1
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Kwiatkowski W, Greenwald J, Murzakhmetov L, Robinson RC, Riek R. Short Peptide Amyloids Are a Potential Sequence Pool for the Emergence of Proteins. J Mol Biol 2024; 436:168495. [PMID: 38360090 DOI: 10.1016/j.jmb.2024.168495] [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: 10/19/2023] [Revised: 01/15/2024] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
Under prebiotic conditions, peptides are capable of self-replication through a structure-based template-assisted mechanism when they form amyloids. Furthermore, peptide amyloids can spontaneously form inside fatty acid vesicles creating membrane enclosed complex structures of variable morphologies. This is possible because fatty acid vesicle membranes act as filters allowing passage of activated amino acids while some amino acids derived from the activated species become non-permeable and trapped in the vesicles. Similarly, nascent peptides derived from the condensation of the activated amino acids are also trapped in the vesicles. It is hypothesized that such preselected peptide amyloids become a sequence pool for the emergence of proteins in life and that after billions of years of cellular evolution, the sequences in the current proteome have diverged significantly from these original seed peptides. If this hypothesis is correct, it could be possible to detect the traces of these seed sequences in current proteomes. Here, we show for all possible 3, 6, 7, 8 or 9 residue sequence motifs that those motifs that are most amyloidogenic/aggregation prone are over-represented in extant proteomes compared to a sequence-randomized proteome. Furthermore, we find that there is a greater proportion of amyloidogenic sequence motifs in archaea proteomes than in the larger primate proteomes. This suggests that the evolution towards larger proteomes leads to smaller proportion of amyloidogenic sequences.
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Affiliation(s)
| | | | | | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand; Research Institute for Interdisciplinary Science, Okayama University, Japan
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2
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Gagnon LG, Czaikowski ME, Peacock-López E. Dynamic properties of a self-replicating peptide network with inhibition. J Chem Phys 2022; 157:225101. [PMID: 36546800 DOI: 10.1063/5.0119945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In this paper, we report an open system consisting of three self-replicating peptides, in which peptide 1 inhibits the duplex template of peptide 2, peptide 2 inhibits duplex 3, and peptide 3 inhibits duplex 1 to complete the negative feedback loop. This interacting chemical network yields oscillations in the concentrations of all species over time and establishes a possible mechanism for pre-biotic chemical systems organization. The first focus of our analysis is the effect of altering rates of duplex formation and inhibition on oscillations. We then examine the autocatalytic rate constant in the symmetric and asymmetric cases.
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Affiliation(s)
- Lucille G Gagnon
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, USA
| | - Maia E Czaikowski
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, USA
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3
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Roy S, Chatterjee A, Bal S, Das D. Cross β Amyloid Nanotubes Demonstrate Promiscuous Catalysis in a Chemical Reaction Network via Co‐option. Angew Chem Int Ed Engl 2022; 61:e202210972. [DOI: 10.1002/anie.202210972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Soumili Roy
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Ayan Chatterjee
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
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4
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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- 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
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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5
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Liu B, Wu J, Geerts M, Markovitch O, Pappas CG, Liu K, Otto S. Out-of-Equilibrium Self-Replication Allows Selection for Dynamic Kinetic Stability in a System of Competing Replicators. Angew Chem Int Ed Engl 2022; 61:e202117605. [PMID: 35179808 PMCID: PMC9314957 DOI: 10.1002/anie.202117605] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 12/16/2022]
Abstract
