1,720,984 research outputs found
A Combination of Bio-Orthogonal Supramolecular Clicking and Proximity Chemical Tagging as a Supramolecular Tool for Discovery of Putative Proteins Associated with Laminopathic Disease
No full textProtein mutations alter protein-protein interactions that can lead to a number of illnesses. Mutations in lamin A (LMNA) have been reported to cause laminopathies. However, the proteins associated with the LMNA mutation have mostly remained unexplored. Herein, a new chemical tool for proximal proteomics is reported, developed by a combination of proximity chemical tagging and a bio-orthogonal supramolecular latching based on cucurbit[7]uril (CB[7])-based host-guest interactions. As this host-guest interaction acts as a noncovalent clickable motif that can be unclicked on-demand, this new chemical tool is exploited for reliable detection of the proximal proteins of LMNA and its mutant that causes laminopathic dilated cardiomyopathy (DCM). Most importantly, a comparison study reveals, for the first time, mutant-dependent alteration in LMNA proteomic environments, which allows to identify putative laminopathic DCM-linked proteins including FOXJ3 and CELF2. This study demonstrates the feasibility of this chemical tool for reliable proximal proteomics, and its immense potential as a new research platform for discovering biomarkers associated with protein mutation-linked diseases.11Nsciescopu
Supramolecular latching system based on ultrastable synthetic binding pairs as versatile tools for protein imaging
Full text linkAbstractHere we report ultrastable synthetic binding pairs between cucurbit[7]uril (CB[7]) and adamantyl- (AdA) or ferrocenyl-ammonium (FcA) as a supramolecular latching system for protein imaging, overcoming the limitations of protein-based binding pairs. Cyanine 3-conjugated CB[7] (Cy3-CB[7]) can visualize AdA- or FcA-labeled proteins to provide clear fluorescence images for accurate and precise analysis of proteins. Furthermore, controllability of the system is demonstrated by treating with a stronger competitor guest. At low temperature, this allows us to selectively detach Cy3-CB[7] from guest-labeled proteins on the cell surface, while leaving Cy3-CB[7] latched to the cytosolic proteins for spatially conditional visualization of target proteins. This work represents a non-protein-based bioimaging tool which has inherent advantages over the widely used protein-based techniques, thereby demonstrating the great potential of this synthetic system.</jats:p
Supra-blot: An accurate and reliable assay for detecting target proteins with a synthetic host molecule-enzyme hybrid
No full text© 2020 The Royal Society of Chemistry.In accordance with the rapid increase in demand for selective and spatial chemical tagging, and accurate detection of proteins of interest, we develop a sensitive protein detection method, termed "Supra-blot" capitalizing on high-affinity host-guest interaction between cucurbit[7]uril (CB[7]) and adamantylammonium (AdA). The method can directly detect chemically tagged proteins without false-positive signals caused by endogenous biomolecules. Not only a single specific protein, but also spatially localized proteins in cells were labeled with AdA, and selectively detected by a host molecule-enzyme hybrid, CB[7]-conjugated horseradish peroxidase (CB[7]-HRP) generating amplified chemiluminescence signals. This study shows the great potential of Supra-blot for accurate and reliable detection of proteins of interest in cell
Autophagy Caught in the Act: A Supramolecular FRET Pair Based on an Ultrastable Synthetic Host-Guest Complex Visualizes Autophagosome-Lysosome Fusion
