1
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Mondal T, Mandal B. Proteolytic functional amyloid digests pathogenic amyloid. J Mater Chem B 2022; 10:4216-4225. [DOI: 10.1039/d2tb00640e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although amyloids are a well-known pathological structure, functional amyloids are beneficial. Functional amyloids can be engineered to cultivate desired functionality that can destroy malicious amyloids. However, not much is known...
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2
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Fialho DM, Karunakaran SC, Greeson KW, Martínez I, Schuster GB, Krishnamurthy R, Hud NV. Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate. J Am Chem Soc 2021; 143:13525-13537. [PMID: 34398608 DOI: 10.1021/jacs.1c02287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Katherine W Greeson
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Isaac Martínez
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gary B Schuster
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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3
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Siegl K, Kolik‐Shmuel L, Zhang M, Prévost S, Vishnia K, Mor A, Appavou M, Jafta CJ, Danino D, Gradzielski M. Directed Assembly of Multi-Walled Nanotubes and Nanoribbons of Amino Acid Amphiphiles Using a Layer-by-Layer Approach. Chemistry 2021; 27:6904-6910. [PMID: 33560564 PMCID: PMC8251557 DOI: 10.1002/chem.202005331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/05/2021] [Indexed: 11/22/2022]
Abstract
Monodisperse unilamellar nanotubes (NTs) and nanoribbons (NRs) were transformed to multilamellar NRs and NTs in a well-defined fashion. This was done by using a step-wise approach in which self-assembled cationic amino acid amphiphile (AAA) formed the initial NTs or NRs, and added polyanion produced an intermediate coating. Successive addition of cationic AAA formed a covering AAA layer, and by repeating this layer-by-layer (LBL) procedure, multi-walled nanotubes (mwNTs) and nanoribbons were formed. This process was structurally investigated by combining small-angle neutron scattering (SANS) and cryogenic-transmission electron microscopy (cryo-TEM), confirming the multilamellar structure and the precise layer spacing. In this way the controlled formation of multi-walled suprastructures was demonstrated in a simple and reproducible fashion, which allowed to control the charge on the surface of these 1D aggregates. This pathway to 1D colloidal materials is interesting for applications in life science and creating well-defined building blocks in nanotechnology.
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Affiliation(s)
- Kathrin Siegl
- Stranski-Laboratorium für Physikalische und Theoretische ChemieInstitut für ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
| | - Luba Kolik‐Shmuel
- CryoEM Laboratory of Soft MatterFaculty of Biotechnology and Food EngineeringTechnion—Israel Institute of TechnologyHaifa3200003Israel
| | - Mingming Zhang
- CryoEM Laboratory of Soft MatterFaculty of Biotechnology and Food EngineeringTechnion—Israel Institute of TechnologyHaifa3200003Israel
| | - Sylvain Prévost
- Institut Max von Laue-Paul Langevin (ILL)71 avenue des Martyrs38042GrenobleFrance
| | - Kalanit Vishnia
- CryoEM Laboratory of Soft MatterFaculty of Biotechnology and Food EngineeringTechnion—Israel Institute of TechnologyHaifa3200003Israel
| | - Amram Mor
- Faculty of Biotechnology and Food EngineeringTechnion—Israel Institute of TechnologyHaifa3200003Israel
| | - Marie‐Sousai Appavou
- Forschungszentrum Jülich GmbH Jülich Centre for Neutron Science (JCNS)Heinz Maier-Leibnitz Zentrum (MLZ)Lichtenbergerstr. 185747GarchingGermany
| | - Charl J. Jafta
- Helmholtz-Zentrum Berlin für Materialien und Energie (HZB)14109BerlinGermany
| | - Dganit Danino
- CryoEM Laboratory of Soft MatterFaculty of Biotechnology and Food EngineeringTechnion—Israel Institute of TechnologyHaifa3200003Israel
- Guangdong Technion—Israel Institute of TechnologyGuangdong ProvinceShantou515063P. R. China
| | - Michael Gradzielski
- Stranski-Laboratorium für Physikalische und Theoretische ChemieInstitut für ChemieTechnische Universität BerlinStraße des 17. Juni 12410623BerlinGermany
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4
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Narayanan T, Rüter A, Olsson U. Multiscale Structural Elucidation of Peptide Nanotubes by X-Ray Scattering Methods. Front Bioeng Biotechnol 2021; 9:654339. [PMID: 33855016 PMCID: PMC8039368 DOI: 10.3389/fbioe.2021.654339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/16/2021] [Indexed: 11/26/2022] Open
Abstract
This mini-review presents the structural investigations of the self-assembled peptide nanotubes using X-ray scattering techniques. As compared to electron microscopy, scattering methods enable studies of nanotubes in solution under the appropriate physicochemical conditions and probe their formation mechanism. In addition, a combination of X-ray scattering methods allow the elucidation of structural organization from the molecular scale to the dimension of nanotubes.
