This work was supported by the National Natural Science Foundation of China (No. 31870746), Shenzhen Basic Research Grants (JCYJ20200109140414636), and Natural Science Foundation of Guangdong Province, China (No. 2021A1515010796) to W. L. We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript.

1. Purification of GST-tagged TRP and His-tagged NORPA fragments
<ol>
	<li>Purify GST-tagged TRP 1261-1275 fragment
	<ol>
		<li>Transform the pGEX 4T-1 TRP 1261-1275 plasmid10 into Escherichia coli (E. coli) BL21 (DE3) cells using the CaCl2 heat-shock transformation method21. Inoculate a single colony in 10 mL of Luria Bertani (LB) medium and grow overnight at 37 &#176;C. Then, amplify the 10 mL of seeding culture in 1 L of LB medium at 37 &#176;C.</li>
		<li>After the optical density (OD600) of the cells reaches 0.5, cool down the cells to 16 &#176;C and add 0.1 mM isopropyl &#946;-D-1-thiogalactopyranoside (IPTG; final concentration) to induce the overexpression of the target protein and incubate at 16 &#176;C for 18 h.</li>
		<li>After overexpression, pellet 1 L of cultured cells by centrifugation at 3,993&#160;&#215; g&#160;for 20 min and resuspend in 40 mL of phosphate-buffered saline (PBS) buffer.</li>
		<li>Load the resuspended cells in a high-pressure homogenizer pre-cooled at 4 &#176;C. Slowly increase the homogenizer pressure to 800 bar. Open the inlet tap and let the resuspended cells circularly pass through a valve with very narrow slits. 
		NOTE: The cells are homogenized by the high shearing forces caused by a large pressure drop and cavitation.</li>
		<li>Load 5 mL of glutathione beads to a gravity flow column and wash the beads with 50 mL of PBS buffer for a total of three times.</li>
		<li>Centrifuge the cell lysate from the high-pressure homogenizer at 48,384 x g. Add the supernatant of the centrifuged cell lysate (40 mL) to the equilibrated glutathione beads in the gravity flow column and incubate for 30 min at 4 &#176;C. Resuspend the glutathione beads every 10 min.</li>
		<li>After 30 min of incubation, open the column outlet tap to separate the beads and flow-through fraction. Discard the flow-through fraction. Rinse the remaining glutathione beads twice with 50 mL of PBS buffer.</li>
		<li>Add 15 mL of elution buffer to the glutathione beads and incubate for 30 min. Resuspend the beads every 10 min.</li>
		<li>After 30 min of incubation, elute the GST-tagged TRP 1261-1275 fragment in a 50 mL conical tube and load in a size-exclusion column (preparation grade), which is equilibrated using 50 mM Tris (pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM DTT) buffer.</li>
		<li>Keep the elution flow rate of the size-exclusion column to 3 mL/min. Collect the eluted proteins at the rate of 5 mL/tube.</li>
		<li>Identify the peak of the target protein in the size-exclusion column by analyzing the UV absorption signals at 280 nm and verify by SDS-PAGE gel analysis (electrophoresis parameters: 150 V for the stacking gel; 200 V for the resolving gel). Stain the gel with Coomassie blue R250.</li>
		<li>Concentrate the purified GST-tagged TRP 1261-1275 fragment from the size-exclusion column to 1 mL using a 15 mL ultrafiltration spin column centrifuged at 3,000 x g at 4 &#176;C in a desk-top refrigerated centrifuge.</li>
		<li>Determine the concentration of concentrated protein using the Beer-Lambert Law. Measure the UV absorption of GST-tagged TRP 1261-1275 fragment at 280 nm using a spectrophotometer.</li>
		<li>Obtain the extinction coefficient at 280 nm by importing the protein sequences into the Protparam program (https://web.expasy.org/protparam/). Typically, 1 L culture of GST-tagged TRP 1261-1275 yields 1 mL of 600 &#956;M of protein (6 x 10-7 mol). See Table 1 for materials needed.</li>
	</ol>
	</li>
	<li>Purification of His-tagged NORPA 863-1095 fragment
	<ol>
		<li>Transform the pETM.3C NORPA 863-1095 plasmid20 into E. coli BL21 (DE3) cells using the CaCl2 heat-shock transformation method21. Inoculate a single colony in 10 mL of LB medium and grow overnight at 37 &#176;C. Then, amplify the 10 mL seeding culture in 1 L of LB medium at 37 &#176;C.</li>
