Name: monitoring gpcr-&#946;-arrestin1/2 interactions in real time living systems to accelerate drug discovery
Uploaded: 2019-06-28T14:15:00
Description: Watch this Scientific Journal Video about Monitoring GPCR-Î²-arrestin1/2 Interactions in Real Time Living Systems to Accelerate Drug Discovery at JoVE.com

This work was supported by grants from the Research Program (NRF- 2015M3A9E7029172) of the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT, and Future Planning.

1. Primer design strategy
<ol>
	<li>Design primers to introduce genes of interest into pBiT1.1-C [TK/LgBiT], pBiT2.1-C [TK/SmBiT], pBiT1.1-N [TK/LgBiT] and pBiT2.1-N [TK/SmBiT] Vectors.</li>
	<li>Select at least one of these three sites as one of the two unique restriction enzymes needed for directional cloning due to the presence of an in-frame stop codon that divides the multicloning site as shown in Figure 111.</li>
	<li>Incorporate nucleotide sequence into the p...

<ol>
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Using the method presented here, interactions between any GPCR and &#946;-arrestin1/2 can be monitored in real time living systems using this GPCR-&#946;-arrestin structural complementation assay. In this regard, we were able to observe differential &#946;-arrestin recruitment between the two &#946;-arrestin isoforms by the GLP-1r (A prototypical Class B GPCR), we also observed a dissociation of the receptor-&#946;-arrestin complex a few minutes after reaching the maximum luminescent signal.
I...

GPCRs represent the target of nearly 35% of current drugs in the market1,2 and a clear understanding of their pharmacology is crucial in the development of novel therapeutic drugs3. One of the key aspects in GPCR drug discovery, particularly during the development of biased agonists is the characterization of novel ligands towards receptor-&#946;-arrestin interactions4 and &#946;-arrestin interactions with other cytosolic proteins such as clathrin5.
It has been documented that &#946;-arrestin dependent signaling plays a key role in neurological disorders such as bipolar disorder, major depression, and schizophrenia6 and also severe side effects in some medications such as morphine7.
Current methods used to monitor these interactions usually do not represent actual endogenous levels of the proteins in study, in some cases they show weak signal, photobleaching and depending of the GPCR it might be technically challenging to set up8. This novel structural complementation assay uses low expression promoter vectors in order to mimic endogenous physiological levels and provides high sensitivity compared to current methods9. Using this approach, it was possible to easily characterize Galanin receptor-&#946;-arrestin1/2 and also &#946;-arrestin2-clathrin interactions10. This methodology can be widely used to any GPCR of particular interest where &#946;-arrestins play a key physiological function or their signaling is relevant in some diseases.