Among the key characteristics of living systems are their ability to self‐replicate and the fact that they exist in an open system away from equilibrium. Herein, we show how the outcome of the competition between two self‐replicators, differing in size and building block composition, is different depending on whether the experiments are conducted in a closed vial or in an open and out‐of‐equilibrium replication–destruction regime. In the closed system, the slower replicator eventually prevails over the faster competitor. In a replication‐destruction regime, implemented through a flow system, the outcome of the competition is reversed and the faster replicator dominates. The interpretation of the experimental observations is supported by a mass‐action‐kinetics model. These results represent one of the few experimental manifestations of selection among competing self‐replicators based on dynamic kinetic stability and pave the way towards Darwinian evolution of abiotic systems.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Juntian Wu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marc Geerts
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Omer Markovitch
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.,Origins Center, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Kai Liu
- 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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6
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Liu B, Wu J, Geerts M, Markovitch O, Pappas CG, Liu K, Otto S. Out‐of‐equilibrium self‐replication allows selection for dynamic kinetic stability in a system of competing replicators. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bin Liu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Juntian Wu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Marc Geerts
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Omer Markovitch
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Charalampos G. Pappas
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Kai Liu
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Sijbren Otto
- Stratingh Institute University of Groningen Centre for Systems Chemistry Nijenborgh 4 9747AG Groningen NETHERLANDS
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7
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Rout SK, Rhyner D, Riek R, Greenwald J. Prebiotically Plausible Autocatalytic Peptide Amyloids. Chemistry 2021; 28:e202103841. [PMID: 34812556 PMCID: PMC9299922 DOI: 10.1002/chem.202103841] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 12/19/2022]
Abstract
The prebiotic emergence of molecules capable both of self-replication and of storing information was a defining event at the dawn of life. Still, no plausible prebiotic self-replication of biologically relevant molecules has been demonstrated. Building upon the known templating nature of amyloids, we present two systems in which the products of a peptide-bond-forming reaction act as self-replicators to enhance the yield and stereoselectivity of their formation. This first report of an amino acid condensation that can undergo autocatalysis further supports the potential role of amyloids in prebiotic molecular evolution as an environment-responsive and information-coding system capable of self-replication.
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Affiliation(s)
- Saroj K Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - David Rhyner
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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8
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Misra S, Mukherjee S, Ghosh A, Singh P, Mondal S, Ray D, Bhattacharya G, Ganguly D, Ghosh A, Aswal VK, Mahapatra AK, Satpati B, Nanda J. Single Amino-Acid Based Self-Assembled Biomaterials with Potent Antimicrobial Activity. Chemistry 2021; 27:16744-16753. [PMID: 34468048 DOI: 10.1002/chem.202103071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 12/18/2022]
Abstract
The design and development of soft biomaterials based on amino acid and short-peptide have gained much attention due to their potent biomedical applications. A slight alteration in the side-chain of single amino acid in a peptide or protein sequence has a huge impact on the structure and function. Phenylalanine is one of the most studied amino acids, which contains an aromatic phenyl group connected through a flexible -CH2 - unit. In this work, we have examined whether flexibility and aromatic functionality of phenylalanine (Phe) are important in gel formation of model gelator Fmoc-Phe-OH or not. To examine this hypothesis, we synthesized Fmoc-derivatives of three analogues unnatural amino acids including cyclohexylalanine, phenylglycine, and homophenylalanine; which are slightly varied from Phe. Interestingly, all these three new analogues formed hydrogels in phosphate buffer at pH 7.0 having different gelation efficacy and kinetics. This study suggests that the presence of aromatic side-chain and flexibility are not mandatory for the gelation of this model gelator. Newly synthesized unnatural amino acid derivatives have also exhibited promising antimicrobial activity towards gram-positive bacteria by inhibiting cellular oxygen consumption. We further determined the biocompatibility of these amino acid derivatives by using a hemolysis assay on human blood cells. Overall studies described the development of single amino acid-based new injectable biomaterials with improved antimicrobial activity by the slight alteration in the side-chain of amino acid.
