1
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Rout SK, Rhyner D, Greenwald J, Riek R. Characterization of self-templating catalytic amyloids. Methods Enzymol 2024; 697:51-75. [PMID: 38816135 DOI: 10.1016/bs.mie.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Amyloid aggregates with unique periodic structures have garnered significant attention due to their association with numerous diseases, including systemic amyloidoses and the neurodegenerative diseases Parkinson's, Alzheimer's, and Creutzfeld-Jakob. However, more recent investigations have expanded our understanding of amyloids, revealing their diverse functional biological roles. Amyloids have also been proposed to have played a significant role in prebiotic molecular evolution because of their exceptional stability, spontaneous formation in a prebiotic environment, catalytic and templating abilities, and cooperative interaction with fatty acids, polysaccharides, and nucleic acids. This chapter summarizes methods and techniques associated with studying short amyloidogenic peptides, including detailed procedures for investigating cross-templating and autocatalytic templating reactions. Since the work with amyloidogenic peptides and their aggregates present unique challenges, we have attempted to address these with essential details throughout the procedures. The lessons herein may be used in any amyloid-related research to ensure more reproducible results and reduce entrance barriers for researchers new to the field.
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Affiliation(s)
- Saroj K Rout
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland; Systems Biophysics, Department of Physics, Ludwig Maximilian University Munich, Munich, Germany
| | - David Rhyner
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland
| | - Jason Greenwald
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland.
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland.
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2
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Duran-Meza E, Araya-Secchi R, Romero-Hasler P, Soto-Bustamante EA, Castro-Fernandez V, Castillo-Caceres C, Monasterio O, Diaz-Espinoza R. Metal Ions Can Modulate the Self-Assembly and Activity of Catalytic Peptide Amyloids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6094-6106. [PMID: 38470353 DOI: 10.1021/acs.langmuir.3c02983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Rational design of peptides has become a powerful tool to produce self-assembled nanostructures with the ability to catalyze different chemical reactions, paving the way to develop minimalistic enzyme-like nanomaterials. Catalytic amyloid-like assemblies have emerged among the most versatile and active, but they often require additional factors for activity. Elucidating how these factors influence the structure and activity is key for the design. Here, we showed that biologically relevant metal ions can guide and modulate the self-assembly of a small peptide into diverse amyloid architectures. The morphology and catalytic activity of the resulting fibrils were tuned by the specific metal ion decorating the surface, whereas X-ray structural analysis of the amyloids showed ion-dependent shape sizes. Molecular dynamics simulations showed that the metals can strongly affect the local conformational space, which can trigger major rearrangements of the fibrils. Our results demonstrate that the conformational landscape of catalytic amyloids is broad and tunable by external factors, which can be critical for future design strategies.
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Affiliation(s)
- Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Raul Araya-Secchi
- Computational Biophysics group, Facultad de Ingenieria, Tecnologia y Diseño, Universidad San Sebastian, Bellavista 7, Recoleta, Santiago 8420524, Chile
- Centro Basal Ciencia & Vida, Universidad San Sebastian, Santiago 8420524, Chile
| | - Patricio Romero-Hasler
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Santiago 81380494, Chile
| | - Eduardo Arturo Soto-Bustamante
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Santiago 81380494, Chile
| | - Victor Castro-Fernandez
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, General Amengual 014, Estación Central, Santiago 9170390, Chile
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3
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Kwiatkowski W, Greenwald J, Murzakhmetov L, Robinson RC, Riek R. Short Peptide Amyloids Are a Potential Sequence Pool for the Emergence of Proteins. J Mol Biol 2024; 436:168495. [PMID: 38360090 DOI: 10.1016/j.jmb.2024.168495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/15/2024] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
Under prebiotic conditions, peptides are capable of self-replication through a structure-based template-assisted mechanism when they form amyloids. Furthermore, peptide amyloids can spontaneously form inside fatty acid vesicles creating membrane enclosed complex structures of variable morphologies. This is possible because fatty acid vesicle membranes act as filters allowing passage of activated amino acids while some amino acids derived from the activated species become non-permeable and trapped in the vesicles. Similarly, nascent peptides derived from the condensation of the activated amino acids are also trapped in the vesicles. It is hypothesized that such preselected peptide amyloids become a sequence pool for the emergence of proteins in life and that after billions of years of cellular evolution, the sequences in the current proteome have diverged significantly from these original seed peptides. If this hypothesis is correct, it could be possible to detect the traces of these seed sequences in current proteomes. Here, we show for all possible 3, 6, 7, 8 or 9 residue sequence motifs that those motifs that are most amyloidogenic/aggregation prone are over-represented in extant proteomes compared to a sequence-randomized proteome. Furthermore, we find that there is a greater proportion of amyloidogenic sequence motifs in archaea proteomes than in the larger primate proteomes. This suggests that the evolution towards larger proteomes leads to smaller proportion of amyloidogenic sequences.
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Affiliation(s)
| | | | | | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand; Research Institute for Interdisciplinary Science, Okayama University, Japan
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4
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Carrillo D, Duran-Meza E, Castillo-Caceres C, Alarcon DE, Guzman H, Diaz-Espinoza R. Catalytic amyloids for nucleotide hydrolysis. Methods Enzymol 2024; 697:269-291. [PMID: 38816126 DOI: 10.1016/bs.mie.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The design of small peptides that assemble into catalytically active intermolecular structures has proven to be a successful strategy towards developing minimalistic catalysts that exhibit some of the unique functional features of enzymes. Among these, catalytic amyloids have emerged as a fruitful source to unravel many different activities. These assemblies can potentially have broad applications that range from biotechnology to prebiotic chemistry. Although many peptides that assemble into catalytic amyloids have been developed in recent years, the elucidation of convergent mechanistic aspects of the catalysis and the structure/function relationship is still a challenge. Novel catalytic activities are necessary to better address these issues and expand the current repertoire of applicability. In this chapter, we described a methodology to produce catalytic amyloids that are specifically active towards the hydrolysis of phosphoanhydride bonds of nucleotides. The design of potentially active amyloid-prone peptide sequences is explored using as template the active site of enzymes with nucleotidyltransferase activity. The procedures include an approach for sequence design, in vitro aggregation assays, morphological characterization of the amyloid state and a comprehensive methodology to measure activity in vitro using nucleoside and deoxynucleosides triphosphates as model substrates. The proposed strategy can also be implemented to explore different types of activities for the design of future catalytic amyloids.
