1
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Chen J, Moreno JL, Zhang W, Gibson-Elias LJ, Lian R, Najafi S, Zhang H, Zhong W, Hooley RJ. Optical discrimination of terpenes in citrus peels with a host:guest sensing array. Chem Commun (Camb) 2024; 60:5598-5601. [PMID: 38712724 DOI: 10.1039/d4cc01309c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
A simple aqueous host:guest sensing array can selectively discriminate between different types of citrus varietal from peel extract samples. It can also distinguish between identical citrus samples at varying stages of ripening. The discrimination effects stem from detection of changes in the terpenoid composition of the peel extracts by the host:guest array, despite the overwhelming excess of a single component, limonene, in each sample. The hosts are insensitive to limonene but bind other monoterpenes strongly, even though they are similar in structure to the major limonene component. This work demonstrates the capability of host:guest arrays in sensing target molecules in environments with the competing agents present at high abundances in the sample matrix.
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Affiliation(s)
- Junyi Chen
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A.
| | - Jose L Moreno
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A.
| | - Wen Zhang
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A.
| | - Lucas J Gibson-Elias
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A.
| | - Ria Lian
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A.
| | - Saba Najafi
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A.
| | - Haofei Zhang
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A.
| | - Wenwan Zhong
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China.
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A.
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2
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Emenike B, Czabala P, Farhi J, Swaminathan J, Anslyn EV, Spangle J, Raj M. Tertiary Amine Coupling by Oxidation for Selective Labeling of Dimethyl Lysine Post-Translational Modifications. J Am Chem Soc 2024; 146:10621-10631. [PMID: 38584362 PMCID: PMC11027136 DOI: 10.1021/jacs.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Lysine dimethylation (Kme2) is a crucial post-translational modification (PTM) that regulates biological processes and is implicated in diseases. There is significant interest in globally identifying these methylation marks. Unfortunately, this remains challenging due to the lack of robust technologies for selectively labeling Kme2. To address this, we present a chemical method named tertiary amine coupling by oxidation (TACO). This method selectively modifies Kme2 to aldehydes using Selectfluor and a base. The resulting aldehydes from Kme2 were then functionalized using reductive amination, thiolamine, and oxime chemistry. We successfully demonstrated the versatility of TACO in selectively labeling Kme2 peptides and proteins in complex cell lysate mixtures with varying payloads, including affinity tags and fluorophores. We further showed the application of TACO chemistry for the identification of Kme2 sites at a single-molecule level by fluorosequencing. We discovered novel 30 Kme2 sites, in addition to previously known 5 Kme2 sites, by proteomics analysis of TACO-modified nuclear extracts. Our work establishes a unique strategy for covalently modifying Kme2, facilitating the global identification of low-abundance Kme2-PTMs and their sites within complex cell lysate mixtures.
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Affiliation(s)
- Benjamin Emenike
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Patrick Czabala
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jonathan Farhi
- Department
of Radiation Oncology, Emory University
School of Medicine, Atlanta, Georgia 30322, United States
| | - Jagannath Swaminathan
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer Spangle
- Department
of Radiation Oncology, Emory University
School of Medicine, Atlanta, Georgia 30322, United States
| | - Monika Raj
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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3
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Chaudhary KN, Brosnahan KI, Gibson-Elias LJ, Moreno JL, Hickey BL, Hooley RJ, Caulkins BG. Investigation of the effects on proton relaxation times upon encapsulation in a water-soluble synthetic receptor. Phys Chem Chem Phys 2024; 26:10183-10190. [PMID: 38497123 DOI: 10.1039/d3cp06099c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Sequestration of small molecule guests in the cavity of a water-soluble deep cavitand host has a variety of effects on their NMR properties. The effects of encapsulation on the longitudinal (T1) and transverse (T2) relaxation times of the protons in variably sized guest molecules are analyzed here, using inversion recovery and spin-echo experiments. Sequestration of neutral organic species from the bulk solvent reduces the overall proton relaxation times, but the magnitude of this effect on different protons in the same molecule has a variety of contributors, from the motion of the guest when bound, to the position of the protons in the cavity and the magnetic anisotropy induced by the aromatic walls of the host. These subtle effects can have large consequences on the environment experienced by the bound guest, and this sheds light on the nature of small molecules in enclosed environments.