<table>
	<tbody>
		<tr>
			<td>Antibiotics penicillin streptomycin</td>
			<td>Welgene</td>
			<td>LS202-02</td>
			<td>Penicillin/Streptomycin</td>
		</tr>
		<tr>
			<td>Bacterial Incubator</td>
			<td>JEIO Tech</td>
			<td>IB-05G</td>
			<td>Incubator (Air-Jacket), Basic</td>
		</tr>
		<tr>
			<td>Cell culture medium</td>
			<td>Welgene</td>
			<td>LM 001-05</td>
			<td>DMEM Cell culture medium</td>
		</tr>
		<tr>
			<td>Cell culture transfection medium</td>
			<td>Gibco</td>
			<td>31985-070</td>
			<td>Optimem 1X cell culture medium</td>
		</tr>
		<tr>
			<td>CO2 Incubator</td>
			<td>NUAIRE</td>
			<td>NU5720</td>
			<td>Direct Heat CO2 Incubator</td>
		</tr>
		<tr>
			<td>Digital water bath</td>
			<td>Lab Tech</td>
			<td>LWB-122D</td>
			<td>Digital water bath lab tech</td>
		</tr>
		<tr>
			<td>DNA Polymerase proof reading</td>
			<td>ELPIS Biotech</td>
			<td>EBT-1011</td>
			<td>PfU DNA polymerase</td>
		</tr>
		<tr>
			<td>DNA purification kit</td>
			<td>Cosmogenetech</td>
			<td>CMP0112</td>
			<td>miniprepLaboPass Purificartion Kit Plasmid Mini</td>
		</tr>
		<tr>
			<td>DNA Taq Polymerase</td>
			<td>Enzynomics</td>
			<td>P750</td>
			<td>nTaq DNA polymerase</td>
		</tr>
		<tr>
			<td>Enzyme restriction BglII</td>
			<td>New England Biolabs</td>
			<td>R0144L</td>
			<td>BglII</td>
		</tr>
		<tr>
			<td>Enzyme restriction buffer</td>
			<td>New England Biolabs</td>
			<td>B72045</td>
			<td>CutSmart 10X Buffer</td>
		</tr>
		<tr>
			<td>Enzyme restriction EcoRI</td>
			<td>New England Biolabs</td>
			<td>R3101L</td>
			<td>EcoRI-HF</td>
		</tr>
		<tr>
			<td>Enzyme restriction NheI</td>
			<td>New England Biolabs</td>
			<td>R01315</td>
			<td>NheI</td>
		</tr>
		<tr>
			<td>Enzyme restriction XhoI</td>
			<td>New England Biolabs</td>
			<td>R0146L</td>
			<td>XhoI</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Gibco Canada</td>
			<td>12483020</td>
			<td>Fetal Bovine Serum</td>
		</tr>
		<tr>
			<td>Gel/PCR DNA MiniKit</td>
			<td>Real Biotech Corporation</td>
			<td>KH23108</td>
			<td>HiYield Gel/PCR DNA MiniKit</td>
		</tr>
		<tr>
			<td>Ligase</td>
			<td>ELPIS Biotech</td>
			<td>EBT-1025</td>
			<td>T4 DNA Ligase</td>
		</tr>
		<tr>
			<td>Light microscope</td>
			<td>Olympus</td>
			<td>CKX53SF</td>
			<td>CKX53 Microscope Olympus</td>
		</tr>
		<tr>
			<td>lipid transfection reagent</td>
			<td>Invitrogen</td>
			<td>11668-019</td>
			<td>Lipofectamine 2000</td>
		</tr>
		<tr>
			<td>Luminometer</td>
			<td>Biotek/Fisher Scientific</td>
			<td>12504386</td>
			<td>Synergy 2 Multi-Mode Microplate Readers</td>
		</tr>
		<tr>
			<td>NanoBiT System</td>
			<td>Promega</td>
			<td>N2014</td>
			<td>NanoBiT PPI MCS Starter System</td>
		</tr>
		<tr>
			<td>Nanoluciferase substrate</td>
			<td>Promega</td>
			<td>N2012</td>
			<td>Nano-Glo Live Cell assay system</td>
		</tr>
		<tr>
			<td>PCR Thermal cycler</td>
			<td>Eppendorf</td>
			<td>6336000015</td>
			<td>Master cycler Nexus SX1</td>
		</tr>
		<tr>
			<td>Poly-L-lysine</td>
			<td>Sigma Aldrich</td>
			<td>P4707-50ML</td>
			<td>Poly-L-lysine solution</td>
		</tr>
		<tr>
			<td>Trypsin EDTA</td>
			<td>Gibco</td>
			<td>25200-056</td>
			<td>Trysin EDTA 10X</td>
		</tr>
		<tr>
			<td>White Cell culture 96 well plates</td>
			<td>Corning</td>
			<td>3917</td>
			<td>Assay Plate 96 well plate</td>
		</tr>
	</tbody>
</table>

monitoring gpcr-&#946;-arrestin1/2 interactions in real time living systems to accelerate drug discovery

