1
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Prieto-Costas LA, Rivera-Cordero GR, Rivera JM. Quantifying and Modulating Protein Encapsulation in Guanosine-Based Supramolecular Particles. Bioconjug Chem 2023; 34:2112-2122. [PMID: 37903569 DOI: 10.1021/acs.bioconjchem.3c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
The encapsulation of proteins is an effective way to preserve their structure and enhance their function. One exciting possibility is adjusting the protective agent to match the specific protein's characteristics to influence its properties. In a recent study, we developed a flow cytometry-based method to quantify the encapsulation of small-molecule dyes in colloidal particles made from guanosine derivatives (supramolecular hacky sacks (SHS) particles). We aimed to determine whether this method could quantify protein encapsulation and track changes and if the particles could be tuned to bind to specific proteins. Our results showed that fluorescein isothiocyanate (FITC)-labeled proteins had apparent association constants in the micromolar range with hydrophobicity as the dominant factor enhancing the affinities. Confocal laser scanning microscopy (CLSM) imaging supported these results and provided additional information about the protein distribution within the particles. We also tested the feasibility of tuning the avidin affinity (AVI) for SHS particles with a biotin ligand. We found that increasing the amount of biotin initially enhanced AVI binding, but then reached saturation, which we hypothesize results from noncovalent cross-linking caused by strong biotin/AVI interactions. CLSM images showed that the linker also impacted the AVI distribution within the particles. Our strategy provides an advantage over other methods for quantifying protein encapsulation by being suitable for high-throughput analysis with high reproducibility. We anticipate that future efforts to use lower-affinity ligands would result in better strategies for modulating protein affinity for drug delivery applications.
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Affiliation(s)
- Luis A Prieto-Costas
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - Génesis R Rivera-Cordero
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - José M Rivera
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
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2
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Hirbawi N, Lin PC, Jarvo ER. Halogenation Reactions of Alkyl Alcohols Employing Methyl Grignard Reagents. J Org Chem 2022; 87:12352-12369. [PMID: 36049783 PMCID: PMC9486953 DOI: 10.1021/acs.joc.2c01590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 11/29/2022]
Abstract
Grignard reagents are commonly used as carbanion equivalents. Herein, we report an example of Grignard reagents acting as halide nucleophiles to form alkyl iodides and bromides. We establish that Grignard reagents can convert alkyl mesylates into alkyl halides, as well as be employed in a one-pot halogenation reaction starting from alcohols, which proceed through mesylate intermediates. The halogenation reaction is confirmed to occur by an SN2 pathway with inversion of configuration and is demonstrated to be efficient on multi-gram scale.
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Affiliation(s)
| | | | - Elizabeth R. Jarvo
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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3
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Seiler DK, Hay JC. Genetically encoded fluorescent tools: Shining a little light on ER-to-Golgi transport. Free Radic Biol Med 2022; 183:14-24. [PMID: 35272000 PMCID: PMC9097910 DOI: 10.1016/j.freeradbiomed.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 12/11/2022]
Abstract
Since the first fluorescent proteins (FPs) were identified and isolated over fifty years ago, FPs have become commonplace yet indispensable tools for studying the constitutive secretory pathway in live cells. At the same time, genetically encoded chemical tags have provided a new use for much older fluorescent dyes. Innovation has also produced several specialized methods to allow synchronous release of cargo proteins from the endoplasmic reticulum (ER), enabling precise characterization of sequential trafficking steps in the secretory pathway. Without the constant innovation of the researchers who design these tools to control, image, and quantitate protein secretion, major discoveries about ER-to-Golgi transport and later stages of the constitutive secretory pathway would not have been possible. We review many of the tools and tricks, some 25 years old and others brand new, that have been successfully implemented to study ER-to-Golgi transport in intact and living cells.
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Affiliation(s)
- Danette Kowal Seiler
- Division of Biological Sciences, Center for Structural & Functional Neuroscience, University of Montana, Missoula, MT, 59812, USA
| | - Jesse C Hay
- Division of Biological Sciences, Center for Structural & Functional Neuroscience, University of Montana, Missoula, MT, 59812, USA.