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Affiliation(s)
- Krishna N Chaudhary
- Department of Natural Sciences, Pitzer and Scripps Colleges, Claremont, California, 91711, USA.
| | - Kyra I Brosnahan
- Department of Natural Sciences, Pitzer and Scripps Colleges, Claremont, California, 91711, USA.
| | - Lucas J Gibson-Elias
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Jose L Moreno
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Briana L Hickey
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Bethany G Caulkins
- Department of Natural Sciences, Pitzer and Scripps Colleges, Claremont, California, 91711, USA.
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4
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Chen J, Fasihianifard P, Raz AAP, Hickey BL, Moreno JL, Chang CEA, Hooley RJ, Zhong W. Selective recognition and discrimination of single isomeric changes in peptide strands with a host : guest sensing array. Chem Sci 2024; 15:1885-1893. [PMID: 38303931 PMCID: PMC10829040 DOI: 10.1039/d3sc06087j] [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: 11/14/2023] [Accepted: 12/30/2023] [Indexed: 02/03/2024] Open
Abstract
An indirect competitive binding mechanism can be exploited to allow a combination of cationic fluorophores and water-soluble synthetic receptors to selectively recognize and discriminate peptide strands containing a single isomeric residue in the backbone. Peptide isomerization occurs in long-lived proteins and has been linked with diseases such as Alzheimer's, cataracts and cancer, so isomers are valuable yet underexplored targets for selective recognition. Planar cationic fluorophores can selectively bind hydrophobic, Trp-containing peptide strands in solution, and when paired with receptors that provide a competitive host for the fluorophore, can form a differential sensing array that enables selective discrimination of peptide isomers. Residue variations such as D- and L-Asp, D- and L-isoAsp, D-Ser and D-Glu can all be recognized, simply by their effects on the folded structure of the flexible peptide. Molecular dynamics simulations were applied to determine the most favorable conformation of the peptide : fluorophore conjugate, indicating that favorable π-stacking with internal tryptophan residues in a folded binding pocket enables micromolar binding affinity.
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Affiliation(s)
- Junyi Chen
- Environmental Toxicology Graduate Program, University of California-Riverside Riverside CA 92521 USA
| | - Parisa Fasihianifard
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Alexie Andrea P Raz
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Briana L Hickey
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Jose L Moreno
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Chia-En A Chang
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
- Environmental Toxicology Graduate Program, University of California-Riverside Riverside CA 92521 USA
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
- Environmental Toxicology Graduate Program, University of California-Riverside Riverside CA 92521 USA
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5
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Selinger AJ, Hof F. Adaptive Supramolecular Networks: Emergent Sensing from Complex Systems. Angew Chem Int Ed Engl 2023; 62:e202312407. [PMID: 37699200 DOI: 10.1002/anie.202312407] [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: 08/23/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
Molecular differentiation by supramolecular sensors is typically achieved through sensor arrays, relying on the pattern recognition responses of large panels of isolated sensing elements. Here we report a new one-pot systems chemistry approach to differential sensing in biological solutions. We constructed an adaptive network of three cross-assembling sensor elements with diverse analyte-binding and photophysical properties. This robust sensing approach exploits complex interconnected sensor-sensor and sensor-analyte equilibria, producing emergent supramolecular and photophysical responses unique to each analyte. We characterize the basic mechanisms by which an adaptive network responds to analytes. The inherently data-rich responses of an adaptive network discriminate among very closely related proteins and protein mixtures without relying on designed protein recognition elements. We show that a single adaptive sensing solution provides better analyte discrimination using fewer response observations than a sensor array built from the same components. We also show the network's ability to adapt and respond to changing biological solutions over time.
