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Mashhadi IS, Safarnejad MR, Shahmirzaie M, Aliahmadi A, Ghassempour A, Aboul-Enein HY. Determination of the epitopic peptides of fig mosaic virus and the single-chain variable fragment antibody by mass spectrometry. Anal Biochem 2023; 681:115319. [PMID: 37716512 DOI: 10.1016/j.ab.2023.115319] [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: 06/30/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023]
Abstract
The study of antibody-antigen interactions, through epitope mapping, enhances our understanding of antibody neutralization and antigenic determinant recognition. Epitope mapping, employing monoclonal antibodies and mass spectrometry, has emerged as a rapid and precise method to investigate viral antigenic determinants. In this report, we propose an approach to improve the accuracy of epitopic peptide interaction rate recognition. To achieve this, we investigated the interaction between the nucleocapsid protein of fig mosaic virus (FMV-NP) and single-chain variable fragment antibodies (scFv-Ab). These scFv-Ab maintain high specificity similar to whole monoclonal antibodies, but they are smaller in size. We coupled this with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The experimental design involved using two different enzymes to digest FMV-NP separately. The resulting peptides were then incubated separately with the desired scFv-Ab at different incubation times and antibody concentrations. This allowed us to monitor the relative rate of epitopic peptide interaction with the antibody. The results demonstrated that, at a 1:1 ratio and after 2 h of interaction, the residues 122-136, 148-157, and 265-276 exhibited high-rate epitopic peptide binding, with reductions in peak intensity of 78%, 21%, and 22%, respectively. Conversely, the residues 250-264 showed low-rate binding, with a 15% reduction in peak intensity. This epitope mapping approach, utilizing scFv-Ab, two different enzymes, and various incubation times, offers a precise and dependable analysis for monitoring and recognizing the binding kinetics of antigenic determinants. Furthermore, this method can be applied to study any kind of antigens.
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Affiliation(s)
- Ilnaz Soleimani Mashhadi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Mohammad Reza Safarnejad
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Morteza Shahmirzaie
- Pharmaceutical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Niayesh Highway, Valiasr Ave, Tehran, Iran
| | - Atousa Aliahmadi
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Alireza Ghassempour
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran.
| | - Hassan Y Aboul-Enein
- Pharmaceutical and Medicinal Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, Giza, 12622, Egypt.
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2
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Hobsteter A, Badajoz MA, Lo Fiego MJ, Silbestri GF. Galactopyranoside-Substituted N-Heterocyclic Carbene Gold(I) Complexes: Synthesis, Stability, and Catalytic Applications to Alkyne Hydration. ACS OMEGA 2022; 7:21788-21799. [PMID: 35785281 PMCID: PMC9245165 DOI: 10.1021/acsomega.2c01878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
A series of novel gold(I) complexes bearing galactopyranoside-based N-heterocyclic carbene ligands have been synthesized via transmetalation of the corresponding Ag(I) complex. Gold(I) complexes have been characterized by NMR, Fourier transform infrared (FTIR), and elemental analysis. An exhaustive NMR analysis shows that the complexes are not stable when hydroxyl groups are deprotected. Catalytic studies, using the alkyne hydration as a model reaction, indicate that the synthesized complexes are active and reusable.
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3
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Mori K, Sakurai K. Clickable gold-nanoparticles as generic probe precursors for facile photoaffinity labeling application. Org Biomol Chem 2021; 19:1268-1273. [DOI: 10.1039/d0ob01688h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Clickable photoreactive gold nanoparticles have been developed to facilitate one-step preparation of photoaffinity probes for bioactive small molecules and their application to target protein analysis.
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Affiliation(s)
- Kanna Mori
- Tokyo University of Agriculture and Technology
- Department of Biotechnology and Life Science
- Tokyo 184-8588
- Japan
| | - Kaori Sakurai
- Tokyo University of Agriculture and Technology
- Department of Biotechnology and Life Science
- Tokyo 184-8588
- Japan
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4
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Taheri Hatkehlouei SF, Mirza B, Soleimani-Amiri S. Solvent-Free One-Pot Synthesis of Diverse Dihydropyrimidinones/Tetrahydropyrimidinones Using Biginelli Reaction Catalyzed by Fe3O4@C@OSO3H. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1781203] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Behrooz Mirza
- Department of Chemistry, Karaj Branch, Islamic Azad University, Karaj, Iran
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5
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Narita S, Kobayashi N, Mori K, Sakurai K. Clickable gold nanoparticles for streamlining capture, enrichment and release of alkyne-labelled proteins. Bioorg Med Chem Lett 2019; 29:126768. [PMID: 31690474 DOI: 10.1016/j.bmcl.2019.126768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 01/08/2023]
Abstract
Alkyne-labelled proteins are generated as key intermediates in the chemical probe-based approaches to proteomics analysis. Their efficient and selective detection and isolation is an important problem. We designed and synthesized azide-functionalized gold nanoparticles as new clickable capture reagents to streamline click chemistry-mediated capture, enrichment and release of the alkyne-labelled proteins in one-pot to expedite the post-labelling analysis. Because hydrophobic surface functionalities are known to render gold nanoparticles poorly water-dispersible, hydrophilic PEG linkers with two different lengths were explored to confer colloidal stability to the clickable capture reagents. We demonstrated the ability of the capture reagents to conjugate the alkyne containing proteins at a nanomolar concentration via click chemistry, which can be immediately followed by their enrichment and elution. Furthermore, a bifunctional clickable capture reagent bearing sulforhodamine and azide groups was shown to conveniently attach a fluorophore to the alkyne-labelled protein upon click capture, which facilitated their rapid detection in the gel analysis.