		<li>After the OD600 of the cells reaches 0.5, cool down the cells to 16 &#176;C and add 0.1 mM IPTG (final concentration) to induce the overexpression of target protein and incubate at 16 &#176;C for 18 h.</li>
		<li>After overexpression, pellet 1 L of cultured cells by centrifugation at 3,993&#160;x g&#160;for 20 min and resuspend in 40 mL of binding buffer. Next, lyse the resuspended cells in a high-pressure homogenizer at 4 &#176;C as described in step 1.1.4.</li>
		<li>Load 5 mL of Ni-beads into a gravity flow column and wash three times with 50 mL of binding buffer.</li>
		<li>Centrifuge the cell lysate from the high-pressure homogenizer at 48,384 x g. Add the supernatant of the centrifuged cell lysate to the equilibrated Ni-beads in the gravity flow column and incubate for 30 min at 4 &#176;C. Resuspend the Ni-beads every 10 min.</li>
		<li>After 30 min of incubation, open the column outlet tap to separate the beads and flow-through fraction. Discard the flow-through fraction and wash the remaining Ni-beads twice with 50 mL of wash buffer.</li>
		<li>Add 15 mL of elution buffer to the Ni-beads and incubate for 30 min. Resuspend the Ni-beads every 10 min.</li>
		<li>After 30 min of incubation, collect the eluted His-tagged NORPA 863-1095 fragment in a 50 mL conical tube and load into a size-exclusion column (preparation grade), which is equilibrated using 50 mM Tris (pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM DTT).</li>
		<li>Keep the elution flow rate of the size-exclusion column to 3 mL/min. Collect the eluted protein at the rate of 5 mL/tube.</li>
		<li>Identify the peak of the target protein in the size-exclusion column by analyzing the UV absorption signals at 280 nm and verify by SDS-PAGE gel analysis (electrophoresis parameters: 150 V for the stacking gel; 200 V for the resolving gel). Stain the gel using Coomassie blue R250.</li>
		<li>Concentrate the purified His-tagged NORPA 863-1095 fragment from the size-exclusion column to 1 mL using a 15 mL ultrafiltration spin column centrifuged at 3,000 x g at 4 &#176;C in a desk-top refrigerated centrifuge.</li>
		<li>Determine the concentration of concentrated protein using the Beer-Lambert Law. Measure the UV absorption of His-tagged NORPA 863-1095 fragment at 280 nm using a spectrophotometer.</li>
		<li>Obtain the extinction coefficient at 280 nm by importing the protein sequences into the Protparam program (https://web.expasy.org/protparam/). Typically, 1 L culture of His-tagged NORPA 863-1095 fragment yields 1 mL of 600 &#956;M of protein (6 x 10-7 mol). See Table 2 for materials needed.</li>
	</ol>
	</li>
</ol>
2. Preparation of Drosophila heads
<ol>
	<li>Collect adult flies in 50 mL conical centrifugation tubes using the CO2 anaesthetization method22,23; immediately freeze in liquid nitrogen for 10 min and store in a -80&#176;C freezer.</li>
	<li>After collecting a sufficient number of flies, vigorously shake the frozen 50 mL conical tubes by hand to separate the flies&#39; legs, heads, wings, and bodies. Transfer the mixture to three sequentially stacked pre-cooled stainless-steel sieves (20/30/40 mesh size, respectively) and shake the sieves.</li>
	<li>Next, since the heads cannot pass through the 40-mesh sieve, use a brush to sweep the fly heads off the 40-mesh sieve, transfer them into 50 mL conical tubes, and store them at &#8722;80 &#176;C.</li>
	<li>Continuously collect the flies and their heads and store them in a -80 &#176;C freezer until they reach the required amount needed for experimentation (0.5 g). Typically, to collect 0.5 g of heads, 35 mL of flies in a 50 mL conical tube are needed. See Table 3 for materials needed.</li>
</ol>
3. Drosophila TRP channel purification
<ol>
	<li>Weigh a total of 0.5 g of heads and completely homogenize in liquid nitrogen using a pre-cooled mortar-pestle. Dissolve the homogenized heads in 10x v/w lysis buffer (5 mL), incubate in a shaker at 4 &#176;C for 20 min, and then centrifuge at 20,817 x g for 20 min at 4 &#176;C.</li>