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Affiliation(s)
| | - Axel Rüter
- Division of Physical Chemistry, Lund University, Lund, Sweden
| | - Ulf Olsson
- Division of Physical Chemistry, Lund University, Lund, Sweden
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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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Boback K, Bacchi K, O’Neill S, Brown S, Dorsainvil J, Smith-Carpenter JE. Impact of C-Terminal Chemistry on Self-Assembled Morphology of Guanosine Containing Nucleopeptides. Molecules 2020; 25:E5493. [PMID: 33255230 PMCID: PMC7727710 DOI: 10.3390/molecules25235493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/16/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023] Open
Abstract
Herein, we report the design and characterization of guanosine-containing self-assembling nucleopeptides that form nanosheets and nanofibers. Through spectroscopy and microscopy analysis, we propose that the peptide component of the nucleopeptide drives the assembly into β-sheet structures with hydrogen-bonded guanosine forming additional secondary structures cooperatively within the peptide framework. Interestingly, the distinct supramolecular morphologies are driven not by metal cation responsiveness common to guanine-based materials, but by the C-terminal peptide chemistry. This work highlights the structural diversity of self-assembling nucleopeptides and will help advance the development of applications for these supramolecular guanosine-containing nucleopeptides.
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Affiliation(s)
| | | | | | | | | | - Jillian E. Smith-Carpenter
- Department of Chemistry and Biochemistry, Fairfield University, 1073 N. Benson Rd, Fairfield, CT 06824, USA; (K.B.); (K.B.); (S.O.); (S.B.); (J.D.)
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7
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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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8
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Liu B, Pappas CG, Ottelé J, Schaeffer G, Jurissek C, Pieters PF, Altay M, Marić I, Stuart MCA, Otto S. Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids. J Am Chem Soc 2020; 142:4184-4192. [PMID: 32023041 PMCID: PMC7059183 DOI: 10.1021/jacs.9b10796] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
The conditions that led to the formation
of the first organisms
and the ways that life originates from a lifeless chemical soup are
poorly understood. The recent hypothesis of “RNA-peptide coevolution”
suggests that the current close relationship between amino acids and
nucleobases may well have extended to the origin of life. We now show
how the interplay between these compound classes can give rise to
new self-replicating molecules using a dynamic combinatorial approach.
