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Mason TO, Shimanovich U. Fibrous Protein Self-Assembly in Biomimetic Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706462. [PMID: 29883013 DOI: 10.1002/adma.201706462] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/28/2018] [Indexed: 05/22/2023]
Abstract
Protein self-assembly processes, by which polypeptides interact and independently form multimeric structures, lead to a wide array of different endpoints. Structures formed range from highly ordered molecular crystals to amorphous aggregates. Order arises in the system from a balance between many low-energy processes occurring due to a set of interactions between residues in a chain, between residues in different chains, and between solute and solvent. In Nature, self-assembling protein systems have evolved over millions of years to organize into supramolecular structures, optimized for specific functions, with this propensity determined by the sequence of their constituent amino acids, of which only 20 are encoded in DNA. The structural materials that arise from biological self-assembly can display remarkable mechanical properties, often as a result of hierarchical structure on the nano- and microscales, and much research has been devoted to mimicking and exploiting these properties for a variety of end uses. This work presents a review of a range of studies in which biological functions are effectively reproduced through the design of self-assembling fibrous protein systems.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, 7610001, Israel
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Guttenplan APM, Young LJ, Matak-Vinkovic D, Kaminski CF, Knowles TPJ, Itzhaki LS. Nanoscale click-reactive scaffolds from peptide self-assembly. J Nanobiotechnology 2017; 15:70. [PMID: 28985740 PMCID: PMC6389178 DOI: 10.1186/s12951-017-0300-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/23/2017] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Due to their natural tendency to self-assemble, proteins and peptides are important components for organic nanotechnology. One particular class of peptides of recent interest is those that form amyloid fibrils, as this self-assembly results in extremely strong, stable quasi-one-dimensional structures which can be used to organise a wide range of cargo species including proteins and oligonucleotides. However, assembly of peptides already conjugated to proteins is limited to cargo species that do not interfere sterically with the assembly process or misfold under the harsh conditions often used for assembly. Therefore, a general method is needed to conjugate proteins and other molecules to amyloid fibrils after the fibrils have self-assembled. RESULTS Here we have designed an amyloidogenic peptide based on the TTR105-115 fragment of transthyretin to form fibrils that display an alkyne functionality, important for bioorthogonal chemical reactions, on their surface. The fibrils were formed and reacted both with an azide-containing amino acid and with an azide-functionalised dye by the Huisgen cycloaddition, one of the class of "click" reactions. Mass spectrometry and total internal reflection fluorescence optical microscopy were used to show that peptides incorporated into the fibrils reacted with the azide while maintaining the structure of the fibril. These click-functionalised amyloid fibrils have a variety of potential uses in materials and as scaffolds for bionanotechnology. DISCUSSION Although previous studies have produced peptides that can both form amyloid fibrils and undergo "click"-type reactions, this is the first example of amyloid fibrils that can undergo such a reaction after they have been formed. Our approach has the advantage that self-assembly takes place before click functionalization rather than pre-functionalised building blocks self-assembling. Therefore, the molecules used to functionalise the fibril do not themselves have to be exposed to harsh, amyloid-forming conditions. This means that a wider range of proteins can be used as ligands in this process. For instance, the fibrils can be functionalised with a green fluorescent protein that retains its fluorescence after it is attached to the fibrils, whereas this protein loses its fluorescence if it is exposed to the conditions used for aggregation.
