1
|
Zhang W, Tian X, Li X. Fabrication of Nanocatalytic Medicine from Self-Assembling Peptides Containing an ATCUN-Like Copper-Binding Motif for Anticancer Therapy. Chembiochem 2024; 25:e202400216. [PMID: 38801354 DOI: 10.1002/cbic.202400216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/06/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
Development of nanomaterials with multiple enzymatic activities via a facile approach receives growing interests in recent years. Although peptide self-assembling provides an effective approach for the construction of biomimetic materials in recent years, fabrication of artificial enzymes from self-assembling peptides with multiple catalytic activities for anticancer therapy is still a challenge. Here, we report a simple method to prepare nanocatalysts with multienzyme-like activities from self-assembling peptides containing ATCUN copper-binding motifs. With the aid of the coordination interactions between the ATCUN motif and Cu(II) ions, these peptides could perform supramolecular self-assembly to form nanomaterials with biomimetic peroxidase, ascorbate oxidase and glutathione peroxidase activities. Moreover, these trienzyme-like effects can elevate oxidative stress levels and suppress the antioxidative capability of cancer cells, which synergistically induce the apoptosis of cancer cells. Because of the high biocompatibility, catalytic activities and drug encapsulation properties, this self-assembled peptide provides a biomimetic platform for the development of new nanocatalytic medicines for multimodal synergistic cancer therapies.
Collapse
Affiliation(s)
- Wenhui Zhang
- College of chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Xin Tian
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou, 215123, China
| | - Xinming Li
- College of chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| |
Collapse
|
2
|
Pirovano V, Brini P, Brambilla E, Gelmi ML, Romanelli A. Au(I) complexes installed on a self-assembled peptide efficiently catalyze intramolecular cyclization reactions. J Pept Sci 2024:e3630. [PMID: 38943521 DOI: 10.1002/psc.3630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 07/01/2024]
Abstract
Self-assembled peptides are used for diverse applications in the biomedical and technological fields. The morphology and function of the assembled systems are dictated by the peptide sequence and length. In this work, a supramolecular catalyst was obtained upon self-assembly of the diphenylalanine peptide conjugated to a triphenylphosphine Au(I) complex in acetonitrile. The assembled molecules were characterized by spectroscopic techniques and by scanning electron microscopy. The activity of the catalyst was tested on two substrates in cyclization reactions. The morphology and the dimensions of the assembled systems vary depending on the presence of a carboxyl versus an amide C-terminal end. The catalyst efficiently promotes intramolecular cyclization reactions. Results obtained encourage the use of self-assembled peptides for the obtainment of new and efficient catalysts.
Collapse
Affiliation(s)
- Valentina Pirovano
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Patrizia Brini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Elisa Brambilla
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Maria Luisa Gelmi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
3
|
Samrout OE, Berlier G, Lambert JF. Amino Acid Polymerization on Silica Surfaces. Chempluschem 2024; 89:e202300642. [PMID: 38226922 DOI: 10.1002/cplu.202300642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.
Collapse
Affiliation(s)
- Ola El Samrout
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Gloria Berlier
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, LRS, Sorbonne Université Place Jussieu, 75005, Paris, France
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Yang Q, Miki T. Characterization of peptide-fused protein assemblies in living cells. Methods Enzymol 2024; 697:293-319. [PMID: 38816127 DOI: 10.1016/bs.mie.2024.01.022] [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
Assembly of de novo peptides designed from scratch is in a semi-rational manner and creates artificial supramolecular structures with unique properties. Considering that the functions of various proteins in living cells are highly regulated by their assemblies, building artificial assemblies within cells holds the potential to simulate the functions of natural protein assemblies and engineer cellular activities for controlled manipulation. How can we evaluate the self-assembly of designed peptides in cells? The most effective approach involves the genetic fusion of fluorescent proteins (FPs). Expressing a self-assembling peptide fused with an FP within cells allows for evaluating assemblies through fluorescence signal. When µm-scale assemblies such as condensates are formed, the peptide assemblies can be directly observed by imaging. For sub-µm-scale assemblies, fluorescence correlation spectroscopy analysis is more practical. Additionally, the fluorescence resonance energy transfer (FRET) signal between FPs is valuable evidence of proximity. The decrease in fluorescence anisotropy associated with homo-FRET reveals the properties of self-assembly. Furthermore, by combining two FPs, one acting as a donor and the other as an acceptor, the heteromeric interaction between two different components can be studied through the FRET signal. In this chapter, we provide detailed protocols, from designing and constructing plasmid DNA expressing the peptide-fused protein to analysis of self-assembly in living cells.
Collapse
Affiliation(s)
- Qinxuan Yang
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Takayuki Miki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
| |
Collapse
|
6
|
Pham TL, Thomas F. Design of Functional Globular β-Sheet Miniproteins. Chembiochem 2024; 25:e202300745. [PMID: 38275210 DOI: 10.1002/cbic.202300745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
Collapse
Affiliation(s)
- Truc Lam Pham
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Marshall LR, Korendovych IV. Screening of oxidative behavior in catalytic amyloid assemblies. Methods Enzymol 2024; 697:15-33. [PMID: 38816121 DOI: 10.1016/bs.mie.2024.01.020] [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
Once considered a thermodynamic minimum of the protein fold or as simply by-products of a misfolding process, amyloids are increasingly showing remarkable potential for promoting enzyme-like catalysis. Recent studies have demonstrated a diverse range of catalytic behaviors that amyloids can promote way beyond the hydrolytic behaviors originally reported. We and others have demonstrated the strong propensity of catalytic amyloids to facilitate redox reactions both in the presence and in the absence of metal cofactors. Here, we present a detailed protocol for measuring the oxidative ability of supramolecular peptide assemblies.
Collapse
Affiliation(s)
- Liam R Marshall
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States.
| | - Ivan V Korendovych
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| |
Collapse
|
9
|
Yang Y, Wang X, Dong H. Simulating chemical reactions promoted by self-assembled peptides with catalytic properties. Methods Enzymol 2024; 697:321-343. [PMID: 38816128 DOI: 10.1016/bs.mie.2024.03.001] [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
Peptides that self-assemble exhibit distinct three-dimensional structures and attributes, positioning them as promising candidates for biocatalysts. Exploring their catalytic processes enhances our comprehension of the catalytic actions inherent to self-assembling peptides, laying a theoretical foundation for creating novel biocatalysts. The investigation into the intricate reaction mechanisms of these entities is rendered challenging due to the vast variability in peptide sequences, their aggregated formations, supportive elements, structures of active sites, types of catalytic reactions, and the interplay between these variables. This complexity hampers the elucidation of the linkage between sequence, structure, and catalytic efficiency in self-assembling peptide catalysts. This chapter delves into the latest progress in understanding the mechanisms behind peptide self-assembly, serving as a catalyst in hydrolysis and oxidation reactions, and employing computational analyses. It discusses the establishment of models, selection of computational strategies, and analysis of computational procedures, emphasizing the application of modeling techniques in probing the catalytic mechanisms of peptide self-assemblies. It also looks ahead to the potential future trajectories within this research domain. Despite facing numerous obstacles, a thorough investigation into the structural and catalytic mechanisms of peptide self-assemblies, combined with the ongoing advancement in computational simulations and experimental methodologies, is set to offer valuable theoretical insights for the development of new biocatalysts, thereby significantly advancing the biocatalysis field.