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Affiliation(s)
- Sho Narita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Life Science, 2-24-16, Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Naohiro Kobayashi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Life Science, 2-24-16, Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Kanna Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Life Science, 2-24-16, Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Kaori Sakurai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Life Science, 2-24-16, Naka-cho, Koganei-shi, Tokyo 184-8588, Japan.
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6
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Liu S, Lämmerhofer M. Functionalized gold nanoparticles for sample preparation: A review. Electrophoresis 2019; 40:2438-2461. [PMID: 31056767 DOI: 10.1002/elps.201900111] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/13/2022]
Abstract
Sample preparation is a crucial step for the reliable and accurate analysis of both small molecule and biopolymers which often involves processes such as isolation, pre-concentration, removal of interferences (purification), and pre-processing (e.g., enzymatic digestion) of targets from a complex matrix. Gold nanoparticle (GNP)-assisted sample preparation and pre-concentration has been extensively applied in many analytical procedures in recent years due to the favorable and unique properties of GNPs such as size-controlled synthesis, large surface-to-volume ratio, surface inertness, straightforward surface modification, easy separation requiring minimal manipulation of samples. This review article primarily focuses on applications of GNPs in sample preparation, in particular for bioaffinity capture and biocatalysis. In addition, their most common synthesis, surface modification and characterization methods are briefly summarized. Proper surface modification for GNPs designed in accordance to their target application directly influence their functionalities, e.g., extraction efficiencies, and catalytic efficiencies. Characterization of GNPs after synthesis and modification is worthwhile for monitoring and controlling the fabrication process to ensure proper quality and functionality. Parameters such as morphology, colloidal stability, and physical/chemical properties can be assessed by methods such as surface plasmon resonance, dynamic light scattering, ζ-potential determinations, transmission electron microscopy, Taylor dispersion analysis, and resonant mass measurement, among others. The accurate determination of the surface coverage appears to be also mandatory for the quality control of functionality of the nanoparticles. Some promising applications of (functionalized) GNPs for bioanalysis and sample preparation are described herein.
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Affiliation(s)
- Siyao Liu
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Tübingen, Germany
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7
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Waniwan JT, Chen YJ, Capangpangan R, Weng SH, Chen YJ. Glycoproteomic Alterations in Drug-Resistant Nonsmall Cell Lung Cancer Cells Revealed by Lectin Magnetic Nanoprobe-Based Mass Spectrometry. J Proteome Res 2018; 17:3761-3773. [PMID: 30261726 DOI: 10.1021/acs.jproteome.8b00433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the functional role of glycosylation-mediated pathogenesis requires deep characterization of glycoproteome, which remains extremely challenging due to the inherently complex nature of glycoproteins. We demonstrate the utility of lectin-magnetic nanoprobe (MNP@lectin) coupled to Orbitrap HCD-CID-MS/MS for complementary glycotope-specific enrichment and site-specific glycosylation analysis of the glycoproteome. By three nanoprobes, MNP@ConA, MNP@AAL, and MNP@SNA, our results revealed the first large-scale glycoproteome of nonsmall cell lung cancer (NSCLC) with 2290 and 2767 nonredundant glycopeptides confidently identified (Byonic score ≥100) in EGFR-TKI-sensitive PC9 and -resistant PC9-IR cells, respectively, especially with more fucosylated and sialylated glycopeptides in PC9-IR cells. The complementary enrichment was demonstrated with only five glycopeptides commonly enriched in three MNP@lectins. Glycotope specificity of 79 and 62% for enrichment was achieved using MNP@AAL and MNP@SNA, respectively. Label-free quantitation revealed predominant fucosylation in PC9-IR cells, suggesting its potential role associated with NSCLC resistance. Moreover, without immunoprecipitation, this multilectin nanoprobe allows the sensitive identification of 51 glycopeptides from 10 of 12 reported sites from onco-protein EGFR. Our results not only demonstrated a sensitive approach to study the vastly under-represented N-glycoprotome but also may pave the way for a glycoproteomic atlas to further explore the site-specific function of glycoproteins associated with drug resistance in NSCLC.
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Affiliation(s)
- Juanilita T Waniwan
- Department of Chemistry , National Taiwan University , Taipei 115 , Taiwan.,Chemical Biology and Molecular Biophysics , Taiwan International Graduate Program , Taipei 115 , Taiwan.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Rey Capangpangan
- Caraga State University , Butuan City 8600 , Philippines.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Shao-Hsing Weng
- Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan.,Genome and Systems Biology Degree Program , National Taiwan University , Taipei 115 , Taiwan
| | - Yu-Ju Chen
- Department of Chemistry , National Taiwan University , Taipei 115 , Taiwan.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
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9
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Abdelhamid HN, Wu HF. Gold nanoparticles assisted laser desorption/ionization mass spectrometry and applications: from simple molecules to intact cells. Anal Bioanal Chem 2016; 408:4485-502. [DOI: 10.1007/s00216-016-9374-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/29/2015] [Accepted: 01/28/2016] [Indexed: 01/05/2023]
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10
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Hao N, Neranon K, Ramström O, Yan M. Glyconanomaterials for biosensing applications. Biosens Bioelectron 2016; 76:113-30. [PMID: 26212205 PMCID: PMC4637221 DOI: 10.1016/j.bios.2015.07.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/11/2015] [Accepted: 07/14/2015] [Indexed: 02/08/2023]
Abstract
Nanomaterials constitute a class of structures that have unique physiochemical properties and are excellent scaffolds for presenting carbohydrates, important biomolecules that mediate a wide variety of important biological events. The fabrication of carbohydrate-presenting nanomaterials, glyconanomaterials, is of high interest and utility, combining the features of nanoscale objects with biomolecular recognition. The structures can also produce strong multivalent effects, where the nanomaterial scaffold greatly enhances the relatively weak affinities of single carbohydrate ligands to the corresponding receptors, and effectively amplifies the carbohydrate-mediated interactions. Glyconanomaterials are thus an appealing platform for biosensing applications. In this review, we discuss the chemistry for conjugation of carbohydrates to nanomaterials, summarize strategies, and tabulate examples of applying glyconanomaterials in in vitro and in vivo sensing applications of proteins, microbes, and cells. The limitations and future perspectives of these emerging glyconanomaterials sensing systems are furthermore discussed.
