1
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Dev D, Wagner N, Pramanik B, Sharma B, Maity I, Cohen-Luria R, Peacock-Lopez E, Ashkenasy G. A Peptide-Based Oscillator. J Am Chem Soc 2023; 145:26279-26286. [PMID: 37984498 DOI: 10.1021/jacs.3c09377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Living organisms are replete with rhythmic and oscillatory behavior at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recent studies of synthetic oscillators that mimic such functions have shown decayed cycles in batch-mode reactions or sustained oscillatory kinetics under flow conditions. Considering the hypothesized functionality of peptides in early chemical evolution and their central role in current bio-nanotechnology, we now reveal a peptide-based oscillator. Oscillatory behavior was achieved by coupling coiled-coil-based replication processes as positive feedback to controlled initiation and inhibition pathways in a continuously stirred tank reactor (CSTR). Our results stress that assembly into the supramolecular structure and specific interactions with the replication substrates are crucial for oscillations. The replication-inhibition processes were first studied in batch mode, which produced a single damped cycle. Thereafter, combined experimental and theoretical characterization of the replication process in a CSTR under different flow and environmental (pH, redox) conditions demonstrated reasonably sustained oscillations. We propose that studies in this direction might pave the way to the design of robust oscillation networks that mimic the autonomous behavior of proteins in cells (e.g., in the cyanobacterial circadian clock) and hence hint at feasible pathways that accelerated the transition from simple peptides to extant enzymes.
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Affiliation(s)
- Dharm Dev
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bapan Pramanik
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bhawna Sharma
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Centre for Nano and Material Sciences, Jain Global Campus, Bangalore, Karnataka 560070, India
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Enrique Peacock-Lopez
- Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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2
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Sadihov-Hanoch H, Bandela AK, Chotera-Ouda A, Ben David O, Cohen-Luria R, Lynn DG, Ashkenasy G. Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras. Soft Matter 2023; 19:3940-3945. [PMID: 37211859 DOI: 10.1039/d2sm01528e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recent attempts to develop the next generation of functional biomaterials focus on systems chemistry approaches exploiting dynamic networks of hybrid molecules. This task is often found challenging, but we herein present ways for profiting from the multiple interaction interfaces forming Nucleic-acid-Peptide assemblies and tuning their formation. We demonstrate that the formation of well-defined structures by double-stranded DNA-peptide conjugates (dsCon) is restricted to a specific range of environmental conditions and that precise DNA hybridization, satisfying the interaction interfaces, is a crucial factor in this process. We further reveal the impact of external stimuli, such as competing free DNA elements or salt additives, which initiate dynamic interconversions, resulting in hybrid structures exhibiting spherical and fibrillar domains or a mixture of spherical and fibrillar particles. This extensive analysis of the co-assembly systems chemistry offers new insights into prebiotic hybrid assemblies that may now facilitate the design of new functional materials. We discuss the implications of these findings for the emergence of function in synthetic materials and during early chemical evolution.
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Affiliation(s)
- Hava Sadihov-Hanoch
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Anil Kumar Bandela
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Agata Chotera-Ouda
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Oshrat Ben David
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - David G Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, USA
| | - Gonen Ashkenasy
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Glionna C, Kumar V, Le Saux G, Pramanik B, Wagner N, Cohen-Luria R, Ashkenasy G, Ashkenasy N. Dynamic Surface Layer Coiled Coil Proteins Processing Analog-to-Digital Information. J Am Chem Soc 2021; 143:17441-17451. [PMID: 34652148 DOI: 10.1021/jacs.1c06356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Surface layer proteins perform multiple functions in prokaryotic cells, including cellular defense, cell-shape maintenance, and regulation of import and export of materials. However, mimicking the complex and dynamic behavior of such two-dimensional biochemical systems is challenging, and hence research has so far focused mainly on the design and manipulation of the structure and functionality of protein assemblies in solution. Motivated by the new opportunities that dynamic surface layer proteins may offer for modern technology, we herein demonstrate that immobilization of coiled coil proteins onto an inorganic surface facilitates complex behavior, manifested by reversible chemical reactions that can be rapidly monitored as digital surface readouts. Using multiple chemical triggers as inputs and several surface characteristics as outputs, we can realize reversible switching and logic gate operations that are read in parallel. Moreover, using the same coiled coil protein monolayers for derivatization of nanopores drilled into silicon nitride membranes facilitates control over ion and mass transport through the pores, thereby expanding the applicability of the dynamic coiled coil system for contemporary stochastic biosensing applications.