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Affiliation(s)
- Daniel Carrillo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile; Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
| | - Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Diego Eduardo Alarcon
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Hardy Guzman
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile.
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5
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Janković P, Kalafatovic D. Determining the esterase activity of peptides and peptide assemblies. Methods Enzymol 2024; 697:423-433. [PMID: 38816131 DOI: 10.1016/bs.mie.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Catalytic peptides are gaining attention as alternatives to enzymes, especially in industrial applications. Recent advances in peptide design have improved their catalytic efficiency with approaches such as self-assembly and metal ion complexation. However, the fundamental principles governing peptide catalysis at the sequence level are still being explored. Ester hydrolysis, a well-studied reaction, serves as a widely employed method to evaluate the catalytic potential of peptides. The standard colorimetric reaction involving para-nitrophenyl acetate hydrolysis acts as a benchmark assay, providing a straightforward and efficient screening method for rapidly identifying potential catalysts. However, maintaining standardized conditions is crucial for reproducible results, given that factors such as pH, temperature, and substrate concentration can introduce unwanted variability. This necessity becomes particularly pronounced when working with peptides, which often exhibit slower reaction rates compared to enzymes, making even minor variations significantly influential on the final outcome. In this context, we present a refined protocol for assessing the catalytic activity of peptides and peptide assemblies, addressing critical considerations for reproducibility and accuracy.
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Affiliation(s)
- Patrizia Janković
- Faculty of Biotechnology and Drug Development, University of Rijeka, Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, Rijeka, Croatia.
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6
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Baek Y, Lee M. Solid-state NMR spectroscopic analysis for structure determination of a zinc-bound catalytic amyloid fibril. Methods Enzymol 2024; 697:435-471. [PMID: 38816132 DOI: 10.1016/bs.mie.2024.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Zinc ions are commonly involved in enzyme catalysis and protein structure stabilization, but their coordination geometry of zinc-protein complex is rarely determined. Here, in this chapter, we introduce a systematic solid-state NMR approach to determine the oligomeric assembly and Zn2+ coordination geometry of a de novo designed amyloid fibrils that catalyze zinc dependent ester hydrolysis. NMR chemical shifts and intermolecular contacts confirm that the peptide forms parallel-in-register β-sheets, with the two forms of Zn2+ bound histidines in each peptide. The amphiphilic parallel β-sheets assemble into stacked bilayers that are stabilized by hydrophobic side chains between β-sheets. The conformations of the histidine side chains, determined by 13C-15N distance measurements, reveal how histidines protrude from the β-sheet. 1H-15N correlation spectra show that the single-Zn2+ coordinated histidine associated with dynamic water. The resulting structure provides insight into how metal ions contribute to stabilizing the protein structure and driving its catalytic reactivity.
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Affiliation(s)
- Yoongyeong Baek
- Department of Chemistry, Drexel University, Philadelphia, PA, United States
| | - Myungwoon Lee
- Department of Chemistry, Drexel University, Philadelphia, PA, United States.
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7
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Rathee P, Moorkkannur SN, Prabhakar R. Structural studies of catalytic peptides using molecular dynamics simulations. Methods Enzymol 2024; 697:151-180. [PMID: 38816122 DOI: 10.1016/bs.mie.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Many self-assembling peptides can form amyloid like structures with different sizes and morphologies. Driven by non-covalent interactions, their aggregation can occur through distinct pathways. Additionally, they can bind metal ions to create enzyme like active sites that allow them to catalyze diverse reactions. Due to the non-crystalline nature of amyloids, it is quite challenging to elucidate their structures using experimental spectroscopic techniques. In this aspect, molecular dynamics (MD) simulations provide a useful tool to derive structures of these macromolecules in solution. They can be further validated by comparing with experimentally measured structural parameters. However, these simulations require a multi-step process starting from the selection of the initial structure to the analysis of MD trajectories. There are multiple force fields, parametrization protocols, equilibration processes, software and analysis tools available for this process. Therefore, it is complicated for non-experts to select the most relevant tools and perform these simulations effectively. In this chapter, a systematic methodology that covers all major aspects of modeling of catalytic peptides is provided in a user-friendly manner. It will be helpful for researchers in this critical area of research.
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Affiliation(s)
- Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL, United States
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, United States.
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8
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Rout S, Cadalbert R, Schröder N, Wang J, Zehnder J, Gampp O, Wiegand T, Güntert P, Klingler D, Kreutz C, Knörlein A, Hall J, Greenwald J, Riek R. An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA. J Am Chem Soc 2023; 145:21915-21924. [PMID: 37782045 PMCID: PMC10571083 DOI: 10.1021/jacs.3c06287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 10/03/2023]
Abstract
Interactions between RNA and proteins are the cornerstone of many important biological processes from transcription and translation to gene regulation, yet little is known about the ancient origin of said interactions. We hypothesized that peptide amyloids played a role in the origin of life and that their repetitive structure lends itself to building interfaces with other polymers through avidity. Here, we report that short RNA with a minimum length of three nucleotides binds in a sequence-dependent manner to peptide amyloids. The 3'-5' linked RNA backbone appears to be well-suited to support these interactions, with the phosphodiester backbone and nucleobases both contributing to the affinity. Sequence-specific RNA-peptide interactions of the kind identified here may provide a path to understanding one of the great mysteries rooted in the origin of life: the origin of the genetic code.