Collapse
Affiliation(s)
- Yuqin Yang
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China
| | - Xiaoyu Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China; State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute for Brain Sciences, Nanjing University, Nanjing, P.R. China.
| |
Collapse
|
10
|
Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Role of Post-Transcriptional Regulation in Learning and Memory in Mammals. Genes (Basel) 2024; 15:337. [PMID: 38540396 PMCID: PMC10970538 DOI: 10.3390/genes15030337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024] Open
Abstract
After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is of the most importance in the brain, where all the steps of mRNA maturation, transport to different regions of the cells and actual expression, in response to specific signals, constitute the molecular basis for neuronal plasticity and, as a consequence, for structural stabilization/modification of synapses; notably, these latter events are fundamental for the highest brain functions, such as learning and memory, and are characterized by long-term potentiation (LTP) of specific synapses. Here, we will discuss the molecular bases of these fundamental events by considering both the role of RNA-binding proteins (RBPs) and the effects of non-coding RNAs involved in controlling splicing, editing, stability and translation of mRNAs. Importantly, it has also been found that dysregulation of mRNA metabolism/localization is involved in many pathological conditions, arising either during brain development or in the adult nervous system.
Collapse
Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
- Neurology and Multiple Sclerosis Center, Unità Operativa Complessa (UOC), Foundation Institute “G. Giglio”, 90015 Cefalù, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
| |
Collapse
|
11
|
Chen J, Shi K, Chen R, Zhai Z, Song P, Chow LW, Chandrawati R, Pashuck ET, Jiao F, Lin Y. Supramolecular Hydrolase Mimics in Equilibrium and Kinetically Trapped States. Angew Chem Int Ed Engl 2024; 63:e202317887. [PMID: 38161176 DOI: 10.1002/anie.202317887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
The folding of proteins into intricate three-dimensional structures to achieve biological functions, such as catalysis, is governed by both kinetic and thermodynamic controls. The quest to design artificial enzymes using minimalist peptides seeks to emulate supramolecular structures existing in a catalytically active state. Drawing inspiration from the nuanced process of protein folding, our study explores the enzyme-like activity of amphiphilic peptide nanosystems in both equilibrium and non-equilibrium states, featuring the formation of supramolecular nanofibrils and nanosheets. In contrast to thermodynamically stable nanosheets, the kinetically trapped nanofibrils exhibit dynamic characteristics (e.g., rapid molecular exchange and relatively weak intermolecular packing), resulting in a higher hydrolase-mimicking activity. We emphasize that a supramolecular microenvironment characterized by an optimal local polarity, microviscosity, and β-sheet hydrogen bonding is conducive to both substrate binding and ester bond hydrolysis. Our work underscores the pivotal role of both thermodynamic and kinetic control in impacting biomimetic catalysis and sheds a light on the development of artificial enzymes.
Collapse
Affiliation(s)
- Jing Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ke Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Rongjing Chen
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoyi Zhai
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peiyong Song
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lesley W Chow
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
- Department of Materials Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Rona Chandrawati
- School of Chemical Engineering, Australian Centre for Nanomedicine (ACN), The University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - E Thomas Pashuck
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Fang Jiao
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiyang Lin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing, 100029, China
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Chen T, Lu Y, Xiong X, Qiu M, Peng Y, Xu Z. Hydrolytic nanozymes: Preparation, properties, and applications. Adv Colloid Interface Sci 2024; 323:103072. [PMID: 38159448 DOI: 10.1016/j.cis.2023.103072] [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: 09/19/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Hydrolytic nanozymes, as promising alternatives to hydrolytic enzymes, can efficiently catalyze the hydrolysis reactions and overcome the operating window limitations of natural enzymes. Moreover, they exhibit several merits such as relatively low cost, easier recovery and reuse, improved operating stability, and adjustable catalytic properties. Consequently, they have found relevance in practical applications such as organic synthesis, chemical weapon degradation, and biosensing. In this review, we highlight recent works addressing the broad topic of the development of hydrolytic nanozymes. We review the preparation, properties, and applications of six types of hydrolytic nanozymes, including AuNP-based nanozymes, polymeric nanozymes, surfactant assemblies, peptide assemblies, metal and metal oxide nanoparticles, and MOFs. Last, we discuss the remaining challenges and future directions. This review will stimulate the development and application of hydrolytic nanozymes.
Collapse
Affiliation(s)
- Tianyou Chen
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China.
| | - Yizhuo Lu
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Xiaorong Xiong
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Meishuang Qiu
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Yan Peng
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Zushun Xu
- Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China.
| |
Collapse
|
15
|
Le NTK, Kang EJ, Park JH, Kang K. Catechol-Amyloid Interactions. Chembiochem 2023; 24:e202300628. [PMID: 37850717 DOI: 10.1002/cbic.202300628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/19/2023]
Abstract
This review introduces multifaceted mutual interactions between molecules containing a catechol moiety and aggregation-prone proteins. The complex relationships between these two molecular species have previously been elucidated primarily in a unidirectional manner, as demonstrated in cases involving the development of catechol-based inhibitors for amyloid aggregation and the elucidation of the role of functional amyloid fibers in melanin biosynthesis. This review aims to consolidate scattered clues pertaining to catechol-based amyloid inhibitors, functional amyloid scaffold of melanin biosynthesis, and chemically designed peptide fibers for providing chemical insights into the role of the local three-dimensional orientation of functional groups in manifesting such interactions. These orientations may play crucial, yet undiscovered, roles in various supramolecular structures.
Collapse
Affiliation(s)
- Nghia T K Le
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| | - Eun Joo Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| | - Ji Hun Park
- Department of Science Education, Ewha Womans University, Seoul, 03760, South Korea
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| |
Collapse
|
16
|
Arad E, Pedersen KB, Malka O, Mambram Kunnath S, Golan N, Aibinder P, Schiøtt B, Rapaport H, Landau M, Jelinek R. Staphylococcus aureus functional amyloids catalyze degradation of β-lactam antibiotics. Nat Commun 2023; 14:8198. [PMID: 38081813 PMCID: PMC10713593 DOI: 10.1038/s41467-023-43624-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Antibiotic resistance of bacteria is considered one of the most alarming developments in modern medicine. While varied pathways for bacteria acquiring antibiotic resistance have been identified, there still are open questions concerning the mechanisms underlying resistance. Here, we show that alpha phenol-soluble modulins (PSMαs), functional bacterial amyloids secreted by Staphylococcus aureus, catalyze hydrolysis of β-lactams, a prominent class of antibiotic compounds. Specifically, we show that PSMα2 and, particularly, PSMα3 catalyze hydrolysis of the amide-like bond of the four membered β-lactam ring of nitrocefin, an antibiotic β-lactam surrogate. Examination of the catalytic activities of several PSMα3 variants allowed mapping of the active sites on the amyloid fibrils' surface, specifically underscoring the key roles of the cross-α fibril organization, and the combined electrostatic and nucleophilic functions of the lysine arrays. Molecular dynamics simulations further illuminate the structural features of β-lactam association upon the fibril surface. Complementary experimental data underscore the generality of the functional amyloid-mediated catalytic phenomenon, demonstrating hydrolysis of clinically employed β-lactams by PSMα3 fibrils, and illustrating antibiotic degradation in actual S. aureus biofilms and live bacteria environments. Overall, this study unveils functional amyloids as catalytic agents inducing degradation of β-lactam antibiotics, underlying possible antibiotic resistance mechanisms associated with bacterial biofilms.