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Affiliation(s)
- Allison J Selinger
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
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6
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Xiong Y, Li M, Cao Y, Li Z, Chang Y, Zhao X, Qing G. Nanofluidic Device for Detection of Lysine Methylpeptides and Sensing of Lysine Methylation. Anal Chem 2023; 95:7761-7769. [PMID: 37140051 DOI: 10.1021/acs.analchem.3c01074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein methylation is the smallest possible yet vitally important post-translational modification (PTM). This small and chemically inert addition in proteins makes the analysis of methylation more challenging, thus calling for an efficient tool for the sake of recognition and detection. Herein, we present a nanofluidic electric sensing device based on a functionalized nanochannel that was constructed by introducing monotriazole-containing p-sulfonatocalix[4]arene (TSC) into a single asymmetric polymeric nanochannel via click chemistry. The device can selectively detect lysine methylpeptides with subpicomole sensitivity, distinguish between different lysine methylation states, and monitor the lysine methylation process by methyltransferase at the peptide level in real time. The introduced TSC molecule, with its confined asymmetric configuration, presents the remarkable ability to selectively bind to lysine methylpeptides, which, coupled with the release of the complexed Cu ions, allows the device to transform the molecular-level recognition to the discernible change in ionic current of the nanofluidic electric device, thus enabling detection. This work could serve as a stepping stone to the development of a new methyltransferase assay and the chemical that specifically targets lysine methylation in PTM proteomics.
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Affiliation(s)
- Yuting Xiong
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
| | - Minmin Li
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuchen Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Zan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yongxin Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinjia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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7
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Qin J, Guo J, Tang G, Li L, Yao SQ. Multiplex Identification of Post-Translational Modifications at Point-of-Care by Deep Learning-Assisted Hydrogel Sensors. Angew Chem Int Ed Engl 2023; 62:e202218412. [PMID: 36815677 DOI: 10.1002/anie.202218412] [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: 12/13/2022] [Revised: 02/02/2023] [Accepted: 02/23/2023] [Indexed: 02/24/2023]
Abstract
Multiplex detection of protein post-translational modifications (PTMs), especially at point-of-care, is of great significance in cancer diagnosis. Herein, we report a machine learning-assisted photonic crystal hydrogel (PCH) sensor for multiplex detection of PTMs. With closely-related PCH sensors microfabricated on a single chip, our design achieved not only rapid screening of PTMs at specific protein sites by using only naked eyes/cellphone, but also the feasibility of real-time monitoring of phosphorylation reactions. By taking advantage of multiplex sensor chips and a neural network algorithm, accurate prediction of PTMs by both their types and concentrations was enabled. This approach was ultimately used to detect and differentiate up/down regulation of different phosphorylation sites within the same protein in live mammalian cells. Our developed method thus holds potential for POC identification of various PTMs in early-stage diagnosis of protein-related diseases.
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Affiliation(s)
- Junjie Qin
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Jia Guo
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, Fujian, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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8
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Harrison EE, Waters ML. Detection and differentiation of per- and polyfluoroalkyl substances (PFAS) in water using a fluorescent imprint-and-report sensor array. Chem Sci 2023; 14:928-936. [PMID: 36755732 PMCID: PMC9891069 DOI: 10.1039/d2sc05685b] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
Widespread industrial use of per- and polyfluoroalkyl substances (PFAS) as surfactants has led to global contamination of water sources with these persistent, highly stable chemicals. As a result, humans and wildlife are regularly exposed to PFAS, which have been shown to bioaccumulate and cause adverse health effects. Methods for detecting PFAS in water are currently limited and primarily utilize mass spectrometry (MS), which is time-consuming and requires expensive instrumentation. Thus, new methods are needed to rapidly and reliably assess the pollution level of water sources. While some fluorescent PFAS sensors exist, they typically function in high nanomolar or micromolar concentration ranges and focus on sensing only 1-2 individual PFAS. Our work aims to address this problem by developing a fluorescent sensor for both individual PFAS, as well as complex PFAS mixtures, and demonstrate its functionality in tap water samples. Here we show that dynamic combinatorial libraries (DCLs) with simple building blocks can be templated with a fluorophore and subsequently used as sensors to form an array that differentially detects each PFAS species and various mixtures thereof. Our method is a high-throughput analysis technique that allows many samples to be analyzed simultaneously with a plate reader. This is one of the first examples of a fluorescent PFAS sensor array that functions at low nanomolar concentrations, and herein we report its use for the rapid detection of PFAS contamination in water.