Interactions between G-protein coupled receptors (GPCRs) and &#946;-arrestins are vital processes with physiological implications of great importance. Currently, the characterization of novel drugs towards their interactions with &#946;-arrestins and other cytosolic proteins is extremely valuable in the field of GPCR drug discovery particularly during the study of GPCR biased agonism. Here, we show the application of a novel structural complementation assay to accurately monitor receptor-&#946;-arrestin interactions in real time living systems. This method is simple, accurate and can be easily extended to any GPCR of interest and also it has the advantage that it overcomes unspecific interactions due to the presence of a low expression promoter present in each vector system. This structural complementation assay provides key features that allow an accurate and precise monitoring of receptor-&#946;-arrestin interactions, making it suitable in the study of biased agonism of any GPCR system as well as GPCR c-terminus &#8216;phosphorylation codes&#8217; written by different GPCR-kinases (GRKs) and post-translational modifications of arrestins that stabilize or destabilize the receptor-&#946;-arrestin complex.

Using the procedure presented here, interactions between a prototypical GPCR and two &#946;-arrestin isoforms were monitored. Glucagon like peptide receptor (GLP-1r) constructs were made using primers containing NheI and EcoRI enzyme restriction sites and cloned into the vectors pBiT1.1-C [TK/LgBiT] and pBiT2.1-C [TK/SmBiT] while in the case of &#946;-arrestins, two additional vectors were used pBiT1.1-N [TK/LgBiT] and pBiT2.1-N [TK/SmBiT] using enzyme restriction sites BgIII and EcoRI in the case of &#946;-arrestin2 and...

Watch this Scientific Journal Video about Monitoring GPCR-Î²-arrestin1/2 Interactions in Real Time Living Systems to Accelerate Drug Discovery at JoVE.com

Monitoring GPCR-&#946;-arrestin1/2 Interactions in Real Time Living Systems to Accelerate Drug Discovery

GPCR-&#946;-arrestin interactions are an emerging field in GPCR drug discovery. Accurate, precise and easy to set up methods are necessary to monitor such interactions in living systems. We show a structural complementation assay to monitor GPCR-&#946;-arrestin interactions in real time living cells, and it can be extended to any GPCR.

Interactions between G-protein coupled receptors (GPCRs) and &#946;-arrestins are vital processes with physiological implications of great importance. ...