We report two strategies for the fabrication of chimeric amino acid/nucleobase
self-replicating macrocycles capable of exponential growth. The first
one relies on mixing nucleobase- and peptide-based building blocks,
where the ligation of these two gives rise to highly specific chimeric
ring structures. The second one starts from peptide nucleic acid (PNA)
building blocks in which nucleobases are already linked to amino acids
from the start. While previously reported nucleic acid-based self-replicating
systems rely on presynthesis of (short) oligonucleotide sequences,
self-replication in the present systems start from units containing
only a single nucleobase. Self-replication is accompanied by self-assembly,
spontaneously giving rise to an ordered one-dimensional arrangement
of nucleobase nanostructures.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Christoph Jurissek
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Priscilla F Pieters
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Meniz Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ivana Marić
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marc C A Stuart
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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9
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Fukunaga K, Tsutsumi H, Mihara H. Self-Assembling Peptides as Building Blocks of Functional Materials for Biomedical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180293] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kazuto Fukunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-40, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hiroshi Tsutsumi
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-40, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-40, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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10
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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11
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Chotera A, Sadihov H, Cohen-Luria R, Monnard PA, Ashkenasy G. Functional Assemblies Emerging in Complex Mixtures of Peptides and Nucleic Acid-Peptide Chimeras. Chemistry 2018; 24:10128-10135. [PMID: 29732630 DOI: 10.1002/chem.201800500] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/29/2018] [Indexed: 01/24/2023]
Abstract
Striking synergy between nucleic acids and proteins is exhibited in living cells. Whether such mutual activity can be performed using simple supramolecular nucleic acid-peptide (NA-pep) architectures remains a mystery. To shed light on this question, we studied the emergence of a primitive synergy in assemblies of short DNA-peptide chimeras. Specifically, we characterized multiple structures forming along gradual mixing trajectory, in which a peptide solution was seeded with increasing amounts of NA-pep chimeras. We report on the systematic change from β-sheet-peptide-based fibrillar architectures into the spherical structures formed by the conjugates. Remarkably, we find that through forming onion-like structures, the conjugates exhibit increased DNA hybridization stability and bind small molecules more efficiently than the peptides or DNA alone. A brief discussion highlights the implications of our findings for the production of new materials and for research on the origin of life.
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Affiliation(s)
- Agata Chotera
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Hava Sadihov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Pierre-Alain Monnard
- Institute for Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
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12
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Maury CPJ. Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities. Cell Mol Life Sci 2018; 75:1499-1507. [PMID: 29550973 PMCID: PMC5897472 DOI: 10.1007/s00018-018-2797-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/19/2018] [Accepted: 03/13/2018] [Indexed: 01/29/2023]
Abstract
A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.
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13
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Wang H, Feng Z, Qin Y, Wang J, Xu B. Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin. Angew Chem Int Ed Engl 2018; 57:4931-4935. [PMID: 29451962 PMCID: PMC6014697 DOI: 10.1002/anie.201712834] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/01/2018] [Indexed: 12/20/2022]
Abstract
Herein, we report that assemblies of nucleopeptides selectively sequester ATP in complex conditions (for example, serum and cytosol). We developed assemblies of nucleopeptides that selectively sequester ATP over ADP. Counteracting enzymes interconvert ATP and ADP to modulate the nanostructures formed by the nucleopeptides and the nucleotides. The nucleopeptides, sequestering ATP effectively in cells, slow down efflux pumps in multidrug-resistant cancer cells, thus boosting the efficacy of doxorubicin, an anticancer drug. Investigation of 11 nucleopeptides (including d- and l-enantiomers) yields five more nucleopeptides that differentiate ATP and ADP through either precipitation or gelation. As the first example of assemblies of nucleopeptides that interact with ATP and disrupt intracellular ATP dynamics, this work illustrates the use of supramolecular assemblies to interact with small and essential biological molecules for controlling cell behavior.
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Affiliation(s)
- Huaimin Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Zhaoqianqi Feng
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Yanan Qin
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Jiaqing Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Bing Xu
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
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14
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Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712834] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Yamagata N, Chen X, Zhou J, Li J, Du X, Xu B. Enzymatic self-assembly of an immunoreceptor tyrosine-based inhibitory motif (ITIM). Org Biomol Chem 2017; 15:5689-5692. [PMID: 28675212 DOI: 10.1039/c7ob01074e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here we show the first example of an immunoreceptor tyrosine-based inhibitory motif (ITIM), LYYYYL, as well as its enantiomeric or retro-inverso peptide, to self-assemble in water via enzyme-instructed self-assembly. Upon enzymatic dephosphorylation, the phosphohexapeptides become hexapeptides, which self-assemble in water to result in supramolecular hydrogels. This work illustrates a new approach to design bioinspired soft materials from a less explored, but important pool of immunomodulatory peptides.