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Affiliation(s)
- Emily E. Harrison
- Department of Chemistry, University of North Carolina at Chapel HillChapel HillNorth Carolina 27599USA
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina at Chapel HillChapel HillNorth Carolina 27599USA
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9
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Chen J, Hooley RJ, Zhong W. Applications of Synthetic Receptors in Bioanalysis and Drug Transport. Bioconjug Chem 2022; 33:2245-2253. [PMID: 35362963 DOI: 10.1021/acs.bioconjchem.2c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Synthetic receptors are powerful tools for molecular recognition. They can bind to guests with high selectivity and affinity, and their structures are tunable and diversified. These features, plus the relatively low cost and high simplicity in synthesis and modification, support the feasibility of array-based molecular analysis with synthetic receptors for improved selectivity in the recognition of a wide range of targets. More attractively, host-guest interaction is reversible and guest displacement allows biocompatible and gentle release of the host-bound molecules, simplifying the stimulation designs needed to control analyte sensing, enrichment, and transportation. Here, we highlight a few recent advancements in using synthetic receptors for molecular analysis and manipulation, with the focus on macrocyclic receptors and their applications in displacement sensing, separation, imaging, and drug transport.
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10
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Sedgi I, Lerner N, Lerner A, Zeiri O. Mixed-Ligand gold nanoparticles based optical sensor array for the recognition and quantification of seven toxic metals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 277:121241. [PMID: 35472706 DOI: 10.1016/j.saa.2022.121241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/17/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Sensor arrays use pattern recognition for the identification and quantification of analytes. In the presented work, a gold nanoparticle (GNP) based optical sensor array was employed to classify and quantify seven toxic metals (arsenic, barium, cadmium, cerium, chromium, lead, and mercury). The sensor array receptors were GNPs functionalized by mercaptoundecanoic acid, 2-mercaptoethanesulfonate, and a 1:1 mixture of the two ligands. The mixed-ligand particle responds to the same analytes as the mono-ligand particles but in a distinctive way. This behavior demonstrates the high potential of mixed-ligand particles in the fabrication of sensor array receptors. The responses of the GNPs to different concentrations of the seven metal ions were analyzed, and a unique "classification trajectory" was produced for every metal. Samples of different metal concentrations were then measured and identified using the "classification trajectories". Once sample composition has been identified, a PLSR model, produced from the concatenated sensor array spectra of four calibration samples for each nanoparticle, was used to determine the metal concentration.
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Affiliation(s)
- Itzhak Sedgi
- Department of Analytical Chemistry, Nuclear Research Center Negev, P.O Box 9001, Beer-Sheva, Israel; Department of Chemistry, Ben-Gurion University, Beer-Sheva, Israel
| | - Nadav Lerner
- Department of Analytical Chemistry, Nuclear Research Center Negev, P.O Box 9001, Beer-Sheva, Israel
| | - Ana Lerner
- Department of Chemistry, Ben-Gurion University, Beer-Sheva, Israel; Chemistry Department, Israel Atomic Energy Commission, Tel Aviv, Israel
| | - Offer Zeiri
- Department of Analytical Chemistry, Nuclear Research Center Negev, P.O Box 9001, Beer-Sheva, Israel.