This protocol has a high impact in the field of drug discovery and development, especially in the development of novel, first-in-class drugs with minimal side effects. The main advantage of this technique is that it can be applied to any GPCR system, and used to obtain accurate information about receptor pharmacology in real-time living systems. The implications of this technique are closely related to new therapies particularly where beta-arrestins are relevant.These include opiod receptors in pain and dopamine receptors in schizophrenia. This method can be useful in many medical scientific research areas from neurology to cardiopulmonary disease. PCR demonstration of our method is important, because it allows for a detailed presentation of the critical steps in the protocol, which would not be possible with conventional publication.Begin by designing primers to introduce genes of interest to the pBiT vectors. Due to the inframe stop codon that divides the multi-cloning site, select at least one of the three sites as one of the two unique restriction enzymes needed for directional cloning. Refer to the manuscript for nucleotide sequences to encode the linker residues and incorporate them into the primers.For the pBiT1.1-C and pBiT2.1-C make sure that the forward primer contains an ATG codon and a potent Kozak consensus sequence. For the pBiT1.1-N and pBiT2.1-N make sure that the reverse primer contains a stop codon. Use the designed primers to amplify the insert DNA of the gene of interest.Combine the PCR reagents according to manuscript directions, making sure to use a high-fidelity DNA polymerase to minimize mutations. Program the thermocycler and start the reaction. After completing PCR, digest the product in a 50-microliter digestion reaction.In a 1.5-milliliter tube, combine 12 microliters of distilled water, five microliters of the appropriate 10X restriction digestion buffer, and 30 microliters of the PCR product. Then add 1.5 microliters of each restriction enzyme. Vortex the reaction mixture.And incubate overnight at 37.5 degrees Celsius. Prepare a second reaction to digest the recipient plasmid. In a 1.5-milliliter tube, combine 23 microliters of water, five microliters of the appropriate 10X restriction digestion buffer, 15 microliters of the recipient plasmid, and 1.5 microliters of each restriction enzyme.Briefly mix the tube. And incubate overnight at 37.5 degrees Celsius. On the day following the cloning and transformation, pick three to 10 individual bacterial colonies and transfer them to one milliliter of LB medium with ampicillin.Incubate the cells for six hours. And then transfer 200 microliters of bacterial suspension to five milliliters of fresh LB medium with ampicillin. Incubate the culture at 37.5 degrees Celsius with shaking at 200 rpm overnight.On the next day, isolate the plasmid with a mini-prep DNA purification kit. Screen the purified plasmid for successful ligation with PCR. One day before transfection, seed the cells on a poly-L-lysine coated 96-well plate using Dulbecco's modified Eagle's medium supplemented with 10%fetal bovine serum, 100 units per milliliter of penicillin G, and 100 microliters per milliliter of streptomycin.Only add cells to the 60 inner wells to minimize potential for thermal gradients across the plate and edge effects from evaporation. Add 200 microliters of sterile distilled water to the 36 outside wells, and 150 microliters into the spaces between the wells. Then incubate the plate overnight at 37.5 degrees Celsius and 5%carbon dioxide.On the next day, perform transfection using a total of 100 nanograms DNA. Set up four different plasmid combinations according to manuscript directions. Using 20 microliters of modified Eagle's minimum essential media buffered with HEPES, and 0.3 microliters of lipidic transfection reagent per well.Add 20 microliters of lipidic transfection reagent and DNA mixture to each well, and mix the plate in circles for 10 seconds. Incubate the plate at 37.5 degrees Celsius and 5%carbon dioxide for six hours. Refresh the medium.And incubate for another 24 hours. After the incubation, aspirate the medium and add 100 microliters of modified Eagle's minimum essential media buffered with HEPES to each well. Allow the plate to stabilize at room temperature for 10 minutes.Meanwhile, prepare the furimazine substrate by combining one volume of the 100X substrate with 19 volumes of LCS dilution buffer, creating a 5X stock to mix with the cell culture medium. When the cells are ready, add 25 microliters of the stock to each well, and gently mix the plate for 10 seconds. Then measure the luminescence for 10 minutes at room temperature for signal stabilization.For experiments with ligand addition, prepare the 13.5X ligand solution in modified Eagle's minimum essential media buffered with HEPES, and add 10 microliters per well using a multichannel pipette. Then mix the plate by hand or with an orbital shaker. This protocol has been successfully used to study interactions between a prototypical GPCR and two beta-arrestin isoforms.Four different plasmid combinations were screened, and the one with the highest luminescent signal was selected for further experiments. The EC50 values for each beta-arrestin isoform were determined using dose-response curves, which were obtained from the maximum response of each concentration from kinetic studies. It's critical to pay special attention when designing the PCR primers.The development of the right constructs is essential to the success of these assays. Following this methodology, you will be able to monitor receptor-beta-arrestin interactions, as well as receptor interactions with other cytosolic proteins. This methodology will help to answer fundamental questions in the field of GPCR pharmacology by studying how GPCR-beta-arrestin interactions can be modulated by modifications in the ligand structure.

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Research

JoVE Journal

Biochemistry

Preparation and In Vivo Use of an Activity-based Probe for N-acylethanolamine Acid Amidase

Activity-based protein profiling (ABPP) is a method for the identification of an enzyme of interest in a complex proteome through the use of a chemical probe that targets the enzyme&#39;s active sites. A reporter tag introduced into the probe allows for the detection of the labeled enzyme by in-gel fluorescence scanning, protein blot, fluorescence microscopy, or liquid chromatography-mass spectrometry. Here, we describe the preparation and use of the compound ARN14686, a click chemistry activity-based probe (CC-ABP) that selectively recognizes the enzyme N-acylethanolamine acid amidase (NAAA). NAAA is a cysteine hydrolase that promotes inflammation by deactivating endogenous peroxisome proliferator-activated receptor (PPAR)-alpha agonists such as palmitoylethanolamide (PEA) and oleoylethanolamide (OEA). NAAA is synthesized as an inactive full-length proenzyme, which is activated by autoproteolysis in the acidic pH of the lysosome. Localization studies have shown that NAAA is predominantly expressed in macrophages and other monocyte-derived cells, as well as in B-lymphocytes. We provide examples of how ARN14686 can be used to detect and quantify active NAAA ex vivo in rodent tissues by protein blot and fluorescence microscopy.