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Affiliation(s)
- Natsuko Yamagata
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA.
| | - Xiaoyi Chen
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA.
| | - Jie Zhou
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA.
| | - Jie Li
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA.
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA.
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA.
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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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Lin Y, Pashuck ET, Thomas MR, Amdursky N, Wang ST, Chow LW, Stevens MM. Plasmonic Chirality Imprinting on Nucleobase-Displaying Supramolecular Nanohelices by Metal-Nucleobase Recognition. Angew Chem Int Ed Engl 2017; 56:2361-2365. [PMID: 28102964 PMCID: PMC5396806 DOI: 10.1002/anie.201610976] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 11/09/2022]
Abstract
Supramolecular self-assembly is an important process that enables the conception of complex structures mimicking biological motifs. Herein, we constructed helical fibrils through chiral self-assembly of nucleobase-peptide conjugates (NPCs), where achiral nucleobases are helically displayed on the surface of fibrils, comparable to polymerized nucleic acids. Selective binding between DNA and the NPC fibrils was observed with fluorescence polarization. Taking advantage of metal-nucleobase recognition, we highlight the possibility of deposition/assembly of plasmonic nanoparticles onto the fibrillar constructs. In this approach, the supramolecular chirality of NPCs can be adaptively imparted to metallic nanoparticles, covering them to generate structures with plasmonic chirality that exhibit significantly improved colloidal stability. The self-assembly of rationally designed NPCs into nanohelices is a promising way to engineer complex, optically diverse nucleobase-derived nanomaterials.
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Affiliation(s)
- Yiyang Lin
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, SW72AZ, London, UK
| | - E. Thomas Pashuck
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, SW72AZ, London, UK
| | - Michael R. Thomas
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, SW72AZ, London, UK
| | - Nadav Amdursky
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, SW72AZ, London, UK
| | - Shih-Ting Wang
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, SW72AZ, London, UK
| | - Lesley W. Chow
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, SW72AZ, London, UK
| | - Molly M. Stevens
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, SW72AZ, London, UK
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18
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Plasmonic Chirality Imprinting on Nucleobase-Displaying Supramolecular Nanohelices by Metal-Nucleobase Recognition. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610976] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Fukunaga K, Tsutsumi H, Mihara H. Self-assembling peptide nanofibers promoting cell adhesion and differentiation. Biopolymers 2016; 100:731-7. [PMID: 23893249 DOI: 10.1002/bip.22309] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/12/2013] [Accepted: 06/04/2013] [Indexed: 01/19/2023]
Abstract
There is an increasing need for the development of functional artificial extracellular matrices (ECMs) for tissue engineering. Recently, we have successfully designed a self-assembling peptide, named E1Y9, to construct functional ECMs. We describe here an enhancement of abilities of E1Y9 materials to promote cell adhesion and differentiation, using functional peptide sequences derived from natural extracellular matrix proteins. We designed functionalized self-assembling peptides, RGDS-conjugated E1Y9 (E1Y9-RGDS) and IKVAV-conjugated E1Y9 (E1Y9-IKVAV). E1Y9-RGDS and E1Y9-IKVAV formed peptide nanofibers in a similar manner to E1Y9, with β-sheet secondary structures. Surfaces coated with peptide nanofibers displayed the higher bioactivities of E1Y9-RGDS for cell adhesion and E1Y9-IKVAV for cell differentiation than those of E1Y9, with the activities being dependent on the concentrations of the functional peptides. These functionalized peptides will be useful for the construction of functional ECMs in cell and tissue engineering.
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Affiliation(s)
- Kazuto Fukunaga
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B40 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
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20
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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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21
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Humenik M, Scheibel T. Self-assembly of nucleic acids, silk and hybrid materials thereof. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:503102. [PMID: 25419786 DOI: 10.1088/0953-8984/26/50/503102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here,we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.