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Affiliation(s)
- Chiara Glionna
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Vinod Kumar
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Guillaume Le Saux
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bapan Pramanik
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nathaniel Wagner
- 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
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,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.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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5
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Maity I, Dev D, Basu K, Wagner N, Ashkenasy G. Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Indrajit Maity
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
- Institute for Macromolecular Chemistry Freiburg Institute for Advanced Studies Albert Ludwigs University of Freiburg 79104 Freiburg Germany
| | - Dharm Dev
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Kingshuk Basu
- Department of Chemistry Ben Gurion University of the Negev Beer Sheva 84105 Israel
| | - Nathaniel Wagner
- Department of Chemistry 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
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6
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Maity I, Dev D, Basu K, Wagner N, Ashkenasy G. Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network. Angew Chem Int Ed Engl 2021; 60:4512-4517. [PMID: 33006406 PMCID: PMC7984337 DOI: 10.1002/anie.202012837] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Indexed: 12/23/2022]
Abstract
Living cells exploit bistable and oscillatory behaviors as memory mechanisms, facilitating the integration of transient stimuli into sustained molecular responses that control downstream functions. Synthetic bistable networks have also been studied as memory entities, but have rarely been utilized to control orthogonal functions in coupled dynamic systems. We herein present a new cascade pathway, for which we have exploited a well-characterized switchable peptide-based replicating network, operating far from equilibrium, that yields two alternative steady-state outputs, which in turn serve as the input signals for consecutive processes that regulate various features of Au nanoparticle shape and assembly. This study further sheds light on how bridging together the fields of systems chemistry and nanotechnology may open up new opportunities for the dynamically controlled design of functional materials.
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Affiliation(s)
- Indrajit Maity
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
- Institute for Macromolecular ChemistryFreiburg Institute for Advanced StudiesAlbert Ludwigs University of Freiburg79104FreiburgGermany
| | - Dharm Dev
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Kingshuk Basu
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Nathaniel Wagner
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
| | - Gonen Ashkenasy
- Department of ChemistryBen Gurion University of the NegevBeer Sheva84105Israel
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7
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Affiliation(s)
- Nathaniel Wagner
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
| | - Rakesh Mukherjee
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
- Institute for chemical sciences and engineeringEcole Polytechnique Federale de Lausanne 1015 Lausanne Switzerland
| | - Indrajit Maity
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
- Institute for Macromolecular ChemistryAlbert Ludwigs University of Freiburg 79104 Freiburg Germany
| | - Sagi Kraun
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
| | - Gonen Ashkenasy
- Department of ChemistryBen-Gurion University of the Negev Beer Sheva 84105 Israel
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8
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Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, 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
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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9
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Affiliation(s)
- Gonen Ashkenasy
- Department of ChemistryBen-Gurion University of the Negev Beer-Sheva 84105 Israel
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10
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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11
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Kroiss D, Ashkenasy G, Braunschweig AB, Tuttle T, Ulijn RV. Catalyst: Can Systems Chemistry Unravel the Mysteries of the Chemical Origins of Life? Chem 2019. [DOI: 10.1016/j.chempr.2019.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Wagner N, Hochberg D, Peacock-Lopez E, Maity I, Ashkenasy G. Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior. Life (Basel) 2019; 9:life9020045. [PMID: 31163645 PMCID: PMC6617095 DOI: 10.3390/life9020045] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 12/05/2022] Open
Abstract
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent to a steady state. In this paper we review the properties of these simple replicating networks, and show, via four working models, how even though closed systems exhibit a wide range of emergent phenomena, many of the more interesting phenomena leading to complexification and emergence indeed require open systems.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra Ajalvir Km. 4, 28850 Torrejón de Ardoz, Madrid, Spain.
| | | | - Indrajit Maity
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
- Present address: Institute for Macromolecular Chemistry, Albert Ludwigs University of Freiburg, D-79104 Freiburg, Germany.
