101
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Gokula RP, Mahato J, Tripathi A, Singh HB, Chowdhury A. Self-Assembly of Nicotinic Acid-Conjugated Selenopeptides into Mesotubes. ACS APPLIED BIO MATERIALS 2021; 4:1912-1919. [PMID: 35014460 DOI: 10.1021/acsabm.0c01551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The study of controlling the morphology for designing advanced supramolecular architectures by tuning the molecular motif at the elemental level has been rarely carried out. Here, we report the synthesis of a nicotinic acid-conjugated selenopeptide, which induced the formation of an unbranched mesoscale elongated tubular morphology. We rationally designed two additional peptides to find out the decisive role played by the nitrogen atom (in nicotinic acid) and selenium (in the peptide backbone) toward the formation of the mesotube. We found that the peptide, devoid of nitrogen, forms a fibrillar structure, whereas the peptide without selenium self-assembled into a cylindrical filled rodlike morphology. Here, we report an entirely different class of peptide inspired from the selenopeptide chemistry that forms a tubular structure and unambiguously establish that both nicotinic acid and selenium are essential toward the formation of such mesotubes.
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Affiliation(s)
- Ram P Gokula
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Jaladhar Mahato
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Abhishek Tripathi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Harkesh B Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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102
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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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103
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Kurbasic M, Garcia AM, Viada S, Marchesan S. Heterochiral tetrapeptide self-assembly into hydrogel biomaterials for hydrolase mimicry. J Pept Sci 2021; 28:e3304. [PMID: 33521995 DOI: 10.1002/psc.3304] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 12/23/2022]
Abstract
Self-assembling short peptides have attracted great interest as enzyme mimics, especially if the catalytic activity resides solely in the supramolecular structure so that it can be switched on/off as needed by controlling assembly/disassembly. Among the various enzyme classes, hydrolases find wide application in biomaterials, and their mimetics often contain His residues, in addition to either divalent cations or other amino acids to mimic the catalytic site. This work reports two self-assembling tetrapeptides based on the Ser-His motif for catalysis and the Phe-Phe motif to drive amyloid structure formation. Both peptides form thermoreversible hydrogels in phosphate buffer at neutral pH that display a mild esterase-like activity, as demonstrated on the hydrolysis of 4-nitrophenyl acetate as a model substrate, although presence of Ser did not enhance catalytic activity. The systems are characterised by circular dichroism, transmission electron microscopy, oscillatory rheology and Thioflavin T fluorescence as an amyloid stain, to provide further insights that may assist the future design of improved supramolecular catalysts.
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Affiliation(s)
- Marina Kurbasic
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Trieste, 34127, Italy
| | - Ana M Garcia
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Trieste, 34127, Italy
| | - Simone Viada
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Trieste, 34127, Italy
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Trieste, 34127, Italy
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104
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Kwiatkowski W, Bomba R, Afanasyev P, Boehringer D, Riek R, Greenwald J. Prebiotic Peptide Synthesis and Spontaneous Amyloid Formation Inside a Proto-Cellular Compartment. Angew Chem Int Ed Engl 2021; 60:5561-5568. [PMID: 33325627 DOI: 10.1002/anie.202015352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 12/12/2022]
Abstract
Cellular life requires a high degree of molecular complexity and self-organization, some of which must have originated in a prebiotic context. Here, we demonstrate how both of these features can emerge in a plausibly prebiotic system. We found that chemical gradients in simple mixtures of activated amino acids and fatty acids can lead to the formation of amyloid-like peptide fibrils that are localized inside of a proto-cellular compartment. In this process, the fatty acid or lipid vesicles act both as a filter, allowing the selective passage of activated amino acids, and as a barrier, blocking the diffusion of the amyloidogenic peptides that form spontaneously inside the vesicles. This synergy between two distinct building blocks of life induces a significant increase in molecular complexity and spatial order thereby providing a route for the early molecular evolution that could give rise to a living cell.
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Affiliation(s)
- Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Radoslaw Bomba
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Pavel Afanasyev
- Scientific Center for Optical and Electron Microscopy, Swiss Federal Institute of Technology, ETH-Hönggerberg, Otto-Stern-Weg 3, CH-8093, Zürich, Switzerland
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, ETH-Hönggerberg, Otto-Stern-Weg 5, CH-8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
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105
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Chen Y, Tao K, Ji W, Makam P, Rencus-Lazar S, Gazit E. Self-Assembly of Cyclic Dipeptides: Platforms for Functional Materials. Protein Pept Lett 2021; 27:688-697. [PMID: 32048950 DOI: 10.2174/0929866527666200212123542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/29/2019] [Accepted: 12/09/2019] [Indexed: 11/22/2022]
Abstract
Supramolecular self-assembled functional materials comprised of cyclic dipeptide building blocks have excellent prospects for biotechnology applications due to their exceptional structural rigidity, morphological flexibility, ease of preparation and modification. Although the pharmacological uses of many natural cyclic dipeptides have been studied in detail, relatively little is reported on the engineering of these supramolecular architectures for the fabrication of functional materials. In this review, we discuss the progress in the design, synthesis, and characterization of cyclic dipeptide supramolecular nanomaterials over the past few decades, highlighting applications in biotechnology and optoelectronics engineering.
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Affiliation(s)
- Yu Chen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Wei Ji
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Pandeeswar Makam
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sigal Rencus-Lazar
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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106
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Pal S, Goswami S, Das D. Cross β amyloid assemblies as complex catalytic machinery. Chem Commun (Camb) 2021; 57:7597-7609. [PMID: 34278403 DOI: 10.1039/d1cc02880d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
How modern enzymes evolved as complex catalytic machineries to facilitate diverse chemical transformations is an open question for the emerging field of systems chemistry. Inspired by Nature's ingenuity in creating complex catalytic structures for exotic functions, short peptide-based cross β amyloid sequences have been shown to access intricate binding surfaces demonstrating the traits of extant enzymes and proteins. Based on their catalytic proficiencies reported recently, these amyloid assemblies have been argued as the earliest protein folds. Herein, we map out the recent progress made by our laboratory and other research groups that demonstrate the catalytic diversity of cross β amyloid assemblies. The important role of morphology and specific mutations in peptide sequences has been underpinned in this review. We have divided the feature article into different sections where examples from biology have been covered demonstrating the mechanism of extant biocatalysts and compared with recent works on cross β amyloid folds showing covalent catalysis, aldolase, hydrolase, peroxidase-like activities and complex cascade catalysis. Beyond equilibrium, we have extended our discussion towards transient catalytic amyloid phases mimicking the energy driven cytoskeleton polymerization. Finally, a future outlook has been provided on the way ahead for short peptide-based systems chemistry approaches that can lead to the development of robust catalytic networks with improved enzyme-like proficiencies and higher complexities. The discussed examples along with the rationale behind selecting specific amino acids sequence will benefit readers to design systems for achieving catalytic reactivity similar to natural complex enzymes.