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Affiliation(s)
- Souvik Misra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.- Botanic Garden, Howrah, 711103, India
| | | | - Anamika Ghosh
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.- Botanic Garden, Howrah, 711103, India
| | - Pijush Singh
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, India
| | - Sanjoy Mondal
- Polymer Science Unit, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debes Ray
- Solid State Physics Division, Bhabha Atomic Research Centre Trombay, Mumbai, 400085, India
| | | | - Debabani Ganguly
- Centre for Health Science and Technology, JIS Institute of Advanced Studies and Research, Kolkata, 700091, India
| | - Alok Ghosh
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - V K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre Trombay, Mumbai, 400085, India
| | - Ajit K Mahapatra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.- Botanic Garden, Howrah, 711103, India
| | - Biswarup Satpati
- Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Jayanta Nanda
- Department of Chemistry, University of North Bengal, Darjeeling, West Bengal, PIN-734301, India
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9
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Lengyel-Zhand Z, Marshall LR, Jung M, Jayachandran M, Kim MC, Kriews A, Makhlynets OV, Fry HC, Geyer A, Korendovych IV. Covalent Linkage and Macrocylization Preserve and Enhance Synergistic Interactions in Catalytic Amyloids. Chembiochem 2021; 22:585-591. [PMID: 32956537 PMCID: PMC8009494 DOI: 10.1002/cbic.202000645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Indexed: 12/14/2022]
Abstract
The self-assembly of short peptides into catalytic amyloid-like nanomaterials has proven to be a powerful tool in both understanding the evolution of early proteins and identifying new catalysts for practically useful chemical reactions. Here we demonstrate that both parallel and antiparallel arrangements of β-sheets can accommodate metal ions in catalytically productive coordination environments. Moreover, synergistic relationships, identified in catalytic amyloid mixtures, can be captured in macrocyclic and sheet-loop-sheet species, that offer faster rates of assembly and provide more complex asymmetric arrangements of functional groups, thus paving the way for future designs of amyloid-like catalytic proteins. Our findings show how initial catalytic activity in amyloid assemblies can be propagated and improved in more-complex molecules, providing another link in a complex evolutionary chain between short, potentially abiotically produced peptides and modern-day enzymes.
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Affiliation(s)
- Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Liam R Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Maximilian Jung
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Megha Jayachandran
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Min-Chul Kim
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Austin Kriews
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - H Christopher Fry
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Armin Geyer
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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10
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Hanopolskyi AI, Smaliak VA, Novichkov AI, Semenov SN. Autocatalysis: Kinetics, Mechanisms and Design. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anton I. Hanopolskyi
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Viktoryia A. Smaliak
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Alexander I. Novichkov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Sergey N. Semenov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
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11
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Sevim İ, Pankau WM, von Kiedrowski G. Re-Evaluation of a Fulvene-Based Self-Replicating Diels-Alder Reaction System. Chemistry 2020; 26:9032-9035. [PMID: 32638430 DOI: 10.1002/chem.201905594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/04/2020] [Indexed: 11/06/2022]
Abstract
We re-evaluate our claim of a high diastereoselectivity in the self-relicating Diels-Alder reaction between maleimide 1 and fulvene 3. It was shown that the system has a diastereoselectivity of 1.8:1 for NN-4:NX-4, which is contrary to the 16:1 ratio claimed by Dieckmann et al. The analysis of 1 H NMR monitoring of the reaction revealed that both replicators show sigmoidal growth which is typical for auto-catalytic systems.
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Affiliation(s)
- İlhan Sevim
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Wolf Matthias Pankau
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Günter von Kiedrowski
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
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12
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self‐Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
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13
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self-Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020; 59:4329-4334. [PMID: 31920004 DOI: 10.1002/anie.201914633] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Indexed: 12/25/2022]
Abstract
Early evolution benefited from a complex network of reactions involving multiple C-C bond forming and breaking events that were critical for primitive metabolism. Nature gradually chose highly evolved and complex enzymes such as lyases to efficiently facilitate C-C bond formation and cleavage with remarkable substrate selectivity. Reported here is a lipidated short peptide which accesses a homogenous nanotubular morphology to efficiently catalyze C-C bond cleavage and formation. This system shows morphology-dependent catalytic rates, suggesting the formation of a binding pocket and registered enhancements in the presence of the hydrogen-bond donor tyrosine, which is exploited by extant aldolases. These assemblies showed excellent substrate selectivity and templated the formation of a specific adduct from a pool of possible adducts. The ability to catalyze metabolically relevant cascade transformations suggests the importance of such systems in early evolution.
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Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
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14
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Wang H, Feng Z, Xu B. Assemblies of Peptides in a Complex Environment and their Applications. Angew Chem Int Ed Engl 2019; 58:10423-10432. [PMID: 30903643 PMCID: PMC6656613 DOI: 10.1002/anie.201814552] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Indexed: 01/28/2023]
Abstract
Using peptide assemblies with emergent properties to achieve elaborate functions has attracted increasing attention in recent years. Besides tailoring the self-assembly of peptides in vitro, peptide research is advancing into a new and exciting frontier: the rational design of peptide assemblies (or their derivatives) for biological functions in a complex environment. This Minireview highlights recent developments in peptide assemblies and their applications in biological systems. After introducing the unique merits of peptide assemblies, we discuss the recent progress in designing peptides (or peptide derivatives) for self-assembly with conformational control. Then, we describe biological functions of peptide assemblies, with an emphasis on approach-instructed assembly for spatiotemporal control of peptide assemblies, in the cellular context. Finally, we discuss the future promises and challenges of this exciting area of chemistry.