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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13
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Abstract
Synthetic and materials chemistry initiatives have enabled the translation of the macromolecular functions of biology into synthetic frameworks. These explorations into alternative chemistries of life attempt to capture the versatile functionality and adaptability of biopolymers in new orthogonal scaffolds. Information storage and transfer, however, so beautifully represented in the central dogma of biology, require multiple components functioning synergistically. Over a single decade, the emerging field of systems chemistry has begun to catalyze the construction of mutualistic biopolymer networks, and this review begins with the foundational small-molecule-based dynamic chemical networks and peptide amyloid-based dynamic physical networks on which this effort builds. The approach both contextualizes the versatile approaches that have been developed to enrich chemical information in synthetic networks and highlights the properties of amyloids as potential alternative genetic elements. The successful integration of both chemical and physical networks through β-sheet assisted replication processes further informs the synergistic potential of these networks. Inspired by the cooperative synergies of nucleic acids and proteins in biology, synthetic nucleic-acid-peptide chimeras are now being explored to extend their informational content. With our growing range of synthetic capabilities, structural analyses, and simulation technologies, this foundation is radically extending the structural space that might cross the Darwinian threshold for the origins of life as well as creating an array of alternative systems capable of achieving the progressive growth of novel informational materials.
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Affiliation(s)
- Yushi Bai
- Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, USA.
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Hordijk W, Shichor S, Ashkenasy G. The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics. Chemphyschem 2018; 19:2437-2444. [PMID: 29813174 DOI: 10.1002/cphc.201800101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Indexed: 11/09/2022]
Abstract
Chemical networks often exhibit emergent, systems-level properties that cannot be simply derived from the linear sum of the individual components. The design and analysis of increasingly complex chemical networks thus constitute a major area of research in Systems Chemistry. In particular, much research is focused on the emergence of functional properties in prebiotic chemical networks relevant to the origin and early evolution of life. Here, we apply a formal framework known as RAF theory to study the dynamics of a complex network of mutually catalytic peptides. We investigate in detail the influence of network modularity, initial template seeding, and product inhibition on the network dynamics. We show that these results can be useful for designing new experiments, and further argue how they are relevant to origin of life studies.
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Affiliation(s)
- Wim Hordijk
- Institute for Advanced Study, University of Amsterdam, The Netherlands
| | - Shira Shichor
- Ben-Gurion University of the Negev, Be'er Sheva, Israel
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16
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Abstract
Correction for 'Achieving biopolymer synergy in systems chemistry' by Yushi Bai et al., Chem. Soc. Rev., 2018, DOI: 10.1039/c8cs00174j.
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Affiliation(s)
- Yushi Bai
- Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, USA.
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17
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Wagner N, Mukherjee R, Maity I, Peacock-Lopez E, Ashkenasy G. Bistability and Bifurcation in Minimal Self-Replication and Nonenzymatic Catalytic Networks. Chemphyschem 2017; 18:1842-1850. [PMID: 28112462 DOI: 10.1002/cphc.201601293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/23/2017] [Indexed: 11/08/2022]
Abstract
Bistability and bifurcation, found in a wide range of biochemical networks, are central to the proper function of living systems. We investigate herein recent model systems that show bistable behavior based on nonenzymatic self-replication reactions. Such models were used before to investigate catalytic growth, chemical logic operations, and additional processes of self-organization leading to complexification. By solving for their steady-state solutions by using various analytical and numerical methods, we analyze how and when these systems yield bistability and bifurcation and discover specific cases and conditions producing bistability. We demonstrate that the onset of bistability requires at least second-order catalysis and results from a mismatch between the various forward and reverse processes. Our findings may have far-reaching implications in understanding early evolutionary processes of complexification, emergence, and potentially the origin of life.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Rakesh Mukherjee
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Indrajit Maity
- Department of Chemistry, 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
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18
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Abstract
A series of exciting phenomena that can occur in supramolecular systems away from equilibrium are reviewed.