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Affiliation(s)
- Saroj
K. Rout
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Nina Schröder
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Julia Wang
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Johannes Zehnder
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Olivia Gampp
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Wiegand
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
- Max
Planck Institute for Chemical Energy Conversion, 45470 Mülheim/Ruhr, Germany
| | - Peter Güntert
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
- Institute
of Biophysical Chemistry, Goethe University, 60438 Frankfurt
am Main, Germany
- Department
of Chemistry, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - David Klingler
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Anna Knörlein
- Institute
of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jason Greenwald
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
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9
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Navarro S, Díaz-Caballero M, Peccati F, Roldán-Martín L, Sodupe M, Ventura S. Amyloid Fibrils Formed by Short Prion-Inspired Peptides Are Metalloenzymes. ACS NANO 2023; 17:16968-16979. [PMID: 37647583 PMCID: PMC10510724 DOI: 10.1021/acsnano.3c04164] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
Enzymes typically fold into defined 3D protein structures exhibiting a high catalytic efficiency and selectivity. It has been proposed that the earliest enzymes may have arisen from the self-assembly of short peptides into supramolecular amyloid-like structures. Several artificial amyloids have been shown to display catalytic activity while offering advantages over natural enzymes in terms of modularity, flexibility, stability, and reusability. Hydrolases, especially esterases, are the most common artificial amyloid-like nanozymes with some reported to act as carbonic anhydrases (CA). Their hydrolytic activity is often dependent on the binding of metallic cofactors through a coordination triad composed of His residues in the β-strands, which mimic the arrangement found in natural metalloenzymes. Tyr residues contribute to the coordination of metal ions in the active center of metalloproteins; however, their use has been mostly neglected in the design of metal-containing amyloid-based nanozymes. We recently reported that four different polar prion-inspired heptapeptides spontaneously self-assembled into amyloid fibrils. Their sequences lack His but contain three alternate Tyr residues exposed to solvent. We combine experiments and simulations to demonstrate that the amyloid fibrils formed by these peptides can efficiently coordinate and retain different divalent metal cations, functioning as both metal scavengers and nanozymes. The metallized fibrils exhibit esterase and CA activities without the need for a histidine triad. These findings highlight the functional versatility of prion-inspired peptide assemblies and provide a new sequential context for the creation of artificial metalloenzymes. Furthermore, our data support amyloid-like structures acting as ancestral catalysts at the origin of life.
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Affiliation(s)
- Susanna Navarro
- Institut
de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Marta Díaz-Caballero
- Institut
de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Francesca Peccati
- Basque
Research and Technology Alliance (BRTA), Center for Cooperative Research in Biosciences (CIC bioGUNE), 48160 Derio, Spain
| | - Lorena Roldán-Martín
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Mariona Sodupe
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut
de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, 08193 Bellaterra (Barcelona), Spain
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10
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Li Z, Joshi SY, Wang Y, Deshmukh SA, Matson JB. Supramolecular Peptide Nanostructures Regulate Catalytic Efficiency and Selectivity. Angew Chem Int Ed Engl 2023; 62:e202303755. [PMID: 37194941 PMCID: PMC10330506 DOI: 10.1002/anie.202303755] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Indexed: 05/18/2023]
Abstract
We report three constitutionally isomeric tetrapeptides, each comprising one glutamic acid (E) residue, one histidine (H) residue, and two lysine (KS ) residues functionalized with side-chain hydrophobic S-aroylthiooxime (SATO) groups. Depending on the order of amino acids, these amphiphilic peptides self-assembled in aqueous solution into different nanostructures:nanoribbons, a mixture of nanotoroids and nanoribbons, or nanocoils. Each nanostructure catalyzed hydrolysis of a model substrate, with the nanocoils exhibiting the greatest rate enhancement and the highest enzymatic efficiency. Coarse-grained molecular dynamics simulations, analyzed with unsupervised machine learning, revealed clusters of H residues in hydrophobic pockets along the outer edge of the nanocoils, providing insight for the observed catalytic rate enhancement. Finally, all three supramolecular nanostructures catalyzed hydrolysis of the l-substrate only when a pair of enantiomeric Boc-l/d-Phe-ONp substrates were tested. This study highlights how subtle molecular-level changes can influence supramolecular nanostructures, and ultimately affect catalytic efficiency.
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Affiliation(s)
- Zhao Li
- Department of Chemistry, Virginia Tech, Blacksburg, VA-24061, USA
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA-24061, USA
| | - Soumil Y Joshi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA-24061, USA
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA-24061, USA
| | - Yin Wang
- Engineering Research Center of Cell & Therapeutic Antibody, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sanket A Deshmukh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA-24061, USA
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA-24061, USA
| | - John B Matson
- Department of Chemistry, Virginia Tech, Blacksburg, VA-24061, USA
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA-24061, USA
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11
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Janković P, Otović E, Mauša G, Kalafatovic D. Manually curated dataset of catalytic peptides for ester hydrolysis. Data Brief 2023; 48:109290. [PMID: 37383747 PMCID: PMC10294096 DOI: 10.1016/j.dib.2023.109290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/12/2023] [Accepted: 05/30/2023] [Indexed: 06/30/2023] Open
Abstract
Catalytic peptides are low cost biomolecules able to catalyse chemical reactions such as ester hydrolysis. This dataset provides a list of catalytic peptides currently reported in literature. Several parameters were evaluated, including sequence length, composition, net charge, isoelectric point, hydrophobicity, self-assembly propensity and mechanism of catalysis. Along with the analysis of physico-chemical properties, the SMILES representation for each sequence was generated to provide an easy-to-use means of training machine learning models. This offers a unique opportunity for the development and validation of proof-of-concept predictive models. Being a reliable manually curated dataset, it also enables the benchmark for comparison of new models or models trained on automatically gathered peptide-oriented datasets. Moreover, the dataset provides an insight in the currently developed catalytic mechanisms and can be used as the foundation for the development of next-generation peptide-based catalysts.