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4
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Díaz-Caballero M, Navarro S, Ventura S. Functionalized Prion-Inspired Amyloids for Biosensor Applications. Biomacromolecules 2021; 22:2822-2833. [PMID: 34196531 PMCID: PMC8483438 DOI: 10.1021/acs.biomac.1c00222] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Protein
amyloid nanofibers provide a biocompatible platform for
the development of functional nanomaterials. However, the functionalities
generated up to date are still limited. Typical building blocks correspond
to aggregation-prone proteins and peptides, which must be modified
by complex and expensive reactions post-assembly. There is high interest
in researching alternative strategies to tailor amyloid-based nanostructures’
functionality on demand. In the present study, the biotin-streptavidin
system was exploited for this purpose. Prion-inspired heptapeptides
(Ac-NYNYNYN-NH2, Ac-QYQYQYQ-NH2, and Ac-SYSYSYS-NH2) were doped with biotin-conjugated counterparts and assembled
into amyloid-like fibers under mild conditions. The scaffolds’
versatile functionalization was demonstrated by decorating them with
different streptavidin conjugates, including gold nanoparticles, quantum
dots, and enzymes. In particular, they were functionalized with peroxidase
or phosphatase activities using streptavidin conjugated with horseradish
peroxidase and alkaline phosphatase, respectively. Modification of
amyloid-like nanostructures has generally been restricted to the addition
of a single protein moiety. We functionalized the fibrils simultaneously
with glucose oxidase and horseradish peroxidase, coupling these activities
to build up a nanostructured glucose biosensor. Overall, we present
a simple, modular, and multivalent approach for developing amyloid-based
nanomaterials functionalized with any desired combination of chemical
and biological moieties.
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Affiliation(s)
- Marta Díaz-Caballero
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
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5
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Nejrotti S, Marra F, Priola E, Maranzana A, Prandi C. Gold(I)-Catalyzed Reactivity of Furan-ynes with N-Oxides: Synthesis of Substituted Dihydropyridinones and Pyranones. J Org Chem 2021; 86:8295-8307. [PMID: 34100288 PMCID: PMC8279485 DOI: 10.1021/acs.joc.1c00746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reactivity of "furan-ynes" in combination with pyridine and quinoline N-oxides in the presence of a Au(I) catalyst, has been studied, enabling the synthesis of three different heterocyclic scaffolds. Selective access to two out of the three possible products, a dihydropyridinone and a furan enone, has been achieved through the fine-tuning of the reaction conditions. The reactions proceed smoothly at room temperature and open-air, and were further extended to a broad substrate scope, thus affording functionalized dihydropyridinones and pyranones.
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Affiliation(s)
- Stefano Nejrotti
- Dipartimento di Chimica, Università degli Studi di Torino, via Pietro Giuria 7, I-10125 Torino, Italy
| | - Francesco Marra
- Dipartimento di Chimica, Università degli Studi di Torino, via Pietro Giuria 7, I-10125 Torino, Italy
| | - Emanuele Priola
- Dipartimento di Chimica, Università degli Studi di Torino, via Pietro Giuria 7, I-10125 Torino, Italy
| | - Andrea Maranzana
- Dipartimento di Chimica, Università degli Studi di Torino, via Pietro Giuria 7, I-10125 Torino, Italy
| | - Cristina Prandi
- Dipartimento di Chimica, Università degli Studi di Torino, via Pietro Giuria 7, I-10125 Torino, Italy
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6
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McCabe JW, Mallis CS, Kocurek KI, Poltash ML, Shirzadeh M, Hebert MJ, Fan L, Walker TE, Zheng X, Jiang T, Dong S, Lin CW, Laganowsky A, Russell DH. First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes. Anal Chem 2020; 92:11155-11163. [PMID: 32662991 PMCID: PMC7967297 DOI: 10.1021/acs.analchem.0c01285] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rotationally averaged collision cross section (CCS) values for a series of proteins and protein complexes ranging in size from 8.6 to 810 kDa are reported. The CCSs were obtained using a native electrospray ionization drift tube ion mobility-Orbitrap mass spectrometer specifically designed to enhance sensitivity while having high-resolution ion mobility and mass capabilities. Periodic focusing (PF)-drift tube (DT)-ion mobility (IM) provides first-principles determination of the CCS of large biomolecules that can then be used as CCS calibrants. The experimental, first-principles CCS values are compared to previously reported experimentally determined and computationally calculated CCS using projected superposition approximation (PSA), the Ion Mobility Projection Approximation Calculation Tool (IMPACT), and Collidoscope. Experimental CCS values are generally in agreement with previously reported CCSs, with values falling within ∼5.5%. In addition, an ion mobility resolution (CCS centroid divided by CCS fwhm) of ∼60 is obtained for pyruvate kinase (MW ∼ 233 kDa); however, ion mobility resolution for bovine serum albumin (MW ∼ 68 kDa) is less than ∼20, which arises from sample impurities and underscores the importance of sample quality. The high resolution afforded by the ion mobility-Orbitrap mass analyzer provides new opportunities to understand the intricate details of protein complexes such as the impact of post-translational modifications (PTMs), stoichiometry, and conformational changes induced by ligand binding.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Klaudia I Kocurek