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Affiliation(s)
- Nanjing Hao
- Department of Chemistry, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Kitjanit Neranon
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm, Sweden
| | - Olof Ramström
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm, Sweden.
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA; Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm, Sweden.
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11
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Sakurai K, Hatai Y, Okada A. Gold nanoparticle-based multivalent carbohydrate probes: selective photoaffinity labeling of carbohydrate-binding proteins. Chem Sci 2016; 7:702-706. [PMID: 28791113 PMCID: PMC5530003 DOI: 10.1039/c5sc03275j] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/19/2015] [Indexed: 12/22/2022] Open
Abstract
Multivalent carbohydrate photoaffinity probes were developed based on gold nanoparticles (AuNPs) to provide a streamlined approach toward identification of carbohydrate-binding proteins. By using AuNPs as scaffolds, a carbohydrate ligand and a photoreactive group could be readily assembled on a probe in a modular fashion, which greatly accelerated the process of optimizing the probe design. The novel AuNP-based probes serve dual functions by facilitating photoaffinity labeling and by directly enriching the crosslinked proteins by centrifugation. We demonstrated that their ability to enhance the affinity and to stringently remove nonspecific proteins allowed selective photoaffinity labeling and isolation of a low affinity carbohydrate-binding protein in cell lysate.
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Affiliation(s)
- Kaori Sakurai
- Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Tokyo 184-8588 , Japan .
| | - Yuki Hatai
- Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Tokyo 184-8588 , Japan .
| | - Ayumi Okada
- Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Tokyo 184-8588 , Japan .
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12
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Adak AK, Li BY, Lin CC. Advances in multifunctional glycosylated nanomaterials: preparation and applications in glycoscience. Carbohydr Res 2015; 405:2-12. [DOI: 10.1016/j.carres.2014.07.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 01/13/2023]
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13
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Kavunja HW, Voss PG, Wang JL, Huang X. Identification of Lectins from Metastatic Cancer Cells through Magnetic Glyconanoparticles. Isr J Chem 2015; 55:423-436. [PMID: 27110035 PMCID: PMC4838199 DOI: 10.1002/ijch.201400156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cancer cells can have characteristic carbohydrate binding properties. Previously, it was shown that a highly metastatic melanoma cell line B16F10 bound to galacto-side-functionalized nanoparticles much stronger than the corresponding less metastatic B16F1 cells. To better understand the carbohydrate binding properties of cancer cells, herein, we report the isolation and characterization of endogenous galactose binding proteins from B16F10 cells using magnetic glyconanoparticles. The galactose-coated magnetic glyconanoparticles could bind with lectins present in the cells and be isolated through magnet-mediated separation. Through Western blot and mass spectrometry, the arginine/serine rich splicing factor Sfrs1 was identified as a galactose-selective endogenous lectin, overexpressed in B16F10 cells, compared with B16F1 cells. In addition, galactin-3 was found in higher amounts in B16F10 cells. Finally, the glyconanoparticles exhibited a superior efficiency in lectin isolation, from both protein mixtures and live cells, than the corresponding more traditional microparticles functionalized with carbohydrates. Thus, the magnetic glyconanoparticles present a useful tool for discovery of endogenous lectins, as well as binding partners of lectins, without prior knowledge of protein identities.