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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
| | - Bing Xu
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA 02454, USA
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15
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Wang H, Feng Z, Xu B. Assemblies of Peptides in a Complex Environment and their Applications. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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
| | - Bing Xu
- Department of Chemistry Brandeis University 415 South St Waltham MA 02454 USA
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16
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Rink WM, Thomas F. De Novo Designed α-Helical Coiled-Coil Peptides as Scaffolds for Chemical Reactions. Chemistry 2018; 25:1665-1677. [DOI: 10.1002/chem.201802849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Indexed: 01/31/2023]
Affiliation(s)
- W. Mathis Rink
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Straße 3a 37075 Göttingen Germany
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17
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Affiliation(s)
- Meniz Altay
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Yigit Altay
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems ChemistryStratingh InstituteUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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18
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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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19
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Altay M, Altay Y, Otto S. Parasitic Behavior of Self-Replicating Molecules. Angew Chem Int Ed Engl 2018; 57:10564-10568. [PMID: 29856109 DOI: 10.1002/anie.201804706] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/16/2022]
Abstract
Self-replication plays a central role in the origin of life and in strategies to synthesize life de novo. Studies on self-replication have focused mostly on isolated systems, while the dynamics of systems containing multiple replicators have received comparatively little attention. Yet most evolutionary scenarios involve the interplay between different replicators. Here we report the emergence of parasitic behavior in a system containing self-replicators derived from two subtly different building blocks 1 and 2. Replicators from 2 form readily through cross-catalysis by pre-existing replicators made from 1. Once formed, the new replicators consume the original replicators to which they owe their existence. These results resemble parasitic and predatory behavior that is normally associated with living systems and show how such lifelike behavior has its roots in relatively simple systems of self-replicating molecules.
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Affiliation(s)
- Meniz Altay
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Yigit Altay
- 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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20
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Middel S, Panse CH, Nawratil S, Diederichsen U. Native Chemical Ligation Directed by Photocleavable Peptide Nucleic Acid (PNA) Templates. Chembiochem 2017; 18:2328-2332. [PMID: 28987009 DOI: 10.1002/cbic.201700487] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Indexed: 11/10/2022]
Abstract
A novel peptide-peptide ligation strategy is introduced that has the potential to provide peptide libraries of linearly or branched coupled fragments and will be suited to introduce simultaneous protein modifications at different ligation sites. Ligation is assisted by templating peptide nucleic acid (PNA) strands, and therefore, ligation specificity is solely encoded by the PNA sequence. PNA templating, in general, allows for various kinds of covalent ligation reactions. As a proof of principle, a native chemical ligation strategy was elaborated. This PNA-templated ligation includes easy on-resin procedures to couple linkers and PNA to the respective peptides, and a traceless photocleavage of the linker/PNA oligomer after the ligation step. A 4,5-dimethoxy-2-nitrobenzaldehyde-based linker that allowed the photocleavable linkage of two bio-oligomers was developed.
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Affiliation(s)
- Stephen Middel
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstrasse 2, 37077, Göttingen, Germany
| | - Cornelia H Panse
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstrasse 2, 37077, Göttingen, Germany
| | - Swantje Nawratil
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstrasse 2, 37077, Göttingen, Germany
| | - Ulf Diederichsen
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstrasse 2, 37077, Göttingen, Germany
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21
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Frederix PWJM, Idé J, Altay Y, Schaeffer G, Surin M, Beljonne D, Bondarenko AS, Jansen TLC, Otto S, Marrink SJ. Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles. ACS NANO 2017; 11:7858-7868. [PMID: 28723067 PMCID: PMC5616102 DOI: 10.1021/acsnano.7b02211] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.