Collapse
Affiliation(s)
- Elad Arad
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Kasper B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Orit Malka
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Sisira Mambram Kunnath
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Nimrod Golan
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Polina Aibinder
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Hanna Rapaport
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
- Centre for Structural Systems Biology (CSSB), and European Molecular Biology Laboratory (EMBL), Hamburg, 22607, Germany
| | - Raz Jelinek
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
| |
Collapse
|
17
|
Sanchis I, Spinelli R, Siano A. Acetylcholine hydrolytic activity of fibrillated β-amyloid (1-40) peptide. Amino Acids 2023; 55:1991-1997. [PMID: 37904049 DOI: 10.1007/s00726-023-03349-3] [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: 06/27/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023]
Abstract
Alzheimer's disease is characterized by the presence of senile plaques composed of β-amyloid peptide (Aβ) aggregates with toxic effects that are still not fully understood. Recently, it was discovered that Aβ(1-42) fibrils possess catalytic activity on acetylcholine hydrolysis. Catalytic amyloids are an emerging and exciting field of research. In this study, we examined the catalytic activity of the fibrils formed by Aβ(1-40), the most abundant Aβ variant, on acetylcholine hydrolysis. Our findings reveal that Aβ(1-40) fibrils exhibit moderate enzymatic activity, indicating that natural peptide aggregates could serve as biocatalysts and provide new insights into the potential role of Aβ in neurological disorders.
Collapse
Affiliation(s)
- Ivan Sanchis
- Laboratory of Bioactive Peptides, Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- Ministry of Science, Technology and Innovation, National Scientific and Technical Research Council (CONICET), Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Roque Spinelli
- Laboratory of Bioactive Peptides, Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- Ministry of Science, Technology and Innovation, National Scientific and Technical Research Council (CONICET), Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Alvaro Siano
- Laboratory of Bioactive Peptides, Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina.
- Ministry of Science, Technology and Innovation, National Scientific and Technical Research Council (CONICET), Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina.
| |
Collapse
|
18
|
Edri R, Fisher S, Menor-Salvan C, Williams LD, Frenkel-Pinter M. Assembly-driven protection from hydrolysis as key selective force during chemical evolution. FEBS Lett 2023; 597:2879-2896. [PMID: 37884438 DOI: 10.1002/1873-3468.14766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.
Collapse
Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Sarah Fisher
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Cesar Menor-Salvan
- Department of Biología de Sistemas, Universidad de Alcalá, Madrid, Spain
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| |
Collapse
|
19
|
Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
Collapse
Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| |
Collapse
|
20
|
Wang X, Li Y, Nie J, Wen G, Li W. Modular co-assembly of peptides and polyoxometalates into underwater adhesives with photoluminescence and adjustable adhesion. SOFT MATTER 2023; 19:8659-8667. [PMID: 37927210 DOI: 10.1039/d3sm01151h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Supramolecular polymerization between cationic peptides and anionic polyoxometalates has emerged as a promising strategy for the creation of peptide-based biomimetic underwater adhesives. However, the extremely rigorous requirements for peptide design are an important obstacle to the fabrication of available peptide adhesives with controlled adhesion and versatile functionality. Inspired by marine sessile organisms in nature, here we reported a modular co-assembly method to easily produce peptide/polyoxometalate underwater adhesive materials through mixing two complementary cationic peptides (Pep1 and Pep2) with a single anionic polyoxometalate K6H[SiW9V3O40] in aqueous solution, which are not possible to be obtained from an individual peptide module. We demonstrated that the relatively hydrophobic Pep1 contributes to the bulk cohesion of the resulting adhesive, while the relatively hydrophilic Pep2 not only enables the interfacial adhesion but also regulates the bulk cohesion of the Pep1/Pep2/SiW9V3 adhesive. Rheological and shear adhesion tests showed that the macroscopic adhesion performance of the resulting adhesive materials could be conveniently adjusted by simply changing the molar ratio of the complementary peptide modules without any complicated peptide design. Interestingly, the luminescence properties of K11[Eu(PW11O39)2] (labelled as EuPW11) could be maintained within the Pep1/Pep2/EuPW11 adhesive even in a water environment. The lifetime of the Pep1/Pep2/EuPW11 adhesive was 2.19 ms. The fluorescence quantum yield of the Pep1/Pep2/EuPW11 adhesive was measured to be 27.46%. This study unveils that the modular co-assembly method can effectively simplify the material design of peptide/polyoxometalate underwater adhesives, which will significantly broaden the horizon of material pools and extend their availability space.
Collapse
Affiliation(s)
- Xinyan Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Yiwen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Junlian Nie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Guang Wen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| |
Collapse
|
21
|
Song Q, Cheng Z, Perrier S. Supramolecular peptide nanotubes as artificial enzymes for catalysing ester hydrolysis. Polym Chem 2023; 14:4712-4718. [PMID: 38013987 PMCID: PMC10594401 DOI: 10.1039/d3py00993a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 11/29/2023]
Abstract
Peptide-based artificial enzymes are attracting significant interest because of their remarkable resemblance in both composition and structure to native enzymes. Herein, we report the construction of histidine-containing cyclic peptide-based supramolecular polymeric nanotubes to function as artificial enzymes for ester hydrolysis. The optimized catalyst shows a ca. 70-fold increase in reaction rate compared to the un-catalysed reaction when using 4-nitrophenyl acetate as a model substrate. Furthermore, the amphiphilic nature of the supramolecular catalysts enables an enhanced catalytic activity towards hydrophobic substrates. By incorporating an internal hydrophobic region within the self-assembled polymeric nanotube, we achieve a 55.4-fold acceleration in hydrolysis rate towards a more hydrophobic substrate, 4-nitrophenyl butyrate. This study introduces supramolecular peptide nanotubes as an innovative class of supramolecular scaffolds for fabricating artificial enzymes with better structural and chemical stability, catalysing not only ester hydrolysis, but also a broader spectrum of catalytic reactions.