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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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Cui H, Cheetham AG, Pashuck ET, Stupp SI. Amino acid sequence in constitutionally isomeric tetrapeptide amphiphiles dictates architecture of one-dimensional nanostructures. J Am Chem Soc 2014; 136:12461-8. [PMID: 25144245 PMCID: PMC4156871 DOI: 10.1021/ja507051w] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 12/19/2022]
Abstract
The switching of two adjacent amino acids can lead to differences in how proteins fold thus affecting their function. This effect has not been extensively explored in synthetic peptides in the context of supramolecular self-assembly. Toward this end, we report here the use of isomeric peptide amphiphiles as molecular building blocks to create one-dimensional (1D) nanostructures. We show that four peptide amphiphile isomers, with identical composition but a different sequence of their four amino acids, can form drastically different types of 1D nanostructures under the same conditions. We found that molecules with a peptide sequence of alternating hydrophobic and hydrophilic amino acids such as VEVE and EVEV self-assemble into flat nanostructures that can be either helical or twisted. On the other hand, nonalternating isomers such as VVEE and EEVV result in the formation of cylindrical nanofibers. Furthermore, we also found that when the glutamic acid is adjacent to the alkyl tail the supramolecular assemblies appear to be internally flexible compared to those with valine as the first amino acid. These results clearly demonstrate the significance of peptide side chain interactions in determining the architectures of supramolecular assemblies.
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Affiliation(s)
- Honggang Cui
- Department of Materials Science
and Engineering, Department of Chemistry, Department of Medicine, and Department of
Biomedical Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Andrew G. Cheetham
- Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - E. Thomas Pashuck
- Department of Materials Science
and Engineering, Department of Chemistry, Department of Medicine, and Department of
Biomedical Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Samuel I. Stupp
- Department of Materials Science
and Engineering, Department of Chemistry, Department of Medicine, and Department of
Biomedical Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
- Simpson
Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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24
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Abstract
The self-assembly of different classes of peptide, including cyclic peptides, amyloid peptides and surfactant-like peptides into nanotube structures is reviewed. The modes of self-assembly are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD (UK).
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26
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Kameta N. Soft nanotube hosts for capsulation and release of molecules, macromolecules, and nanomaterials. J INCL PHENOM MACRO 2014. [DOI: 10.1007/s10847-014-0397-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Gong B, Shao Z. Self-assembling organic nanotubes with precisely defined, sub-nanometer pores: formation and mass transport characteristics. Acc Chem Res 2013; 46:2856-66. [PMID: 23597055 DOI: 10.1021/ar400030e] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The transport of molecules and ions across nanometer-scaled pores, created by natural or artificial molecules, is a phenomenon of both fundamental and practical significance. Biological channels are the most remarkable examples of mass transport across membranes and demonstrate nearly exclusive selectivity and high efficiency with a diverse collection of molecules. These channels are critical for many basic biological functions, such as membrane potential, signal transduction, and osmotic homeostasis. If such highly specific and efficient mass transport or separation could be achieved with artificial nanostructures under controlled conditions, they could create revolutionary technologies in a variety of areas. For this reason, investigators from diverse disciplines have vigorously studied small nondeformable nanopores. The most exciting studies have focused on carbon nanotubes (CNTs), which have exhibited fast mass transport and high ion selectivity despite their very simple structure. However, the limitations of CNTs and the dearth of other small (≤2 nm) nanopores have severely hampered the systematic investigation of nanopore-mediated mass transport, which will be essential for designing artificial nanopores with desired functions en masse. Researchers can overcome the difficulties associated with CNT and other artificial pores by stacking macrocyclic building blocks with persistent shapes to construct tunable, self-assembling organic pores. This effort started when we discovered a highly efficient, one-pot macrocyclization process to efficiently prepare several classes of macrocycles with rigid backbones containing nondeformable cavities. Such macrocycles, if stacked atop one another, should lead to nanotubular assemblies with defined inner pores determined by their constituent macrocycles. One class of macrocycles with aromatic oligoamide backbones had a very high propensity for directional assembly, forming nanotubular structures containing nanometer and sub-nanometer hydrophilic pores. These self-assembling hydrophilic pores can form ion channels in lipid membranes with very large ion conductances. To control the assembly, we have further introduced multiple hydrogen-bonding side chains to enforce the stacking of rigid macrocycles into self-assembling nanotubes. This strategy has produced a self-assembling, sub-nanometer hydrophobic pore that not only acted as a transmembrane channel with surprisingly high ion selectivity, but also mediated a significant transmembrane water flux. The stacking of rigid macrocycles that can be chemically modified in either the lumen or the exterior surface can produce self-assembling organic nanotubes with inner pores of defined sizes. The combination of our approach with the availability and synthetic tunability of various rigid macrocycles should produce a variety of organic nanopores. Such structures would allow researchers to systematically explore mass transport in the sub-nanometer regime. Further advances should lead to novel applications such as biosensing, materials separation, and molecular purifications.