No full textA supramolecular FRET pair based on the ultrahigh binding affinity between cyanine 3 conjugated cucurbit[7]uril (CB[7]-Cy3) and cyanine 5 conjugated adamantylamine (AdA-Cy5) was exploited as a new synthetic tool for imaging cellular processes in live cells. Confocal laser scanning microscopy revealed that CB[7]-Cy3 and AdA-Cy5 were intracellularly translocated and accumulated in lysosomes and mitochondria, respectively. CB[7]-Cy3 and AdA-Cy5 then formed a host-guest complex, reported by a FRET signal, as a result of the fusion of lysosomes and mitochondria. This observation not only indicated that CB[7] forms a stable complex with AdA in a live cell, but also suggested that this FRET pair can visualize dynamic organelle fusion processes, such as those involved in the degradation of mitochondria through autophagy (mitophagy), by virtue of its small size, chemical stability, and ease of us
Direct Profiling the Post-Translational Modification Codes of a Single Protein Immobilized on a Surface Using Cu-free Click Chemistry
Full text linkCombinatorial
post-translational modifications (PTMs), which can
serve as dynamic “molecular barcodes”, have been proposed
to regulate distinct protein functions. However, studies of combinatorial
PTMs on single protein molecules have been hindered by a lack of suitable
analytical methods. Here, we describe erasable single-molecule blotting
(eSiMBlot) for combinatorial PTM profiling. This assay is performed
in a highly multiplexed manner and leverages the benefits of covalent
protein immobilization, cyclic probing with different antibodies,
and single molecule fluorescence imaging. Especially, facile and efficient
covalent immobilization on a surface using Cu-free click chemistry
permits multiple rounds (>10) of antibody erasing/reprobing without
loss of antigenicity. Moreover, cumulative detection of coregistered
multiple data sets for immobilized single-epitope molecules, such
as HA peptide, can be used to increase the antibody detection rate.
Finally, eSiMBlot enables direct visualization and quantitative profiling
of combinatorial PTM codes at the single-molecule level, as we demonstrate
by revealing the novel phospho-codes of ligand-induced epidermal growth
factor receptor. Thus, eSiMBlot provides an unprecedentedly simple,
rapid, and versatile platform for analyzing the vast number of combinatorial
PTMs in biological pathways
Raman Scattering of 4-Aminobenzenethiol and Its Analog Molecules on Ag, Au, and Pt Nanostructures: Contribution of Photoinduced Charge-Transfer
Full text link학위논문 (박사)-- 서울대학교 대학원 : 화학부, 2013. 2. 김관.The surface-enhanced Raman scattering (SERS) of 4-aminobenzenehtiol (4-ABT) has seen a surge of interest recently, since its SERS spectral features are dependent not only on the kinds of SERS substrates but also on the measurement conditions. A problem was initially encountered in the interpretation of the SERS spectrum of 4-ABT due to difficulty in correlating several peaks therein with the normal Raman peaks, but the SERS spectral pattern of 4-ABT looked similar to that of 4,4′-dimercaptoazobenzene (4,4′-DMAB). To clarify the issue, the SERS characteristics of 4-ABT and its analog molecules adsorbed on metal surfaces are carefully reinvestigated to understand the charge-transfer chemical enhancement mechanism in this Ph.D. thesis.
In chapter 1, the general overview of the Raman scattering theory and SERS mechanisms are described concisely. SERS is an abnormal surface optical phenomenon resulting in strongly increased Raman signals for molecules adsorbed onto nanostructured coinage metals. In recent years, it has been reported that even single-molecule detection is possible by surface-enhanced resonance Raman scattering (SERRS), suggesting that the enhancement factor (EF) can reach as much as 1014-1015. Two enhancement mechanisms, one called a long-range electromagnetic (EM) effect and the other called a short-range charge-transfer (CT) chemical effect, are simultaneously operative. Both mechanisms suggest the possibility of enhanced absorption and enhanced photochemistry for surface-adsorbed molecules.