Collapse
Affiliation(s)
- Qiao Song
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
- Shenzhen Grubbs Institute, Southern University of Science and Technology Shenzhen 518055 China
| | - Zihe Cheng
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Sébastien Perrier
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
- Warwick Medical School, University of Warwick Coventry CV4 7AL UK
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| |
Collapse
|
22
|
Vicente-Garcia C, Colomer I. Lipopeptides as tools in catalysis, supramolecular, materials and medicinal chemistry. Nat Rev Chem 2023; 7:710-731. [PMID: 37726383 DOI: 10.1038/s41570-023-00532-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/21/2023]
Abstract
Lipopeptides are amphiphilic peptides in which an aliphatic chain is attached to either the C or N terminus of peptides. Their self-assembly - into micelles, vesicles, nanotubes, fibres or nanobelts - leads to applications in nanotechnology, catalysis or medicinal chemistry. Self-organization of lipopeptides is dependent on both the length of the lipid tail and the amino acid sequence, in which the chirality of the peptide sequence can be transmitted into the supramolecular species. This Review describes the use of lipopeptides to design synthetic advanced dynamic supramolecular systems, nanostructured materials or self-responsive delivery systems in the area of medical biotechnology. We examine the influence of external stimuli, the ability of lipopeptide-derived structures to adapt over time and their application as medicinal agents with antibacterial, antifungal, antiviral or anticancer activities. Finally, we discuss the catalytic efficiency of lipopeptides, with the aim of building minimal synthetic enzymes, and recent efforts to incorporate metals into lipopeptide assemblies.
Collapse
Affiliation(s)
| | - Ignacio Colomer
- IMDEA-Nanociencia, Madrid, Spain.
- Instituto de Química Orgánica General (IQOG-CSIC), Madrid, Spain.
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Parra RD. Hydrogen-Bond-Driven Peptide Nanotube Formation: A DFT Study. Molecules 2023; 28:6217. [PMID: 37687047 PMCID: PMC10488343 DOI: 10.3390/molecules28176217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
DFT calculations were carried out to examine geometries and binding energies of H-bond-driven peptide nanotubes. A bolaamphiphile molecule, consisting of two N-α amido glycylglycine head groups linked by either one CH2 group or seven CH2 groups, is used as a building block for nanotube self-assembly. In addition to hydrogen bonds between adjacent carboxy or amide groups, nanotube formation is also driven by weak C-H· · ·O hydrogen bonds between a methylene group and the carboxy OH group, and between a methylene group and an amide O=C group. The intratubular O-H· · ·O=C hydrogen bonds account for approximately a third of the binding energies. Binding energies calculated with the wB97XD/DGDZVP method show that the hydrocarbon chains play a stabilizing role in nanotube self-assembly. The shortest nanotube has the length of a single monomer and a diameter than increases with the number of monomers. Lengthening of the tubular structure occurs through intertubular O-H· · ·O=C hydrogen bonds. The average intertubular O-H· · ·O=C hydrogen bond binding energy is estimated to change with the size of the nanotubes, decreasing slightly towards some plateau value near 15 kcal/mol according to the wB97XD/DGDZVP method.
Collapse
Affiliation(s)
- Rubén D Parra
- Department of Chemistry and Biochemistry, DePaul University, Chicago, IL 60614, USA
| |
Collapse
|
25
|
Alletto P, Garcia AM, Marchesan S. Short Peptides for Hydrolase Supramolecular Mimicry and Their Potential Applications. Gels 2023; 9:678. [PMID: 37754360 PMCID: PMC10529927 DOI: 10.3390/gels9090678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023] Open
Abstract
Hydrolases are enzymes that have found numerous applications in various industrial sectors spanning from pharmaceuticals to foodstuff and beverages, consumers' products such as detergents and personal care, textiles, and even for biodiesel production and environmental bioremediation. Self-assembling and gelling short peptides have been designed for their mimicry so that their supramolecular organization leads to the creation of hydrophobic pockets for catalysis to occur. Catalytic gels of this kind can also find numerous industrial applications to address important global challenges of our time. This concise review focuses on the last 5 years of progress in this fast-paced, popular field of research with an eye towards the future.
Collapse
Affiliation(s)
- Paola Alletto
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
- Instituto Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
- Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Ana Maria Garcia
- Instituto Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
- Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| |
Collapse
|
26
|
Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
Collapse
Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
| |
Collapse
|
27
|
Parkman JA, Barlow CD, Sheppert AP, Jacobsen S, Barksdale CA, Wayment AX, Newton MP, Burt SR, Michaelis DJ. Structural Analysis of Non-native Peptide-Based Catalysts Using 2D NMR-Guided MD Simulations. J Phys Chem A 2023; 127:5602-5608. [PMID: 37347770 PMCID: PMC10722561 DOI: 10.1021/acs.jpca.3c03389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Proteins and enzymes generally achieve their functions by creating well-defined 3D architectures that pre-organize reactive functionalities. Mimicking this approach to supramolecular pre-organization is leading to the development of highly versatile artificial chemical environments, including new biomaterials, medicines, artificial enzymes, and enzyme-like catalysts. The use of β-turn and α-helical motifs is one approach that enables the precise placement of reactive functional groups to enable selective substrate activation and reactivity/selectivity that approaches natural enzymes. Our recent work has demonstrated that helical peptides can serve as scaffolds for pre-organizing two reactive groups to achieve enzyme-like catalysis. In this study, we used CYANA and AmberTools to develop a computational approach for determining how the structure of our peptide catalysts can lead to enhancements in reactivity. These results support our hypothesis that the bifunctional nature of the peptide enables catalysis by pre-organizing the two catalysts in reactive conformations that accelerate catalysis by proximity. We also present evidence that the low reactivity of monofunctional peptides can be attributed to interactions between the peptide-bound catalyst and the helical backbone, which are not observed in the bifunctional peptide.
Collapse
Affiliation(s)
- Jacob A Parkman
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Connor D Barlow
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Alexander P Sheppert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Steven Jacobsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Caleb A Barksdale
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Adam X Wayment
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Madison P Newton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Scott R Burt
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - David J Michaelis
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| |
Collapse
|
28
|
Hou Y, Xu X, Kong X. K +-Selectivity Due to Coordination with a D4d-Symmetric Homochiral Proline Octamer Verified by Mass Spectrometry and Infrared Photodissociation Spectroscopy. J Phys Chem Lett 2023; 14:2660-2664. [PMID: 36892259 DOI: 10.1021/acs.jpclett.2c03838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Both phenomena of homochirality and sodium-potassium ion selectivity in cells have been regarded as important issues in the process of the origin of life. However, whether K+/Na+ selectivity was involved in homochirogenesis has never been considered. Herein, we report that a homochiral proline octamer shows high K+-selectivity. Coordination of K+ results in formation of a stable, noncovalent, D4d-symmetric complex, as demonstrated by mass spectrometry, infrared photodissociation spectroscopy, and calculations. A cooperative relationship between an eight-coordinated metal cation and a homochirality-restricted topological hydrogen-bonded proline network is the key for the K+/Na+ selectivity. As the complex comprises merely the basic chiral amino acid, it provides a possible linkage between K+/Na+ selectivity and the origin of chirality on the prebiotic Earth.
Collapse
Affiliation(s)
- Yameng Hou
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xingshi Xu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| |
Collapse
|
29
|
Li Q, Wang Y, Zhang G, Su R, Qi W. Biomimetic mineralization based on self-assembling peptides. Chem Soc Rev 2023; 52:1549-1590. [PMID: 36602188 DOI: 10.1039/d2cs00725h] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.