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Affiliation(s)
- Herbert W. Kavunja
- Department of Chemistry, Chemistry Building, Room 426, 578 S. Shaw Lane, Michigan State University, East Lansing, MI 48824 (USA)
| | - Patricia G. Voss
- Department of Biochemistry and Molecular Biology, Biochemistry Building, Room 402, 603 Wilson Road, Michigan State University, East Lansing, MI 48824 (USA)
| | - John L. Wang
- Department of Biochemistry and Molecular Biology, Biochemistry Building, Room 402, 603 Wilson Road, Michigan State University, East Lansing, MI 48824 (USA)
| | - Xuefei Huang
- Department of Chemistry, Chemistry Building, Room 426, 578 S. Shaw Lane, Michigan State University, East Lansing, MI 48824 (USA)
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14
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Kailasa SK, Wu HF. Nanomaterial-based miniaturized extraction and preconcentration techniques coupled to matrix-assisted laser desorption/ionization mass spectrometry for assaying biomolecules. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.09.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Abdelhamid HN, Wu HF. Proteomics analysis of the mode of antibacterial action of nanoparticles and their interactions with proteins. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.09.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Lai CH, Lai NC, Chuang YJ, Chou FI, Yang CM, Lin CC. Trivalent galactosyl-functionalized mesoporous silica nanoparticles as a target-specific delivery system for boron neutron capture therapy. NANOSCALE 2013; 5:9412-9418. [PMID: 23958787 DOI: 10.1039/c3nr02594b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A multi-functional mesoporous silica nanoparticle (MSN)-based boron neutron capture therapy (BNCT) agent, designated as T-Gal-B-Cy3@MSN, was synthesized with hydrophobic mesopores for incorporating a large amount of o-carborane (almost 60% (w/w) boron atoms per MSN), and the amines on the external surface were conjugated with trivalent galactosyl ligands and fluorescent dyes for cell targeting and imaging, respectively. The polar and hydrophilic galactosyl ligands enhance the water dispersibility of the BNCT agent and inhibit the possible leakage of o-carborane loaded in the MSN. Confocal microscopic images showed that T-Gal-B-Cy3@MSNs were endocytosed by cells and were then released from lysosomes into the cytoplasm of cells. Moreover, in comparison with the commonly used clinical BNCT agent, sodium borocaptate (BSH), T-Gal-B-Cy3@MSN provides a higher delivery efficiency (over 40-50 fold) of boron atoms and a better effect of BNCT in neutron irradiation experiments. MTT assays show a very low cytotoxicity for T-Gal-B-Cy3@MSN over a 2 h incubation time. The results are promising for the design of multifunctional MSNs as potential BNCT agents for clinical use.
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Affiliation(s)
- Chian-Hui Lai
- Department of Chemistry, National Tsing Hua University 101, Sec. 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan.
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17
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Wu CC, Han CC, Chang HC. Applications of Surface-Functionalized Diamond Nanoparticles for Mass-Spectrometry-Based Proteomics. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Lin PC, Yu CC, Wu HT, Lu YW, Han CL, Su AK, Chen YJ, Lin CC. A chemically functionalized magnetic nanoplatform for rapid and specific biomolecular recognition and separation. Biomacromolecules 2012. [PMID: 23198853 DOI: 10.1021/bm301567w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have developed a target-molecule-functionalized magnetic nanoparticle (MNP)-based method to facilitate the study of biomolecular recognition and separation. The superparamagnetic property of MNPs allows the corresponding biomolecules to be rapidly separated from crude biofluids with a significant improvement in recovery yield and specificity. Various MNPs functionalized with tag molecules (chitin, heparin, and amylose) were synthesized for recombinant protein purification, and several probe-functionalized MNPs, such as nitrilotriacetic acid (NTA)@MNP and P(k)@MNP, exhibited excellent extraction efficiency for proteins. In a cell recognition study, mannose-functionalized MNPs allowed specific purification of Escherichia coli with FimH adhesin on the surface. In an immunoprecipitation assay, the antibody-conjugated MNPs reduced the incubation time from 12 to 1 h while maintaining a comparable efficiency. The functionalized MNPs were also used in a membrane proteomic study that utilized the interaction between streptavidin-functionalized MNPs and biotinylated cell membrane proteins. Overall, the functionalized MNPs were demonstrated to be promising probes for the specific separation of targets from proteins to cells and proteomics.
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Affiliation(s)
- Po-Chiao Lin
- Department of Chemistry, National Sun Yat-sen University, 70, Lienhai Road, Kaohsiung 80424, Taiwan.
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Yeh PR, Tseng WL. Human serum albumin-coated gold nanoparticles for selective extraction of lysozyme from real-world samples prior to capillary electrophoresis. J Chromatogr A 2012; 1268:166-72. [DOI: 10.1016/j.chroma.2012.09.103] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/27/2012] [Accepted: 09/28/2012] [Indexed: 12/24/2022]
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Yang L, Zhang X, Ye M, Jiang J, Yang R, Fu T, Chen Y, Wang K, Liu C, Tan W. Aptamer-conjugated nanomaterials and their applications. Adv Drug Deliv Rev 2011; 63:1361-70. [PMID: 22016112 PMCID: PMC3245877 DOI: 10.1016/j.addr.2011.10.002] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 10/11/2011] [Accepted: 10/11/2011] [Indexed: 11/26/2022]
Abstract
The combination of aptamers with novel nanomaterials, including nanomaterial-based aptamer bioconjugates has attracted considerable interest and has led to a wide variety of applications. In this review, we discuss how a variety of nanomaterials, including gold, silica and magnetic nanoparticles, as well as carbon nanotubes, hydrogels, liposomes and micelles, have been used to functionalize aptamers for a variety of applications. These aptamer functionalized materials have led to advances in amplified biosensing, cancer cell-specific recognition, high-efficiency separation, and targeted drug delivery.
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Affiliation(s)
- Liu Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, PR China
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21
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Gold nanomaterials as a new tool for bioanalytical applications of laser desorption ionization mass spectrometry. Anal Bioanal Chem 2011; 402:601-23. [DOI: 10.1007/s00216-011-5120-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 05/13/2011] [Accepted: 05/17/2011] [Indexed: 10/18/2022]
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22
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Bakry R, Rainer M, Huck C, Bonn G. Protein profiling for cancer biomarker discovery using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and infrared imaging: A review. Anal Chim Acta 2011; 690:26-34. [DOI: 10.1016/j.aca.2011.01.044] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 01/18/2011] [Accepted: 01/20/2011] [Indexed: 10/18/2022]
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23
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006. MASS SPECTROMETRY REVIEWS 2011; 30:1-100. [PMID: 20222147 DOI: 10.1002/mas.20265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK.