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11
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Harrison EE, Waters ML. Application of an Imprint‐and‐Report Sensor Array for Detection of the Dietary Metabolite Trimethylamine N‐Oxide and Its Precursors in Complex Mixtures. Angew Chem Int Ed Engl 2022; 61:e202205193. [DOI: 10.1002/anie.202205193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Emily E. Harrison
- Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Marcey L. Waters
- Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
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12
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Das Saha N, Pradhan S, Sasmal R, Sarkar A, Berač CM, Kölsch JC, Pahwa M, Show S, Rozenholc Y, Topçu Z, Alessandrini V, Guibourdenche J, Tsatsaris V, Gagey-Eilstein N, Agasti SS. Cucurbit[7]uril Macrocyclic Sensors for Optical Fingerprinting: Predicting Protein Structural Changes to Identifying Disease-Specific Amyloid Assemblies. J Am Chem Soc 2022; 144:14363-14379. [PMID: 35913703 DOI: 10.1021/jacs.2c05969] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a three-dimensional (3D) representation, each protein molecule displays a specific pattern of chemical and topological features, which are altered during its misfolding and aggregation pathway. Generating a recognizable fingerprint from such features could provide an enticing approach not only to identify these biomolecules but also to gain clues regarding their folding state and the occurrence of pathologically lethal misfolded aggregates. We report here a universal strategy to generate a fluorescent fingerprint from biomolecules by employing the pan-selective molecular recognition feature of a cucurbit[7]uril (CB[7]) macrocyclic receptor. We implemented a direct sensing strategy by covalently tethering CB[7] with a library of fluorescent reporters. When CB[7] recognizes the chemical and geometrical features of a biomolecule, it brings the tethered fluorophore into the vicinity, concomitantly reporting the nature of its binding microenvironment through a change in their optical signature. The photophysical properties of the fluorophores allow a multitude of probing modes, while their structural features provide additional binding diversity, generating a distinct fluorescence fingerprint from the biomolecule. We first used this strategy to rapidly discriminate a diverse range of protein analytes. The macrocyclic sensor was then applied to probe conformational changes in the protein structure and identify the formation of oligomeric and fibrillar species from misfolded proteins. Notably, the sensor system allowed us to differentiate between different self-assembled forms of the disease-specific amyloid-β (Aβ) aggregates and segregated them from other generic amyloid structures with a 100% identification accuracy. Ultimately, this sensor system predicted clinically relevant changes by fingerprinting serum samples from a cohort of pregnant women.
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Affiliation(s)
- Nilanjana Das Saha
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.,Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Soumen Pradhan
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Ranjan Sasmal
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Aritra Sarkar
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Christian M Berač
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.,Graduate School of Materials Science in Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Jonas C Kölsch
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Meenakshi Pahwa
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Sushanta Show
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Yves Rozenholc
- UR 7537 BioSTM, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Zeki Topçu
- UR 7537 BioSTM, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Vivien Alessandrini
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | - Jean Guibourdenche
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | - Vassilis Tsatsaris
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | | | - Sarit S Agasti
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.,Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
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13
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Tian JH, Hu XY, Hu ZY, Tian HW, Li JJ, Pan YC, Li HB, Guo DS. A facile way to construct sensor array library via supramolecular chemistry for discriminating complex systems. Nat Commun 2022; 13:4293. [PMID: 35879312 PMCID: PMC9314354 DOI: 10.1038/s41467-022-31986-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/13/2022] [Indexed: 12/15/2022] Open
Abstract
Differential sensing, which discriminates analytes via pattern recognition by sensor arrays, plays an important role in our understanding of many chemical and biological systems. However, it remains challenging to develop new methods to build a sensor unit library without incurring a high workload of synthesis. Herein, we propose a supramolecular approach to construct a sensor unit library by taking full advantage of recognition and assembly. Ten sensor arrays are developed by replacing the building block combinations, adjusting the ratio between system components, and changing the environment. Using proteins as model analytes, we examine the discriminative abilities of these supramolecular sensor arrays. Then the practical applicability for discriminating complex analytes is further demonstrated using honey as an example. This sensor array construction strategy is simple, tunable, and capable of developing many sensor units with as few syntheses as possible.
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Affiliation(s)
- Jia-Hong Tian
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Xin-Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Zong-Ying Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Han-Wen Tian
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Juan-Juan Li
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Yu-Chen Pan
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Hua-Bin Li
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Dong-Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China.