In chapter 2, the current status of SERS studies on 4-ABT are described. For a long time, 4-ABT, also known as p-aminothiophenol (PATP) or p-mercaptoaniline (pMA), is one of the important surface probe molecules in SERS community and the nanoscience field. The main reasons are that 4-ABT molecules are strongly and easily adsorbed onto the most metal substrates and generate a strong and unique SERS signal which is very sensitive to the type of substrates and measurement conditions. The normal Raman (NR) spectrum of 4-ABT is mostly featureless in the region of 1100~1500 cm-1, but three to four peaks appear newly in that region in its SERS spectra. Since these peaks can be assigned to the b2-type vibration, which are arising from charge transfer process through the Herzberg-Teller vibronic coupling term, 4-ABT has been regarded for two decades as a model adsorbate for probing the CM effect in SERS. Very recently, however, a number of researchers have come up with a different explanation for the appearance of these b2-type bands that the b2-type bands appearing in the SERS of 4-ABT must be the N=N stretching vibrations of 4,4-DMAB produced from 4-ABT via a catalytic coupling reaction on the metal substrates. The elucidation of the SERS characteristics of 4-ABT and its analog molecules including 4,4-DMAB is thus needed to see another or why we have made a wrong assignment during the past 15 years.
In chapter 3, the SERS characteristics of 4-ABT and 4-ABT adsorbed on Pt nanoparticles are investigated. Pt is a well-known catalyst that has a high catalytic activity. It is found, however, that 4-nitrobenzenethiol (4-NBT) is barely subjected to photoreaction on a Pt surface. On the contrary, the SERS spectra of 4-ABT on Pt clearly show that the b2-type bands are increasing in relative intensity toward shorter wavelength. In addition, the SERS spectral pattern of 4-ABT on Pt is variable not only with changes in the electrode potential but also by altering the excitation wavelength. These spectral variations could be understood by presuming that the chemical enhancement mechanism is also operating in this system, along with the electromagnetic enhancement. Interestingly, similar spectral variation is also observed even under ambient conditions by exposure of 4-ABT on Ag to volatile organic chemicals (VOCs) such as acetone and ammonia. Based on the potential-dependent SERS data, the effect of acetone appeared to correspond to an application of +0.15 V to the Ag substrate vs a saturated Ag/AgCl electrode, while the effect of ammonia corresponded to the application of -0.45 V to Ag.
In chapter 4, as one of several attempts to explore the origin of the b2-type bands observable in the SERS of 4-ABT, the pH dependence has been investigated. Consulting the claim that those b2-type bands might be associated with a surface-induced photoreaction product such as 4,4′-DMAB, the pH dependence of the SERS spectral feature of 4,4′-DMAB was also examined. Distinct differences were observed in the SERS spectra of 4-ABT and 4,4′-DMAB. The SERS spectral feature of 4,4′-DMAB had virtually no dependence either on the excitation wavelength or on the kind of metal substrate or even on the solution pH. On the other hand, the SERS spectral pattern of 4-ABT displayed substantial changes, depending not only on the excitation wavelength and the kind of SERS substrates but also on the solution pH. It is presumed that when the amine group of 4-ABT is protonated at acidic pHs, the electron population in the benzene ring moiety decreases, resulting in the up-shift of the LUMO level of 4-ABT, as revealed by UV-vis spectra and from an ab initio calculation, thereby prohibiting the charge transfer resonance chemical enhancement.
In chapter 5, the similarity and dissimilarity in the SERS of 4-ABT and 4,4′-DMAB, along with the SERS spectrum of their analog molecule 4,4′-dimercaptohydrazobenzene (4,4′-DMHAB) were carefully examined. Under ambient conditions, the SERS spectra of 4-ABT, 4,4′-DMAB, and 4,4′-DMHAB on Ag looked in fact comparable to one another, but the spectral dissimilarity was evidenced not only from the SERS spectra taken after treating the probing substrates with a borohydride solution but also from the potential-dependent SERS spectra. It was found that 4,4′-DMAB on Ag could convert to 4-ABT not only by contact with a 100 mM borohydride but also by lowering the potential below -1.0 V. The reverse reaction from 4-ABT on Ag to 4,4′-DMAB appeared insignificant electrochemically as well as photochemically. Furthermore, it was found that the conversion of 4,4′-DMAB to 4-ABT on Ag is a more feasible process upon irradiation with a 514.5-nm (not 632.8-nm) laser under ambient conditions. The SERS spectral pattern of 4,4-DMAB on Ag varied as a function of laser irradiation time, finally becoming the same as that of 4-ABT on Ag. The photoconversion of 4,4-DMAB upon 514.5-nm radiation was further confirmed not only by the coupling reaction with 4-cyanobenzoic acid to form amide bonds but also by the selective growth of calcium carbonate.