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Affiliation(s)
- Patrizia Janković
- University of Rijeka, Department of Biotechnology, Rijeka 51000, Croatia
| | - Erik Otović
- University of Rijeka, Faculty of Engineering, Rijeka 51000, Croatia
- University of Rijeka, Center for Artificial Intelligence and Cybersecurity, Rijeka 51000, Croatia
| | - Goran Mauša
- University of Rijeka, Faculty of Engineering, Rijeka 51000, Croatia
- University of Rijeka, Center for Artificial Intelligence and Cybersecurity, Rijeka 51000, Croatia
| | - Daniela Kalafatovic
- University of Rijeka, Department of Biotechnology, Rijeka 51000, Croatia
- University of Rijeka, Center for Artificial Intelligence and Cybersecurity, Rijeka 51000, Croatia
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12
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Mandal R, Ghosh A, Rout NK, Prasad M, Hazra B, Sar S, Das S, Datta A, Tarafdar PK. Self-assembled prebiotic amphiphile-mixture exhibits tunable catalytic properties. Org Biomol Chem 2023; 21:4473-4481. [PMID: 37194351 DOI: 10.1039/d3ob00606a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protocellular surface formation via the self-assembly of amphiphiles, and catalysis by simple peptides/proto-RNA are two important pillars in the evolution of protocells. To hunt for prebiotic self-assembly-supported catalytic reactions, we thought that amino-acid-based amphiphiles might play an important role. In this paper, we investigate the formation of histidine-based and serine-based amphiphiles under mild prebiotic conditions from amino acid : fatty alcohol and amino acid : fatty acid mixtures. The histidine-based amphiphiles were able to catalyze hydrolytic reactions at the self-assembled surface (with a rate increase of ∼1000-fold), and the catalytic ability can be tuned by linkage of the fatty carbon part to histidine (N-acylated vs. O-acylated). Moreover, the presence of cationic serine-based amphiphiles on the surface enhances the catalytic efficiency by another ∼2-fold, whereas the presence of anionic aspartic acid-based amphiphiles reduces the catalytic activity. Ester partitioning into the surface, reactivity, and the accumulation of liberated fatty acid explain the substrate selectivity of the catalytic surface, where the hexyl esters were found to be more hydrolytic than other fatty acyl esters. Di-methylation of the -NH2 of OLH increases the catalytic efficacy by a further ∼2-fold, whereas trimethylation reduces the catalytic ability. The self-assembly, charge-charge repulsion, and the H-bonding to the ester carbonyl are likely to be responsible for the superior (∼2500-fold higher rate than the pre-micellar OLH) catalytic efficiency of O-lauryl dimethyl histidine (OLDMH). Thus, prebiotic amino-acid-based surfaces served as an efficient catalyst that exhibits regulation of catalytic function, substrate selectivity, and further adaptability to perform bio-catalysis.
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Affiliation(s)
- Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Anupam Ghosh
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Nilesh K Rout
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Sanu Sar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Subrata Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Ayan Datta
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
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13
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Tian Y, Yang L, Peng X, Qi W, Wang M. A covalent crosslinking strategy to construct a robust peptide-based artificial esterase. SOFT MATTER 2023; 19:3458-3463. [PMID: 37129250 DOI: 10.1039/d3sm00284e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Peptide-based artificial enzymes derived from the supramolecular assembly of short peptides have attracted growing attention in recent years. However, the stability of these artificial enzymes is still a problem since their noncovalent supramolecular structure is quite sensitive and frail under environmental conditions. In this study, we reported a covalent crosslinking strategy for the fabrication of a robust peptide-based artificial esterase. Inspired by the di-tyrosine bonds in many natural structural proteins, multi-tyrosines were designed into a peptide sequence with histidine as the catalytic residue for the ester hydrolysis reaction. Upon the photo-induced oxidation reaction, the short peptide YYHYY rapidly transferred into nanoparticle-shaped aggregates (CL-YYHYY) and displayed improved esterase-like catalytic activity than some previously reported noncovalent-based artificial esterases. Impressively, CL-YYHYY showed outstanding reusability and superior stability under high temperature, strong acid and alkaline and organic solvent conditions. This study provides a promising approach to improving the catalytic activity and stability of peptide-based artificial enzymes.
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Affiliation(s)
- Yi Tian
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
| | - Lijun Yang
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
| | - Xin Peng
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China.
| | - Wei Qi
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300350, P. R. China.
- The Co-Innovation Centre of Chemistry and Chemical Engineering of Tianjin, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, 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.
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China.
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300350, P. R. China
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14
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Diaz-Espinoza R. Catalytically Active Amyloids as Future Bionanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3802. [PMID: 36364578 PMCID: PMC9656882 DOI: 10.3390/nano12213802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/14/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Peptides and proteins can aggregate into highly ordered and structured conformations called amyloids. These supramolecular structures generally have convergent features, such as the formation of intermolecular beta sheets, that lead to fibrillary architectures. The resulting fibrils have unique mechanical properties that can be exploited to develop novel nanomaterials. In recent years, sequences of small peptides have been rationally designed to self-assemble into amyloids that catalyze several chemical reactions. These amyloids exhibit reactive surfaces that can mimic the active sites of enzymes. In this review, I provide a state-of-the-art summary of the development of catalytically active amyloids. I will focus especially on catalytic activities mediated by hydrolysis, which are the most studied examples to date, as well as novel types of recently reported activities that promise to expand the possible repertoires. The combination of mechanical properties with catalytic activity in an amyloid scaffold has great potential for the development of future bionanomaterials aimed at specific applications.
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Affiliation(s)
- Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 3363, Chile
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15
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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16
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Catalytic Peptides: the Challenge between Simplicity and Functionality. Isr J Chem 2022. [DOI: 10.1002/ijch.202200029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022; 31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
Abstract
How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.
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Affiliation(s)
- Vijay Jayaraman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Saacnicteh Toledo‐Patiño
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Lianet Noda‐García
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentHebrew University of JerusalemRehovotIsrael
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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18
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Ghosh D, Konar M, Mondal T, Govindaraju T. Differential copper-guided architectures of amyloid β peptidomimetics modulate oxidation states and catalysis. NANOSCALE ADVANCES 2022; 4:2196-2200. [PMID: 36133442 PMCID: PMC9419866 DOI: 10.1039/d2na00161f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/30/2022] [Indexed: 06/16/2023]
Abstract
Orchestration of differential architectures of designer peptidomimetics that modulate metal oxidation states to perform multiple chemical transformations remains a challenge. Cu-chelation and self-assembly properties of amyloid β (Aβ14-23) peptide were tuned by the incorporation of cyclic dipeptide (CDP) and pyrene (Py) as the assembly directing and reporting units, respectively. We explore the molecular architectonics of Aβ14-23 derived peptidomimetics (AkdNMCPy) to form differential architectures that stabilize distinct Cu oxidation states. The fibrillar self-assembly of AkdNMCPy is modulated to form nanosheets by the one-off addition of CuII. Notably, the serial addition of CuII resulted in the formation of micelle-like core-shell architectures. The micelle-like and nanosheet architectures were found to differentially stabilize CuII and CuI states and catalyze tandem oxidative-hydrolysis and alkyne-azide cycloaddition reactions, respectively.