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Hu C, Jochmann T, Chakraborty P, Neumaier M, Levkin PA, Kappes MM, Biedermann F. Further Dimensions for Sensing in Biofluids: Distinguishing Bioorganic Analytes by the Salt-Induced Adaptation of a Cucurbit[7]uril-Based Chemosensor. J Am Chem Soc 2022; 144:13084-13095. [PMID: 35850489 PMCID: PMC9335531 DOI: 10.1021/jacs.2c01520] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insufficient binding selectivity of chemosensors often renders biorelevant metabolites indistinguishable by the widely used indicator displacement assay. Array-based chemosensing methods are a common workaround but require additional effort for synthesizing a chemosensor library and setting up a sensing array. Moreover, it can be very challenging to tune the inherent binding preference of macrocyclic systems such as cucurbit[n]urils (CBn) by synthetic means. Using a novel cucurbit[7]uril-dye conjugate that undergoes salt-induced adaptation, we now succeeded in distinguishing 14 bioorganic analytes from each other through the facile stepwise addition of salts. The salt-specific concentration-resolved emission provides additional information about the system at a low synthetic effort. We present a data-driven approach to translate the human-visible curve differences into intuitive pairwise difference measures. Ion mobility experiments combined with density functional theory calculations gave further insights into the binding mechanism and uncovered an unprecedented ternary complex geometry for CB7. TThis work introduces the non-selectively binding, salt-adaptive cucurbit[n]uril system for sensing applications in biofluids such as urine, saliva, and blood serum.
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Affiliation(s)
- Changming Hu
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, Eggenstein-Leopoldshafen 76344, Germany
| | - Thomas Jochmann
- Department of Computer Science and Automation, Technische Universität Ilmenau, Gustav-Kirchhoff-Str. 2, Ilmenau 98693, Germany
| | - Papri Chakraborty
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, Eggenstein-Leopoldshafen 76344, Germany.,Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Karlsruhe 76131, Germany
| | - Marco Neumaier
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, Eggenstein-Leopoldshafen 76344, Germany
| | - Pavel A Levkin
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz-1, Eggenstein-Leopoldshafen 76344, Germany
| | - Manfred M Kappes
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, Eggenstein-Leopoldshafen 76344, Germany.,Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Karlsruhe 76131, Germany
| | - Frank Biedermann
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz-1, Eggenstein-Leopoldshafen 76344, Germany
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15
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Emenike B, Nwajiobi O, Raj M. Covalent Chemical Tools for Profiling Post-Translational Modifications. Front Chem 2022; 10:868773. [PMID: 35860626 PMCID: PMC9289218 DOI: 10.3389/fchem.2022.868773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Nature increases the functional diversity of the proteome through posttranslational modifications (PTMs); a process that involves the proteolytic processing or catalytic attachment of diverse functional groups onto proteins. These modifications modulate a host of biological activities and responses. Consequently, anomalous PTMs often correlate to a host of diseases, hence there is a need to detect these transformations, both qualitatively and quantitatively. One technique that has gained traction is the use of robust chemical strategies to label different PTMs. By utilizing the intrinsic chemical reactivity of the different chemical groups on the target amino acid residues, this strategy can facilitate the delineation of the overarching and inclusionary roles of these different modifications. Herein, we will discuss the current state of the art in post-translational modification analysis, with a direct focus on covalent chemical methods used for detecting them.
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16
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Harrison EE, Waters ML. Application of an Imprint‐and‐Report Sensor Array for Detection of the Dietary Metabolite Trimethylamine N‐Oxide and Its Precursors in Complex Mixtures. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Emily E. Harrison
- University of North Carolina at Chapel Hill Kenan Science Library: The University of North Carolina at Chapel Hill Chemistry UNITED STATES
| | - Marcey L. Waters
- UNC Chapel Hill Dept. of Chemistry CB 3290 27599 Chapel Hill UNITED STATES
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17
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