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Affiliation(s)
- Gonen Ashkenasy
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer Sheva
- Israel
| | | | - Sijbren Otto
- Centre for Systems Chemistry
- Stratingh Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Annette F. Taylor
- Chemical and Biological Engineering
- University of Sheffield
- Sheffield S1 3JD
- UK
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Abstract
Theoretical modeling of quasispecies has progressed in several directions. In this chapter, we review the works of Emmanuel Tannenbaum, who, together with Eugene Shakhnovich at Harvard University and later with colleagues and students at Ben-Gurion University in Beersheva, implemented one of the more useful approaches, by progressively setting up various formulations for the quasispecies model and solving them analytically. Our review will focus on these papers that have explored new models, assumed the relevant mathematical approximations, and proceeded to analytically solve for the steady-state solutions and run stochastic simulations . When applicable, these models were related to real-life problems and situations, including changing environments, presence of chemical mutagens, evolution of cancer and tumor cells , mutations in Escherichia coli, stem cells , chromosomal instability (CIN), propagation of antibiotic drug resistance , dynamics of bacteria with plasmids , DNA proofreading mechanisms, and more.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, 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
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel.
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Lerner Yardeni J, Amit M, Ashkenasy G, Ashkenasy N. Sequence dependent proton conduction in self-assembled peptide nanostructures. Nanoscale 2016; 8:2358-2366. [PMID: 26750973 DOI: 10.1039/c5nr06750b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The advancement of diverse electrochemistry technologies depends on the development of novel proton conducting polymers. Inspired by the efficacy of proton transport through proteins, we show in this work that self-assembling peptide nanostructures may be a promising alternative for such organic proton conducting materials. We demonstrate that aromatic amino acids, which participate in charge transport in nature, unprecedentedly promote proton conduction under both high and low relative humidity conditions for d,l α-cyclic peptide nanotubes. For dehydrated networks long-range order of the assemblies, induced by the aromatic side chains, is shown to be a dominating factor for promoting conductivity. However, for hydrated networks this order of effect is less significant and conductivity can be improved by the introduction of proton donating carboxylic acid peptide side chains in addition to the aromatic side chains despite the lower order of the assemblies. Based on these observations, a novel cyclic peptide that incorporates non-natural naphthyl side chains was designed. Self-assembled nanotubes of this peptide show greatly improved dehydrated conductivity, while maintaining high conductivity under hydrated conditions. We envision that the demonstrated modularity and versatility of these bio inspired nanostructures will make them extremely attractive building blocks for the fabrication of devices for energy conversion and storage applications, as well as other applications that involve proton transport, whether dry or wet conductivity is desired.
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Affiliation(s)
- Jenny Lerner Yardeni
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel. and Department of chemistry, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Moran Amit
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel.