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Affiliation(s)
- Pim W. J. M. Frederix
- University
of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747AG Groningen, The Netherlands
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
- E-mail:
| | - Julien Idé
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - Yigit Altay
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
| | - Gaël Schaeffer
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
| | - Mathieu Surin
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - David Beljonne
- Laboratory
of Chemistry of Novel Materials, University
of Mons − UMONS, Place du Parc 20, B-7000 Mons, Belgium
| | - Anna S. Bondarenko
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Sijbren Otto
- University
of Groningen, Center for Systems Chemistry, Stratingh Institute for
Chemistry, Nijenborgh
4, 9747AG Groningen, The Netherlands
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
- E-mail:
| | - Siewert J. Marrink
- University
of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747AG Groningen, The Netherlands
- University
of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747AG Groningen, The Netherlands
- E-mail:
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22
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Chi H, Keiderling TA. Structural Rearrangement from Oligomer to Fibril Detected with FRET in a Designed Amphiphilic Peptide. Chembiochem 2016; 18:195-205. [DOI: 10.1002/cbic.201600436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Heng Chi
- Department of Chemistry (M/C 111); University of Illinois at Chicago; 845 W. Taylor Street Chicago IL 60607 USA
- Department of Pharmacy; Jiangsu Food and Pharmaceutical Science College; 4 E. Meicheng Rd. Huai'an Jiangsu Province 223005 China
| | - Timothy A. Keiderling
- Department of Chemistry (M/C 111); University of Illinois at Chicago; 845 W. Taylor Street Chicago IL 60607 USA
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23
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Singh N, Kumar M, Miravet JF, Ulijn RV, Escuder B. Peptide-Based Molecular Hydrogels as Supramolecular Protein Mimics. Chemistry 2016; 23:981-993. [PMID: 27530095 DOI: 10.1002/chem.201602624] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Indexed: 12/14/2022]
Abstract
This Minireview concerns recent advances in the design, synthesis, and application of low molecular-weight peptidic hydrogelators. The sequence-specific combinations of amino acid side chain functionalities combined with hydrogen bonding of amide backbones and hydrophobic (aromatic) capping groups give these peptidic molecules the intrinsic tendency to self-assemble. The most prevalent designs include N-capped amino acid residues, bolamphiphilic peptides, and amphipathic peptides. Factors such as hydrophobic effects, the Hofmeister effect, and tunable ionization influence their aggregation properties. The self-assembly of simple bio-inspired building blocks into higher organized structures allows comparisons to be drawn with proteins and their complex functionalities, providing preliminary insights into complex biological functions and also enabling their application in a wide range of fields including catalysis, biomedical applications, and mimicry of natural dissipative systems. The Minireview is concluded by a short summary and outlook, highlighting the advances and steps required to bridge the gaps in the understanding of such systems.
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Affiliation(s)
- Nishant Singh
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Av. Sos Baynat, s/n, 12071, Castelló, Spain
| | - Mohit Kumar
- Advanced Science Research Centre (ASRC), City University of New York, 85 St Nicholas Terrace, New York, NY, 10031, USA
| | - Juan F Miravet
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Av. Sos Baynat, s/n, 12071, Castelló, Spain
| | - Rein V Ulijn
- Advanced Science Research Centre (ASRC), City University of New York, 85 St Nicholas Terrace, New York, NY, 10031, USA.,WestCHEM/Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.,Department of Chemistry and Biochemistry, City University of New York-Hunter College, 695 Park Ave., New York, NY, 10065, USA.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Beatriu Escuder
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Av. Sos Baynat, s/n, 12071, Castelló, Spain
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24
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Ivnitski D, Amit M, Silberbush O, Atsmon-Raz Y, Nanda J, Cohen-Luria R, Miller Y, Ashkenasy G, Ashkenasy N. The Strong Influence of Structure Polymorphism on the Conductivity of Peptide Fibrils. Angew Chem Int Ed Engl 2016; 55:9988-92. [DOI: 10.1002/anie.201604833] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Denis Ivnitski
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Moran Amit
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Ohad Silberbush
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Yoav Atsmon-Raz
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- Department of Biological Science; University of Calgary, Center of Molecular Simulation; 2500 University Drive NW Calgary Alberta T2N 1N4 Canada
| | - Jayanta Nanda
- 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
| | - Yifat Miller
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Gonen Ashkenasy
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
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25