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Affiliation(s)
- Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhifeng Shao
- Key Laboratory of Systems Biomedicine, State Key Laboratory for Oncogenes & Related Genes and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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28
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Kameta N, Ishikawa K, Masuda M, Shimizu T. Control of self-assembled morphology and molecular packing of asymmetric glycolipids by association/dissociation with poly(thiopheneboronic acid). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:13291-13298. [PMID: 24090115 DOI: 10.1021/la4028018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The molecular packing and self-assembled morphologies of asymmetric bolaamphiphiles, N-(2-aminoethyl)-N'-(β-d-glucopyranosyl)alkanediamide [1(n), n = 12, 14, 16, 17, 18, and 20], were precisely controlled by association/dissociation with poly(thiopheneboronic acid) (PTB). Differential scanning calorimetry, X-ray diffraction, and infrared spectroscopy revealed that the starting film of 1(n) associated with 1 equiv of the boronic acid moiety of PTB, (Film-1(n)PTB), had antiparallel molecular packing of 1(n) moiety within the monolayer membranes. However, the molecular packing of the starting film that contained 0.5 equiv of the boronic acid moiety of PTB (Film-2eq1(n)PTB) was parallel. The dispersion of Film-1(n)PTB in water gave only nanotapes, whereas that of Film-2eq1(n)PTB in water selectively formed nanotubes, through a dissociation reaction of PTB based on the hydrolysis of the boronate esters in the complexes. The nanotapes and nanotubes memorized the antiparallel and parallel molecular packing of the starting films, respectively. Changes in the length of the oligomethylene spacer of 1(n) never affected the molecular packing or self-assembled morphologies. However, the inner diameters of the nanotubes increased irregularly in the range of 67.9-79.6 nm as the length of the oligomethylene spacer of 1(n) increased from n = 12 to n = 18.