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Liqi Fan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Ting Jiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shiyu Dong
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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7
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López-Andarias J, Saarbach J, Moreau D, Cheng Y, Derivery E, Laurent Q, González-Gaitán M, Winssinger N, Sakai N, Matile S. Cell-Penetrating Streptavidin: A General Tool for Bifunctional Delivery with Spatiotemporal Control, Mediated by Transport Systems Such as Adaptive Benzopolysulfane Networks. J Am Chem Soc 2020; 142:4784-4792. [PMID: 32109058 PMCID: PMC7307903 DOI: 10.1021/jacs.9b13621] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/17/2022]
Abstract
In this report, cell-penetrating streptavidin (CPS) is introduced to exploit the full power of streptavidin-biotin biotechnology in cellular uptake. For this purpose, transporters, here cyclic oligochalcogenides (COCs), are covalently attached to lysines of wild-type streptavidin. This leaves all four biotin binding sites free for at least bifunctional delivery. To maximize the standards of the quantitative evaluation of cytosolic delivery, the recent chloroalkane penetration assay (CAPA) is coupled with automated high content (HC) imaging, a technique that combines the advantages of fluorescence microscopy and flow cytometry. According to the resulting HC-CAPA, cytosolic delivery of CPS equipped with four benzopolysulfanes was the best among all tested CPSs, also better than the much smaller TAT peptide, the original cell-penetrating peptide from HIV. HaloTag-GFP fusion proteins expressed on mitochondria were successfully targeted using CPS carrying two different biotinylated ligands, HaloTag substrates or anti-GFP nanobodies, interfaced with peptide nucleic acids, flipper force probes, or fluorescent substrates. The delivered substrates could be released from CPS into the cytosol through desthiobiotin-biotin exchange. These results validate CPS as a general tool which enables unrestricted use of streptavidin-biotin biotechnology in cellular uptake.
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Affiliation(s)
- Javier López-Andarias
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Jacques Saarbach
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Dimitri Moreau
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Yangyang Cheng
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Emmanuel Derivery
- MRC
Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Quentin Laurent
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Marcos González-Gaitán
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Nicolas Winssinger
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Naomi Sakai
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Stefan Matile
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
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8
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Liu P, Zhao L, Loos F, Marty C, Xie W, Martins I, Lachkar S, Qu B, Waeckel-Énée E, Plo I, Vainchenker W, Perez F, Rodriguez D, López-Otin C, van Endert P, Zitvogel L, Kepp O, Kroemer G. Immunosuppression by Mutated Calreticulin Released from Malignant Cells. Mol Cell 2019; 77:748-760.e9. [PMID: 31785928 DOI: 10.1016/j.molcel.2019.11.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/23/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022]
Abstract
Mutations affecting exon 9 of the CALR gene lead to the generation of a C-terminally modified calreticulin (CALR) protein that lacks the KDEL endoplasmic reticulum (ER) retention signal and consequently mislocalizes outside of the ER where it activates the thrombopoietin receptor in a cell-autonomous fashion, thus driving myeloproliferative diseases. Here, we used the retention using selective hooks (RUSH) assay to monitor the trafficking of CALR. We found that exon-9-mutated CALR was released from cells in response to the biotin-mediated detachment from its ER-localized hook, in vitro and in vivo. Cellular CALR release was confirmed in suitable mouse models bearing exon-9-mutated hematopoietic systems or tumors. Extracellular CALR mediated immunomodulatory effects and inhibited the phagocytosis of dying cancer cells by dendritic cells (DC), thereby suppressing antineoplastic immune responses elicited by chemotherapeutic agents or by PD-1 blockade. Altogether, our results demonstrate paracrine immunosuppressive effects for exon-9-mutated CALR.