Preparation and In Vivo Use of an Activity-based Probe for N-acylethanolamine Acid Amidase

Here, we describe the preparation and use of an activity-based probe (ARN14686, undec-10-ynyl-N-[(3S)-2-oxoazetidin-3-yl]carbamate) that allows for the detection and quantification of the active form of the proinflammatory enzyme N-acylethanolamine acid amidase (NAAA), both in vitro and ex vivo.

Activity-based protein profiling (ABPP) is a method for the identification of an enzyme of interest in a complex proteome through the use of a chemical ...

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size. This technique has advanced greatly in the last several decades, including the ability to monitor HDX labeling times on the millisecond time scale. In addition, by incorporating the HDX workflow onto a microfluidic platform housing an acidic protease microreactor, we are able to localize dynamic properties at the peptide level. In this study, Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS) coupled to HDX was used to provide a detailed picture of residual structure in the tau protein, as well as the conformational shifts induced upon hyperphosphorylation.

Conformational flexibility plays a critical role in protein function. Herein, we describe the use of time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange for probing the rapid structural changes that drive function in ordered and disordered proteins.

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. ...

Real-time Tracking of DNA Fragment Separation by Smartphone

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.

Traditional slab gel electrophoresis (SGE) experiments require a complicated apparatus and high chemical consumption. This work presents a protocol that describes a low-cost method to separate DNA fragments within a short timeframe.

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and ...

Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions

Secreted factors, membrane-tethered receptors, and their interacting partners are main regulators of cellular communication and initiation of signaling cascades during homeostasis and disease, and as such represent prime therapeutic targets. Despite their relevance, these interaction networks remain significantly underrepresented in current databases; therefore, most extracellular proteins have no documented binding partner. This discrepancy is primarily due to the challenges associated with the study of the extracellular proteins, including expression of functional proteins, and the weak, low affinity, protein interactions often established between cell surface receptors. The purpose of this method is to describe the printing of a library of extracellular proteins in a microarray format for screening of protein-protein interactions. To enable detection of weak interactions, a method based on multimerization of the query protein under study is described. Coupled to this microbead-based multimerization approach for increased multivalency, the protein microarray allows robust detection of transient protein-protein interactions in high throughput. This method offers a rapid and low sample consuming-approach for identification of new interactions applicable to any extracellular protein. Protein microarray printing and screening protocol are described. This technology will be useful for investigators seeking a robust method for discovery of protein interactions in the extracellular space.

Here, we present a protocol to screen extracellular protein microarrays for identification of novel receptor-ligand interactions in high throughput. We also describe a method to enhance detection of transient protein-protein interactions by using protein-microbead complexes.

Secreted factors, membrane-tethered receptors, and their interacting partners are main regulators of cellular communication and initiation of signaling ...

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and the degradation of target proteins in live cells. By using short (pulse) radiolabeling times (&lt;30 min) and tightly controlled chase times, it is possible to label only a small fraction of the total protein pool and follow its folding. When combined with nonreducing/reducing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoprecipitation with (conformation-specific) antibodies, folding processes can be examined in great detail. This system has been used to analyze the folding of proteins with a huge variation in properties such as soluble proteins, single and multi-pass transmembrane proteins, heavily N- and O-glycosylated proteins, and proteins with and without extensive disulfide bonding. Pulse-chase methods are the basis of kinetic studies into a range of additional features, including co- and posttranslational modifications, oligomerization, and polymerization, essentially allowing the analysis of a protein from birth to death. Pulse-chase studies on protein folding are complementary with other biochemical and biophysical methods for studying proteins in vitro by providing increased temporal resolution and physiological information. The methods as described within this paper are adapted easily to study the folding of almost any protein that can be expressed in mammalian or insect-cell systems.