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Affiliation(s)
- Debasis Ghosh
- 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
| | - Mouli Konar
- 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
| | - Tanmay Mondal
- 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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19
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Castillo-Caceres C, Duran-Meza E, Diaz-Espinoza R. Design and Testing of Synthetic Catalytic Amyloids Based on the Active Site of Enzymes. Methods Mol Biol 2022; 2538:207-216. [PMID: 35951302 DOI: 10.1007/978-1-0716-2529-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The amyloid fold is nowadays recognized as an alternative conformation accessible to different proteins and peptides. The highly stable and ordered structural organization of amyloid fibrils can be exploited for the design of novel nanomaterials with emergent properties. Recent works have demonstrated that the functional features of the active site of enzymes can be partially recreated using this fold as a scaffold to develop catalytically active amyloids. We describe in this chapter a protocol to design functionally active amyloids that emerge from the self-assembly in vitro of synthetic peptides with sequences based on the active site of enzymes. Using this protocol, we show the development of amyloids that catalyze the metal-dependent hydrolysis of the phosphoanhydride bonds of nucleoside triphosphates.
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Affiliation(s)
- Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
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20
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Rout SK, Rhyner D, Riek R, Greenwald J. Prebiotically Plausible Autocatalytic Peptide Amyloids. Chemistry 2021; 28:e202103841. [PMID: 34812556 PMCID: PMC9299922 DOI: 10.1002/chem.202103841] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 12/19/2022]
Abstract
The prebiotic emergence of molecules capable both of self-replication and of storing information was a defining event at the dawn of life. Still, no plausible prebiotic self-replication of biologically relevant molecules has been demonstrated. Building upon the known templating nature of amyloids, we present two systems in which the products of a peptide-bond-forming reaction act as self-replicators to enhance the yield and stereoselectivity of their formation. This first report of an amino acid condensation that can undergo autocatalysis further supports the potential role of amyloids in prebiotic molecular evolution as an environment-responsive and information-coding system capable of self-replication.
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Affiliation(s)
- Saroj K Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - David Rhyner
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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21
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Gülseren G. Catalytic, theoretical, and biological investigation of an enzyme mimic model. Turk J Chem 2021; 45:1270-1278. [PMID: 34707450 PMCID: PMC8517613 DOI: 10.3906/kim-2104-51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/12/2021] [Indexed: 11/30/2022] Open
Abstract
Artificial catalyst studies were always stayed at the kinetics investigation level, in this work bioactivity of designed catalyst were shown by the induction of biomineralization of the cells, indicating the possible use of enzyme mimics for biological applications. The development of artificial enzymes is a continuous quest for the development of tailored catalysts with improved activity and stability. Understanding the catalytic mechanism is a replaceable step for catalytic studies and artificial enzyme mimics provide an alternative way for catalysis and a better understanding of catalytic pathways at the same time. Here we designed an artificial catalyst model by decorating peptide nanofibers with a covalently conjugated catalytic triad sequence. Owing to the self-assembling nature of the peptide amphiphiles, multiple action units can be presented on the surface for enhanced catalytic performance. The designed catalyst has shown an enzyme-like kinetics profile with a significant substrate affinity. The cooperative action in between catalytic triad amino acids has shown improved catalytic activity in comparison to only the histidine-containing control group. Histidine is an irreplaceable contributor to catalytic action and this is an additional reason for control group selection. This new method based on the self-assembly of covalently conjugated action units offers a new platform for enzyme investigations and their further applications. Artificial catalyst studies always stayed at the kinetics investigation level, in this work bioactivity of the designed catalyst was shown by the induction of biomineralization of the cells, indicating the possible use of enzyme mimics for biological applications.
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Affiliation(s)
- Gülcihan Gülseren
- Department of Molecular Biology and Genetics, Faculty of Agriculture and Natural Sciences, Konya Food and Agriculture University Turkey
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22
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Marshall LR, Korendovych IV. Catalytic amyloids: Is misfolding folding? Curr Opin Chem Biol 2021; 64:145-153. [PMID: 34425319 PMCID: PMC8585703 DOI: 10.1016/j.cbpa.2021.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/24/2022]
Abstract
Originally regarded as a disease symptom, amyloids have shown a rich diversity of functions, including biologically beneficial ones. As such, the traditional view of polypeptide aggregation into amyloid-like structures being 'misfolding' should rather be viewed as 'alternative folding.' Various amyloid folds have been recently used to create highly efficient catalysts with specific catalytic efficiencies rivaling those of enzymes. Here we summarize recent developments and applications of catalytic amyloids, derived from both de novo and bioinspired designs, and discuss how progress in the last 2 years reflects on the field as a whole.
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Affiliation(s)
- Liam R Marshall
- 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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23
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Gülseren G, Saylam A, Marion A, Özçubukçu S. Fullerene-Based Mimics of Biocatalysts Show Remarkable Activity and Modularity. ACS APPLIED MATERIALS & INTERFACES 2021; 13:45854-45863. [PMID: 34520162 DOI: 10.1021/acsami.1c11516] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The design of catalysts with greater control over catalytic activity and stability is a major challenge with substantial impact on fundamental chemistry and industrial applications. Due to their unparalleled diversity, selectivity, and efficiency, enzymes are promising models for next-generation catalysts, and considerable efforts have been devoted to incorporating the principles of their mechanisms of action into artificial systems. We report a heretofore undocumented catalyst design that introduces fullerenes to the field of biocatalysis, which we refer to as fullerene nanocatalysts, and that emulates enzymatic active sites through multifunctional self-assembled nanostructures. As a proof-of-concept, we mimicked the reactivity of hydrolases using fullerene nanocatalysts functionalized with the basic components of the parent enzyme with remarkable activity. Owing to the versatile amino acid-based functionalization repertoire of fullerene nanocatalysts, these next-generation carbon/biomolecule hybrids have potential to mimic the activity of other families of enzymes and, therefore, offer new perspectives for the design of biocompatible, high-efficiency artificial nanocatalysts.