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Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Surashree Goswami
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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107
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Kurbasic M, Garcia AM, Viada S, Marchesan S. Tripeptide Self-Assembly into Bioactive Hydrogels: Effects of Terminus Modification on Biocatalysis. Molecules 2020; 26:E173. [PMID: 33396543 PMCID: PMC7794889 DOI: 10.3390/molecules26010173] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022] Open
Abstract
Bioactive hydrogels based on the self-assembly of tripeptides have attracted great interest in recent years. In particular, the search is active for sequences that are able to mimic enzymes when they are self-organized in a nanostructured hydrogel, so as to provide a smart catalytic (bio)material whose activity can be switched on/off with assembly/disassembly. Within the diverse enzymes that have been targeted for mimicry, hydrolases find wide application in biomaterials, ranging from their use to convert prodrugs into active compounds to their ability to work in reverse and catalyze a plethora of reactions. We recently reported the minimalistic l-His-d-Phe-d-Phe for its ability to self-organize into thermoreversible and biocatalytic hydrogels for esterase mimicry. In this work, we analyze the effects of terminus modifications that mimic the inclusion of the tripeptide in a longer sequence. Therefore, three analogues, i.e., N-acetylated, C-amidated, or both, were synthesized, purified, characterized by several techniques, and probed for self-assembly, hydrogelation, and esterase-like biocatalysis. This work provides useful insights into how chemical modifications at the termini affect self-assembly into biocatalytic hydrogels, and these data may become useful for the future design of supramolecular catalysts for enhanced performance.
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Affiliation(s)
| | | | | | - Silvia Marchesan
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (M.K.); (A.M.G.); (S.V.)
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108
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Liu S, Du P, Sun H, Yu HY, Wang ZG. Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03753] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Siyuan Liu
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Peidong Du
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hai-Yin Yu
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
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109
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Choi W, Sun H, Battistella C, Berger O, Vratsanos MA, Wang MM, Gianneschi NC. Biomolecular Densely Grafted Brush Polymers: Oligonucleotides, Oligosaccharides and Oligopeptides. Angew Chem Int Ed Engl 2020; 59:19762-19772. [PMID: 32436259 PMCID: PMC11042487 DOI: 10.1002/anie.202005379] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 01/19/2023]
Abstract
In this Minireview, we describe synthetic polymers densely functionalized with sequence-defined biomolecular sidechains. We focus on synthetic brush polymers of oligonucleotides, oligosaccharides, and oligopeptides, prepared via graft-through polymerization from biomolecule functionalized monomers. The resulting structures are brush polymers wherein a biomolecular graft is positioned at each monomer backbone unit. We describe key synthetic milestones, identify synthetic opportunities, and highlight recent advances in the field, including biological applications.
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Affiliation(s)
- Wonmin Choi
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Hao Sun
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Claudia Battistella
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Or Berger
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Maria A. Vratsanos
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Max M. Wang
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Nathan C. Gianneschi
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
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110
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Choi W, Sun H, Battistella C, Berger O, Vratsanos MA, Wang MM, Gianneschi NC. Biomolecular Densely Grafted Brush Polymers: Oligonucleotides, Oligosaccharides and Oligopeptides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Wonmin Choi
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Hao Sun
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Claudia Battistella
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Or Berger
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Maria A. Vratsanos
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Max M. Wang
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Nathan C. Gianneschi
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
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111
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Rimoldi I, Bucci R, Feni L, Santagostini L, Facchetti G, Pellegrino S. Exploring the copper binding ability of Mets7 hCtr-1 protein domain and His7 derivative: An insight in Michael addition catalysis. J Pept Sci 2020; 27:e3289. [PMID: 33094563 DOI: 10.1002/psc.3289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022]
Abstract
Mets7 is a methionine-rich motif present in hCtr-1 transporter that is involved in copper cellular trafficking. Its ability to bind Cu(I) was recently exploited to develop metallopeptide catalysts for Henry condensation. Here, the catalytic activity of Mets7-Cu(I) complex in Michael addition reactions has been evaluated. Furthermore, His7 peptide, in which Met residues have been substituted with His ones, was also prepared. This substitution allowed His7 to coordinate Cu (II), with the obtainment of a stable turn conformation as evicted by CD experiments. His7-Cu (II) proved also to be a better catalyst than Mets7-Cu(I) in the addition reaction. In particular, when the substrate was the (E)-1-phenyl-3-(pyridin-2-yl)prop-2-en-1-one, a conversion of 71% and a significative 58% of e.e. was observed.
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Affiliation(s)
- Isabella Rimoldi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Raffaella Bucci
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Lucia Feni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | | | - Giorgio Facchetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Sara Pellegrino
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
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112
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He C, Wu S, Liu D, Chi C, Zhang W, Ma M, Lai L, Dong S. Glycopeptide Self-Assembly Modulated by Glycan Stereochemistry through Glycan–Aromatic Interactions. J Am Chem Soc 2020; 142:17015-17023. [DOI: 10.1021/jacs.0c06360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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113
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Chien CY, Yu SS. Ester-mediated peptide formation promoted by deep eutectic solvents: a facile pathway to proto-peptides. Chem Commun (Camb) 2020; 56:11949-11952. [PMID: 32929424 DOI: 10.1039/d0cc03319g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ester-amide exchange reaction enables spontaneous formation of prebiotic proto-peptides under mild conditions. However, this reaction also leads to oligomers with a vast sequence diversity of ester and amide linkages. Here, we demonstrate using deep eutectic solvents as a universal strategy to regulate the reaction pathways and promote the formation of amino acid-enriched oligomers with peptide backbones.