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Fabrication and Applications of Glyconanomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 705:727-55. [DOI: 10.1007/978-1-4419-7877-6_38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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25
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Wu CS, Liu FK, Ko FH. Potential role of gold nanoparticles for improved analytical methods: an introduction to characterizations and applications. Anal Bioanal Chem 2010; 399:103-18. [DOI: 10.1007/s00216-010-4094-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/01/2010] [Accepted: 08/03/2010] [Indexed: 01/13/2023]
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26
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Kim MH, Choi YL, Heo JN, Min YK, Kim SH. Identification of Vimentin Binding to the Derivative of Saurolactam with Antiresorptive Activity by Using Its Chemical Affinity Probe. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.7.2047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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28
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Barrientos AG, Fuente JMDL, Jiménez M, Solís D, Cañada FJ, Martín-Lomas M, Penadés S. Modulating glycosidase degradation and lectin recognition of gold glyconanoparticles. Carbohydr Res 2009; 344:1474-8. [DOI: 10.1016/j.carres.2009.04.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Revised: 04/07/2009] [Accepted: 04/27/2009] [Indexed: 11/25/2022]
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30
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Miyachi A, Dohi H, Neri P, Mori H, Uzawa H, Seto Y, Nishida Y. Multivalent Galacto-trehaloses: Design, Synthesis, and Biological Evaluation under the Concept of Carbohydrate Modules. Biomacromolecules 2009; 10:1846-53. [DOI: 10.1021/bm900283x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akira Miyachi
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan, Faculty of Biomolecular Chemistry, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan, Department of Public Health Pharmacy, Gifu Pharmaceutical University, Gifu 502-8585, Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8586, Japan, and National Research Institute of Police Science (NRIPS), 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Hirofumi Dohi
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan, Faculty of Biomolecular Chemistry, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan, Department of Public Health Pharmacy, Gifu Pharmaceutical University, Gifu 502-8585, Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8586, Japan, and National Research Institute of Police Science (NRIPS), 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Paola Neri
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan, Faculty of Biomolecular Chemistry, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan, Department of Public Health Pharmacy, Gifu Pharmaceutical University, Gifu 502-8585, Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8586, Japan, and National Research Institute of Police Science (NRIPS), 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Hiroshi Mori
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan, Faculty of Biomolecular Chemistry, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan, Department of Public Health Pharmacy, Gifu Pharmaceutical University, Gifu 502-8585, Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8586, Japan, and National Research Institute of Police Science (NRIPS), 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Hirotaka Uzawa
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan, Faculty of Biomolecular Chemistry, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan, Department of Public Health Pharmacy, Gifu Pharmaceutical University, Gifu 502-8585, Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8586, Japan, and National Research Institute of Police Science (NRIPS), 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yasuo Seto
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan, Faculty of Biomolecular Chemistry, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan, Department of Public Health Pharmacy, Gifu Pharmaceutical University, Gifu 502-8585, Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8586, Japan, and National Research Institute of Police Science (NRIPS), 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yoshihiro Nishida
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan, Faculty of Biomolecular Chemistry, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan, Department of Public Health Pharmacy, Gifu Pharmaceutical University, Gifu 502-8585, Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8586, Japan, and National Research Institute of Police Science (NRIPS), 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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31
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Singh S, Patel P, Jaiswal S, Prabhune AA, Ramana CV, Prasad BLV. A direct method for the preparation of glycolipid–metal nanoparticle conjugates: sophorolipids as reducing and capping agents for the synthesis of water re-dispersible silver nanoparticles and their antibacterial activity. NEW J CHEM 2009. [DOI: 10.1039/b811829a] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Castellana ET, Sherrod SD, Russell DH. Nanoparticles for Selective Laser Desorption/Ionization in Mass Spectrometry. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.jala.2008.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The selective desorption/ionization of analytes using nanomaterials is investigated using metallic nanoparticles. By replacing the sodium citrate capping of gold nanoparticles with self-assembled monolayers, we are able to both enhance analyte ionization and selectively capture analytes. Capping gold nanoparticles with a monolayer of 4-mercaptobenzoic acid enhances analyte ionization while greatly decreasing chemical noise resulting from alkali adducted species. Selective capture and sequential desorption/ionization of the peptide bradykinin (1–7) from a two peptide mixture is achieved using β-cyclodextrin capped gold nanoparticles. Finally, by switching from gold to silver nanoparticles, we are able to ionize both folic acid and amphotericin B. These results demonstrate that through careful control of nanoparticle surface chemistry and composition one can achieve selective analyte ionization for MS applications.