Collapse
Affiliation(s)
- Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Gong Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou Industrial Park, Suzhou 215123, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| |
Collapse
|
30
|
Crone NSA, van Hilten N, van der Ham A, Risselada HJ, Kros A, Boyle AL. Azobenzene-Based Amino Acids for the Photocontrol of Coiled-Coil Peptides. Bioconjug Chem 2023; 34:345-357. [PMID: 36705971 PMCID: PMC9936496 DOI: 10.1021/acs.bioconjchem.2c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Coiled-coil peptides are high-affinity, selective, self-assembling binding motifs, making them attractive components for the preparation of functional biomaterials. Photocontrol of coiled-coil self-assembly allows for the precise localization of their activity. To rationally explore photoactivity in a model coiled coil, three azobenzene-containing amino acids were prepared and substituted into the hydrophobic core of the E3/K3 coiled-coil heterodimer. Two of the non-natural amino acids, APhe1 and APhe2, are based on phenylalanine and differ in the presence of a carboxylic acid group. These have previously been demonstrated to modulate protein activity. When incorporated into peptide K3, coiled-coil binding strength was affected upon isomerization, with the two variants differing in their most folded state. The third azobenzene-containing amino acid, APgly, is based on phenylglycine and was prepared to investigate the effect of amino acid size on photoisomerization. When APgly is incorporated into the coiled coil, a 4.7-fold decrease in folding constant is observed upon trans-to-cis isomerization─the largest difference for all three amino acids. Omitting the methylene group between azobenzene and α-carbon was theorized to both position the diazene of APgly closer to the hydrophobic amino acids and reduce the possible rotations of the amino acid, with molecular dynamics simulations supporting these hypotheses. These results demonstrate the ability of photoswitchable amino acids to control coiled-coil assembly through disruption of the hydrophobic interface, a strategy that should be widely applicable.
Collapse
Affiliation(s)
- Niek S A Crone
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Alex van der Ham
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Alexander Kros
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| |
Collapse
|
31
|
Huo Y, Hu J, Yin Y, Liu P, Cai K, Ji W. Self-Assembling Peptide-Based Functional Biomaterials. Chembiochem 2023; 24:e202200582. [PMID: 36346708 DOI: 10.1002/cbic.202200582] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Peptides can self-assemble into various hierarchical nanostructures through noncovalent interactions and form functional materials exhibiting excellent chemical and physical properties, which have broad applications in bio-/nanotechnology. The self-assembly mechanism, self-assembly morphology of peptide supramolecular architecture and their various applications, have been widely explored which have the merit of biocompatibility, easy preparation, and controllable functionality. Herein, we introduce the latest research progress of self-assembling peptide-based nanomaterials and review their applications in biomedicine and optoelectronics, including tissue engineering, anticancer therapy, biomimetic catalysis, energy harvesting. We believe that this review will inspire the rational design and development of novel peptide-based functional bio-inspired materials in the future.
Collapse
Affiliation(s)
- Yehong Huo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Jian Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Yuanyuan Yin
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital of Chongqing Medical University, Chongqing, 401147, P. R. China
| | - Peng Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Wei Ji
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| |
Collapse
|
32
|
Jeong S, Lee K, Yoo SH, Lee HS, Kwon S. Crystalline Metal-Peptide Networks: Structures, Applications, and Future Outlook. Chembiochem 2023; 24:e202200448. [PMID: 36161687 DOI: 10.1002/cbic.202200448] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/23/2022] [Indexed: 01/20/2023]
Abstract
Metal-peptide networks (MPNs), which are assembled from short peptides and metal ions, are considered one of the most fascinating metal-organic coordinated architectures because of their unique and complicated structures. Although MPNs have considerable potential for development into versatile materials, they have not been developed for practical applications because of several underlying limitations, such as designability, stability, and modifiability. In this review, we summarise several important milestones in the development of crystalline MPNs and thoroughly analyse their structural features, such as peptide sequence designs, coordination geometries, cross-linking types, and network topologies. In addition, potential applications such as gas adsorption, guest encapsulation, and chiral recognition are introduced. We believe that this review is a useful survey that can provide insights into the development of new MPNs with more sophisticated structures and novel functions.
Collapse
Affiliation(s)
- Seoneun Jeong
- Center for Multiscale Chiral Architectures, Department of Chemistry, KAIST 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Kwonjung Lee
- Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Korea
| | - Sung Hyun Yoo
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Hee-Seung Lee
- Center for Multiscale Chiral Architectures, Department of Chemistry, KAIST 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Sunbum Kwon
- Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Korea
| |
Collapse
|
33
|
El Samrout O, Berlier G, Lambert JF, Martra G. Polypeptide Chain Growth Mechanisms and Secondary Structure Formation in Glycine Gas-Phase Deposition on Silica Surfaces. J Phys Chem B 2023; 127:673-684. [PMID: 36637235 PMCID: PMC9884078 DOI: 10.1021/acs.jpcb.2c07382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Peptide formation by amino acids condensation represents a crucial reaction in the quest of the origins of life as well as in synthetic chemistry. However, it is still poorly understood in terms of efficiency and reaction mechanism. In the present work, peptide formation has been investigated through thermal condensation of gas-phase glycine in fluctuating silica environments as a model of prebiotic environments. In-situ IR spectroscopy measurements under a controlled atmosphere reveal that a humidity fluctuating system subjected to both temperature and water activity variations results in the formation of more abundant peptides compared to a dehydrated system subjected only to temperature fluctuations cycles. A model is proposed in which hydration steps result in the hydrolysis and redistribution of the oligomers formed during previous deposition in dry conditions. This results in the formation of self-assembled aggregates with well-defined secondary structures (especially β-sheets). Upon further monomers feeding, structural elements are conserved in newly growing chains, with indications of templated polymerization. The structural dynamics of peptides were also evaluated. Rigid self-assembled structures with a high resistance to further wetting/drying cycles and inaccessibility to isotopic exchange were present in the humidity fluctuating system compared to more flexible structures in the dehydrated system. The resistance and growth of self-assembled structures were also investigated for an extended duration of Gly deposition using isotope labeling.
Collapse
Affiliation(s)
- Ola El Samrout
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy,Laboratoire
de Réactivité de Surface, LRS (UMR 7197 CNRS), Sorbonne Université, Place Jussieu, 75005Paris, France
| | - Gloria Berlier
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy,
| | - Jean-François Lambert
- Laboratoire
de Réactivité de Surface, LRS (UMR 7197 CNRS), Sorbonne Université, Place Jussieu, 75005Paris, France,
| | - Gianmario Martra
- Department
of Chemistry and NIS Centre, University
of Torino, Via P. Giuria 7, 10125Torino, Italy
| |
Collapse
|
34
|
Mkrtchyan S, Shkoor M, Phanindrudu M, Medved′ M, Sevastyanova O, Iaroshenko VO. Mechanochemical Defluorinative Arylation of Trifluoroacetamides: An Entry to Aromatic Amides. J Org Chem 2023; 88:863-870. [PMID: 36622848 PMCID: PMC9872087 DOI: 10.1021/acs.joc.2c02197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The amide bond is prominent in natural and synthetic organic molecules endowed with activity in various fields. Among a wide array of amide synthetic methods, substitution on a pre-existing (O)C-N moiety is an underexplored strategy for the synthesis of amides. In this work, we disclose a new protocol for the defluorinative arylation of aliphatic and aromatic trifluoroacetamides yielding aromatic amides. The mechanochemically induced reaction of either arylboronic acids, trimethoxyphenylsilanes, diaryliodonium salts, or dimethyl(phenyl)sulfonium salts with trifluoroacetamides affords substituted aromatic amides in good to excellent yields. These nickel-catalyzed reactions are enabled by C-CF3 bond activation using Dy2O3 as an additive. The current protocol provides versatile and scalable routes for accessing a wide variety of substituted aromatic amides. Moreover, the protocol described in this work overcomes the drawbacks and limitations in the previously reported methods.