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Affiliation(s)
- Alexander P. M. Guttenplan
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Laurence J. Young
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS UK
| | - Dijana Matak-Vinkovic
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS UK
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD UK
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Reynolds NP, Charnley M, Bongiovanni MN, Hartley PG, Gras SL. Biomimetic Topography and Chemistry Control Cell Attachment to Amyloid Fibrils. Biomacromolecules 2015; 16:1556-65. [DOI: 10.1021/acs.biomac.5b00114] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Nicholas P. Reynolds
- Manufacturing
Flagship, CSIRO, Bayview Avenue, Clayton, Victoria 3169, Australia
| | | | - Marie N. Bongiovanni
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Patrick G. Hartley
- Energy
Flagship, CSIRO, Private Bag 10, Bayview Avenue, Clayton, Victoria 3169, Australia
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Bongiovanni MN, Gras SL. Bioactive TTR105-115-based amyloid fibrils reduce the viability of mammalian cells. Biomaterials 2015; 46:105-16. [PMID: 25678120 DOI: 10.1016/j.biomaterials.2014.12.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/09/2014] [Accepted: 12/20/2014] [Indexed: 12/29/2022]
Abstract
A growing number of protein-based fibrous biomaterials have been produced with a cross-β amyloid core yet the long-term effect of these materials on cell viability and the influence of core and non-core protein sequences on viability is not well understood. Here, synthetic bioactive TTR1-RGD and control TTR1-RAD or TTR1 fibrils were used to test the response of mammalian cells. At high fibril concentrations cell viability was reduced, as assessed by mitochondrial reduction assays, lactate dehydrogenase membrane integrity assays and apoptotic biomarkers. This reduction occurred despite the high density of RGD cell adhesion ligands and use of cells displaying integrin receptors. Cell viability was affected by fibril size, maturity and whether fibrils were added to the cell media or as a pre-coated surface layer. These findings show that while cells initially interact well with synthetic fibrils, cellular integrity can be compromised over longer periods of time, suggesting a better understanding of the role of core and non-core residues in determining cellular interactions is required before TTR1-based fibrils are used as biomaterials.
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Affiliation(s)
- Marie N Bongiovanni
- The ARC Dairy Innovation Hub, 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
| | - Sally L Gras
- The ARC Dairy Innovation Hub, 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.
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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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Kang L, Janowska MK, Moriarty GM, Baum J. Mechanistic insight into the relationship between N-terminal acetylation of α-synuclein and fibril formation rates by NMR and fluorescence. PLoS One 2013; 8:e75018. [PMID: 24058647 PMCID: PMC3776725 DOI: 10.1371/journal.pone.0075018] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/09/2013] [Indexed: 11/20/2022] Open
Abstract
Aggregation of α-synuclein (αSyn), the primary protein component in Lewy body inclusions of patients with Parkinson’s disease, arises when the normally soluble intrinsically disordered protein converts to amyloid fibrils. In this work, we provide a mechanistic view of the role of N-terminal acetylation on fibrillation by first establishing a quantitative relationship between monomer secondary structural propensity and fibril assembly kinetics, and secondly by demonstrating in the N-terminal acetylated form of the early onset A53T mutation, that N-terminal transient helices formed and/or inhibited by N-terminal acetylation modulate the fibril assembly rates. Using NMR chemical shifts and fluorescence experiments, we report that secondary structural propensity in residues 5–8, 14–31, and 50–57 are highly correlated to fibril growth rate. A four-way comparison of secondary structure propensity and fibril growth rates of N-terminally acetylated A53T and WT αSyn with non-acetylated A53T and WT αSyn present novel mechanistic insight into the role of N-terminal acetylation in amyloid fibril formation. We show that N-terminal acetylation inhibits the formation of the “fibrillation promoting” transient helix at residues 14–31 resulting from the A53T mutation in the non-acetylated variant and supports the formation of the “fibrillation inhibiting” transient helix in residues 1–12 thereby resulting in slower fibrillation rates relative to the previously studied non-acetylated A53T variant. Our results highlight the critical interplay of the region-specific transient secondary structure of the N-terminal region with fibrillation, and the inhibitory role of the N-terminal acetyl group in fibril formation.
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Affiliation(s)
- Lijuan Kang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Maria K. Janowska
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Gina M. Moriarty
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey, United States of America
- * E-mail:
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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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Rodríguez-Pérez JC, Hamley IW, Gras SL, Squires AM. Local orientational disorder in peptide fibrils probed by a combination of residue-specific 13C–18O labelling, polarised infrared spectroscopy and molecular combing. Chem Commun (Camb) 2012; 48:11835-7. [DOI: 10.1039/c2cc35586h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
In this chapter we provided the overall background to the subject of protein aggregation and fibrillogenesis in amyloidogenesis, with introduction and brief discussion of the various topics that are included with the coming chapters. The division of the book into basic science and clinical science sections enables correlation of the topics to be made. The many proteins and peptides that have currently been found to undergo fibrillogenesis are tabulated. A broad technical survey is made, to indicate the vast array of techniques currently available to study aspects of protein oligomerization, aggregation and fibrillogenesis. These are split into three groups and tabulated, as the microscopical techniques, the analytical and biophysical methods, and the biochemical and cellular techniques. A few techniques are discussed, but in most cases only a link to relevant recent literature is provided.
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