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Affiliation(s)
- Peng Liu
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Liwei Zhao
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France; Université Paris-Saclay, Villejuif, France
| | - Friedemann Loos
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Caroline Marty
- Université Paris-Saclay, Villejuif, France; INSERM, UMR 1170, Villejuif, France; Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - Wei Xie
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Isabelle Martins
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Sylvie Lachkar
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France
| | - Bo Qu
- Gustave Roussy Comprehensive Cancer Center, Villejuif, France; INSERM, U1015, Villejuif, France; Center of Clinical Investigations, CIC1428, Villejuif, France
| | - Emmanuelle Waeckel-Énée
- Université of Paris, Paris, France; INSERM, U1151, Paris, France; CNRS UMR8253, Paris, France
| | - Isabelle Plo
- Université Paris-Saclay, Villejuif, France; INSERM, UMR 1170, Villejuif, France; Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - William Vainchenker
- Université Paris-Saclay, Villejuif, France; INSERM, UMR 1170, Villejuif, France; Gustave Roussy Comprehensive Cancer Center, Villejuif, France
| | - Franck Perez
- Cell Biology and Cancer Unit, Institut Curie, PSL Research University, CNRS, Paris, France
| | - David Rodriguez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Carlos López-Otin
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France; Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Peter van Endert
- Université of Paris, Paris, France; INSERM, U1151, Paris, France; CNRS UMR8253, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Comprehensive Cancer Center, Villejuif, France; INSERM, U1015, Villejuif, France; Center of Clinical Investigations, CIC1428, Villejuif, France
| | - Oliver Kepp
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France.
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM UMR 1138, Paris, France; Sorbonne Université, Paris, France; Université of Paris, Paris, France; Suzhou Institute for Systems Medicine, Chinese Academy of Sciences, Suzhou, China; Karolinska Institutet, Department of Women's and Children's Health, Stockholm, Sweden; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
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9
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Recent advances in the engineering and application of streptavidin-like molecules. Appl Microbiol Biotechnol 2019; 103:7355-7365. [DOI: 10.1007/s00253-019-10036-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 01/24/2023]
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10
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Reversible association with motor proteins (RAMP): A streptavidin-based method to manipulate organelle positioning. PLoS Biol 2019; 17:e3000279. [PMID: 31100061 PMCID: PMC6542540 DOI: 10.1371/journal.pbio.3000279] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/30/2019] [Accepted: 05/03/2019] [Indexed: 01/18/2023] Open
Abstract
We report the development and characterization of a method, named reversible association with motor proteins (RAMP), for manipulation of organelle positioning within the cytoplasm. RAMP consists of coexpressing in cultured cells (i) an organellar protein fused to the streptavidin-binding peptide (SBP) and (ii) motor, neck, and coiled-coil domains from a plus-end-directed or minus-end-directed kinesin fused to streptavidin. The SBP-streptavidin interaction drives accumulation of organelles at the plus or minus end of microtubules, respectively. Importantly, competition of the streptavidin-SBP interaction by the addition of biotin to the culture medium rapidly dissociates the motor construct from the organelle, allowing restoration of normal patterns of organelle transport and distribution. A distinctive feature of this method is that organelles initially accumulate at either end of the microtubule network in the initial state and are subsequently released from this accumulation, allowing analyses of the movement of a synchronized population of organelles by endogenous motors.