| | - Gonen Ashkenasy
- Department of chemistry, Ben-Gurion University of the Negev, Beer Sheva, Israel and The Ilze Katz Institute for Nanoscale Science Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel. and The Ilze Katz Institute for Nanoscale Science Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
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24
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Mukherjee R, Cohen-Luria R, Wagner N, Ashkenasy G. A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template-Directed Ligation. Angew Chem Int Ed Engl 2015; 54:12452-6. [DOI: 10.1002/anie.201503898] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/21/2015] [Indexed: 11/08/2022]
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25
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Mukherjee R, Cohen-Luria R, Wagner N, Ashkenasy G. A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template-Directed Ligation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503898] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Ashkenasy G, Pross A. Origin of Life: Special Issue Honoring Prof. Albert Eschenmoser on the Occasion of his 90 thBirthday. Isr J Chem 2015. [DOI: 10.1002/ijch.201510008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Ivnitski D, Amit M, Rubinov B, Cohen-Luria R, Ashkenasy N, Ashkenasy G. Introducing charge transfer functionality into prebiotically relevant β-sheet peptide fibrils. Chem Commun (Camb) 2015; 50:6733-6. [PMID: 24828820 DOI: 10.1039/c4cc00717d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Incorporation of naphthalene diimide moieties as side chains of short amphiphilic peptide results in the formation of fibrils that exhibit substantial intermolecular π-stacking interactions. These interactions can be manipulated without affecting the structure. The new system is suggested as a first step towards functional self-synthesizing materials.
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Affiliation(s)
- Denis Ivnitski
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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28
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29
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Gurevich L, Cohen-Luria R, Wagner N, Ashkenasy G. Robustness of synthetic circadian clocks to multiple environmental changes. Chem Commun (Camb) 2015; 51:5672-5. [PMID: 25714790 DOI: 10.1039/c5cc00098j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A molecular network that mimics circadian clocks from cyanobacteria is constructed in silico. Simulating its oscillatory behaviour under variable conditions reveals its robustness relative to networks of alternative topologies. The principles for synthetic chemical circadian networks to work properly are consequently highlighted.
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Affiliation(s)
- Lilia Gurevich
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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30
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Abstract
Living organisms often display rhythmic and oscillatory behavior. We investigate here a challenge in contemporary Systems Chemistry, that is, to construct "bottom-up" molecular networks that display such complex behavior. We first describe oscillations during self-replication by applying kinetic parameters relevant to peptide replication in an open environment. Small networks of coupled oscillators are then constructed in silico, producing various functions such as logic gates, integrators, counters, triggers, and detectors. These networks are finally utilized to simulate the connectivity and network topology of the Kai proteins circadian clocks from the S. elongatus cyanobacteria, thus producing rhythms whose constant frequency is independent of the input intake rate and robust toward concentration fluctuations. We suggest that this study helps further reveal the underlying principles of biological clocks and may provide clues into their emergence in early molecular evolution.
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Affiliation(s)
- Nathaniel Wagner
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
| | - Samaa Alasibi
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
| | - Enrique Peacock-Lopez
- ‡Department of Chemistry, Williams College, Williamstown, Massachusetts 02167, United States
| | - Gonen Ashkenasy
- †Department of Chemistry, Ben Gurion University of the Negev, Be'er Sheva, 84105 Israel
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31
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Dadon Z, Wagner N, Alasibi S, Samiappan M, Mukherjee R, Ashkenasy G. Competition and Cooperation in Dynamic Replication Networks. Chemistry 2014; 21:648-54. [DOI: 10.1002/chem.201405195] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Indexed: 11/09/2022]
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32
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Shamay Y, Shpirt L, Ashkenasy G, David A. Complexation of Cell-Penetrating Peptide–Polymer Conjugates with Polyanions Controls Cells Uptake of HPMA Copolymers and Anti-tumor Activity. Pharm Res 2013; 31:768-79. [DOI: 10.1007/s11095-013-1198-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/21/2013] [Indexed: 12/22/2022]
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33
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Dadon Z, Samiappan M, Shahar A, Zarivach R, Ashkenasy G. A High-Resolution Structure that Provides Insight into Coiled-Coil Thiodepsipeptide Dynamic Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303900] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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34
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Dadon Z, Samiappan M, Shahar A, Zarivach R, Ashkenasy G. A high-resolution structure that provides insight into coiled-coil thiodepsipeptide dynamic chemistry. Angew Chem Int Ed Engl 2013; 52:9944-7. [PMID: 23929823 DOI: 10.1002/anie.201303900] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/16/2013] [Indexed: 01/29/2023]
Abstract
Stable and reactive: A crystal structure at 1.35 Å of a thioester coiled-coil protein reveals high similarity to all-peptide-bond proteins. In these assemblies, the thioester bonds are kept reactive towards thiol molecules in the mixture. This enables efficient domain exchange between proteins in response to changes in folding conditions or introduction of external templates.