After considering all the experiments conducted in the work, it is concluded that the appearance of the so-called b2-type bands in the SERS of 4-ABT must be attributed wholly to the involvement of the chemical enhancement mechanism, not due to the formation of 4,4′-DMAB.Contents
Abstract (i)
Contents (vi)
List of Figures (x)
List of Tables (xxi)
List of Scheme (xxi)
Chapter 1. General Concepts (1)
1. Raman Scattering Theory (2)
2. Raman Spectroscopy (5)
3. Surface-enhanced Raman Scattering (SERS) (7)
4. The Electromagnetic Theory of SERS (9)
5. SERS from Transition Metal (15)
6. The Chemical Enhancement Theory of SERS (18) References (24)
Chapter 2. History of 4-Aminobenzenethiol (4-ABT) from SERS Field (28)
1. Introduction (29)
2. United Experimental Section (34)
3. References (40)
Chapter 3. The SERS of 4-ABT on Pt and The Volatile Organic Chemicals (VOCs) Effects of 4-ABT on Ag (43)
3-1. SERS on Aggregates of Pt Nanoparticles with Definite Size (44)
1. Introduction (44)
2. Results and Discussion (46)
3. Summary and Conclusion (61)
4. References (62)
3-2. Effect of VOCs on SERS of 4-ABT on Ag: Comparison with the Potential Dependence (65)
1. Introduction (65)
2. Results and Discussion (68)
3. Summary and Conclusion (79)
4. References (81)
Chapter 4. SERS of 4-ABT And 4,4-Dimercaptoazobenzene (4,4′-DMAB) on Ag And Au: pH Dependence of b2-Type Bands (84)
1. Introduction (85)
2. Results and Discussion (87)
3. Summary and Conclusion (97)
4. References (98)
Chapter 5. Similarity and Dissimilarity in SERS of 4-ABT And Its Analog molecules (100)
5-1. Similarity And Dissimilarity in SERS of 4-ABT, 4,4-DMAB, And 4,4-Dimercaptohydrazobenzene (4,4-DMHAB) on Ag (101)
1. Introduction (101)
2. Results and Discussion (104)
3. Summary and Conclusion (118)
4. References (119)
5-2. Photoreduction of 4,4-DMAB on Ag Revealed by Raman Scattering Spectroscopy (122)
1. Introduction (122)
2. Results and Discussion (125)
3. Summary and Conclusion (138)
4. References (142)
5-3. Visible-Light Response of 4-ABT and 4,4-DMAB Silver Salts (145)
1. Introduction (145)
2. Results and Discussion (147)
3. Summary and Conclusion (160)
4. References (161)
IV. Appendix
1. List of Publications (164)
2. List of Presentations (167)
Abstract (Korean) (169)Docto
Iodide-Selective Synthetic Ion Channels Based on Shape-Persistent Organic Cages
No full textWe report here a synthetic ion channel developed from a shape-persistent porphyrin-based covalent organic cage. The cage was synthesized by employing a synthetically economical dynamic covalent chemistry (DCC) approach. The organic cage selectively transports biologically relevant iodide ions over other inorganic anions by a dehydration-driven, channel mechanism as evidenced by vesicle-based fluorescence assays and planar lipid bilayer-based single channel recordings. Furthermore, the organic cage appears to facilitate iodide transport across the membrane of a living cell, suggesting that the cage could be useful as a biological tool that may replace defective iodide channels in living systems. © 2017 American Chemical Society101
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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