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33
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Sudhir PR, Shrivas K, Zhou ZC, Wu HF. Single drop microextraction using silver nanoparticles as electrostatic probes for peptide analysis in atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry and comparison with gold electrostatic probes and silver hydrophobic probes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:3076-3086. [PMID: 18777509 DOI: 10.1002/rcm.3710] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Single drop microextraction using tetraalkylammonium bromide coated silver nanoparticles (SDME-AgNPs) prepared in toluene has been successfully applied as electrostatic affinity probes to preconcentrate peptide mixtures in biological samples prior to atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry (AP-MALDI-MS) analysis. This approach is based on the isoelectric point (pI) of peptides and surface charge of AgNPs. Using the SDME-AgNPs technique, from a peptide mixture, Met- and Leu-enkephalins (Met-enk and Leu-enk) were extracted into a droplet of toluene containing AgNPs, but not the neutral peptides (gramicidins). The best peptide extraction efficiency for SDME-AgNPs was observed with the optimized parameters: extraction time 2 min, sample agitation rate 240 rpm, and sample pH 7. The limits of detection (LODs) of the SDME-AgNPs/AP-MALDI-MS technique for Met-enk and Leu-enk peptides were 160 and 210 nM, respectively. Furthermore, the application of the technique has been shown for the analysis of peptides from a sample containing high matrix interferences such as 1% Triton X-100 and 6 M urea. Finally, this approach has been compared with the SDME-AuNPs technique and the results have clearly revealed that the SDME-AgNP affinity probe exhibits higher affinity to extract the sulfur-bearing peptide (Met-enk). We also compared this electrostatic affinity probe of AgNPs with the previously demonstrated hydrophobic affinity probe of AgNPs and found that the electrostatic probe can greatly reduce the extraction time from 1.5 h to 2 min. This is due to the fact that electrostatic attraction forces are much stronger than the hydrophobic attraction forces. Therefore, we concluded that the electrostatic affinity probe based on SDME-AgNPs coupled with AP-MALDI-MS is a high-throughput technique for the analysis of low-abundance peptides from biological samples containing complex matrices.
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Affiliation(s)
- Putty-Reddy Sudhir
- Graduate Institute of Life Sciences, Tamkang University, Tamsui 251, Taiwan
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34
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Aili D, Enander K, Baltzer L, Liedberg B. Assembly of polypeptide-functionalized gold nanoparticles through a heteroassociation- and folding-dependent bridging. NANO LETTERS 2008; 8:2473-2478. [PMID: 18578553 DOI: 10.1021/nl8014796] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Gold nanoparticles were functionalized with a synthetic polypeptide, de novo-designed to associate with a charge complementary linker polypeptide in a folding-dependent manner. A heterotrimeric complex that folds into two disulphide-linked four-helix bundles is formed when the linker polypeptide associates with two of the immobilized peptides. The heterotrimer forms in between separate particles and induces a rapid and extensive aggregation with a well-defined interparticle spacing. The aggregated particles are redispersed when the disulphide bridge in the linker polypeptide is reduced.
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Affiliation(s)
- Daniel Aili
- Division of Sensor Science and Molecular Physics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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35
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Wei H, Chen C, Han B, Wang E. Enzyme Colorimetric Assay Using Unmodified Silver Nanoparticles. Anal Chem 2008; 80:7051-5. [DOI: 10.1021/ac801144t] [Citation(s) in RCA: 268] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui Wei
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Chaogui Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Bingyan Han
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
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36
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Chien YY, Jan MD, Adak AK, Tzeng HC, Lin YP, Chen YJ, Wang KT, Chen CT, Chen CC, Lin CC. Globotriose-functionalized gold nanoparticles as multivalent probes for Shiga-like toxin. Chembiochem 2008; 9:1100-9. [PMID: 18398881 DOI: 10.1002/cbic.200700590] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Compared to monovalent carbohydrates, multivalent carbohydrate ligands exhibit significantly enhanced binding affinities to their interacting proteins. Here, we report globotriose (P(k) ligand)-functionalized gold nanoparticle (AuNP) probes for the investigation of multivalent interactions with the B(5) subunit of Shiga-like toxin I (B-Slt). Six P(k)-ligand-encapsulated AuNPs (P(k)-AuNPs) of varying particle size and linker length were synthesized and evaluated for their potential as multivalent affinity probes by using a surface plasmon resonance competition assay. The affinity of these probes for the interacting proteins was greatly affected by nanoparticle size, linker length, and ligand density on nanoparticle surface. For example, the 20-nm 20-P(k)-l-AuNP, which had a relatively long linker showed a >10(8)-fold increase in affinity compared with the mono P(k) ligand. This intrinsic high-affinity AuNP probe specifically captured the recombinant B-Slt from Escherichia coli lysate, and the resulting purity of the B-Slt was >95 %. We also developed a robust P(k)-AuNP-based detection method for Slt-I by combining the technique with silver enhancement.
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Affiliation(s)
- Yuh-Yih Chien
- Institute of Chemistry, and Genomics Research Centre, Academia Sinica, 128 Taipei, Taiwan
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37
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Park S, Lee MR, Shin I. Chemical tools for functional studies of glycans. Chem Soc Rev 2008; 37:1579-91. [DOI: 10.1039/b713011m] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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38
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Srinivasan B, Huang X. Functionalization of magnetic nanoparticles with organic molecules: Loading level determination and evaluation of linker length effect on immobilization. Chirality 2008; 20:265-77. [PMID: 17568438 DOI: 10.1002/chir.20418] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A general method is introduced to immobilize organic molecules on magnetic nanoparticles through silanization reactions and determine the maximum loading level by UV-vis spectroscopy. Loading levels of 1.5 x 10(-3) mol per gram of nanoparticle were obtained with structurally diverse compounds such as rhodamine B and glucosamine. The length of the linker did not have a significant effect on loading as comparable maximum amounts of rhodamine B were immobilized on magnetic nanoparticles regardless of the linker length. Interestingly, rhodamine B derivatives lost conjugation during synthetic manipulations due to reversible spiroisobenzofuran formation. Full regeneration of conjugation was found to be slow with rhodamine B attached on magnetic nanoparticles. The results obtained from these studies will be useful for studying surface functionalization of MNPs in general.