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Affiliation(s)
- Zehavit Dadon
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 84105 (Israel)
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35
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Eisenberg M, Shumacher I, Cohen-Luria R, Ashkenasy G. Dynamic combinatorial libraries of artificial repeat proteins. Bioorg Med Chem 2013; 21:3450-7. [PMID: 23582443 DOI: 10.1016/j.bmc.2013.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/10/2013] [Accepted: 03/11/2013] [Indexed: 10/27/2022]
Abstract
Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (~14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.
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Affiliation(s)
- Margarita Eisenberg
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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36
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Atanassov A, Hendler Z, Berkovich I, Ashkenasy G, Ashkenasy N. Force modulated conductance of artificial coiled-coil protein monolayers. Biopolymers 2013; 100:93-9. [DOI: 10.1002/bip.22181] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 10/04/2012] [Accepted: 10/30/2012] [Indexed: 11/07/2022]
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37
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Raz Y, Rubinov B, Matmor M, Rapaport H, Ashkenasy G, Miller Y. Effects of mutations in de novo designed synthetic amphiphilic β-sheet peptides on self-assembly of fibrils. Chem Commun (Camb) 2013; 49:6561-3. [DOI: 10.1039/c3cc42879f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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38
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Rubinov B, Wagner N, Matmor M, Regev O, Ashkenasy N, Ashkenasy G. Transient fibril structures facilitating nonenzymatic self-replication. ACS Nano 2012; 6:7893-901. [PMID: 22856322 DOI: 10.1021/nn302223v] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An emerging new direction of research focuses on developing "self-synthesizing materials", those supramolecular structures that can promote their own formation by accelerating the synthesis of building blocks and/or an entire assembly. It was postulated recently that practical design of such systems can benefit from the ability to control the assembly of amphiphilic molecules into nanostructures. We describe here the self-assembly pathway of short amphiphilic peptides into various forms of soluble β-sheet structures--β-plates, fibrils, and hollow nanotubes--and their consequent activity as autocatalysts for the synthesis of monomeric peptides from simpler building blocks. A detailed kinetic analysis of both the self-assembly and self-replication processes allows us to suggest a full model and simulate the replication process, revealing that only specific structures, primarily fibrils that are stable within the solution for a time shorter than a few hours, can be active as catalysts. Interestingly, we have found that such a process also induces fibril reproduction, in a mechanism very similar to the propagation of prion proteins by transmission of misfolded states.
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Affiliation(s)
- Boris Rubinov
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
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39
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40
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Samiappan M, Alasibi S, Cohen-Luria R, Shanzer A, Ashkenasy G. Allosteric effects in coiled-coil proteins folding and lanthanide-ion binding. Chem Commun (Camb) 2012; 48:9577-9. [DOI: 10.1039/c2cc35166h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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41
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Dadon Z, Samiappan M, Wagner N, Ashkenasy G. Chemical and light triggering of peptide networks under partial thermodynamic control. Chem Commun (Camb) 2012; 48:1419-21. [DOI: 10.1039/c1cc14301h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Bourbo V, Matmor M, Shtelman E, Rubinov B, Ashkenasy N, Ashkenasy G. Self-assembly and self-replication of short amphiphilic β-sheet peptides. ORIGINS LIFE EVOL B 2011; 41:563-7. [PMID: 22139518 DOI: 10.1007/s11084-011-9257-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 08/28/2011] [Indexed: 12/01/2022]
Abstract
Most self-replicating peptide systems are made of α-helix forming sequences. However, it has been postulated that shorter and simpler peptides may also serve as templates for replication when arranged into well-defined structures. We describe here the design and characterization of new peptides that form soluble β-sheet aggregates that serve to significantly accelerate their ligation and self-replication. We then discuss the relevance of these phenomena to early molecular evolution, in light of additional functionality associated with β-sheet assemblies.