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live cells.

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and ...

Real-time Observation of the DNA Strand Exchange Reaction Mediated by Rad51

The DNA strand exchange reaction mediated by Rad51 is a critical step of homologous recombination. In this reaction, Rad51 forms a nucleoprotein filament on single-stranded DNA (ssDNA) and captures double-stranded DNA (dsDNA) non-specifically to interrogate it for a homologous sequence. After encountering homology, Rad51 catalyzes DNA strand exchange to mediate pairing of the ssDNA with the complementary strand of the dsDNA. This reaction is highly regulated by numerous accessary proteins in vivo. Although conventional biochemical assays have been successfully employed to examine the role of such accessory protein in vitro, kinetic analysis of intermediate formation and its progression into a final product has proven challenging due to the unstable and transient nature of the reaction intermediates. To observe these reaction steps directly in solution, fluorescence resonance energy transfer (FRET)-based real-time observation systems of this reaction were established. Kinetic analysis of real-time observations shows that the DNA strand exchange reaction mediated by Rad51 obeys a three-step reaction model involving the formation of a three-strand DNA intermediate, maturation of this intermediate, and the release of ssDNA from the mature intermediate. The Swi5-Sfr1 complex, an accessary protein conserved in eukaryotes, strongly enhances the second and third steps of this reaction. The FRET-based assays presented here enable us to uncover the molecular mechanisms through which recombination accessary proteins stimulate the DNA strand exchange activity of Rad51. The primary goal of this protocol is to enhance the repertoire of techniques available to researchers in the field of homologous recombination, particularly those working with proteins from species other than Schizosaccharomyces pombe, so that the evolutionary conservation of the findings presented herein can be determined.

Fluorescence resonance energy transfer-based real-time observation systems of the DNA strand exchange reaction mediated by Rad51 were developed. Using the protocols presented here, we are able to detect the formation of reaction intermediates and their conversion into products, while also analyzing the enzymatic kinetics of the reaction.

The DNA strand exchange reaction mediated by Rad51 is a critical step of homologous recombination. In this reaction, Rad51 forms a nucleoprotein filament ...

Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis

Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal transduction; from sensing environmental signals to biological response; from metabolic regulation to developmental control. Accurate structural information of protein-protein interactions is crucial for understanding the molecular mechanisms of membrane protein complexes and for the design of highly specific molecules to modulate these proteins. Many in vivo and in vitro approaches have been developed for the detection and analysis of protein-protein interactions. Among them the structural biology approach is unique in that it can provide direct structural information of protein-protein interactions at the atomic level. However, current membrane protein structural biology is still largely limited to detergent-based methods. The major drawback of detergent-based methods is that they often dissociate or denature membrane protein complexes once their native lipid bilayer environment is removed by detergent molecules. We have been developing a&#160;native cell membrane nanoparticle system for membrane protein structural biology. Here, we demonstrate the use of this system in the analysis of protein-protein interactions on the cell membrane with a case study of the oligomeric state of AcrB.

Presented here is a protocol for the determination of oligomeric state of membrane proteins that utilizes a native cell membrane nanoparticle system in conjunction with electron microscopy.

Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal ...

Measuring Nucleotide Binding to Intact, Functional Membrane Proteins in Real Time

We have developed a method to measure binding of adenine nucleotides to intact, functional transmembrane receptors in a cellular or membrane environment. This method combines expression of proteins tagged with the fluorescent non-canonical amino acid ANAP, and FRET between ANAP and fluorescent (trinitrophenyl) nucleotide derivatives. We present examples of nucleotide binding to ANAP-tagged KATP ion channels measured in unroofed plasma membranes and excised, inside-out membrane patches under voltage clamp. The latter allows for simultaneous measurements of ligand binding and channel current, a direct readout of protein function. Data treatment and analysis are discussed extensively, along with potential pitfalls and artefacts. This method provides rich mechanistic insights into the ligand-dependent gating of KATP channels and can readily be adapted to the study of other nucleotide-regulated proteins or any receptor for which a suitable fluorescent ligand can be identified.