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Affiliation(s)
- Naohiro Kameta
- Nanosystem Research Institute (NRI) and ‡Nanotube Research Center (NTRC), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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29
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Abstract
Living matter is the most elaborate, elegant, and complex hierarchical material known and is consequently the natural target for an ever-expanding scientific and technological effort to unlock and deconvolute its marvelous forms and functions. Our current understanding suggests that biological materials are derived from a bottom-up process, a spontaneous emergence of molecular networks in the course of chemical evolution. Polymer cooperation, so beautifully manifested in the ribosome, appeared in these dynamic networks, and the special physicochemical properties of the nucleic and amino acid polymers made possible the critical threshold for the emergence of extant cellular life. These properties include the precise and geometrically discrete hydrogen bonding patterns that dominate the complementary interactions of nucleic acid base-pairing that guide replication and ensure replication fidelity. In contrast, complex and highly context-dependent sets of intra- and intermolecular interactions guide protein folding. These diverse interactions allow the more analog environmental chemical potential fluctuations to dictate conformational template-directed propagation. When these two different strategies converged in the remarkable synergistic ribonucleoprotein that is the ribosome, this resulting molecular digital-to-analog converter achieved the capacity for both persistent information storage and adaptive responses to an ever-changing environment. The ancestral chemical networks that preceded the Central Dogma of Earth's biology must reflect the dynamic chemical evolutionary landscapes that allowed for selection, propagation, and diversification and ultimately the demarcation and specialization of function that modern biopolymers manifest. Not only should modern biopolymers contain molecular fossils of this earlier age, but it should be possible to use this information to reinvent these dynamic functional networks. In this Account, we review the first dynamic network created by modification of a nucleic acid backbone and show how it has exploited the digital-like base pairing for reversible polymer construction and information transfer. We further review how these lessons have been extended to the complex folding landscapes of templated peptide assembly. These insights have allowed for the construction of molecular hybrids of each biopolymer class and made possible the reimagining of chemical evolution. Such elaboration of biopolymer chimeras has already led to applications in therapeutics and diagnostics, to the construction of novel nanostructured materials, and toward orthogonal biochemical pathways that expand the evolution of existing biochemical systems. The ability to look beyond the primordial emergence of the ribosome may allow us to better define the origins of chemical evolution, to extend its horizons beyond the biology of today and ask whether evolution is an inherent property of matter unbounded by physical limitations imposed by our planet's diverse environments.
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Affiliation(s)
- Jay T. Goodwin
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Departments of Chemistry and Biology, Emory University, Atlanta, Georgia, United States
| | - Anil K. Mehta
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Departments of Chemistry and Biology, Emory University, Atlanta, Georgia, United States
| | - David G. Lynn
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Departments of Chemistry and Biology, Emory University, Atlanta, Georgia, United States
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30
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Zhou X, Liu G, Yamato K, Shen Y, Cheng R, Wei X, Bai W, Gao Y, Li H, Liu Y, Liu F, Czajkowsky DM, Wang J, Dabney MJ, Cai Z, Hu J, Bright FV, He L, Zeng XC, Shao Z, Gong B. Self-assembling subnanometer pores with unusual mass-transport properties. Nat Commun 2012; 3:949. [DOI: 10.1038/ncomms1949] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 06/11/2012] [Indexed: 11/09/2022] Open
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31
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Wang T, Cai Y, Wang Z, Guan E, Yu D, Qin A, Sun J, Tang BZ, Gao C. Decomposition-Assembly of Tetraphenylethylene Nanoparticles With Uniform Size and Aggregation-Induced Emission property. Macromol Rapid Commun 2012; 33:1584-9. [DOI: 10.1002/marc.201200324] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/09/2012] [Indexed: 11/08/2022]
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32
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Eichner T, Radford SE. A diversity of assembly mechanisms of a generic amyloid fold. Mol Cell 2011; 43:8-18. [PMID: 21726806 DOI: 10.1016/j.molcel.2011.05.012] [Citation(s) in RCA: 224] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 04/21/2011] [Accepted: 04/26/2011] [Indexed: 12/28/2022]
Abstract
Protein misfolding and amyloid assembly have long been recognized as being responsible for many devastating human diseases. Recent findings indicate that amyloid assemblies may facilitate crucial biological processes from bacteria to mammals. This review focuses on the mechanistic understanding of amyloid formation, including the transformation of initially innocuous proteins into oligomers and fibrils. The result is a competing folding and assembly energy landscape, which contains a number of routes by which the polypeptide chain can convert its primary sequence into functional structures, dysfunctional assemblies, or epigenetic entities that provide both threats and opportunities in the evolution of life.
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Affiliation(s)
- Timo Eichner
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
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33
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Liu D, Yao M, Li Q, Cui W, Zou B, Cui T, Liu B, Sundqvist B, Wågberg T. High pressure and high temperature induced polymerization of C60 nanotubes. CrystEngComm 2011. [DOI: 10.1039/c0ce00953a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Chan JCC. Solid-state NMR techniques for the structural determination of amyloid fibrils. Top Curr Chem (Cham) 2011; 306:47-88. [PMID: 21630137 DOI: 10.1007/128_2011_154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.