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Affiliation(s)
- Gülcihan Gülseren
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
- Department of Molecular Biology and Genetics, Konya Food and Agriculture University, Konya 42080, Turkey
| | - Aytül Saylam
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
| | - Antoine Marion
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
| | - Salih Özçubukçu
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
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24
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Duran-Meza E, Diaz-Espinoza R. Catalytic Amyloids as Novel Synthetic Hydrolases. Int J Mol Sci 2021; 22:ijms22179166. [PMID: 34502074 PMCID: PMC8431744 DOI: 10.3390/ijms22179166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 11/23/2022] Open
Abstract
Amyloids are supramolecular assemblies composed of polypeptides stabilized by an intermolecular beta-sheet core. These misfolded conformations have been traditionally associated with pathological conditions such as Alzheimer’s and Parkinson´s diseases. However, this classical paradigm has changed in the last decade since the discovery that the amyloid state represents a universal alternative fold accessible to virtually any polypeptide chain. Moreover, recent findings have demonstrated that the amyloid fold can serve as catalytic scaffolds, creating new opportunities for the design of novel active bionanomaterials. Here, we review the latest advances in this area, with particular emphasis on the design and development of catalytic amyloids that exhibit hydrolytic activities. To date, three different types of activities have been demonstrated: esterase, phosphoesterase and di-phosphohydrolase. These artificial hydrolases emerge upon the self-assembly of small peptides into amyloids, giving rise to catalytically active surfaces. The highly stable nature of the amyloid fold can provide an attractive alternative for the design of future synthetic hydrolases with diverse applications in the industry, such as the in situ decontamination of xenobiotics.
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Affiliation(s)
- Eva Duran-Meza
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170022, Chile
- Correspondence:
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25
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Hamley IW. Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures. Biomacromolecules 2021; 22:1835-1855. [PMID: 33843196 PMCID: PMC8154259 DOI: 10.1021/acs.biomac.1c00240] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.
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Affiliation(s)
- Ian W. Hamley
- Department of Chemistry, University of Reading, RG6 6AD Reading, United Kingdom
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26
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Zozulia O, Marshall LR, Kim I, Kohn EM, Korendovych IV. Self-Assembling Catalytic Peptide Nanomaterials Capable of Highly Efficient Peroxidase Activity. Chemistry 2021; 27:5388-5392. [PMID: 33460473 PMCID: PMC8208039 DOI: 10.1002/chem.202100182] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Indexed: 12/13/2022]
Abstract
The self-assembly of short peptides gives rise to versatile nanomaterials capable of promoting efficient catalysis. We have shown that short, seven-residue peptides bind hemin to produce functional catalytic materials which display highly efficient peroxidation activity, reaching a catalytic efficiency of 3×105 m-1 s-1 . Self-assembly is essential for catalysis as non-assembling controls show no activity. We have also observed peroxidase activity even in the absence of hemin, suggesting the potential to alter redox properties of substrates upon association with the assemblies. These results demonstrate the practical utility of self-assembled peptides in various catalytic applications and further support the evolutionary link between amyloids and modern-day enzymes.
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Affiliation(s)
- Oleksii Zozulia
- 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)
| | - Inhye Kim
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244 (USA)
| | - Eric M. Kohn
- 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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27
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Kwiatkowski W, Bomba R, Afanasyev P, Boehringer D, Riek R, Greenwald J. Präbiotische Peptid‐Synthese und spontane Amyloid‐Bildung im Inneren eines protozellulären Kompartiments. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Witek Kwiatkowski
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Radoslaw Bomba
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Pavel Afanasyev
- Wissenschaftliches Zentrum für optische und Elektronenmikroskopie Eidgenössische Technische Hochschule, ETH-Hönggerberg Otto-Stern-Weg 3 CH-8093 Zürich Schweiz
| | - Daniel Boehringer
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule, ETH-Hönggerberg Otto-Stern-Weg 5 CH-8093 Zürich Schweiz
| | - Roland Riek
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Jason Greenwald
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
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28
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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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29
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Abstract
Self-assembly of proteins and peptides into the amyloid fold is a widespread phenomenon in the natural world. The structural hallmark of self-assembly into amyloid fibrillar assemblies is the cross-beta motif, which conveys distinct morphological and mechanical properties. The amyloid fibril formation has contrasting results depending on the organism, in the sense that it can bestow an organism with the advantages of mechanical strength and improved functionality or, on the contrary, could give rise to pathological states. In this chapter we review the existing information on amyloid-like peptide aggregates, which could either be derived from protein sequences, but also could be rationally or de novo designed in order to self-assemble into amyloid fibrils under physiological conditions. Moreover, the development of self-assembled fibrillar biomaterials that are tailored for the desired properties towards applications in biomedical or environmental areas is extensively analyzed. We also review computational studies predicting the amyloid propensity of the natural amino acid sequences and the structure of amyloids, as well as designing novel functional amyloid materials.
