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Reddi RN, Rogel A, Resnick E, Gabizon R, Prasad PK, Gurwicz N, Barr H, Shulman Z, London N. Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry. J Am Chem Soc 2021; 143:20095-20108. [PMID: 34817989 PMCID: PMC8662641 DOI: 10.1021/jacs.1c06167] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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Chemical modifications
of native proteins can affect their stability,
activity, interactions, localization, and more. However, there are
few nongenetic methods for the installation of chemical modifications
at a specific protein site in cells. Here we report a covalent ligand
directed release (CoLDR) site-specific labeling strategy, which enables
the installation of a variety of functional tags on a target protein
while releasing the directing ligand. Using this approach, we were
able to label various proteins such as BTK, K-RasG12C,
and SARS-CoV-2 PLpro with different tags. For BTK we have
shown selective labeling in cells of both alkyne and fluorophores
tags. Protein labeling by traditional affinity methods often inhibits
protein activity since the directing ligand permanently occupies the
target binding pocket. We have shown that using CoLDR chemistry, modification
of BTK by these probes in cells preserves its activity. We demonstrated
several applications for this approach including determining the half-life
of BTK in its native environment with minimal perturbation, as well
as quantification of BTK degradation by a noncovalent proteolysis
targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive
“turn-on” fluorescent probe, we were able to monitor
ligand binding to the active site of BTK. Finally, we have demonstrated
efficient CoLDR-based BTK PROTACs (DC50 < 100 nM), which
installed a CRBN binder onto BTK. This approach joins very few available
labeling strategies that maintain the target protein activity and
thus makes an important addition to the toolbox of chemical biology.
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Affiliation(s)
- Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Resnick
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Pragati Kishore Prasad
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Shulman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
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Regulation of retinal membrane guanylyl cyclase (RetGC) by negative calcium feedback and RD3 protein. Pflugers Arch 2021; 473:1393-1410. [PMID: 33537894 PMCID: PMC8329130 DOI: 10.1007/s00424-021-02523-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 11/07/2022]
Abstract
This article presents a brief overview of the main biochemical and cellular processes involved in regulation of cyclic GMP production in photoreceptors. The main focus is on how the fluctuations of free calcium concentrations in photoreceptors between light and dark regulate the activity of retinal membrane guanylyl cyclase (RetGC) via calcium sensor proteins. The emphasis of the review is on the structure of RetGC and guanylyl cyclase activating proteins (GCAPs) in relation to their functional role in photoreceptors and congenital diseases of photoreceptors. In addition to that, the structure and function of retinal degeneration-3 protein (RD3), which regulates RetGC in a calcium-independent manner, is discussed in detail in connections with its role in photoreceptor biology and inherited retinal blindness.
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Tawfik H, Puza S, Seemann R, Fleury JB. Transport Properties of Gramicidin A Ion Channel in a Free-Standing Lipid Bilayer Filled With Oil Inclusions. Front Cell Dev Biol 2020; 8:531229. [PMID: 33015051 PMCID: PMC7498540 DOI: 10.3389/fcell.2020.531229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/14/2020] [Indexed: 11/13/2022] Open
Abstract
Ion channels are key proteins in mammalian cell membranes. They have a central role in the physiology of excitable cells such as neurons, muscle, and heart cells. They also play a crucial role in kidney physiology. The gramicidin ion channel is one of the most studied ion channels, in particular it was intensively employed to investigate the lipid–protein interactions in model cell membranes. For example, even though the sequence of gramicidin is extremely hydrophobic, its motion is impaired in membrane bilayer, i.e., it does not rapidly flip to the other membrane leaflet, and low channel activity were observed when gramicidin is added asymmetrically to only one leaflet of a model cell membrane. In this article, we study the transport properties of gramicidin channel in a heterogeneous model membrane. Using microfluidics, we are forming freestanding bilayers as model cell membranes including heterogeneous domains that are created by oil inclusions. The presence of oil inclusions is then demonstrated by measuring the bilayer capacity via a patch-clamp amplifier and fluorescent confocal inspection. Based on electrophysiological and optical measurements Gramicidin A (gA) ion channels are dispersed into the buffer phases on both side of the formed lipid bilayer and insert spontaneously into the bilayer upon formation. The presence of functional Gramicidin A is then demonstrated by measuring conductivity signals. Based on electrophysiological and optical measurements, we explore the consequence of the presence of these oil inclusions on the functionality of incorporated gA ion channels. For low oil concentration, we measure a decrease of gA transport properties due to the reduction of the bilayer tension. For large oil concentration, we measure a saturation of gA transport properties due to an increase of the bilayer thickness.
