51
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Friscourt F, Fahrni CJ, Boons GJ. A fluorogenic probe for the catalyst-free detection of azide-tagged molecules. J Am Chem Soc 2012; 134:18809-15. [PMID: 23095037 DOI: 10.1021/ja309000s] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fluorogenic reactions in which non- or weakly fluorescent reagents produce highly fluorescent products can be exploited to detect a broad range of compounds including biomolecules and materials. We describe a modified dibenzocyclooctyne that under catalyst-free conditions undergoes fast strain-promoted cycloadditions with azides to yield strongly fluorescent triazoles. The cycloaddition products are more than 1000-fold brighter compared to the starting cyclooctyne, exhibit large Stokes shift, and can be excited above 350 nm, which is required for many applications. Quantum mechanical calculations indicate that the fluorescence increase upon triazole formation is due to large differences in oscillator strengths of the S(0) ↔ S(1) transitions in the planar C(2v)-symmetric starting material compared to the symmetry-broken and nonplanar cycloaddition products. The new fluorogenic probe was successfully employed for labeling of proteins modified by an azide moiety.
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Affiliation(s)
- Frédéric Friscourt
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30602, United States
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52
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Shaw BF, Schneider GF, Whitesides GM. Effect of surfactant hydrophobicity on the pathway for unfolding of ubiquitin. J Am Chem Soc 2012; 134:18739-45. [PMID: 23095057 DOI: 10.1021/ja3079863] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This paper describes the interaction between ubiquitin (UBI) and three sodium n-alkyl sulfates (SC(n)S) that have the same charge (Z = -1) but different hydrophobicity (n = 10, 12, or 14). Increasing the hydrophobicity of the n-alkyl sulfate resulted in (i) an increase in the number of distinct intermediates (that is, complexes of UBI and surfactant) that form along the pathway of unfolding, (ii) a decrease in the minimum concentrations of surfactant at which intermediates begin to form (i.e., a more negative ΔG(binding) of surfactant for UBI), and (iii) an increase in the number of surfactant molecules bound to UBI in each intermediate or complex. These results demonstrate that small changes in the hydrophobicity of a surfactant can significantly alter the binding interactions with a folded or unfolded cytosolic protein.
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Affiliation(s)
- Bryan F Shaw
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.
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53
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McLeod D, McNulty J. Mild Chemical and Biological Synthesis of Donor-Acceptor Flanked Reporter Stilbenes: Demonstration of a Physiological Wittig Olefination Reaction. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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54
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Tandem photoaffinity labeling-bioorthogonal conjugation in medicinal chemistry. Bioorg Med Chem 2012; 20:6237-47. [PMID: 23026086 DOI: 10.1016/j.bmc.2012.09.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/30/2012] [Accepted: 09/05/2012] [Indexed: 12/24/2022]
Abstract
Photoaffinity labeling has a longstanding history as a powerful biochemical technique. However, photoaffinity labeling has significantly evolved over the past decade principally due to its coupling with bioorthogonal/click chemistry reactions. This review aims to highlight tandem photoaffinity labeling-bioorthogonal conjugation as a chemical approach in medicinal chemistry and chemical biology. In particular, recent examples of using this strategy for affinity-based protein profiling (AfBPP), drug target identification, binding ensemble profiling, studying endogenous biological molecules, and imaging applications will be presented. Additionally, recent advances in the development of 'all-in-one' compact moieties possessing a photoreactive group and clickable handle will be discussed.
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55
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Chakrabarty R, Stang PJ. Post-assembly functionalization of organoplatinum(II) metallacycles via copper-free click chemistry. J Am Chem Soc 2012; 134:14738-41. [PMID: 22917086 DOI: 10.1021/ja3070073] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe the use of a strain-promoted copper-free click reaction in the post-self-assembly functionalization of organoplatinum(II) metallacycles. The coordination-driven self-assembly of a 120° cyclooctyne-tethered dipyridyl donor with 60° and 120° di-Pt(II) acceptors forms molecular rhomboids and hexagons bearing cyclooctynes. These species undergo post-self-assembly [3+2] Huisgen cycloaddition with a variety of azides to give functionalized ensembles under mild conditions.