	<li>Collect the spin-down supernatant (&#34;20817 g S&#34;, Figure 4) and further centrifuge it at 100,000 x g for 60 min at 4 &#176;C. Use the spin-down supernatant (&#34;100,000 g S&#34;, Figure 4) for the following pull-down assay.</li>
	<li>Add 1 mL of Ni-beads into the gravity flow column and wash the beads with 10 mL of double-distilled H2O (ddH2O) at 4 &#176;C for a total of three times. Equilibrate the beads with 10 column volumes of lysis buffer three times at 4 &#176;C.</li>
	<li>Add 500 &#181;L of 600 &#181;M purified His-tagged NORPA 863-1095 protein (3 x 10-7 mol) into the Ni-column and incubate for 30 min at 4 &#176;C. Resuspend the beads every 10 min.</li>
	<li>Open the column outlet tap to separate the beads and flow-through fraction. Take the flow-through fraction for SDS-PAGE analysis (NORPA F, Figure 4). In this section, the bait proteins are immobilized on the Ni-beads.</li>
	<li>Wash the Ni-beads with 10 column volumes of lysis buffer (10 mL) at 4 &#176;C and keep the washing fraction for SDS-PAGE analysis (Wash 1, Figure 4A). Repeat the above steps and keep the sample for SDS-PAGE analysis (Wash 2, Figure 4A). In this section, the excessive bait proteins on the Ni-beads are removed.</li>
	<li>Add the supernatant of Drosophila head homogenate after 100,000 x g centrifugation into the Ni-column at 4 &#176;C, where the His-tagged NORPA 863-1095 fragment has been immobilized.</li>
	<li>Incubate the supernatant with the Ni-beads at 4 &#176;C for 30 min. Resuspend the beads every 10 min. Then, open the column outlet tap to separate the beads and flow-through fraction.</li>
	<li>Collect the supernatant for SDS-PAGE analysis (Dro head lysis F, Figure 4A). In this section, the INAD protein complexes (INAD/TRP/ePKC) in the head homogenates are captured by the immobilized NORPA 863-1095 fragments on the Ni-beads.</li>
	<li>Wash the Ni-beads with 10 column volumes of lysis buffer (10 mL) at 4 &#176;C and keep the supernatant from gravity precipitation for SDS-PAGE analysis (Wash 3, Figure 4A). Repeat the above steps and collect the supernatant for SDS-PAGE analysis (Wash 4, Figure 4A). In this section, the unbound proteins on the Ni-beads are removed.</li>
	<li>Add 500 &#181;L of 600 &#181;M of GST-tagged TRP 1261-1275 protein (3 x 10-7 mol) into the Ni-beads and incubate for 20 min at 4 &#176;C. Resuspend the beads every 10 min.</li>
	<li>Collect the eluted fraction from the gravity column (TRP E1, Figure 4B), which contains the endogenous Drosophila TRP channel. Repeat the above stepsand collect the elution fraction (TRP E2, Figure 4B). In this step, by using the GST-tagged TRP 1261-1275 fragments as the competitor, the TRP channels are eluted from the captured INAD protein complexes (INAD/TRP/ePKC) on the Ni-beads.</li>
	<li>Wash the Ni-beads with 10 column volumes of binding buffer (10 mL; Table 1) at 4 &#176;C and collect the washing fraction for SDS-PAGE analysis (Wash 5, Figure 4B).</li>
	<li>Add 500 &#181;L of elution buffer (Table 1) into the Ni-beads and incubate for 20 min at 4 &#176;C. Collect the elution fraction from the gravity flow column (NORPA E1, Figure 4B). Repeat the above steps, and collect the elution fraction (NORPA E2, Figure 4B).</li>
	<li>Using the elution buffer, elute the His-tagged NORPA 863-1095 fragment accompanied with the INAD/ePKC protein complexes. Next, resuspend the Ni-beads in 500 &#181;L of binding buffer.</li>
	<li>Take the resuspended Ni-beads to run the SDS-PAGE (stained by Coomassie blue R250) to analyze the efficiency of the elution and evaluate whether the elute buffer works (beads, Figure 4B). See Table 4 for materials needed.</li>
</ol>
4. Size-exclusion column purification of Drosophila TRP channel
<ol>
	<li>Install a size-exclusion column (analytical grade) on the protein purification system. Equilibrate the column with the column buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM DTT, 0.75 mM DDM), which is filtered by a 0.45 &#181;m filter.</li>