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11
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Li JS, Yang Q, Chen GQ, Li ZW, Huang PM. Facile Reagent-Free Synthesis of Furo[3,2-c
]pyridinones and Their Polynuclear Analogues with DDQ as Precursor. ChemistrySelect 2018. [DOI: 10.1002/slct.201802686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jiang-Sheng Li
- Hunan Provincial Key Laboratory of Materials; Protection for Electric Power and Transportation; School of Chemistry and Biological Engineering; Changsha University of Science & Technology; Changsha 410114 People's Republic of China
| | - Qian Yang
- Hunan Provincial Key Laboratory of Materials; Protection for Electric Power and Transportation; School of Chemistry and Biological Engineering; Changsha University of Science & Technology; Changsha 410114 People's Republic of China
| | - Guo-Qin Chen
- Hunan Provincial Key Laboratory of Materials; Protection for Electric Power and Transportation; School of Chemistry and Biological Engineering; Changsha University of Science & Technology; Changsha 410114 People's Republic of China
| | - Zhi-Wei Li
- Hunan Provincial Key Laboratory of Materials; Protection for Electric Power and Transportation; School of Chemistry and Biological Engineering; Changsha University of Science & Technology; Changsha 410114 People's Republic of China
| | - Peng-Mian Huang
- Hunan Provincial Key Laboratory of Materials; Protection for Electric Power and Transportation; School of Chemistry and Biological Engineering; Changsha University of Science & Technology; Changsha 410114 People's Republic of China
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12
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Yahodkina-Yakovenko MS, Bol’but AV, Vovk MV. Synthesis of benzofuro[3,2-b]furo[2,3-d]pyridin-4(5H)-ones, derivatives of a novel heterocyclic system. HETEROCYCL COMMUN 2018. [DOI: 10.1515/hc-2017-0143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractMethyl 2-[(cyanophenoxy)methyl]-3-furoates obtained from methyl 2-(chloromethyl)-3-furoate and salicylonitriles undergo tandem cyclization in the presence of excess t-BuOK in N,N-dimethylformamide (DMF) solution at 65°C to give substituted benzofuro[3,2-b]furo[2,3-d]pyridin-4(5H)-ones, derivatives of a novel heterocyclic system.
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Affiliation(s)
| | - Andriy V. Bol’but
- Institute of Organic Chemistry, National Academy of Science of ukraine, 5 Murmanska str., Kyiv 02660, Ukraine
- RPA “Enamine”, 78 Chervonotkatska str., Kyiv 02660, Ukraine
| | - Mykhailo V. Vovk
- Institute of Organic Chemistry, National Academy of Science of ukraine, 5 Murmanska str., Kyiv 02660, Ukraine
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13
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Raines DJ, Clarke JE, Blagova EV, Dodson EJ, Wilson KS, Duhme-Klair AK. Redox-switchable siderophore anchor enables reversible artificial metalloenzyme assembly. Nat Catal 2018. [DOI: 10.1038/s41929-018-0124-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Blanco PM, Garcés JL, Madurga S, Mas F. Macromolecular diffusion in crowded media beyond the hard-sphere model. SOFT MATTER 2018; 14:3105-3114. [PMID: 29620120 DOI: 10.1039/c8sm00201k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shoulder-shaped interaction potential that is implemented in the Brownian Dynamics (BD) computations. The interaction potential contains only one parameter associated with the chain entanglement energetic cost (Ur). The hydrodynamic interactions are included in the BD computations via Tokuyama mean-field equations. The model is used to analyze the diffusion of a streptavidin protein among different sized dextran obstacles. For this system, Ur is obtained by fitting the streptavidin experimental long-time diffusion coefficient Dlongversus the macromolecular concentration for D50 (indicating their molecular weight in kg mol-1) dextran obstacles. The obtained Dlong values show better quantitative agreement with experiments than those obtained with hard-core spheres. Moreover, once parametrized, the CESP model is also able to quantitatively predict Dlong and the anomalous exponent (α) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. Dlong, the short-time diffusion coefficient (Dshort) and α are obtained from the BD simulations by using a new empirical expression, able to describe the full temporal evolution of the diffusion coefficient.
