials in physiologically extreme conditions and disease. NATURE MATERIALS 2009; 8:175-88. [PMID: 19229265 DOI: 10.1038/nmat2387] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Biological protein materials feature hierarchical structures that make up a diverse range of physiological materials. The analysis of protein materials is an emerging field that uses the relationships between biological structures, processes and properties to probe deformation and failure phenomena at the molecular and microscopic level. Here we discuss how advanced experimental, computational and theoretical methods can be used to assess structure-process-property relations and to monitor and predict mechanisms associated with failure of protein materials. Case studies are presented to examine failure phenomena in the progression of disease. From this materials science perspective, a de novo basis for understanding biological processes can be used to develop new approaches for treating medical disorders. We highlight opportunities to use knowledge gained from the integration of multiple scales with physical, biological and chemical concepts for potential applications in materials design and nanotechnology.
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Affiliation(s)
- Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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Diegelmann SR, Gorham JM, Tovar JD. One-Dimensional Optoelectronic Nanostructures Derived from the Aqueous Self-Assembly of π-Conjugated Oligopeptides. J Am Chem Soc 2008; 130:13840-1. [DOI: 10.1021/ja805491d] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Justin M. Gorham
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
| | - John D. Tovar
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
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Wenger MPE, Horton MA, Mesquida P. Nanoscale scraping and dissection of collagen fibrils. NANOTECHNOLOGY 2008; 19:384006. [PMID: 21832566 DOI: 10.1088/0957-4484/19/38/384006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The main function of collagen is mechanical, hence there is a fundamental scientific interest in experimentally investigating the mechanical and structural properties of collagen fibrils on the nanometre scale. Here, we present a novel atomic force microscopy (AFM) based scraping technique that can dissect the outer layer of a biological specimen. Applied to individual collagen fibrils, the technique was successfully used to expose the fibril core and reveal the presence of a D-banding-like structure. AFM nanoindentation measurements of fibril shell and core indicated no significant differences in mechanical properties such as stiffness (reduced modulus), hardness, adhesion and adhesion work. This suggests that collagen fibrils are mechanically homogeneous structures. The scraping technique can be applied to other biological specimens, as demonstrated on the example of bacteria.
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Affiliation(s)
- M P E Wenger
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
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