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Affiliation(s)
- Rajesh Chakrabarty
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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56
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McNulty J, Keskar K. Discovery of a Robust and Efficient Homogeneous Silver(I) Catalyst for the Cycloaddition of Azides onto Terminal Alkynes. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200930] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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57
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Yang J, Šečkutė J, Cole CM, Devaraj NK. Live-cell imaging of cyclopropene tags with fluorogenic tetrazine cycloadditions. Angew Chem Int Ed Engl 2012; 51:7476-9. [PMID: 22696426 PMCID: PMC3431913 DOI: 10.1002/anie.201202122] [Citation(s) in RCA: 264] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 04/26/2012] [Indexed: 01/04/2023]
Affiliation(s)
- Jun Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA), Homepage: http://devarajgroup.ucsd.edu/
| | - Jolita Šečkutė
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA), Homepage: http://devarajgroup.ucsd.edu/
| | - Christian M. Cole
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA), Homepage: http://devarajgroup.ucsd.edu/
| | - Neal K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 (USA), Homepage: http://devarajgroup.ucsd.edu/
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58
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Yang J, Šečkutė J, Cole CM, Devaraj NK. Live-Cell Imaging of Cyclopropene Tags with Fluorogenic Tetrazine Cycloadditions. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202122] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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59
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Demchenko AP. Modern views on the structure and dynamics of biological membranes. ACTA ACUST UNITED AC 2012. [DOI: 10.7124/bc.000029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- A. P. Demchenko
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine
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60
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Lamani M, Devadig P, Prabhu KR. A non-metal catalysed oxidation of primary azides to nitriles at ambient temperature. Org Biomol Chem 2012; 10:2753-9. [DOI: 10.1039/c2ob06949k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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61
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Ito H, Kamachi T, Yashima E. Specific surface modification of the acetylene-linked glycolipid vesicle by click chemistry. Chem Commun (Camb) 2012; 48:5650-2. [DOI: 10.1039/c2cc31666h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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62
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Loosli F, Doval DA, Grassi D, Zaffalon PL, Favarger F, Zumbuehl A. Clickosomes—using triazole-linked phospholipid connectors to fuse vesicles. Chem Commun (Camb) 2012; 48:1604-6. [DOI: 10.1039/c2cc16827h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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63
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Bostic HE, Smith MD, Poloukhtine AA, Popik VV, Best MD. Membrane labeling and immobilization viacopper-free click chemistry. Chem Commun (Camb) 2012; 48:1431-3. [DOI: 10.1039/c1cc14415d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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64
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Rowland MM, Gong D, Bostic HE, Lucas N, Cho W, Best MD. Microarray analysis of Akt PH domain binding employing synthetic biotinylated analogs of all seven phosphoinositide headgroup isomers. Chem Phys Lipids 2011; 165:207-15. [PMID: 22178158 DOI: 10.1016/j.chemphyslip.2011.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/29/2011] [Accepted: 12/02/2011] [Indexed: 12/19/2022]
Abstract
Signaling lipids control many of the most important biological pathways, typically by recruiting cognate protein binding targets to cell surfaces, thereby regulating both their function and subcellular localization. A critical family of signaling lipids is that of the phosphatidylinositol polyphosphates (PIP(n)s), which is composed of seven isomers that vary based on phosphorylation pattern. A key protein that is activated upon PIP(n) binding is Akt, which then plays important roles in regulating the cell cycle, and is thus aberrant in disease. Characterization of protein-PIP(n) binding interactions is hindered by the complexity of the membrane environment and of the PIP(n) structures. Herein, we describe two rapid assays of use for characterizing protein-PIP(n) binding interactions. First, a microplate-based binding assay was devised to characterize the binding of effectors to immobilized synthetic PIP(n) headgroup-biotin conjugates corresponding to all seven isomers. The assay was implemented for simultaneous analysis of Akt-PH domain, indicating PI(3,4,5)P(3) and PI(3,4)P(2) as the primary ligands. In addition, density-dependant studies indicated that the amount of ligand immobilized on the surface affected the amplitude of protein binding, but not the affinity, for Akt-PH. Since the PIP(n) ligand motifs used in this analysis lack the membrane environment and glycerolipid backbone, yet still exhibit high-affinity protein binding, these results narrow down the structural requirements for Akt recognition. Additionally, binding detection was also achieved through microarray analysis via the robotic pin printing of ligands onto glass slides in a miniaturized format. Here, fluorescence-based detection provided sensitive detection of binding using minimal amounts of materials. Due to their high-throughput and versatile attributes, these assays provide invaluable tools for probing and perturbing protein-membrane binding interactions.