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Affiliation(s)
- Chen-Yu Chien
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Road, Tainan City, 70101, Taiwan, Republic of China.
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114
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Sasselli IR, Syrgiannis Z. Small Molecules Organic Co‐Assemblies as Functional Nanomaterials. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ivan R. Sasselli
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE) Basque Research and Technology Alliance (BRTA) Paseo de Miramon 182 20014 Donostia San Sebastián Spain
| | - Zois Syrgiannis
- Centre of Excellence for Nanostructured Materials (CENMAT) INSTM, unit of Trieste, Dipartimento di Scienze Chimiche e Farmaceutiche Università di Trieste via L. Giorgieri 1 34127 Trieste Italy
- Simpson Querrey Institute Northwestern University 303 East Superior Street 60611 Chicago IL USA
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115
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Wang C, Fei J, Wang K, Li J. A Dipeptide‐Based Hierarchical Nanoarchitecture with Enhanced Catalytic Activity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006994] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chenlei Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Colloid, Interface and Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Colloid, Interface and Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Keqing Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Colloid, Interface and Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Colloid, Interface and Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
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116
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Wang C, Fei J, Wang K, Li J. A Dipeptide‐Based Hierarchical Nanoarchitecture with Enhanced Catalytic Activity. Angew Chem Int Ed Engl 2020; 59:18960-18963. [DOI: 10.1002/anie.202006994] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/14/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Chenlei Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Colloid, Interface and Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Colloid, Interface and Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Keqing Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Colloid, Interface and Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Colloid, Interface and Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
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117
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Protoenzymes: The Case of Hyperbranched Polymer-Scaffolded ZnS Nanocrystals. Life (Basel) 2020; 10:life10080150. [PMID: 32823487 PMCID: PMC7460482 DOI: 10.3390/life10080150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2020] [Accepted: 07/04/2020] [Indexed: 12/15/2022] Open
Abstract
Enzymes are biological catalysts that are comprised of small-molecule, metal, or cluster catalysts augmented by biopolymeric scaffolds. It is conceivable that early in chemical evolution, ancestral enzymes opted for simpler, easier to assemble scaffolds. Herein, we describe such possible protoenzymes: hyperbranched polymer-scaffolded metal-sulfide nanocrystals. Hyperbranched polyethyleneimine (HyPEI) and glycerol citrate polymer-supported ZnS nanocrystals (NCs) are formed in a simple process. Transmission electron microscopy (TEM) analyses of HyPEI-supported NCs reveal spherical particles with an average size of 10 nm that undergo only a modest aggregation over a 14-day incubation. The polymer-supported ZnS NCs are shown to possess a high photocatalytic activity in an eosin B photodegradation assay, making them an attractive model for the study of the origin of life under the “Zn world” theory dominated by a photocatalytic proto-metabolic redox reaction network. The catalyst, however, could be easily adapted to apply broadly to different protoenzymatic systems.
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118
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Li J, Zhu M, Wang M, Qi W, Su R, He Z. Molecularly imprinted peptide-based enzyme mimics with enhanced activity and specificity. SOFT MATTER 2020; 16:7033-7039. [PMID: 32667008 DOI: 10.1039/d0sm00635a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We herein report the construction of peroxidase (POD)-mimicking catalysts based on the strategy of peptide assembly and molecular imprinting. Upon co-assembly of Fmoc-FFH and Hemin, we firstly fabricated CA-H/Hemin which displayed POD-like catalytic activity and showed a 21-fold rate acceleration in the oxidation of 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) compared to the uncatalyzed reaction. Then, upon combining CA-H/Hemin with the ABTS-imprinted polymer, the obtained imprinted catalyst (MIP-H/Hemin) showed 52-fold acceleration due to the enhanced re-binding toward ABTS. Moreover, by introducing cationic monomers, a 137-fold rate enhancement was further achieved for the positively charged imprinted catalyst (MIP+-H/Hemin), from the synergistic effect of molecular imprinting and electrostatic attraction. Remarkably, by comparing the catalytic activity of these POD mimics towards ABTS and 3,3',5,5'-tetramethylbenzidine (TMB), we also highlighted the substrate specificity of MIP-H/Hemin and MIP+-H/Hemin toward ABTS. This study provides a promising approach to improve the catalytic activity and specificity of peptide-based enzyme mimics.