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39
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Kumaraswamy G, Ankamma K, Pitchaiah A. Tandem Epoxide or Aziridine Ring Opening by Azide/Copper Catalyzed [3+2] Cycloaddition: Efficient Synthesis of 1,2,3-Triazolo β-Hydroxy or β-Tosylamino Functionality Motif. J Org Chem 2007; 72:9822-5. [DOI: 10.1021/jo701724f] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gullapalli Kumaraswamy
- Organic Division III, Fine Chemicals Laboratory, Indian Institute of Chemical Technology, Hyderabad-500 007, India ;
| | - Kukkadapu Ankamma
- Organic Division III, Fine Chemicals Laboratory, Indian Institute of Chemical Technology, Hyderabad-500 007, India ;
| | - Arigala Pitchaiah
- Organic Division III, Fine Chemicals Laboratory, Indian Institute of Chemical Technology, Hyderabad-500 007, India ;
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40
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Kasture M, Singh S, Patel P, Joy PA, Prabhune AA, Ramana CV, Prasad BLV. Multiutility sophorolipids as nanoparticle capping agents: synthesis of stable and water dispersible Co nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:11409-11412. [PMID: 17935370 DOI: 10.1021/la702931j] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Sophorolipids are a class of glycolipids that can be obtained from fatty acids by simply treating them with yeast cells (Candida bombicola, ATCC 22214) and glucose. In this letter, we demonstrate the application of sophorolipids obtained from oleic acid as a capping agent for Co nanoparticles. Upon capping the nanoparticle surface, the sugar moiety of these sophorolipids is exposed to the solvent environment, making the nanoparticles stable and water-redispersible.
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Affiliation(s)
- Manasi Kasture
- Materials Chemistry Division, National Chemical Laboratory, Pune-411 008, India
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41
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Turner RA, Oliver AG, Lokey RS. Click Chemistry as a Macrocyclization Tool in the Solid-Phase Synthesis of Small Cyclic Peptides. Org Lett 2007; 9:5011-4. [DOI: 10.1021/ol702228u] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rushia A. Turner
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, 1156 High Street, Santa Cruz, California 95064
| | - Allen G. Oliver
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, 1156 High Street, Santa Cruz, California 95064
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, 1156 High Street, Santa Cruz, California 95064
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42
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Pirali T, Tron GC, Zhu J. One-pot synthesis of macrocycles by a tandem three-component reaction and intramolecular [3+2] cycloaddition. Org Lett 2007; 8:4145-8. [PMID: 16928095 DOI: 10.1021/ol061782p] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
By combining three appropriately designed simple substrates, a programmed sequence involving an alpha-isocyano acetamide-based three-component reaction followed by a copper-catalyzed intramolecular [3+2] cycloaddition of alkyne and azide took place to afford complex macrocycles in moderate to good yields. One macrocycle and two heterocycles were produced with concurrent formation of five chemical bonds in this operationally simple process.
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Affiliation(s)
- Tracey Pirali
- Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche and Drug and Food Biotechnology Center, Università degli Studi del Piemonte Orientale A. Avogadro, Via Bovio 6, 28100 Novara, Italy
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43
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Zhao W, Chiuman W, Brook MA, Li Y. Simple and rapid colorimetric biosensors based on DNA aptamer and noncrosslinking gold nanoparticle aggregation. Chembiochem 2007; 8:727-31. [PMID: 17410623 DOI: 10.1002/cbic.200700014] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Weian Zhao
- Department of Chemistry, McMaster University, 1280 Main St., W. Hamilton, ON, L8S 4M1, Canada
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44
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Han SY, Hwan Kim S. Introduction to Chemical Proteomics for Drug Discovery and Development. Arch Pharm (Weinheim) 2007; 340:169-77. [PMID: 17351965 DOI: 10.1002/ardp.200600153] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A fundamental goal of chemical proteomics is to identify target proteins for bioactive small molecules and then apply them to drug discovery and development as valid and drugable targets. Here, we introduce integrated technologies for the rapid identification of target proteins, methodologies for validating them as drugable targets, and applications of chemical proteomics in drug discovery and development.
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Affiliation(s)
- Sung-Young Han
- Department of Chemistry, University of Texas at Dallas, Richardson, TX, USA
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45
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Step by step towards understanding gold glyconanoparticles as elements of the nanoworld. CHEMICAL PAPERS 2007. [DOI: 10.2478/s11696-007-0029-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AbstractGold glyconanoparticles as elements of the nanoworld belong to a group of particles with diameters not exceeding 100 nm. This size scale makes them conformable to common biomolecules. A gold glyconanoparticle consists of three different parts: the gold core, the linkers, and saccharide ligands. The glycocalyx-like surface of these particles mimics the presentation of carbohydrate epitopes of cell surface glycoconjugates. As a consequence, gold glyconanoparticles provide inimitable tools for probing and manipulating the mechanisms of biological processes based on carbohydrate interactions. Each component of the gold glyconanoparticle has a profound effect on the nanoparticle’s properties. Therefore, in this review, elucidation of the overall behavior and properties of gold glyconanoparticles is based on a step by step (component by component) description of the system.