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Affiliation(s)
- C. Kokotidou
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
| | - P. Tamamis
- Texas A&M University, Artie McFerrin Department of Chemical Engineering College Station Texas 77843-3122 USA
| | - A. Mitraki
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
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30
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Wang J, Wang C, Ge Y, Sun Y, Wang D, Xu H. Self‐assembly
of hairpin peptides mediated by Cu(
II
) ion: Effect of amino acid sequence. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jiqian Wang
- State Key Laboratory of Heavy Oil Processing, Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Qingdao China
| | - Chengdong Wang
- Qingdao Industrial Energy Storage Research Institute, Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences Qingdao China
| | - Yanqing Ge
- State Key Laboratory of Heavy Oil Processing, Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Qingdao China
| | - Yawei Sun
- State Key Laboratory of Heavy Oil Processing, Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Qingdao China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing, Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Qingdao China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing, Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Qingdao China
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31
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Marshall LR, Jayachandran M, Lengyel-Zhand Z, Rufo CM, Kriews A, Kim MC, Korendovych IV. Synergistic Interactions Are Prevalent in Catalytic Amyloids. Chembiochem 2020; 21:2611-2614. [PMID: 32329215 PMCID: PMC7605102 DOI: 10.1002/cbic.202000205] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/20/2020] [Indexed: 11/05/2022]
Abstract
Interactions between multiple functional groups are key to catalysis. Previously, we reported synergistic interactions in catalytic amyloids formed by mixtures of heptameric peptides that lead to significant improvements in esterase activity. Herein, we describe the in-depth investigation of synergistic interactions within a family of amyloid fibrils, exploring the results of functional group interactions, the effects of chirality and the use of mixed enantiomers within fibrils. Remarkably, we find that synergistic interactions (either positive or negative) are found in the vast majority of binary mixtures of catalytic amyloid-forming peptides. The productive arrangements of functionalities rapidly identified by mixing different peptides will undoubtedly lead to the development of more active catalysts for a variety of different transformations.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Megha Jayachandran
- 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
| | - Caroline M. Rufo
- 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
| | - Min-Chul Kim
- 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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32
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Functional characterization of the ATPase-like activity displayed by a catalytic amyloid. Biochim Biophys Acta Gen Subj 2020; 1865:129729. [PMID: 32916204 DOI: 10.1016/j.bbagen.2020.129729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/17/2020] [Accepted: 09/04/2020] [Indexed: 01/20/2023]
Abstract
BACKGROUND Amyloids are highly ordered polypeptide aggregates stabilized by a beta-sheet structural core. Though classically associated to pathology, reports on novel functional roles of these proteins have increasingly emerged in the past decade. Moreover, the recent discovery that amyloids formed with rationally designed small peptides can exhibit catalytic reactivity has opened up new opportunities in both biology and biotechnology. The observed activities typically require the binding of divalent metals, giving rise to active metal-amyloid complexes. METHODS Peptide (SDIDVFI) was aggregated in vitro. The structure of the self-assembled species was analyzed using fluorescence, transmission electron microscopy, circular dichroism and computational modeling. A kinetic characterization of the emerging catalytic activity was performed. RESULTS The peptide self-assembled into canonical amyloids that exhibited catalytic activity towards hydrolysis of the phosphoanhydride bonds of adenosine triphosphate (ATP), partially mimicking an ATPase-like enzyme. Both amyloid formation and activity are shown to depend on manganese (Mn2+) binding. The activity was not restricted to ATP but also affected all other ribonucleotides (GTP, CTP and UTP). Peptides carrying a single aspartate exhibited a similar activity. CONCLUSIONS The phosphoanhydride bonds appear as the main specificity target of the Mn2+-amyloid complex. A single aspartate per peptide is sufficient to enable the hydrolytic activity. GENERAL SIGNIFICANCE Catalytic amyloids are shown for the first time to catalyze the hydrolysis of all four ribonucleotides. Our results should contribute towards understanding the biological implications of amyloid-mediated reactivity as well as in the design of future catalytic amyloids for biotechnological applications.
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33
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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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34
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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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35
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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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36
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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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37
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Sarkhel B, Chatterjee A, Das D. Covalent Catalysis by Cross β Amyloid Nanotubes. J Am Chem Soc 2020; 142:4098-4103. [PMID: 32083482 DOI: 10.1021/jacs.9b13517] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The binding pockets of extant enzymes feature precise positioning of amino acid residues that facilitate multiple complex transformations exploiting covalent and non-covalent interactions. Reversible covalent anchoring is extensively used as an efficient tool by Nature for activating modern enzymes such as esterases and dehydratases and also for proteins like opsins for the complex process of visual phototransduction. Here we construct paracrystalline amyloid surfaces through the self-propagation of short peptides which offer binding pockets exposed with arrays of imidazoles and lysines. As covalent catalysis is utilized by modern-day enzymes, these homogeneous amyloid nanotubes exploit Schiff imine formation via the exposed lysines to efficiently hydrolyze both activated and inactivated esters. Controls where lysines were mutated with charged residues accessed similar morphologies but did not augment the rate. The designed amyloid microphases thus foreshadow the generation of binding pockets of advanced proteins and have the potential to contribute to the development of functional materials.
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Affiliation(s)
- Baishakhi Sarkhel
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Ayan Chatterjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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38
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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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39
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Bomba R, Rout SK, Bütikofer M, Kwiatkowski W, Riek R, Greenwald J. Carbonyl Sulfide as a Prebiotic Activation Agent for Stereo- and Sequence-Selective, Amyloid-Templated Peptide Elongation. ORIGINS LIFE EVOL B 2019; 49:213-224. [PMID: 31845164 DOI: 10.1007/s11084-019-09586-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/26/2019] [Indexed: 01/28/2023]
Abstract
Prebiotic chemical replication is a commonly assumed precursor to and prerequisite for life and as such is the one of the goals of our research. We have previously reported on the role that short peptide amyloids could have played in a template-based chemical elongation. Here we take a step closer to the goal by reproducing amyloid-templated peptide elongation with carbonyl sulfide (COS) in place of the less-prebiotically relevant carbonyldiimidazole (CDI) used in the earlier study. Our investigation shows that the sequence-selectivity and stereoselectivity of the amyloid-templated reaction is similar for both activation chemistries. Notably, the amyloid protects the peptides from some of the side-reactions that take place with the COS-activation.
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Affiliation(s)
- Radoslaw Bomba
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Saroj K Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Matthias Bütikofer
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland.
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland.
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40
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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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41
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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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42
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Designed peptides that assemble into cross-α amyloid-like structures. Nat Chem Biol 2018; 14:870-875. [PMID: 30061717 DOI: 10.1038/s41589-018-0105-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 11/08/2022]
Abstract
Amyloids adopt 'cross-β' structures composed of long, twisted fibrils with β-strands running perpendicular to the fibril axis. Recently, a toxic peptide was proposed to form amyloid-like cross-α structures in solution, with a planar bilayer-like assembly observed in the crystal structure. Here we crystallographically characterize designed peptides that assemble into spiraling cross-α amyloid-like structures, which resemble twisted β-amyloid fibrils. The peptides form helical dimers, stabilized by packing of small and apolar residues, and the dimers further assemble into cross-α amyloid-like fibrils with superhelical pitches ranging from 170 Å to 200 Å. When a small residue that appeared critical for packing was converted to leucine, it resulted in structural rearrangement to a helical polymer. Fluorescently tagged versions of the designed peptides form puncta in mammalian cells, which recover from photobleaching with markedly different kinetics. These structural folds could be potentially useful for directing in vivo protein assemblies with predetermined spacing and stabilities.