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Ivnitski D, Amit M, Silberbush O, Atsmon-Raz Y, Nanda J, Cohen-Luria R, Miller Y, Ashkenasy G, Ashkenasy N. The Strong Influence of Structure Polymorphism on the Conductivity of Peptide Fibrils. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Denis Ivnitski
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Moran Amit
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Ohad Silberbush
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Yoav Atsmon-Raz
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- Department of Biological Science; University of Calgary, Center of Molecular Simulation; 2500 University Drive NW Calgary Alberta T2N 1N4 Canada
| | - Jayanta Nanda
- 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
| | - Yifat Miller
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Gonen Ashkenasy
- Department of Chemistry; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
- The Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
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26
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Tena-Solsona M, Nanda J, Díaz-Oltra S, Chotera A, Ashkenasy G, Escuder B. Emergent Catalytic Behavior of Self-Assembled Low Molecular Weight Peptide-Based Aggregates and Hydrogels. Chemistry 2016; 22:6687-94. [PMID: 27004623 DOI: 10.1002/chem.201600344] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 01/19/2023]
Abstract
We report a series of short peptides possessing the sequence (FE)n or (EF)n and bearing l-proline at their N-terminus that self-assemble into high aspect ratio aggregates and hydrogels. We show that these aggregates are able to catalyze the aldol reaction, whereas non-aggregated analogues are catalytically inactive. We have undertaken an analysis of the results, considering the accessibility of catalytic sites, pKa value shifts, and the presence of hydrophobic pockets. We conclude that the presence of hydrophobic regions is indeed relevant for substrate solubilization, but that the active site accessibility is the key factor for the observed differences in reaction rates. The results presented here provide an example of the emergence of a new chemical property caused by self-assembly, and support the relevant role played by self-assembled peptides in prebiotic scenarios. In this sense, the reported systems can be seen as primitive aldolase I mimics, and have been successfully tested for the synthesis of simple carbohydrate precursors.
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Affiliation(s)
- Marta Tena-Solsona
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain
| | - Jayanta Nanda
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Santiago Díaz-Oltra
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain
| | - Agata Chotera
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Beatriu Escuder
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain.
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27
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Rasale DB, Konda M, Biswas S, Das AK. Controlling Peptide Self-Assembly through a Native Chemical Ligation/Desulfurization Strategy. Chem Asian J 2016; 11:926-35. [DOI: 10.1002/asia.201501458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Dnyaneshwar B. Rasale
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 452020 India
| | - Maruthi Konda
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 452020 India
| | - Sagar Biswas
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 452020 India
| | - Apurba K. Das
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 452020 India
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28
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Controlling the Structure and Length of Self-Synthesizing Supramolecular Polymers through Nucleated Growth and Disassembly. Angew Chem Int Ed Engl 2015; 54:7852-6. [DOI: 10.1002/anie.201501965] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 12/19/2022]
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29
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Pal A, Malakoutikhah M, Leonetti G, Tezcan M, Colomb-Delsuc M, Nguyen VD, van der Gucht J, Otto S. Controlling the Structure and Length of Self-Synthesizing Supramolecular Polymers through Nucleated Growth and Disassembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501965] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Atcher J, Moure A, Bujons J, Alfonso I. Salt-Induced Adaptation of a Dynamic Combinatorial Library of Pseudopeptidic Macrocycles: Unraveling the Electrostatic Effects in Mixed Aqueous Media. Chemistry 2015; 21:6869-78. [DOI: 10.1002/chem.201406155] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Joan Atcher
- Department of Biological Chemistry and Molecular Modeling, IQAC-CSIC, Jordi Girona 18-26, 08034, Barcelona (Spain)
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31
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Nowak P, Saggiomo V, Salehian F, Colomb-Delsuc M, Han Y, Otto S. Localized Template-Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry. Angew Chem Int Ed Engl 2015; 54:4192-7. [DOI: 10.1002/anie.201409667] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/21/2015] [Indexed: 12/18/2022]
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32
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Nowak P, Saggiomo V, Salehian F, Colomb-Delsuc M, Han Y, Otto S. Localized Template-Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409667] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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33