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Affiliation(s)
- Pablo M Blanco
- Department of Material Science and Physical Chemistry, Barcelona University, 08028 Barcelona, Spain. and Institute of Theoretical and Computational Chemistry (IQTC), Barcelona University, 08028 Barcelona, Spain
| | - Josep Lluís Garcés
- Department of Chemistry, University of Lleida (UdL), 25003 Lleida, Spain.
| | - Sergio Madurga
- Department of Material Science and Physical Chemistry, Barcelona University, 08028 Barcelona, Spain. and Institute of Theoretical and Computational Chemistry (IQTC), Barcelona University, 08028 Barcelona, Spain
| | - Francesc Mas
- Department of Material Science and Physical Chemistry, Barcelona University, 08028 Barcelona, Spain. and Institute of Theoretical and Computational Chemistry (IQTC), Barcelona University, 08028 Barcelona, Spain
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15
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Triadon A, Ngo Ndimba A, Richy N, Amar A, Boucekkine A, Roisnel T, Cifuentes MP, Humphrey MG, Blanchard-Desce M, Mongin O, Paul F. Diphenylamino-substituted tristyryl vs. triphenyl isocyanurates: improved conjugation has minimal impact on two-photon absorption. NEW J CHEM 2018. [DOI: 10.1039/c8nj01904e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Planarization and extension of the central π-system does not increase two-photon absorption cross-section.
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16
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Laszlo KJ, Bush MF. Interpreting the Collision Cross Sections of Native-like Protein Ions: Insights from Cation-to-Anion Proton-Transfer Reactions. Anal Chem 2017. [PMID: 28636334 DOI: 10.1021/acs.analchem.7b01474] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of charge state on structures of native-like cations of serum albumin, streptavidin, avidin, and alcohol dehydrogenase were probed using cation-to-anion proton-transfer reactions (CAPTR), ion mobility, mass spectrometry, and complementary energy-dependent experiments. The CAPTR products all have collision cross-section (Ω) values that are within 5.5% of the original precursor cations. The first CAPTR event for each precursor yields products that have smaller Ω values and frequently exhibit the greatest magnitude of change in Ω resulting from a single CAPTR event. To investigate how the structures of the precursors affect the structures of the products, ions were activated as a function of energy prior to CAPTR. In each case, the Ω values of the activated precursors increase with increasing energy, but the Ω values of the CAPTR products are smaller than the activated precursors. To investigate the stabilities of the CAPTR products, the products were activated immediately prior to ion mobility. These results show that additional structures with smaller or larger Ω values can be populated and that the structures and stabilities of these ions depend most strongly on the identity of the protein and the charge state of the product, rather than the charge state of the precursor or the number of CAPTR events. Together, these results indicate that the excess charges initially present on native-like ions have a modest, but sometimes statistically significant, effect on their Ω values. Therefore, potential contributions from charge state should be considered when using experimental Ω values to elucidate structures in solution.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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17
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Abstract
Biotin/(strept)avidin self-assembly is a powerful platform for nanoscale fabrication and capture with many different applications in science, medicine, and nanotechnology. However, biotin/(strept)avidin self-assembly has several well-recognized drawbacks that limit performance in certain technical areas and there is a need for synthetic mimics that can either become superior replacements or operational partners with bio-orthogonal recognition properties. The goal of this tutorial review is to describe the recent progress in making high affinity synthetic association partners that operate in water or biological media. The review starts with a background summary of biotin/(strept)avidin self-assembly and the current design rules for creating synthetic mimics. A series of case studies are presented that describe recent success using synthetic derivatives of cyclodextrins, cucurbiturils, and various organic cyclophanes such as calixarenes, deep cavitands, pillararenes, and tetralactams. In some cases, two complementary partners associate to produce a nanoscale complex and in other cases a ditopic host molecule is used to link two partners. The article concludes with a short discussion of future directions and likely challenges.