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Affiliation(s)
- Jingyi Li
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
| | - Mingjie Zhu
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
| | - Mengfan Wang
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China. and Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China
| | - Wei Qi
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China. and Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China and The Co-Innovation Centre of Chemistry and Chemical Engineering of Tianjin, Tianjin, 300350, P. R. China
| | - Rongxin Su
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China. and Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China and The Co-Innovation Centre of Chemistry and Chemical Engineering of Tianjin, Tianjin, 300350, P. R. China
| | - Zhimin He
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
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119
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Ren CZJ, Solís-Muñana P, Warr GG, Chen JLY. Dynamic and Modular Formation of a Synergistic Transphosphorylation Catalyst. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01321] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Chloe Z.-J. Ren
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Pablo Solís-Muñana
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Gregory G. Warr
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jack L.-Y. Chen
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Auckland 1010, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences, Università degli Studi di Siena, 53100 Siena, Italy
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120
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Gao P, Feng Y, Wang M, Jiang N, Qi W, Su R, He Z. Ferrocene-Modified Metal–Organic Frameworks as a Peroxidase-Mimicking Catalyst. Catal Letters 2020. [DOI: 10.1007/s10562-020-03314-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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121
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Guan M, Wang M, Qi W, Su R, He Z. Biomineralization-inspired copper-cystine nanoleaves capable of laccase-like catalysis for the colorimetric detection of epinephrine. Front Chem Sci Eng 2020. [DOI: 10.1007/s11705-020-1940-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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122
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Rodon Fores J, Criado‐Gonzalez M, Chaumont A, Carvalho A, Blanck C, Schmutz M, Boulmedais F, Schaaf P, Jierry L. Autonomous Growth of a Spatially Localized Supramolecular Hydrogel with Autocatalytic Ability. Angew Chem Int Ed Engl 2020; 59:14558-14563. [DOI: 10.1002/anie.202005377] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Jennifer Rodon Fores
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Miryam Criado‐Gonzalez
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche Médicale INSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de Strasbourg Faculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Alain Chaumont
- Université de Strasbourg Faculté de Chimie, UMR7140 1 rue Blaise Pascal 67008 Strasbourg Cedex France
| | - Alain Carvalho
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christian Blanck
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Marc Schmutz
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Fouzia Boulmedais
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Pierre Schaaf
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche Médicale INSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de Strasbourg Faculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Loïc Jierry
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
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123
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Rodon Fores J, Criado‐Gonzalez M, Chaumont A, Carvalho A, Blanck C, Schmutz M, Boulmedais F, Schaaf P, Jierry L. Autonomous Growth of a Spatially Localized Supramolecular Hydrogel with Autocatalytic Ability. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jennifer Rodon Fores
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Miryam Criado‐Gonzalez
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche Médicale INSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de Strasbourg Faculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Alain Chaumont
- Université de Strasbourg Faculté de Chimie, UMR7140 1 rue Blaise Pascal 67008 Strasbourg Cedex France
| | - Alain Carvalho
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christian Blanck
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Marc Schmutz
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Fouzia Boulmedais
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Pierre Schaaf
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche Médicale INSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de Strasbourg Faculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Loïc Jierry
- Université de Strasbourg CNRS, Institut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
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124
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Longo LM, Despotović D, Weil-Ktorza O, Walker MJ, Jabłońska J, Fridmann-Sirkis Y, Varani G, Metanis N, Tawfik DS. Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion. Proc Natl Acad Sci U S A 2020; 117:15731-15739. [PMID: 32561643 PMCID: PMC7355028 DOI: 10.1073/pnas.2001989117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
De novo emergence demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can polypeptides confer functions of evolutionary relevance, and how might such polypeptides evolve into modern proteins? The earliest proteins present an even greater challenge, as they were likely based on abiotic, spontaneously synthesized amino acids. Here we asked whether a primordial function, such as nucleic acid binding, could emerge with ornithine, a basic amino acid that forms abiotically yet is absent in modern-day proteins. We combined ancestral sequence reconstruction and empiric deconstruction to unravel a gradual evolutionary trajectory leading from a polypeptide to a ubiquitous nucleic acid-binding protein. Intermediates along this trajectory comprise sequence-duplicated functional proteins built from 10 amino acid types, with ornithine as the only basic amino acid. Ornithine side chains were further modified into arginine by an abiotic chemical reaction, improving both structure and function. Along this trajectory, function evolved from phase separation with RNA (coacervates) to avid and specific double-stranded DNA binding. Our results suggest that phase-separating polypeptides may have been an evolutionary resource for the emergence of early proteins, and that ornithine, together with its postsynthesis modification to arginine, could have been the earliest basic amino acids.
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Affiliation(s)
- Liam M Longo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dragana Despotović
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orit Weil-Ktorza
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Jagoda Jabłońska
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael Fridmann-Sirkis
- Life Sciences Core Facility, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Norman Metanis
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
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125
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Stevenson MJ, Janisse SE, Tao L, Neil RL, Pham QD, Britt RD, Heffern MC. Elucidation of a Copper Binding Site in Proinsulin C-peptide and Its Implications for Metal-Modulated Activity. Inorg Chem 2020; 59:9339-9349. [PMID: 32510934 PMCID: PMC8023225 DOI: 10.1021/acs.inorgchem.0c01212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The connecting peptide (C-peptide) is a hormone with promising health benefits in ameliorating diabetes-related complications, yet mechanisms remain elusive. Emerging studies point to a possible dependence of peptide activity on bioavailable metals, particularly Cu(II) and Zn(II). However, little is known about the chemical nature of the interactions, hindering advances in its therapeutic applications. This work uncovers the Cu(II)-binding site in C-peptide that may be key to understanding its metal-dependent function. A combination of spectroscopic studies reveal that Cu(II) and Zn(II) bind to C-peptide at specific residues in the N-terminal region of the peptide and that Cu(II) is able to displace Zn(II) for C-peptide binding. The data point to a Cu(II)-binding site consisting of 1N3O square-planar coordination that is entropically driven. Furthermore, the entire random coil peptide sequence is needed for specific metal binding as mutations and truncations reshuffle the coordinating residues. These results expand our understanding of how metals influence hormone activity and facilitate the discovery and validation of both new and established paradigms in peptide biology.
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Affiliation(s)
- Michael J Stevenson
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Samuel E Janisse
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Lizhi Tao
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Ryan L Neil
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Quang D Pham
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Marie C Heffern
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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127
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Carlomagno T, Cringoli MC, Kralj S, Kurbasic M, Fornasiero P, Pengo P, Marchesan S. Biocatalysis of D,L-Peptide Nanofibrillar Hydrogel. Molecules 2020; 25:E2995. [PMID: 32630001 PMCID: PMC7411710 DOI: 10.3390/molecules25132995] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 01/30/2023] Open
Abstract
Self-assembling peptides are attracting wide interest as biodegradable building blocks to achieve functional nanomaterials that do not persist in the environment. Amongst the many applications, biocatalysis is gaining momentum, although a clear structure-to-activity relationship is still lacking. This work applied emerging design rules to the heterochiral octapeptide sequence His-Leu-DLeu-Ile-His-Leu-DLeu-Ile for self-assembly into nanofibrils that, at higher concentration, give rise to a supramolecular hydrogel for the mimicry of esterase-like activity. The peptide was synthesized by solid-phase and purified by HPLC, while its identity was confirmed by 1H-NMR and electrospray ionization (ESI)-MS. The hydrogel formed by this peptide was studied with oscillatory rheometry, and the supramolecular behavior of the peptide was investigated with transmission electron microscopy (TEM) analysis, circular dichroism (CD) spectroscopy, thioflavin T amyloid fluorescence assay, and attenuated total reflectance (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The biocatalytic activity was studied by monitoring the hydrolysis of p-nitrophenyl acetate (pNPA) at neutral pH, and the reaction kinetics followed an apparent Michaelis-Menten model, for which a Lineweaver-Burk plot was produced to determine its enzymatic parameters for a comparison with the literature. Finally, LC-MS analysis was conducted on a series of experiments to evaluate the extent of, if any, undesired peptide acetylation at the N-terminus. In conclusion, we provide new insights that allow gaining a clearer picture of self-assembling peptide design rules for biocatalysis.