Collapse
Affiliation(s)
- Satenik Mkrtchyan
- Department
of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, 97401 Banská Bystrica, Slovakia,
| | - Mohanad Shkoor
- Department
of Chemistry and Earth Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mandalaparthi Phanindrudu
- Inorganic
and Physical Chemistry Division, CSIR-Indian
Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500607, India
| | - Miroslav Medved′
- Department
of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, 97401 Banská Bystrica, Slovakia,Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacky University
Olomouc, Křížkovského 511/8, 77900 Olomouc, Czech Republic
| | - Olena Sevastyanova
- Wallenberg
Wood Science Center, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-10044 Stockholm, Sweden,Division
of Wood Chemistry and Pulp Technology, Department of Fiber and Polymer
Technology, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden
| | - Viktor O. Iaroshenko
- Department
of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, 97401 Banská Bystrica, Slovakia,Wallenberg
Wood Science Center, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-10044 Stockholm, Sweden,Division
of Wood Chemistry and Pulp Technology, Department of Fiber and Polymer
Technology, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden,Department
of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, 00014 Helsinki, Finland,Department
of Biology/Chemistry, Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Barbarastr. 7, D-49076 Osnabrück, Germany,; ; ;
| |
Collapse
|
35
|
Babić M, Janković P, Marchesan S, Mauša G, Kalafatovic D. Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs. J Chem Inf Model 2022; 62:6398-6410. [PMID: 36223497 DOI: 10.1021/acs.jcim.2c00977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ester hydrolysis is of wide biomedical interest, spanning from the green synthesis of pharmaceuticals to biomaterials' development. Existing peptide-based catalysts exhibit low catalytic efficiency compared to natural enzymes, due to the conformational heterogeneity of peptides. Moreover, there is lack of understanding of the correlation between the primary sequence and catalytic function. For this purpose, we statistically analyzed 22 EC 3.1 hydrolases with known catalytic triads, characterized by unique and well-defined mechanisms. The aim was to identify patterns at the sequence level that will better inform the creation of short peptides containing important information for catalysis, based on the catalytic triad, oxyanion holes and the triad residues microenvironments. Moreover, fragmentation schemes of the primary sequence of selected enzymes alongside the study of their amino acid frequencies, composition, and physicochemical properties are proposed. The results showed highly conserved catalytic sites with distinct positional patterns and chemical microenvironments that favor catalysis and revealed variations in catalytic site composition that could be useful for the design of minimalistic catalysts.
Collapse
Affiliation(s)
- Marko Babić
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia
| | - Patrizia Janković
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127Trieste, Italy
| | - Goran Mauša
- Faculty of Engineering, University of Rijeka, 51000Rijeka, Croatia
| | - Daniela Kalafatovic
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia.,Center for Advanced Computing and Modeling, University of Rijeka, 51000Rijeka, Croatia
| |
Collapse
|
36
|
Abstract
Natural enzymes catalyze biochemical transformations in superior catalytic efficiency and remarkable substrate specificity. The excellent catalytic repertoire of enzymes is attributed to the sophisticated chemical structures of their active sites, as a result of billions-of-years natural evolution. However, large-scale practical applications of natural enzymes are restricted due to their poor stability, difficulty in modification, and high costs of production. One viable solution is to fabricate supramolecular catalysts with enzyme-mimetic active sites. In this review, we introduce the principles and strategies of designing peptide-based artificial enzymes which display catalytic activities similar to those of natural enzymes, such as aldolases, laccases, peroxidases, and hydrolases (mainly the esterases and phosphatases). We also discuss some multifunctional enzyme-mimicking systems which are capable of catalyzing orthogonal or cascade reactions. We highlight the relationship between structures of enzyme-like active sites and the catalytic properties, as well as the significance of these studies from an evolutionary point of view.
Collapse
|
37
|
Hierarchical metal-peptide assemblies with chirality-encoded spiral architecture and catalytic activity. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1351-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
38
|
Di Liegro CM, Schiera G, Schirò G, Di Liegro I. RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration. Int J Mol Sci 2022; 23:ijms232314622. [PMID: 36498959 PMCID: PMC9739182 DOI: 10.3390/ijms232314622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
A central aspect of nervous system development and function is the post-transcriptional regulation of mRNA fate, which implies time- and site-dependent translation, in response to cues originating from cell-to-cell crosstalk. Such events are fundamental for the establishment of brain cell asymmetry, as well as of long-lasting modifications of synapses (long-term potentiation: LTP), responsible for learning, memory, and higher cognitive functions. Post-transcriptional regulation is in turn dependent on RNA-binding proteins that, by recognizing and binding brief RNA sequences, base modifications, or secondary/tertiary structures, are able to control maturation, localization, stability, and translation of the transcripts. Notably, most RBPs contain intrinsically disordered regions (IDRs) that are thought to be involved in the formation of membrane-less structures, probably due to liquid-liquid phase separation (LLPS). Such structures are evidenced as a variety of granules that contain proteins and different classes of RNAs. The other side of the peculiar properties of IDRs is, however, that, under altered cellular conditions, they are also prone to form aggregates, as observed in neurodegeneration. Interestingly, RBPs, as part of both normal and aggregated complexes, are also able to enter extracellular vesicles (EVs), and in doing so, they can also reach cells other than those that produced them.
Collapse
Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
- Correspondence: ; Tel.: +39-091-238-97 (ext. 415/446)
| |
Collapse
|
39
|
Beasley MA, Dunkelberger AD, Thum MD, Ryland ES, Fears KP, Grafton AB, Owrutsky JC, Lundin JG, So CR. Extremophilic behavior of catalytic amyloids sustained by backbone structuring. J Mater Chem B 2022; 10:9400-9412. [PMID: 36285764 DOI: 10.1039/d2tb01605b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Enzyme function relies on the placement of chemistry defined by solvent and self-associative hydrogen bonding displayed by the protein backbone. Amyloids, long-range multi-peptide and -protein materials, can mimic enzyme functions while having a high proportion of stable self-associative backbone hydrogen bonds. Though catalytic amyloid structures have exhibited a degree of temperature and solvent stability, defining their full extremophilic properties and the molecular basis for such extreme activity has yet to be realized. Here we demonstrate that, like thermophilic enzymes, catalytic amyloid activity persists across high temperatures with an optimum activity at 81 °C where they are 30-fold more active than at room temperature. Unlike thermophilic enzymes, catalytic amyloids retain both activity and structure well above 100 °C as well as in the presence of co-solvents. Changes in backbone vibrational states are resolved in situ using non-linear 2D infrared spectroscopy (2DIR) to reveal that activity is sustained by reorganized backbone hydrogen bonds in extreme environments, evidenced by an emergent vibrational mode centered at 1612 cm-1. Restructuring also occurs in organic solvents, and facilitates complete retention of hydrolysis activity in co-solvents of lesser polarity. We support these findings with molecular modeling, where the displacement of water by co-solvents leads to shorter, less competitive, bonding lifetimes that further stabilize self-associative backbone interactions. Our work defines amyloid properties that counter classical proteins, where extreme environments induce mechanisms of restructuring to support enzyme-like functions necessary for synthetic applications.