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43
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Jaworek MW, Schuabb V, Winter R. Pressure and cosolvent modulation of the catalytic activity of amyloid fibrils. Chem Commun (Camb) 2018; 54:5696-5699. [PMID: 29691524 DOI: 10.1039/c8cc00699g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report on the effects of pressure and cosolvents on the catalytic activity of a designed amyloid fibril by applying a high-pressure stopped-flow methodology with rapid spectroscopic detection. FTIR spectroscopic data revealed a remarkable pressure and temperature stability of the fibrillar catalyst. The activity is further enhanced by osmolytes and macromolecular crowding.
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Affiliation(s)
- Michel W Jaworek
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
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44
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Greenwald J, Kwiatkowski W, Riek R. Peptide Amyloids in the Origin of Life. J Mol Biol 2018; 430:3735-3750. [PMID: 29890117 DOI: 10.1016/j.jmb.2018.05.046] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
How life can emerge from non-living matter is one of the fundamental mysteries of the universe. A bottom-up approach to this problem focuses on the potential chemical precursors of life, in particular the nature of the first replicative molecules. Such thinking has led to the currently most popular idea: that an RNA-like molecule played a central role as the first replicative and catalytic molecule. Here, we review an alternative hypothesis that has recently gained experimental support, focusing on the role of amyloidogenic peptides rather than nucleic acids, in what has been by some termed "the amyloid-world" hypothesis. Amyloids are well-ordered peptide aggregates that have a fibrillar morphology due to their underlying structure of a one-dimensional crystal-like array of peptides in a β-strand conformation. While they are notorious for their implication in several neurodegenerative diseases including Alzheimer's disease, amyloids also have many biological functions. In this review, we will elaborate on the following properties of amyloids in relation to their fitness as a prebiotic entity: they can be formed by very short peptides with simple amino acids sequences; as aggregates they are more chemically stable than their isolated component peptides; they can possess diverse catalytic activities; they can form spontaneously during the prebiotic condensation of amino acids; they can act as templates in their own chemical replication; they have a structurally repetitive nature that enables them to interact with other structurally repetitive biopolymers like RNA/DNA and polysaccharides, as well as with structurally repetitive surfaces like amphiphilic membranes and minerals.
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Affiliation(s)
- Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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45
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Vitas M, Dobovišek A. In the Beginning was a Mutualism - On the Origin of Translation. ORIGINS LIFE EVOL B 2018; 48:223-243. [PMID: 29713988 DOI: 10.1007/s11084-018-9557-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/23/2018] [Indexed: 12/28/2022]
Abstract
The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.
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Affiliation(s)
- Marko Vitas
- , Laze pri Borovnici 38, Borovnica, Slovenia.
| | - Andrej Dobovišek
- Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000, Maribor, Slovenia
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46
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Abstract
Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.
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Affiliation(s)
- O Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA.
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47
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A prebiotic template-directed peptide synthesis based on amyloids. Nat Commun 2018; 9:234. [PMID: 29339755 PMCID: PMC5770463 DOI: 10.1038/s41467-017-02742-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/21/2017] [Indexed: 11/24/2022] Open
Abstract
The prebiotic replication of information-coding molecules is a central problem concerning life’s origins. Here, we report that amyloids composed of short peptides can direct the sequence-selective, regioselective and stereoselective condensation of amino acids. The addition of activated DL-arginine and DL-phenylalanine to the peptide RFRFR-NH2 in the presence of the complementary template peptide Ac-FEFEFEFE-NH2 yields the isotactic product FRFRFRFR-NH2, 1 of 64 possible triple addition products, under conditions in which the absence of template yields only single and double additions of mixed stereochemistry. The templating mechanism appears to be general in that a different amyloid formed by (Orn)V(Orn)V(Orn)V(Orn)V-NH2 and Ac-VDVDVDVDV-NH2 is regioselective and stereoselective for N-terminal, L-amino-acid addition while the ornithine-valine peptide alone yields predominantly sidechain condensation products with little stereoselectivity. Furthermore, the templating reaction is stable over a wide range of pH (5.6–8.6), salt concentration (0–4 M NaCl), and temperature (25–90 °C), making the amyloid an attractive model for a prebiotic peptide replicating system. Amyloids may have played an important role in prebiotic molecular evolution but understanding replication of such information-coding molecules is still a problem. Here the authors design a model amyloid substrate and demonstrate sequence regio- and stereoselectivity during template-based replication.
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48
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Lengyel Z, Rufo CM, Moroz YS, Makhlynets OV, Korendovych IV. Copper-Containing Catalytic Amyloids Promote Phosphoester Hydrolysis and Tandem Reactions. ACS Catal 2018; 8:59-62. [PMID: 30319881 PMCID: PMC6181230 DOI: 10.1021/acscatal.7b03323] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Self-assembly of short de novo designed peptides gives rise to catalytic amyloids capable of facilitating multiple chemical transformations. We show that catalytic amyloids can efficiently hydrolyze paraoxon, a widely used, highly toxic organophosphate pesticide. Moreover, these robust and inexpensive metal-containing materials can be easily deposited on various surfaces producing catalytic flow devices. Finally, functional promiscuity of catalytic amyloids promotes tandem hydrolysis/oxidation reactions. High efficiency discovered in a very small library of peptides suggests an enormous potential for further improvement of catalytic properties both in terms of catalytic efficiency and substrate scope.
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Affiliation(s)
- Zsófia Lengyel
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244
| | - Caroline M. Rufo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244
| | | | - Olga V. Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244
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49
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Abstract
Aggregation of proteins into amyloids has long been recognized as one of the major contributors to disease and aging. Amyloids are known to catalyze their own formation but they have been considered the rock-bottom thermodynamic minimum of the protein fold without much functionality. We have recently demonstrated that aggregation of short peptides in the presence of metal ions gives rise to efficient catalytic activity. Here we present a detailed protocol for the synthesis and purification of these peptides and the preparation of amyloid-like fibrils. Then we describe an easy-to-perform, high-throughput assay to measure their hydrolytic activity.
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Affiliation(s)
- Zsofia Lengyel
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Caroline M Rufo
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
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50
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Taran O, Chen C, Omosun TO, Hsieh MC, Rha A, Goodwin JT, Mehta AK, Grover MA, Lynn DG. Expanding the informational chemistries of life: peptide/RNA networks. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0356. [PMID: 29133453 DOI: 10.1098/rsta.2016.0356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Olga Taran
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Chenrui Chen
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Ming-Chien Hsieh
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Allisandra Rha
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jay T Goodwin
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
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