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Affiliation(s)
- Tiziano Carlomagno
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
| | - Maria C. Cringoli
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
- INSTM Trieste Research Unit, 34127 Trieste, Italy
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, 1000 Ljubljana, Slovenia;
| | - Marina Kurbasic
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
| | - Paolo Fornasiero
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
- INSTM Trieste Research Unit, 34127 Trieste, Italy
- ICCOM-CNR Trieste Research Unit, 34127 Trieste, Italy
| | - Paolo Pengo
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
| | - Silvia Marchesan
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
- INSTM Trieste Research Unit, 34127 Trieste, Italy
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Abstract
Enzymes are predominantly proteins able to effectively and selectively catalyze highly complex biochemical reactions in mild reaction conditions. Nevertheless, they are limited to the arsenal of reactions that have emerged during natural evolution in compliance with their intrinsic nature, three-dimensional structures and dynamics. They optimally work in physiological conditions for a limited range of reactions, and thus exhibit a low tolerance for solvent and temperature conditions. The de novo design of synthetic highly stable enzymes able to catalyze a broad range of chemical reactions in variable conditions is a great challenge, which requires the development of programmable and finely tunable artificial tools. Interestingly, over the last two decades, chemists developed protein secondary structure mimics to achieve some desirable features of proteins, which are able to interfere with the biological processes. Such non-natural oligomers, so called foldamers, can adopt highly stable and predictable architectures and have extensively demonstrated their attractiveness for widespread applications in fields from biomedical to material science. Foldamer science was more recently considered to provide original solutions to the de novo design of artificial enzymes. This review covers recent developments related to peptidomimetic foldamers with catalytic properties and the principles that have guided their design.
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129
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Du ZH, Tao BX, Yuan M, Qin WJ, Xu YL, Wang P, Da CS. Peptide-Catalyzed Highly Asymmetric Cross-Aldol Reaction of Aldehydes to Biomimetically Synthesize 1,4-Dicarbonyls. Org Lett 2020; 22:4444-4450. [PMID: 32463241 DOI: 10.1021/acs.orglett.0c01407] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Turn tetrapeptides were demonstrated to catalyze asymmetric aldol reaction of α-branched aldehydes and α-carbonyl aldehydes, i.e. glyoxylates and α-ketoaldehydes, to biomimetically synthesize acyclic all-carbon quaternary center-bearing 1,4-dicarbonyls in high yield and excellent enantioselectivity under mild conditions. The spatially restricted environment of the tetrapeptide warrants high enantioselectivity and yield with broad substrates. Using this protocol, (R)-pantolactone, the key intermediate of vitamin B5, was readily accessed in a practical, efficient, and environmentally benign process from inexpensive starting materials.
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Affiliation(s)
- Zhi-Hong Du
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Bao-Xiu Tao
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Meng Yuan
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Wen-Juan Qin
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yan-Li Xu
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Pei Wang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan 750004, China
| | - Chao-Shan Da
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.,State Key Laboratory of Applied Organic Chemistry, and Key Lab of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou 730000, China
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Zozulia O, Korendovych IV. Semi-Rationally Designed Short Peptides Self-Assemble and Bind Hemin to Promote Cyclopropanation. Angew Chem Int Ed Engl 2020; 59:8108-8112. [PMID: 32128962 PMCID: PMC7274867 DOI: 10.1002/anie.201916712] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Indexed: 11/11/2022]
Abstract
The self-assembly of short peptides gives rise to versatile nanoassemblies capable of promoting efficient catalysis. We have semi-rationally designed a series of seven-residue peptides that form hemin-binding catalytic amyloids to facilitate enantioselective cyclopropanation with efficiencies that rival those of engineered hemin proteins. These results demonstrate that: 1) Catalytic amyloids can bind complex metallocofactors to promote practically important multisubstrate transformations. 2) Even essentially flat surfaces of amyloid assemblies can impart a substantial degree of enantioselectivity without the need for extensive optimization. 3) The ease of peptide preparation allows for straightforward incorporation of unnatural amino acids and the preparation of peptides made from d-amino acids with complete reversal of enantioselectivity.
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Affiliation(s)
- Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
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Roy B, Pal S, Govindaraju T. Intrinsic Role of Molecular Architectonics in Enhancing the Catalytic Activity of Lead in Glucose Hydrolysis. ACS APPLIED MATERIALS & INTERFACES 2020; 12:14057-14063. [PMID: 32134618 DOI: 10.1021/acsami.0c01803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lewis acidity plays a key role in the catalytic activity of lead ion (PbII) in the hydrolysis of glucose in solution under harsh synthetic conditions. We report a number of structurally similar d-gluconamide amphiphiles as functional organic ligands with active an -NH center capable of coordinating PbII (viz., PbII-N-C) in basic condition to enhance the catalytic efficiency through the scheme of molecular architectonics. Amphiphiles with different hydrophobic unit form assembly-architectures with a varying second coordination sphere around the active metal ion center. As a result, the active PbII center in each architecture exhibits substantially different efficiency toward catalyzing the glucose hydrolysis under ambient temperature. The catalytic performance of the dynamic and reversible gluconamide-PbII assembly-architectures are highly dependent on their chemical environments in solution. Further, the active PbII center of gluconamide-PbII complex in the assembly architecture and dispersed states exhibits distinct outcomes with the former being a superior catalyst than the latter as well as PbII alone. The current study demonstrates the potential of molecular architectonics that relies on the hydrophobic units of designer functional amphiphiles to enrich surface electron density with enhanced σ-donation ability through space which substantially improves the catalytic efficiency of PbII toward glucose hydrolysis at ambient temperature.