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Affiliation(s)
- Harvey Tawfik
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Sevde Puza
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Ralf Seemann
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Jean-Baptiste Fleury
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
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Yu J, Chen Y, Xiong L, Zhang X, Zheng Y. Conductance Changes in Bovine Serum Albumin Caused by Drug-Binding Triggered Structural Transitions. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E1022. [PMID: 30925667 PMCID: PMC6479529 DOI: 10.3390/ma12071022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 12/13/2022]
Abstract
Proteins, due to their binding selectivity, are promising candidates for fabricating nanoscale bio-sensors. However, the influence of structural change on protein conductance caused by specific protein-ligand interactions and disease-induced degeneration still remains unknown. Here, we excavated the relationship between circular dichroism (CD) spectroscopy and conductive atomic force microscopy (CAFM) to reveal the effect of the protein secondary structures changes on conductance. The secondary structure of bovine serum albumin (BSA) was altered by the binding of drugs, like amoxicillin (Amox), cephalexin (Cefa), and azithromycin (Azit). The CD spectroscopy shows that the α-helical and β-sheet content of BSA, which varied according to the molar ratio between the drug and BSA, changed by up to 6%. The conductance of BSA monolayers in varying drug concentrations was further characterized via CAFM. We found that BSA conductance has a monotonic relation with α-helical content. Moreover, BSA conductance seems to be in connection with the binding ability of drugs and proteins. This work elucidates that protein conductance variations caused by secondary structure transitions are triggered by drug-binding and indicate that electrical methods are of potential application in protein secondary structure analysis.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, China.
- Micro&Nano Physics and Mechanics Research Laboratory, School of Physics, Sun Yat-sen University, Guangzhou 510275, China.
| | - Yun Chen
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, China.
- Micro&Nano Physics and Mechanics Research Laboratory, School of Physics, Sun Yat-sen University, Guangzhou 510275, China.
| | - Liqun Xiong
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, China.
- Micro&Nano Physics and Mechanics Research Laboratory, School of Physics, Sun Yat-sen University, Guangzhou 510275, China.
| | - Xiaoyue Zhang
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, China.
- Micro&Nano Physics and Mechanics Research Laboratory, School of Physics, Sun Yat-sen University, Guangzhou 510275, China.
- Sino-French Institute of Nuclear Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China.
| | - Yue Zheng
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, China.
- Micro&Nano Physics and Mechanics Research Laboratory, School of Physics, Sun Yat-sen University, Guangzhou 510275, China.
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Zang J, Neuhauss SCF. The Binding Properties and Physiological Functions of Recoverin. Front Mol Neurosci 2018; 11:473. [PMID: 30618620 PMCID: PMC6306944 DOI: 10.3389/fnmol.2018.00473] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Recoverin (Rcv) is a low molecular-weight, neuronal calcium sensor (NCS) primarily located in photoreceptor outer segments of the vertebrate retina. Calcium ions (Ca2+)-bound Rcv has been proposed to inhibit G-protein-coupled receptor kinase (GRKs) in darkness. During the light response, the Ca2+-free Rcv releases GRK, which in turn phosphorylates visual pigment, ultimately leading to the cessation of the visual transduction cascade. Technological advances over the last decade have contributed significantly to a deeper understanding of Rcv function. These include both biophysical and biochemical approaches that will be discussed in this review article. Furthermore, electrophysiological experiments uncovered additional functions of Rcv, such as regulation of the lifetime of Phosphodiesterase-Transducin complex. Recently, attention has been drawn to different roles in rod and cone photoreceptors.This review article focuses on Rcv binding properties to Ca2+, disc membrane and GRK, and its physiological functions in phototransduction and signal transmission.