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Affiliation(s)
- Wenqi Liu
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Soumen K. Samanta
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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18
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Tachibana R, Terai T, Boncompain G, Sugiyama S, Saito N, Perez F, Urano Y. Improving the Solubility of Artificial Ligands of Streptavidin to Enable More Practical Reversible Switching of Protein Localization in Cells. Chembiochem 2017; 18:358-362. [PMID: 27905160 DOI: 10.1002/cbic.201600640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 12/21/2022]
Abstract
Chemical inducers that can control target-protein localization in living cells are powerful tools to investigate dynamic biological systems. We recently reported the retention using selective hook or "RUSH" system for reversible localization change of proteins of interest by addition/washout of small-molecule artificial ligands of streptavidin (ALiS). However, the utility of previously developed ALiS was restricted by limited solubility in water. Here, we overcame this problem by X-ray crystal structure-guided design of a more soluble ALiS derivative (ALiS-3), which retains sufficient streptavidin-binding affinity for use in the RUSH system. The ALiS-3-streptavidin interaction was characterized in detail. ALiS-3 is a convenient and effective tool for dynamic control of α-mannosidase II localization between ER and Golgi in living cells.
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Affiliation(s)
- Ryo Tachibana
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Present address: Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Gaelle Boncompain
- Institut Curie, Centre de Recherche, PSL Research University, 26, rue d'Ulm, Paris, 75248, France.,CNRS, UMR144, PSL Research University, 26, rue d'Ulm, Paris, 75248, France
| | - Shigeru Sugiyama
- Graduate School of Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nae Saito
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Franck Perez
- Institut Curie, Centre de Recherche, PSL Research University, 26, rue d'Ulm, Paris, 75248, France.,CNRS, UMR144, PSL Research University, 26, rue d'Ulm, Paris, 75248, France
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,CREST, JST, 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan
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19
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Lee M, Peterson BR. Quantification of Small Molecule-Protein Interactions using FRET between Tryptophan and the Pacific Blue Fluorophore. ACS OMEGA 2016; 1:1266-1276. [PMID: 28058293 PMCID: PMC5204206 DOI: 10.1021/acsomega.6b00356] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/06/2016] [Indexed: 05/14/2023]
Abstract
We report a new method to quantify the affinity of small molecules for proteins. This method is based on Förster resonance energy transfer (FRET) between endogenous tryptophan (Trp) residues and the coumarin-derived fluorophore Pacific Blue (PB). Tryptophan residues are frequently found in proteins near ligand-binding sites, making this approach potentially applicable to a wide range of systems. To improve access to PB, we developed a scalable multigram synthesis of this fluorophore, starting with inexpensive 2,3,4,5-tetrafluorobenzoic acid. This route was used to synthesize fluorescent derivatives of biotin, as well as lower affinity thiobiotin, iminobiotin, and imidazolidinethione analogues that bind the protein streptavidin. Compared with previously published FRET acceptors for tryptophan, PB proved to be superior in both sensitivity and efficiency. These unique properties of PB enabled direct quantification of dissociation constants (Kd) as well as competitive inhibition constants (Ki) in the micromolar to nanomolar range. In comparison to analogous binding studies using fluorescence polarization, fluorescence quenching, or fluorescence enhancement, affinities determined using Trp-FRET were more precise and accurate as validated using independent isothermal titration calorimetry studies. FRET between tryptophan and PB represents a new tool for the characterization of protein-ligand complexes.
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20
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Abstract
The strong interaction between streptavidin (SA) and biotin is widely utilized in biotechnological applications. A SA variant, monovalent SA, was developed with a single and high affinity biotin-binding site within the intact tetramer. However, its structural characterization remains undetermined. Here, we seek to determine the crystal structure of monovalent SA at 1.7-Å resolution. We show that, in contrast to its ‘close-state’ in the only wild-type subunit, the L3,4 loops of three Dead SA subunits are free from crystal packing and remain in an ‘open state’, stabilized by a consistent H-bonding network involving S52. This H-bonding network also applies to the previously reported open state of the wild-type apo-SA. These results suggest that specific substitutions (N23A/S27D/S45A) at biotin-binding sites stabilize the open state of SA L3,4 loop, thereby further reducing biotin-binding affinity. The general features of the ‘open state’ SA among different SA variants may facilitate its rational design. The structural information of monovalent SA will be valuable for its applications across a wide range of biotechnological areas.
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21
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Popa V, Trecroce DA, McAllister RG, Konermann L. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons. J Phys Chem B 2016; 120:5114-24. [DOI: 10.1021/acs.jpcb.6b03035] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Vlad Popa
- Department
of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Danielle A. Trecroce
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Robert G. McAllister
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Lars Konermann
- Department
of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
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