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Affiliation(s)
- Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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35
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Caporini MA, Bajaj VS, Veshtort M, Fitzpatrick A, MacPhee CE, Vendruscolo M, Dobson CM, Griffin RG. Accurate determination of interstrand distances and alignment in amyloid fibrils by magic angle spinning NMR. J Phys Chem B 2010; 114:13555-61. [PMID: 20925357 PMCID: PMC2959142 DOI: 10.1021/jp106675h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid fibrils are structurally ordered aggregates of proteins whose formation is associated with many neurodegenerative and other diseases. For that reason, their high-resolution structures are of considerable interest and have been studied using a wide range of techniques, notably electron microscopy, X-ray diffraction, and magic angle spinning (MAS) NMR. Because of the excellent resolution in the spectra, MAS NMR is uniquely capable of delivering site-specific, atomic resolution information about all levels of amyloid structure: (1) the monomer, which packs into several (2) protofilaments that in turn associate to form a (3) fibril. Building upon our high-resolution structure of the monomer of an amyloid-forming peptide from transthyretin (TTR(105-115)), we introduce single 1-(13)C labeled amino acids at seven different sites in the peptide and measure intermolecular carbonyl-carbonyl distances with an accuracy of ~0.11 A. Our results conclusively establish a parallel, in register, topology for the packing of this peptide into a β-sheet and provide constraints essential for the determination of an atomic resolution structure of the fibril. Furthermore, the approach we employ, based on a combination of a double-quantum filtered variant of the DRAWS recoupling sequence and multispin numerical simulations in SPINEVOLUTION, is general and should be applicable to a wide range of systems.
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Affiliation(s)
- Marc A Caporini
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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36
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Giraldo R. Amyloid Assemblies: Protein Legos at a Crossroads in Bottom-Up Synthetic Biology. Chembiochem 2010; 11:2347-57. [DOI: 10.1002/cbic.201000412] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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37
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Childers W, Mehta A, Ni R, Taylor J, Lynn D. Peptides Organized as Bilayer Membranes. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000212] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Childers W, Mehta A, Ni R, Taylor J, Lynn D. Peptides Organized as Bilayer Membranes. Angew Chem Int Ed Engl 2010; 49:4104-7. [DOI: 10.1002/anie.201000212] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Childers WS, Ni R, Mehta AK, Lynn DG. Peptide membranes in chemical evolution. Curr Opin Chem Biol 2009; 13:652-9. [PMID: 19879180 PMCID: PMC2801140 DOI: 10.1016/j.cbpa.2009.09.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/23/2009] [Accepted: 09/28/2009] [Indexed: 11/21/2022]
Abstract
Simple surfactants achieve remarkable long-range order in aqueous environments. This organizing potential is seen most dramatically in biological membranes where phospholipid assemblies both define cell boundaries and provide a ubiquitous structural scaffold for controlling cellular chemistry. Here we consider simple peptides that also spontaneously assemble into exceptionally ordered scaffolds, and review early data suggesting that these structures maintain the functional diversity of proteins. We argue that such scaffolds can achieve the required molecular order and catalytic agility for the emergence of chemical evolution.
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Affiliation(s)
- W Seth Childers
- Center for Fundamental and Applied Molecular Evolution and Center for Chemical Evolution, Department of Chemistry and Biology, Emory University, Atlanta, GA, United States
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40
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Sawada T, Takahashi T, Mihara H. Affinity-Based Screening of Peptides Recognizing Assembly States of Self-Assembling Peptide Nanomaterials. J Am Chem Soc 2009; 131:14434-41. [DOI: 10.1021/ja905250u] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toshiki Sawada
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Yokohama 226-8501, Japan
| | - Tsuyoshi Takahashi
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Yokohama 226-8501, Japan
| | - Hisakazu Mihara
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Yokohama 226-8501, Japan
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