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Affiliation(s)
- Valery Bourbo
- Department of Chemistry, Ben Gurion University of Negev, Beer Sheva, Israel
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43
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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44
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Wagner N, Alesebi S, Ashkenasy G. How Symmetry and Order Affect Logic Operations and Computation in Catalytic Chemical Networks. ACTA ACUST UNITED AC 2011. [DOI: 10.1166/jctn.2011.1712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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46
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47
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Abstract
Cell-penetrating peptides (CPPs) can be used for intracellular delivery of a broad variety of cargoes, including various nanoparticulate pharmaceutical carriers. However, the cationic nature of all CPP sequences, and thus lack of cell specificity, limits their in vivo use for drug delivery applications. Here, we have devised and tested a strategy for site-specific delivery of dyes and drugs into cancer cells by using polymers bearing a light activated caged CPP (cCPP). The positive charge of Lys residues on the minimum sequence of the CPP penetratin ((52)RRMKWKK(58)) was masked with photo-cleavable groups to minimize non-specific adsorption and cellular uptake. Once illuminated by UV light, these protecting groups were cleaved, the positively charged CPP regained its activity and facilitated rapid intracellular delivery of the polymer-dye or polymer-drug conjugates into cancer cells. We have found that a 10-min light illumination time was sufficient to enhance the penetration of the polymer-CPP conjugates bearing the proapoptotic peptide, (D)(KLAKLAK)(2), into 80% of the target cells, and to promote a 'switch' like cytotoxic activity resulting a shift from 100% to 10% in cell viability after 2 h. This report provides an example for tumor targeting by means of light activation of cell-penetrating peptides for intracellular drug delivery.
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Affiliation(s)
- Yosi Shamay
- Department of Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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48
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Shlizerman C, Atanassov A, Berkovich I, Ashkenasy G, Ashkenasy N. De novo designed coiled-coil proteins with variable conformations as components of molecular electronic devices. J Am Chem Soc 2010; 132:5070-6. [PMID: 20235538 DOI: 10.1021/ja907902h] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Conformational changes of proteins are widely used in nature for controlling cellular functions, including ligand binding, oligomerization, and catalysis. Despite the fact that different proteins and artificial peptides have been utilized as electron-transfer mediators in electronic devices, the unique propensity of proteins to switch between different conformations has not been used as a mechanism to control device properties and performance. Toward this aim, we have designed and prepared new dimeric coiled-coil proteins that adopt different conformations due to parallel or antiparallel relative orientations of their monomers. We show here that controlling the conformation of these proteins attached as monolayers to gold, which dictates the direction and magnitude of the molecular dipole relative to the surface, results in quantitative modulation of the gold work function. Furthermore, charge transport through the proteins as molecular bridges is controlled by the different protein conformations, producing either rectifying or ohmic-like behavior.
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Affiliation(s)
- Clara Shlizerman
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
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50
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Wagner N, Tannenbaum E, Ashkenasy G. Second order catalytic quasispecies yields discontinuous mean fitness at error threshold. Phys Rev Lett 2010; 104:188101. [PMID: 20482213 DOI: 10.1103/physrevlett.104.188101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Indexed: 05/29/2023]
Abstract
The quasispecies model describes processes related to the origin of life and viral evolutionary dynamics. We discuss how the error catastrophe that reflects the transition from localized to delocalized quasispecies population is affected by catalytic replication of different reaction orders. Specifically, we find that second order mechanisms lead to a discontinuity in the mean fitness of the population at the error threshold. This is in contrast to the behavior of the first order, autocatalytic replication mechanism considered in the standard quasispecies model. This suggests that quasispecies models with higher order replication mechanisms produce discontinuities in the mean fitness, and hence the viable population fraction as well, at the error threshold, while lower order replication mechanisms yield a continuous mean fitness function. We discuss potential implications for understanding replication in the RNA world and in virology.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
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