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Affiliation(s)
- Bappaditya Roy
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Satyajit Pal
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
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132
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Pelin JBD, Gerbelli BB, Edwards-Gayle CJC, Aguilar AM, Castelletto V, Hamley IW, Alves WA. Amyloid Peptide Mixtures: Self-Assembly, Hydrogelation, Nematic Ordering, and Catalysts in Aldol Reactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2767-2774. [PMID: 32131599 PMCID: PMC7146849 DOI: 10.1021/acs.langmuir.0c00198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/04/2020] [Indexed: 05/23/2023]
Abstract
Morphological, spectroscopic, and scattering studies of the self-assembly and aggregation of mixtures of [RF]4 and P[RF]4 peptides (where R = arginine; F = phenylalanine; P = proline), in solution and as hydrogels, were performed to obtain information about polymorphism. CD data confirmed a β-sheet secondary structure in aqueous solution, and TEM images revealed nanofibers with diameters of ∼10 nm and micrometer lengths. SAXS curves were fitted using a mass fractal-component and a long cylinder shell form factor for the liquid samples, and only a long cylinder shell form factor for the gels. Increasing the P[RF]4 content in the systems leads to a reduction in cylinder radius and core scattering density, suggesting an increase in packing of the peptide molecules; however, the opposite effect is observed for the gels, where the scattering density is higher in the shell for the systems containing higher P[RF]4 content. These compounds show potential as catalysts in the asymmetric aldol reactions, with cyclohexanone and p-nitrobenzaldehyde in aqueous media. A moderate conversion (36.9%) and a good stereoselectivity (69:31) were observed for the system containing only [RF]4. With increasing P[RF]4 content, a considerable decrease of the conversion was observed, suggesting differences in the self-assembly and packing factor. Rheological measurements were performed to determine the shear moduli for the soft gels.
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Affiliation(s)
- Juliane
N. B. D. Pelin
- Centro
de Ciências Naturais e Humanas, Universidade
Federal do ABC, 09210-580, Santo André, Brazil
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
| | - Barbara B. Gerbelli
- Centro
de Ciências Naturais e Humanas, Universidade
Federal do ABC, 09210-580, Santo André, Brazil
| | | | - Andrea M. Aguilar
- Instituto
de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, 09972-270, Brazil
| | - Valeria Castelletto
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
| | - Ian W. Hamley
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
| | - Wendel A. Alves
- Centro
de Ciências Naturais e Humanas, Universidade
Federal do ABC, 09210-580, Santo André, Brazil
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133
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Zozulia O, Korendovych IV. Semi‐Rationally Designed Short Peptides Self‐Assemble and Bind Hemin to Promote Cyclopropanation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Oleksii Zozulia
- Department of ChemistrySyracuse University 111 College Place Syracuse NY 13244 USA
| | - Ivan V. Korendovych
- Department of ChemistrySyracuse University 111 College Place Syracuse NY 13244 USA
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134
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Kleinsmann AJ, Nachtsheim BJ. A minimalistic hydrolase based on co-assembled cyclic dipeptides. Org Biomol Chem 2020; 18:102-107. [PMID: 31799587 DOI: 10.1039/c9ob02198a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The self-assembly of small peptides into larger aggregates is an important process for the fundamental understanding of abiogenesis. In this article we demonstrate that blends of cyclic dipeptides (2,5-diketopiperazines - DKPs) bearing either histidine or cysteine in combination with a lipophilic amino acid form highly stable aggregates in aqueous solution with esterase-like activity. We demonstrate that the catalytic activity is based on an intermolecular cooperative behavior between histidine and cysteine. A high control of the molecular arrangement of the peptide assemblies was gained by C-H-π interactions between Phe and Leu or Val sidechains, resulting in a significant increase in catalytic activity. These interactions were strongly supported by Hartree-Fock calculations and finally confirmed via1H-NMR HRMAS NOE spectroscopy.
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Affiliation(s)
- Alexander J Kleinsmann
- Institut für Organische Chemie Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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135
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Huang KY, Yu CC, Horng JC. Conjugating Catalytic Polyproline Fragments with a Self-Assembling Peptide Produces Efficient Artificial Hydrolases. Biomacromolecules 2020; 21:1195-1201. [PMID: 31951389 DOI: 10.1021/acs.biomac.9b01620] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A polyproline fragment containing a catalytic dyad of His-His or Ser-His was coupled with a self-assembling peptide MAX1 to design new hydrolases (H2H5 and H2S5) for catalyzing ester hydrolysis. Circular dichroism measurements indicated that the peptides change their conformation from random coils to β-sheets when pH increases from 5 to 10. IR spectra also displayed the vibration modes corresponding to their β-structures at pH 9.0. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) measurements showed that in solution, the designed peptides self-assemble into network fibrils having a significantly increased catalytic efficiency on ester hydrolysis. On p-nitrophenyl acetate (p-NPA) substrate, the designed peptides exhibit high catalytic efficiency at pH 9.0 (kcat/KM = 12.1 M-1 s-1 for H2H5, 13.3 M-1 s-1 for H2S5), and their efficiency is even better at pH 10.0 (kcat/KM = 24.3 M-1 s-1 for H2H5, 99.4 M-1 s-1 for H2S5). Additionally, H2H5 and H2S5 also display good activity on catalyzing the hydrolysis of p-nitrophenyl-(2-phenyl)-propanoate (p-NPP) and p-nitrophenyl methoxyacetate (p-NPMA). Combining the polyproline-based catalytic scaffold with a self-assembling peptide generates an efficient hydrolase, providing a new design for effective artificial enzymes.