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Affiliation(s)
- Jingjing Zang
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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Elbers D, Scholten A, Koch KW. Zebrafish Recoverin Isoforms Display Differences in Calcium Switch Mechanisms. Front Mol Neurosci 2018; 11:355. [PMID: 30323742 PMCID: PMC6172410 DOI: 10.3389/fnmol.2018.00355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/11/2018] [Indexed: 12/29/2022] Open
Abstract
Primary steps in vertebrate vision occur in rod and cone cells of the retina and require precise molecular switches in excitation, recovery, and adaptation. In particular, recovery of the photoresponse and light adaptation processes are under control of neuronal Ca2+ sensor (NCS) proteins. Among them, the Ca2+ sensor recoverin undergoes a pronounced Ca2+-dependent conformational change, a prototypical so-called Ca2+-myristoyl switch, which allows selective targeting of G protein-coupled receptor kinase. Zebrafish (Danio rerio) has gained attention as a model organism in vision research. It expresses four different recoverin isoforms (zRec1a, zRec1b, zRec2a, and zRec2b) that are orthologs to the one known mammalian variant. The expression pattern of the four isoforms cover both rod and cone cells, but the differential distribution in cones points to versatile functions of recoverin in these cell types. Initial functional studies on zebrafish larvae indicate different Ca2+-sensitive working modes for zebrafish recoverins, but experimental evidence is lacking so far. The aims of the present study are (1) to measure specific Ca2+-sensing properties of the different recoverin isoforms, (2) to ask whether switch mechanisms triggered by Ca2+ resemble that one observed with mammalian recoverin, and (3) to investigate a possible impact of an attached myristoyl moiety. For addressing these questions, we employ fluorescence spectroscopy, surface plasmon resonance (SPR), dynamic light scattering, and equilibrium centrifugation. Exposure of hydrophobic amino acids, due to the myristoyl switch, differed among isoforms and depended also on the myristoylation state of the particular recoverin. Ca2+-induced rearrangement of the protein-water shell was for all variants less pronounced than for the bovine ortholog indicating either a modified Ca2+-myristoyl switch or no switch. Our results have implications for a step-by-step response of recoverin isoforms to changing intracellular Ca2+ during illumination.
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Affiliation(s)
- Dana Elbers
- Department of Neuroscience, Biochemistry, University of Oldenburg, Oldenburg, Germany
| | - Alexander Scholten
- Department of Neuroscience, Biochemistry, University of Oldenburg, Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Biochemistry, University of Oldenburg, Oldenburg, Germany
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Chandra B, Maity BK, Das A, Maiti S. Fluorescence quenching by lipid encased nanoparticles shows that amyloid-β has a preferred orientation in the membrane. Chem Commun (Camb) 2018; 54:7750-7753. [DOI: 10.1039/c8cc02108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Short range plasmonic fields around a nanoparticle can modulate fluorescence or Raman processes.
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Affiliation(s)
| | | | - Anirban Das
- Tata Institute of Fundamental Research
- Homi Bhabha Road
- Mumbai
- India
| | - Sudipta Maiti
- Tata Institute of Fundamental Research
- Homi Bhabha Road
- Mumbai
- India
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Kim JM, Seong BL. Highly chromophoric Cy5-methionine for N-terminal fluorescent tagging of proteins in eukaryotic translation systems. Sci Rep 2017; 7:11642. [PMID: 28912467 PMCID: PMC5599622 DOI: 10.1038/s41598-017-12028-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022] Open
Abstract
Despite significant advances on fluorescent labeling of target proteins to study their structural dynamics and function, there has been need for labeling with high quantum yield ensuring high sensitivity and selectivity without sacrificing the biological function of the protein. Here as a technical advancement over non-canonical amino acid incorporation, we provided a conceptual design of the N-terminal fluorescent tagging of proteins. Cy5-labeled methionine (Cy5-Met) was chemically synthesized, and then the purified Cy5-Met was coupled with synthetic human initiator tRNA by methionine tRNA synthetase. Cy5-Met-initiator tRNA (Cy5-Met-tRNAi) was purified and transfected into HeLa cells with HIV-Tat plasmid, resulting in an efficient production of Cy5-labeled HIV-Tat protein. Based on the universal requirement in translational initiation, the approach provides co-translational incorporation of N-terminal probe to a repertoire of proteins in the eukaryote system. This methodology has potential utility in the single molecule analysis of human proteins in vitro and in vivo for addressing to their complex biological structural and functional dynamics.
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Affiliation(s)
- Jung Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea. .,Vaccine Translational Research Center, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea.
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Potvin-Fournier K, Valois-Paillard G, Lefèvre T, Cantin L, Salesse C, Auger M. Membrane fluidity is a driving force for recoverin myristoyl immobilization in zwitterionic lipids. Biochem Biophys Res Commun 2017; 490:1268-1273. [DOI: 10.1016/j.bbrc.2017.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/02/2017] [Indexed: 01/08/2023]
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