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46
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Whiting M, Tripp JC, Lin YC, Lindstrom W, Olson AJ, Elder JH, Sharpless KB, Fokin VV. Rapid Discovery and Structure−Activity Profiling of Novel Inhibitors of Human Immunodeficiency Virus Type 1 Protease Enabled by the Copper(I)-Catalyzed Synthesis of 1,2,3-Triazoles and Their Further Functionalization. J Med Chem 2006; 49:7697-710. [PMID: 17181152 DOI: 10.1021/jm060754+] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Building from the results of a computational screen of a range of triazole-containing compounds for binding efficiency to human immunodeficiency virus type 1 protease (HIV-1-Pr), a novel series of potent inhibitors has been developed. The copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), which provides ready access to 1,4-disubstituted-1,2,3-triazoles, was used to unite a focused library of azide-containing fragments with a diverse array of functionalized alkyne-containing building blocks. In combination with direct screening of the crude reaction products, this method led to the rapid identification of a lead structure and readily enabled optimization of both azide and alkyne fragments. Replacement of the triazole with a range of alternative linkers led to greatly reduced protease inhibition; however, further functionalization of the triazoles at the 5-position gave a series of compounds with increased activity, exhibiting Ki values as low as 8 nM.
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Affiliation(s)
- Matthew Whiting
- Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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47
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Bock VD, Perciaccante R, Jansen TP, Hiemstra H, van Maarseveen JH. Click chemistry as a route to cyclic tetrapeptide analogues: synthesis of cyclo-[Pro-Val-psi(triazole)-Pro-Tyr]. Org Lett 2006; 8:919-22. [PMID: 16494474 DOI: 10.1021/ol053095o] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the plethora of techniques to cyclize small peptides, a synthesis of cyclo-[(L)Pro-(L)Tyr-(L)Pro-(L)Val], a potent tyrosinase inhibitor, remains elusive because of the unfavorable transition state leading to the cyclic product. Herein, we report the successful synthesis of its triazole analogue, cyclo-[(L)Pro-(L)Val-psi(triazole)-(L)Pro-(L)Tyr]. Attempted cyclization via peptide bond formation at room temperature fails to provide the desired product, but Cu(I)-catalyzed alkyne-azide coupling at 110 degrees C affords the triazole tetrapeptide in 70% yield, demonstrating the utility of "click" chemistry.
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Affiliation(s)
- Victoria D Bock
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands
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48
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Interaction of a Novel Biotin-tagged Photoaffinity Probe with Its Target Protein, VEGFR-2. B KOREAN CHEM SOC 2006. [DOI: 10.5012/bkcs.2006.27.9.1285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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49
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Aly MRE, Rochaix P, Amessou M, Johannes L, Florent JC. Synthesis of globo- and isoglobotriosides bearing a cinnamoylphenyl tag as novel electrophilic thiol-specific carbohydrate reagents. Carbohydr Res 2006; 341:2026-36. [PMID: 16777082 DOI: 10.1016/j.carres.2006.03.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Revised: 03/07/2006] [Accepted: 03/07/2006] [Indexed: 10/24/2022]
Abstract
The galactosyl donor, 4,6-di-O-acetyl-2,3-di-O-benzyl-D-galactopyranosyl trichloroacetimidate, was efficiently coupled with regioselectively benzylated lactoside acceptors under standard conditions to stereoselectively afford the corresponding globotrioside and isoglobotrioside derivatives in very good yields. These glycosides were smoothly functionalized with a 6-(p-cinnamoylphenoxy)-hexyl tether tag as novel electrophilic thiol-specific carbohydrate reagents. Immobilization of the globotrioside conjugate to Thiopropyl Sepharose 6B for purification of B-subunit of Shiga toxin (StxB) and coupling of a model cysteine-containing protein (StxB-Z(n)-Cys) to the isoglobotrioside conjugate were both performed with high efficiency.
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Affiliation(s)
- Mohamed R E Aly
- Laboratoire de Chimie UMR 176 CNRS-Institut Curie, 26 rue d'Ulm, F-75248 Paris, France
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50
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Larsen K, Thygesen MB, Guillaumie F, Willats WGT, Jensen KJ. Solid-phase chemical tools for glycobiology. Carbohydr Res 2006; 341:1209-34. [PMID: 16716275 DOI: 10.1016/j.carres.2006.04.045] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 04/25/2006] [Accepted: 04/28/2006] [Indexed: 11/16/2022]
Abstract
Techniques involving solid supports have played crucial roles in the development of genomics, proteomics, and in molecular biology in general. Similarly, methods for immobilization or attachment to surfaces and resins have become ubiquitous in sequencing, synthesis, analysis, and screening of oligonucleotides, peptides, and proteins. However, solid-phase tools have been employed to a much lesser extent in glycobiology and glycomics. This review provides a comprehensive overview of solid-phase chemical tools for glycobiology including methodologies and applications. We provide a broad perspective of different approaches, including some well-established ones, such as immobilization in microtiter plates and to cross-linked polymers. Emerging areas such as glycan microarrays and glycan sequencing, quantum dots, and gold nanoparticles for nanobioscience applications are also discussed. The applications reviewed here include enzymology, immunology, elucidation of biosynthesis, and systems biology, as well as first steps toward solid-supported sequencing. From these methods and applications emerge a general vision for the use of solid-phase chemical tools in glycobiology.
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Affiliation(s)
- Kim Larsen
- Department of Natural Sciences, Section for Bioorganic Chemistry, Royal Veterinary and Agricultural University, DK-1871 Frederiksberg, Denmark
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