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Affiliation(s)
- Kuei-Yen Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C
| | - Chi-Ching Yu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C
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136
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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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137
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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138
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Song S, Wang J, Song N, Di H, Liu D, Yu Z. Peptide interdigitation-induced twisted nanoribbons as chiral scaffolds for supramolecular nanozymes. NANOSCALE 2020; 12:2422-2433. [PMID: 31916547 DOI: 10.1039/c9nr09492j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Establishing reliable strategies for rationally manipulating the organization of peptide building blocks and thereby precisely creating chiral nanostructures is challenging, while meaningful toward development of advanced functional materials. Here we report on a peptide-interdigitating mechanism for the reliable self-assembly of lipid-inspired amphiphiles (LIPIAs) into robust twisted nanoribbons by grafting domains to one alkyl tail of lipids as an extended element. Peptide interdigitation promoted the self-assembly of LIPIAs into twisted or flat nanoribbons driven by antiparallel or parallel β-sheet hydrogen bonds, respectively, strongly associated with the connecting direction of the incorporated domains. We found that the LIPIAs containing N-terminus-connected domains with either bulky or small side chain groups formed twisted nanoribbons in a broad pH range, thus implying a sequence- and pH-independent strategy for creation of robust chiral nanostructures. Integrating the resulting twisted nanoribbons with gold nanoparticles led to supramolecular nanozymes exhibiting the excellent catalytic activity and enantioselectivity of asymmetric oxidation of 3,4-dihyroxy-phenylalanine molecules. Our finding demonstrates that the peptide-interdigitating mechanism is a reliable strategy for precise creation of chiral nanostructures serving as chiral matrices for supramolecular nanozymes with improved catalytic performance, thus potentially paving the way towards advanced biomimetic systems resembling natural systems.
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Affiliation(s)
- Shuxin Song
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Jingyu Wang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, China
| | - Na Song
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Huixia Di
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin 300071, China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin 300071, China
| | - Zhilin Yu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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139
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Xie X, Wang L, Liu X, Du Z, Li Y, Li B, Wu L, Li W. Light-powered and transient peptide two-dimensional assembly driven by trans-to-cis isomerization of azobenzene side chains. Chem Commun (Camb) 2020; 56:1867-1870. [DOI: 10.1039/c9cc09448b] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A 2D dissipative system is initiated by photo-powered trans-to-cis isomerization of azobenzene, which usually results in the collapse of ordered assemblies.
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Affiliation(s)
- Xiaoming Xie
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
| | - Liang Wang
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
| | - Xiaohuan Liu
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
| | - Zhanglei Du
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
| | - Yiwen Li
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
| | - Bao Li
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- College of Chemistry
- Jilin University
- Changchun 130012
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140
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Jeong WJ, Yu J, Song WJ. Proteins as diverse, efficient, and evolvable scaffolds for artificial metalloenzymes. Chem Commun (Camb) 2020; 56:9586-9599. [DOI: 10.1039/d0cc03137b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have extracted and categorized the desirable properties of proteins that are adapted as the scaffolds for artificial metalloenzymes.
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Affiliation(s)
- Woo Jae Jeong
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jaeseung Yu
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Woon Ju Song
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
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141
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Du ZH, Qin WJ, Tao BX, Yuan M, Da CS. N-Primary-amine tetrapeptide-catalyzed highly asymmetric Michael addition of aliphatic aldehydes to maleimides. Org Biomol Chem 2020; 18:6899-6904. [DOI: 10.1039/d0ob01457e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The highly asymmetric Michael addition reaction between maleimides and aldehydes catalyzed by N-primary-amine β-turn tetrapeptides with excellent yields and enantioselectivities was reported.
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Affiliation(s)
- Zhi-Hong Du
- Institute of Biochemistry and Molecular Biology
- School of Life Sciences
- Lanzhou University
- Lanzhou 730000
- China
| | - Wen-Juan Qin
- Institute of Biochemistry and Molecular Biology
- School of Life Sciences
- Lanzhou University
- Lanzhou 730000
- China
| | - Bao-Xiu Tao
- Institute of Biochemistry and Molecular Biology
- School of Life Sciences
- Lanzhou University
- Lanzhou 730000
- China
| | - Meng Yuan
- Institute of Biochemistry and Molecular Biology
- School of Life Sciences
- Lanzhou University
- Lanzhou 730000
- China
| | - Chao-Shan Da
- Institute of Biochemistry and Molecular Biology
- School of Life Sciences
- Lanzhou University
- Lanzhou 730000
- China
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142
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Adsorption of Rose Bengal on a self-assembled fibrillar network affords a thermally switchable oxygenation photocatalyst and a thermochromic soft material. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2019.112142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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143
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Biswas S, Kumar M, Levine AM, Jimenez I, Ulijn RV, Braunschweig AB. Visible-light photooxidation in water by 1O2-generating supramolecular hydrogels. Chem Sci 2020. [DOI: 10.1039/c9sc06481h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
An aqueous photocatalytic system exploits photophysical properties arising from the formation of supramolecular hydrogels, with properties and assembly modulated by the amino acids appended to an organic chromophore.