Collapse
Affiliation(s)
- Maryssa A Beasley
- NRC Postdoctoral Associate Sited in Chemistry Division, Code 6176, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
| | - Adam D Dunkelberger
- Chemistry Division, Code 6121, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA
| | - Matthew D Thum
- ASEE Postdoctoral Associate Sited in Chemistry Division, Code 6124, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
| | - Elizabeth S Ryland
- NRC Postdoctoral Associate Sited in Chemistry Division, Code 6121, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
| | - Kenan P Fears
- Chemistry Division, Code 6176, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA.
| | - Andrea B Grafton
- NRC Postdoctoral Associate Sited in Chemistry Division, Code 6121, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
| | - Jeffrey C Owrutsky
- Chemistry Division, Code 6121, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA
| | - Jeffrey G Lundin
- Chemistry Division, Code 6124, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA
| | - Christopher R So
- Chemistry Division, Code 6176, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA.
| |
Collapse
|
40
|
Min J, Liu J, Wang Z, Wang Y, Zhou Y, Zhang L, Zhang J, Shen Y, Li Q, Su R, Qi W. Coordination-Induced Self-Assembly of a Dipeptide into Multifunctional Chiral Nanostructures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:14261-14268. [PMID: 36367454 DOI: 10.1021/acs.langmuir.2c02298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Short peptides could be used as chiral motifs to self-assemble into various artificial nanostructures with supramolecular or nanoscale chirality, but their applications still need to be expanded. Here, under the mediation of metal ions, the ferrocene-diphenylalanine (Fc-LFLF) peptide can self-assemble into various chiral nanostructures, including right-handed helical microflowers mediated by Cu2+, left-handed nanofibers mediated by Ag+, and right-handed nanofibers mediated by Zn2+ and Cd2+. Meanwhile, the gold nanoparticles could be mineralized and deposited on Cu2+/Fc-LFLF microflowers to form AuNPs@Cu2+/Fc-LFLF, which showed significantly improved catalytic activity. The Ag+ could be further mineralized on the peptide nanofibers to form AgNPs@Fc-LFLF, showing an excellent antibacterial effect. Overall, this study provides new insights into the chiral self-assembly of short peptides and demonstrates that the chiral peptide-metal assemblies may have broad prospects in the fields of biocatalysis and antimicrobials.
Collapse
Affiliation(s)
- Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Jiayu Liu
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Zixuan Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
- Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Soochow University, Suzhou 215123, China
| | - Yu Zhou
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Liwei Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yuhe Shen
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
- The Co-Innovation Centre of Chemistry and Chemical Engineering of Tianjin, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
- The Co-Innovation Centre of Chemistry and Chemical Engineering of Tianjin, Tianjin 300072, P. R. China
| |
Collapse
|
41
|
Jia X, Liu Y, Qu Y, Li YQ, Liu X, Liu P, Li W. Electric Field-Controlled Peptide Self-Assembly through Funnel-Shaped Two-Dimensional Nanopores. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51183-51189. [PMID: 36329605 DOI: 10.1021/acsami.2c13590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Self-assembly of biomolecules is critical for the realization of biological functions. Thus, the precise control of self-assembly has great significance in the design of biochips and biomedical agents. In this report, we design a Y-shaped funnel on a two-dimensional (2D) heterostructure, called 2D funnel, based on monolayered polyaniline carbon nitride (C3N) and boron carbide (BC3), and study its application in the self-assembly state regulation of the peptide oligomer, using Aβ16-21 as the representative model. Structurally, the 2D funnel is composed of three regions: channel area, triangle area, and barrier area. The channel and triangle areas show higher binding affinity to the peptide than that of the barrier area, which leads to the confinement of the peptide in the 2D funnel. Our results show that when an external electric field is applied along the 2D funnel, the oligomer is driven to migrate across the funnel. Its trajectory is confined inside the narrow channel area, which effectively causes peptide dissociation into the individual peptide chains. Then, when the external electric field is turned off, the separated peptide chains spontaneously assemble in the triangle area and tend to reunite. Our present findings propose a novel heterostructure platform, which enables the manipulation of the self-assembly state of peptides by switching the electric field, which could guide the design and fabrication of nanodevices for sensing and sequencing applications.
Collapse
Affiliation(s)
- Xiao Jia
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yang Liu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yong-Qiang Li
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Xiangdong Liu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Peng Liu
- Institute of Frontier and Interdisciplinary Science and Key Laboratory of Particle Physics and Particle Irradiation (MOE), Shandong University, Qingdao, Shandong 266237, China
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| |
Collapse
|
42
|
Zhao Z, Zhang Z, Zhang H, Liang Z. Small Peptides in the Detection of Mycotoxins and Their Potential Applications in Mycotoxin Removal. Toxins (Basel) 2022; 14:toxins14110795. [PMID: 36422969 PMCID: PMC9698726 DOI: 10.3390/toxins14110795] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/29/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
Mycotoxins pose significant risks to humans and livestock. In addition, contaminated food- and feedstuffs can only be discarded, leading to increased economic losses and potential ecological pollution. Mycotoxin removal and real-time toxin level monitoring are effective approaches to solve this problem. As a hot research hotspot, small peptides derived from phage display peptide libraries, combinatorial peptide libraries, and rational design approaches can act as coating antigens, competitive antigens, and anti-immune complexes in immunoassays for the detection of mycotoxins. Furthermore, as a potential approach to mycotoxin degradation, small peptides can mimic the natural enzyme catalytic site to construct artificial enzymes containing oxidoreductases, hydrolase, and lyase activities. In summary, with the advantages of mature synthesis protocols, diverse structures, and excellent biocompatibility, also sharing their chemical structure with natural proteins, small peptides are widely used for mycotoxin detection and artificial enzyme construction, which have promising applications in mycotoxin degradation. This paper mainly reviews the advances of small peptides in the detection of mycotoxins, the construction of peptide-based artificial enzymes, and their potential applications in mycotoxin control.