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Li J, Cvrtila I, Colomb-Delsuc M, Otten E, Otto S. An “Ingredients” Approach to Functional Self-Synthesizing Materials: A Metal-Ion-Selective, Multi-Responsive, Self-Assembled Hydrogel. Chemistry 2014; 20:15709-14. [DOI: 10.1002/chem.201404977] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Indexed: 12/22/2022]
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34
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Asencio-Hernández J, Ruhlmann C, McEwen A, Eberling P, Nominé Y, Céraline J, Starck JP, Delsuc MA. Reversible Amyloid Fiber Formation in the N Terminus of Androgen Receptor. Chembiochem 2014; 15:2370-3. [DOI: 10.1002/cbic.201402420] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Indexed: 01/17/2023]
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35
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Brauckhoff N, Hahne G, Yeh JTH, Grossmann TN. Protein-vermittelte Peptidverknüpfung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Brauckhoff N, Hahne G, Yeh JTH, Grossmann TN. Protein-Templated Peptide Ligation. Angew Chem Int Ed Engl 2014; 53:4337-40. [DOI: 10.1002/anie.201400681] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Indexed: 12/13/2022]
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37
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38
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Bissette AJ, Fletcher SP. Mechanisms of Autocatalysis. Angew Chem Int Ed Engl 2013; 52:12800-26. [DOI: 10.1002/anie.201303822] [Citation(s) in RCA: 273] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Indexed: 12/17/2022]
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39
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Sonti R, Gopi HN, Muddegowda U, Ragothama S, Balaram P. A Designed Three-Stranded β-Sheet in an α/β Hybrid Peptide. Chemistry 2013; 19:5955-65. [DOI: 10.1002/chem.201204327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Indexed: 01/25/2023]
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40
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Wagner N, Rubinov B, Ashkenasy G. β-Sheet-induced chirogenesis in polymerization of oligopeptides. Chemphyschem 2011; 12:2771-80. [PMID: 21898751 DOI: 10.1002/cphc.201100292] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 07/17/2011] [Indexed: 11/07/2022]
Abstract
The origin of long homochiral biopolymers in living systems has recently been the focus of intense research. In one particular research line, scientists studied, experimentally and theoretically, chiral amplification obtained during peptide formation by polymerization of amino acid building blocks. It was suggested that processes leading to temporal or spatial separation, and thus, to the growth of homochiral polymers at the expense of their heterochiral counterparts, can explain the chirality observed in larger molecules. We introduce a simple model and stochastic simulation for the polymerization of amino acids and β-sheet formation, showing the crucial effects of the β sheets on the distributions of peptide lengths. When chiral affinities are included, racemic β sheets of alternating homochiral strands lead to the formation of chiral peptides, the isotacticity of which increases with length, consistent with previous experimental results in aqueous solutions. The tendency to form isotactic peptides is shown for both initially racemic and initially nonracemic systems, as well as for closed and open systems. We suggest that these or similar mechanisms may explain the origin of chiroselectivity in prebiotic environments.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel
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41
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Dieckmann A, Beniken S, Lorenz CD, Doltsinis NL, von Kiedrowski G. Elucidating the origin of diastereoselectivity in a self-replicating system: selfishness versus altruism. Chemistry 2011; 17:468-80. [PMID: 21207563 DOI: 10.1002/chem.201002325] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have investigated a diastereoselective self-replicating system based on a cycloaddition of a fulvene derivative and a maleimide using a two-pronged approach of combining NMR spectroscopy with computational modelling. Two diastereomers are formed with identical rates in the absence of replication. When replication is enabled, one diastereomer takes over the resources as a "selfish" autocatalyst, while exploiting the competitor as a weak "altruist", resulting in a diastereoselectivity of 16:1. We applied 1D and 2D NMR spectroscopic techniques supported by ab initio chemical shifts as well as ab initio molecular dynamics simulations to study the structure and dynamics of the underlying network. This powerful combination allowed us to decipher the energetic and structural rationale behind the observed behaviour, while static computational methods currently used in the field did not.
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Affiliation(s)
- Arne Dieckmann
- Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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42
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Dadon Z, Samiappan M, Safranchik EY, Ashkenasy G. Light-Induced Peptide Replication Controls Logic Operations in Small Networks. Chemistry 2010; 16:12096-9. [DOI: 10.1002/chem.201001488] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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