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Affiliation(s)
- Sankarsan Biswas
- Advanced Science Research Center
- Graduate Center
- City University of New York
- New York
- USA
| | - Mohit Kumar
- Advanced Science Research Center
- Graduate Center
- City University of New York
- New York
- USA
| | - Andrew M. Levine
- Advanced Science Research Center
- Graduate Center
- City University of New York
- New York
- USA
| | - Ian Jimenez
- Advanced Science Research Center
- Graduate Center
- City University of New York
- New York
- USA
| | - Rein V. Ulijn
- Advanced Science Research Center
- Graduate Center
- City University of New York
- New York
- USA
| | - Adam B. Braunschweig
- Advanced Science Research Center
- Graduate Center
- City University of New York
- New York
- USA
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144
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Rodon Fores J, Criado‐Gonzalez M, Chaumont A, Carvalho A, Blanck C, Schmutz M, Serra CA, Boulmedais F, Schaaf P, Jierry L. Supported Catalytically Active Supramolecular Hydrogels for Continuous Flow Chemistry. Angew Chem Int Ed Engl 2019; 58:18817-18822. [DOI: 10.1002/anie.201909424] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/18/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Jennifer Rodon Fores
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Miryam Criado‐Gonzalez
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche MédicaleINSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de StrasbourgFaculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Alain Chaumont
- Université de StrasbourgFaculté de Chimie, UMR7140 1 rue Blaise Pascal 67008 Strasbourg Cedex France
| | - Alain Carvalho
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christian Blanck
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Marc Schmutz
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christophe A. Serra
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - F. Boulmedais
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Pierre Schaaf
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche MédicaleINSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de StrasbourgFaculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Loïc Jierry
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
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145
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146
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Rodon Fores J, Criado‐Gonzalez M, Chaumont A, Carvalho A, Blanck C, Schmutz M, Serra CA, Boulmedais F, Schaaf P, Jierry L. Supported Catalytically Active Supramolecular Hydrogels for Continuous Flow Chemistry. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jennifer Rodon Fores
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Miryam Criado‐Gonzalez
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche MédicaleINSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de StrasbourgFaculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Alain Chaumont
- Université de StrasbourgFaculté de Chimie, UMR7140 1 rue Blaise Pascal 67008 Strasbourg Cedex France
| | - Alain Carvalho
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christian Blanck
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Marc Schmutz
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christophe A. Serra
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - F. Boulmedais
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Pierre Schaaf
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche MédicaleINSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de StrasbourgFaculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Loïc Jierry
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
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147
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Makam P, Yamijala SSRKC, Tao K, Shimon LJW, Eisenberg DS, Sawaya MR, Wong BM, Gazit E. Non-proteinaceous hydrolase comprised of a phenylalanine metallo-supramolecular amyloid-like structure. Nat Catal 2019; 2:977-985. [PMID: 31742246 PMCID: PMC6861134 DOI: 10.1038/s41929-019-0348-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Enzymatic activity is crucial for various technological applications, yet the complex structures and limited stability of enzymes often hinder their use. Hence, de novo design of robust biocatalysts that are much simpler than their natural counterparts and possess enhanced catalytic activity has long been a goal in biotechnology. Here, we present evidence for the ability of a single amino acid to self-assemble into a potent and stable catalytic structural entity. Spontaneously, phenylalanine (F) molecules coordinate with zinc ions to form a robust, layered, supramolecular amyloid-like ordered architecture (F-Zn(ii)) and exhibit remarkable carbonic anhydrase-like catalytic activity. Notably, amongst the reported artificial biomolecular hydrolases, F-Zn(ii) displays the lowest molecular mass and highest catalytic efficiency, in addition to reusability, thermal stability, substrate specificity, stereoselectivity and rapid catalytic CO2 hydration ability. Thus, this report provides a rational path towards future de novo design of minimalistic biocatalysts for biotechnological and industrial applications.
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Affiliation(s)
- Pandeeswar Makam
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Linda J. W. Shimon
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - David S. Eisenberg
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael R. Sawaya
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Bryan M. Wong
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Department of Physics and Astronomy, and Materials Science and Engineering Program, University of California, Riverside, CA, USA
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
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148
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Grayson KJ, Anderson JLR. Designed for life: biocompatible de novo designed proteins and components. J R Soc Interface 2019; 15:rsif.2018.0472. [PMID: 30158186 PMCID: PMC6127164 DOI: 10.1098/rsif.2018.0472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
A principal goal of synthetic biology is the de novo design or redesign of biomolecular components. In addition to revealing fundamentally important information regarding natural biomolecular engineering and biochemistry, functional building blocks will ultimately be provided for applications including the manufacture of valuable products and therapeutics. To fully realize this ambitious goal, the designed components must be biocompatible, working in concert with natural biochemical processes and pathways, while not adversely affecting cellular function. For example, de novo protein design has provided us with a wide repertoire of structures and functions, including those that can be assembled and function in vivo. Here we discuss such biocompatible designs, as well as others that have the potential to become biocompatible, including non-protein molecules, and routes to achieving full biological integration.
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Affiliation(s)
- Katie J Grayson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK .,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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149
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Marshall LR, Zozulia O, Lengyel-Zhand Z, Korendovych IV. Minimalist de novo Design of Protein Catalysts. ACS Catal 2019; 9:9265-9275. [PMID: 34094654 PMCID: PMC8174531 DOI: 10.1021/acscatal.9b02509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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150
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Dolan MA, Basa PN, Zozulia O, Lengyel Z, Lebl R, Kohn EM, Bhattacharya S, Korendovych IV. Catalytic Nanoassemblies Formed by Short Peptides Promote Highly Enantioselective Transfer Hydrogenation. ACS NANO 2019; 13:9292-9297. [PMID: 31314486 PMCID: PMC7235949 DOI: 10.1021/acsnano.9b03880] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Self-assembly enables formation of incredibly diverse supramolecular structures with practically important functions from simple and inexpensive building blocks. Here, we show how a semirational, bottom-up approach to create emerging properties can be extended to a design of highly enantioselective catalytic nanoassemblies. The designed peptides comprising as few as two amino acid residues spontaneously self-assemble in the presence of metal ions to form supramolecular, vesicle-like nanoassemblies that promote transfer hydrogenation of ketones in an aqueous phase with excellent conversion rates and enantioselectivities (>90% ee).
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Affiliation(s)
- Martin A Dolan
- Department of Chemistry , Syracuse University , 111 College Place , Syracuse , New York 13244 , United States
| | - Prem N Basa
- Department of Chemistry , Syracuse University , 111 College Place , Syracuse , New York 13244 , United States
| | - Oleksii Zozulia
- Department of Chemistry , Syracuse University , 111 College Place , Syracuse , New York 13244 , United States
| | - Zsófia Lengyel
- Department of Chemistry , Syracuse University , 111 College Place , Syracuse , New York 13244 , United States
| | - René Lebl
- Department of Chemistry , Syracuse University , 111 College Place , Syracuse , New York 13244 , United States
| | - Eric M Kohn
- Department of Chemistry , Syracuse University , 111 College Place , Syracuse , New York 13244 , United States
| | - Sagar Bhattacharya
- Department of Chemistry , Syracuse University , 111 College Place , Syracuse , New York 13244 , United States
| | - Ivan V Korendovych
- Department of Chemistry , Syracuse University , 111 College Place , Syracuse , New York 13244 , United States
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