Collapse
Affiliation(s)
- Zitong Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhenzhen Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Haoxiang Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Correspondence: ; Tel.: +86-010-62737055
| |
Collapse
|
43
|
Liu Y, Gan L, Feng P, Huang L, Chen L, Li S, Chen H. An artificial self-assembling peptide with carboxylesterase activity and substrate specificity restricted to short-chain acid p-nitrophenyl esters. Front Chem 2022; 10:996641. [PMID: 36199662 PMCID: PMC9527324 DOI: 10.3389/fchem.2022.996641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/07/2022] [Indexed: 11/19/2022] Open
Abstract
Natural enzymes possess remarkable catalytic activity and high substrate specificity. Many efforts have been dedicated to construct artificial enzymes with high catalytic activity. However, how to mimic the exquisite substrate specificity of a natural enzyme remains challenging because of the complexity of the enzyme structure. Here, we report artificial carboxylesterases that are specific for short chain fatty acids and were constructed via peptide self-assembly. These artificial systems have esterase-like activity rather than lipase-like activity towards p-nitrophenyl esters. The designer peptides self-assembled into nanofibers with strong β-sheet character. The extending histidine units and the hydrophobic edge of the fibrillar structure collectively form the active center of the artificial esterase. These artificial esterases show substrate specificity for short-chain acids esters. Moreover, 1-isopropoxy-4-nitrobenzene could function as a competitive inhibitor of hydrolysis of p-nitrophenyl acetate for an artificial esterase.
Collapse
Affiliation(s)
- Yanfei Liu
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, China
- *Correspondence: Yanfei Liu,
| | - Lili Gan
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Peili Feng
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Lei Huang
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Luoying Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Shuhua Li
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Hui Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, China
| |
Collapse
|
44
|
Liang S, Wu XL, Zong MH, Lou WY. Construction of Zn-heptapeptide bionanozymes with intrinsic hydrolase-like activity for degradation of di(2-ethylhexyl) phthalate. J Colloid Interface Sci 2022; 622:860-870. [PMID: 35561606 DOI: 10.1016/j.jcis.2022.04.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/28/2022]
Abstract
Nanozyme with intrinsic enzyme-like activity has emerged as favorite artificial catalyst during recent years. However, current nanozymes are mainly limited to inorganic-derived nanomaterials, while biomolecule-sourced nanozyme (bionanozyme) are rarely reported. Herein, inspired by the basic structure of natural hydrolase family, we constructed 3 oligopeptide-based bionanozymes with intrinsic hydrolase-like activity by implementing zinc induced self-assembly of histidine-rich heptapeptides. Under mild condition, divalent zinc (Zn2+) impelled the spontaneous assembly of short peptides (i.e. Ac-IHIHIQI-CONH2, Ac-IHIHIYI-CONH2, and Ac-IHVHLQI-CONH2), forming hydrolase-mimicking bionanozymes with β-sheet secondary conformation and nanofibrous architecture. As expected, the resultant bionanozymes were able to hydrolyze a serious of p-nitrophenyl esters, including not only the simple substrate with short side-chain (p-NPA), but also more complicated ones (p-NPB, p-NPH, p-NPO, and p-NPS). Moreover, the self-assembled Zn-heptapeptide bionanozymes were also proven to be capable of degrading di(2-ethylhexyl) phthalate (DEHP), a typical plasticizer, showing great potential for environmental remediation. Based on this study, we aim to provide theoretical references and exemplify a specific case for directing the construction and application of bionanozyme.
Collapse
Affiliation(s)
- Shan Liang
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Xiao-Ling Wu
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Min-Hua Zong
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Wen-Yong Lou
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, China.
| |
Collapse
|
45
|
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]
|
46
|
Arad E, Jelinek R. Catalytic amyloids. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
47
|
Runser JY, Criado-Gonzalez M, Fneich F, Rabineau M, Senger B, Weiss P, Jierry L, Schaaf P. Non-monotonous enzyme-assisted self-assembly profiles resulting from reaction-diffusion processes in host gels. J Colloid Interface Sci 2022; 620:234-241. [DOI: 10.1016/j.jcis.2022.03.150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022]
|
48
|
Li H, Xiong Z, Jia Y, Gao F, Wang C, Li Q, Li J. Flexible Recyclable Cellulose Paper Templated Cu-Doped Polydopamine Membranes with Dual Enzyme-Like Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202405. [PMID: 35908156 DOI: 10.1002/smll.202202405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/02/2022] [Indexed: 06/15/2023]
Abstract
The development of high-efficiency enzyme mimics is of great significance in the field of biocatalysis. However, it remains challenging to design novel enzyme mimics with multiple enzyme-like activities, excellent stability, and good reusability. Herein, a facile molecular assembly strategy to construct dialdehyde cellulose (DAC) templated Cu-doped polydopamine (DAC@PDA/Cu) membrane with dual enzyme-like activities is presented. The Schiff base bonds formed between polydopamine (PDA) and DAC can not only accelerate the adhesion of PDA thin layer but also contribute to Cu-loading and high stability of DAC@PDA/Cu membrane. Importantly, the assembled DAC@PDA/Cu membrane exhibits a remarkable catalytic activity that is superior to the natural laccase along with high stability and excellent reusability. Moreover, the DAC@PDA/Cu membrane also demonstrates peroxidase-like activity, and it is successfully applied in the sensitive detection of ascorbic acid (AA). This work will provide a new paradigm methodology for rational design and practical applications of enzyme mimics based on bioinspired molecular assemblies.
Collapse
Affiliation(s)
- Hong Li
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Zhuzhu Xiong
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Fan Gao
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Chenlei Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Qi Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
49
|
Boruah A, Roy A. Advances in hybrid peptide-based self-assembly systems and their applications. Biomater Sci 2022; 10:4694-4723. [PMID: 35899853 DOI: 10.1039/d2bm00775d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.
Collapse
Affiliation(s)
- Alpana Boruah
- Applied Organic Chemistry Group, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST), Pulibor, Jorhat-785006, Assam, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Arup Roy
- Applied Organic Chemistry Group, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST), Pulibor, Jorhat-785006, Assam, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| |
Collapse
|
50
|
Bioinspired enzymatic compartments constructed by spatiotemporally confined in situ self-assembly of catalytic peptide. Commun Chem 2022; 5:81. [PMID: 36697908 PMCID: PMC9814850 DOI: 10.1038/s42004-022-00700-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/29/2022] [Indexed: 01/28/2023] Open
Abstract
Enzymatic compartments, inspired by cell compartmentalization, which bring enzymes and substrates together in confined environments, are of particular interest in ensuring the enhanced catalytic efficiency and increased lifetime of encapsulated enzymes. Herein, we constructed bioinspired enzymatic compartments (TPE-Q18H@GPs) with semi-permeability by spatiotemporally controllable self-assembly of catalytic peptide TPE-Q18H in hollow porous glucan particles (GPs), allowing substrates and products to pass in/out freely, while enzymatic aggregations were retained. Due to the enrichment of substrates and synergistic effect of catalytic nanofibers formed in the confined environment, the enzymatic compartments exhibited stronger substrate binding affinity and over two-fold enhancement of second-order kinetic constant (kcat/Km) compared to TPE-Q18H nanofibers in disperse system. Moreover, GPs enabled the compartments sufficient stability against perturbation conditions, such as high temperature and degradation. This work opens an intriguing avenue to construct enzymatic compartments using porous biomass materials and has fundamental implications for constructing artificial organelles and even artificial cells.
Collapse
|