This protocol presents a method for measuring adenine nucleotide binding to receptors in real time in a cellular environment. Binding is measured as F&#246;rster resonance energy transfer (FRET) between trinitrophenyl nucleotide derivatives and protein labeled with a non-canonical, fluorescent amino acid.

We have developed a method to measure binding of adenine nucleotides to intact, functional transmembrane receptors in a cellular or membrane environment. ...

Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes

Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area of proteins. This technique relies on the reaction of amino acid side chains with hydroxyl radicals freely diffusing in solution. FPOP generates these radicals in situ by laser photolysis of hydrogen peroxide, creating a burst of hydroxyl radicals that is depleted on the order of a microsecond. When these hydroxyl radicals react with a solvent-accessible amino acid side chain, the reaction products exhibit a mass shift that can be measured and quantified by mass spectrometry. Since the rate of reaction of an amino acid depends in part on the average solvent accessible surface of that amino acid, measured changes in the amount of oxidation of a given region of a protein can be directly correlated to changes in the solvent accessibility of that region between different conformations (e.g., ligand-bound versus ligand-free, monomer vs. aggregate, etc.) FPOP has been applied in a number of problems in biology, including protein-protein interactions, protein conformational changes, and protein-ligand binding. As the available concentration of hydroxyl radicals varies based on many experimental conditions in the FPOP experiment, it is important to monitor the effective radical dose to which the protein analyte is exposed. This monitoring is efficiently achieved by incorporating an inline dosimeter to measure the signal from the FPOP reaction, with laser fluence adjusted in real-time to achieve the desired amount of oxidation. With this compensation, changes in protein topography reflecting conformational changes, ligand-binding surfaces, and/or protein-protein interaction interfaces can be determined in heterogeneous samples using relatively low sample amounts.

Fast photochemical oxidation of proteins is an emerging technique for the structural characterization of proteins. Different solvent additives and ligands have varied hydroxyl radical scavenging properties. To compare the protein structure in different conditions, real-time compensation of hydroxyl radicals generated in the reaction is required to normalize reaction conditions.

Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area ...

A Competent Hepatocyte Model Examining Hepatitis B Virus Entry through Sodium Taurocholate Cotransporting Polypeptide as a Therapeutic Target

Hepatitis B virus (HBV) infection has been considered a crucial risk factor for hepatocellular carcinoma. Current treatment can only lessen the viral load but not result in complete remission. An efficient hepatocyte model for HBV infection would offer a true-to-life viral life cycle that would be crucial for the screening of therapeutic agents. Most available anti-HBV agents target lifecycle stages post viral entry but not before viral entry. This protocol details the generation of a competent hepatocyte model capable of screening for therapeutic agents targeting pre-viral entry and post viral entry lifecycle stages. This includes the targeting of sodium taurocholate cotransporting polypeptide (NTCP) binding, cccDNA formation, transcription, and viral assembly based on imHC or HepaRG as host cells. Here, the HBV entry inhibition assay used curcumin to inhibit HBV binding and transporting functions via NTCP. The inhibitors were evaluated for binding affinity (KD) with NTCP using isothermal titration calorimetry (ITC)-a universal tool for HBV drug screening based on thermodynamic parameters.

We present a protocol to screen anti-hepatitis B virus (HBV) compounds targeting pre- and post-viral entry lifecycle stages, using isothermal titration calorimetry to measure binding affinity (KD) with host sodium taurocholate cotransporting polypeptide. Antiviral efficacy was determined through the suppression of viral lifecycle markers (cccDNA formation, transcription, and viral assembly).

Hepatitis B virus (HBV) infection has been considered a crucial risk factor for hepatocellular carcinoma. Current treatment can only lessen the viral load ...