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Affiliation(s)
- Meng M Rowland
- Department of Chemistry, The University of Tennessee, Knoxville, TN 37996, United States
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65
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Rowland MM, Bostic HE, Gong D, Speers AE, Lucas N, Cho W, Cravatt BF, Best MD. Phosphatidylinositol 3,4,5-trisphosphate activity probes for the labeling and proteomic characterization of protein binding partners. Biochemistry 2011; 50:11143-61. [PMID: 22074223 DOI: 10.1021/bi201636s] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Phosphatidylinositol polyphosphate lipids, such as phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P₃], regulate critical biological processes, many of which are aberrant in disease. These lipids often act as site-specific ligands in interactions that enforce membrane association of protein binding partners. Herein, we describe the development of bifunctional activity probes corresponding to the headgroup of PI(3,4,5)P₃ that are effective for identifying and characterizing protein binding partners from complex samples, namely cancer cell extracts. These probes contain both a photoaffinity tag for covalent labeling of target proteins and a secondary handle for subsequent detection or manipulation of labeled proteins. Probes bearing different secondary tags were exploited, either by direct attachment of a fluorescent dye for optical detection or by using an alkyne that can be derivatized after protein labeling via click chemistry. First, we describe the design and modular synthetic strategy used to generate multiple probes with different reporter tags of use for characterizing probe-labeled proteins. Next, we report initial labeling studies using purified protein, the PH domain of Akt, in which probes were found to label this target, as judged by in-gel detection. Furthermore, protein labeling was abrogated by controls including competition with an unlabeled PI(3,4,5)P₃ headgroup analogue as well as through protein denaturation, indicating specific labeling. In addition, probes featuring linkers of different lengths between the PI(3,4,5)P₃ headgroup and photoaffinity tag led to variations in protein labeling, indicating that a shorter linker was more effective in this case. Finally, proteomic labeling studies were performed using cell extracts; labeled proteins were observed by in-gel detection and characterized using postlabeling with biotin, affinity chromatography, and identification via tandem mass spectrometry. These studies yielded a total of 265 proteins, including both known and novel candidate PI(3,4,5)P₃-binding proteins.
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Affiliation(s)
- Meng M Rowland
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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66
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McNulty J, Keskar K, Vemula R. The first well-defined silver(I)-complex-catalyzed cycloaddition of azides onto terminal alkynes at room temperature. Chemistry 2011; 17:14727-30. [PMID: 22125272 DOI: 10.1002/chem.201103244] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Indexed: 11/07/2022]
Affiliation(s)
- James McNulty
- Department of Chemistry and Chemical-Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada.
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67
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Kyro K, Manandhar SP, Mullen D, Schmidt WK, Distefano MD. Photoaffinity labeling of Ras converting enzyme using peptide substrates that incorporate benzoylphenylalanine (Bpa) residues: improved labeling and structural implications. Bioorg Med Chem 2011; 19:7559-69. [PMID: 22079863 DOI: 10.1016/j.bmc.2011.10.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/04/2011] [Accepted: 10/10/2011] [Indexed: 11/17/2022]
Abstract
Rce1p catalyzes the proteolytic trimming of C-terminal tripeptides from isoprenylated proteins containing CAAX-box sequences. Because Rce1p processing is a necessary component in the Ras pathway of oncogenic signal transduction, Rce1p holds promise as a potential target for therapeutic intervention. However, its mechanism of proteolysis and active site have yet to be defined. Here, we describe synthetic peptide analogues that mimic the natural lipidated Rce1p substrate and incorporate photolabile groups for photoaffinity-labeling applications. These photoactive peptides are designed to crosslink to residues in or near the Rce1p active site. By incorporating the photoactive group via p-benzoyl-l-phenylalanine (Bpa) residues directly into the peptide substrate sequence, the labeling efficiency was substantially increased relative to a previously-synthesized compound. Incorporation of biotin on the N-terminus of the peptides permitted photolabeled Rce1p to be isolated via streptavidin affinity capture. Our findings further suggest that residues outside the CAAX-box sequence are in contact with Rce1p, which has implications for future inhibitor design.
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Affiliation(s)
- Kelly Kyro
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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