	<li>Concentrate the TRP E1 and E2 fraction from step 3.14 using a 4 mL ultrafiltration spin column, centrifuged at 3,000 x g at 4 &#176;C in a refrigerated centrifuge.</li>
	<li>Rinse the sample loop with the column buffer and load the sample into the sample loop. Inject the sample into the size-exclusion column and elute the proteins with a proper flow rate (0.5 mL/min).</li>
	<li>Identify the peak of the target protein by absorption at 280 nm and run an SDS-PAGE gel to detect the purified endogenous Drosophila TRP channel (Figure 5). See Table 5 for materials needed.</li>
</ol>

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The authors have nothing to disclose.

INAD, which contains five PDZ domains, is the core organizer of Drosophila phototransduction machinery. Previous studies showed that INAD PDZ3 binds to the TRP channel C-terminal tail with exquisite specificity (KD = 0.3 &#181;M)18. INAD PDZ45 tandem interacts with NORPA 863-1095 fragment with an extremely high binding affinity (KD = 30 nM). These findings provide a solid biochemical basis to design the affinity purification plus competition strategy, which enables t...

Phototransduction is a process where absorbed photons are converted into electrical codes of neurons. It exclusively relays opsins and the following G protein-coupled signaling cascade in both vertebrates and invertebrates. In Drosophila, by using its five PDZ domains, scaffold protein inactivation-no-after-potential D (INAD) organizes a supramolecular signaling complex, which consists of a transient receptor potential (TRP) channel, phospholipase C&#946;/No receptor potential A (PLC&#946;/NORPA), and eye-specific protein kinase C (ePKC)1. The formation of this supramolecular signaling complex guarantees the correct subcellular localization, high efficiency, and specificity of Drosophila phototransduction machinery. In this complex, light-sensitive TRP channels act as downstream effectors of NORPA and mediate calcium influx and the depolarization of photoreceptors. Previous studies showed that the opening of the Drosophila TRP channel is mediated by protons, disruption of the local lipid environment, or mechanical force2,3,4. The Drosophila TRP channel also interacts with calmodulin5 and is modulated by calcium by both positive and negative feedback6,7,8.
So far, electrophysiology studies on the gating mechanism of Drosophila TRP and TRP-like (TRPL) channels were based on excised membrane patches, whole-cell recordings from dissociated wild-type Drosophila photoreceptors, and hetero-expressed channels in S2, SF9, or HEK cells2,9,10,11,12,13, but not on purified channels. The structural information of the full-length Drosophila TRP channel also remains unclear. In order to study the electrophysiological properties of purified protein in a reconstituted membrane environment and to gain structural information of the full-length Drosophila TRP channel, obtaining purified full-length TRP channels is the necessary first step, similar to the methodologies used in mammalian TRP channel studies14,15,16,17.
Recently, based on the assembling mechanism of INAD protein complex18,19,20, an affinity purification plus competition strategy was first developed to purify the TRP channel from Drosophila head homogenates by streptavidin beads5. Considering the low capacity and expensive cost of streptavidin beads, an improved purification protocol is introduced here that uses His-tagged bait protein and corresponding low-cost Ni-beads with much higher capacity. The proposed method will help to study the gating mechanism of the TRP channel from structural angles and to measure the electrophysiological properties of the TRP channel with purified proteins.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Bacterial strains</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>BL21(DE3) Competent Cells</td>
			<td>Novagen</td>
			<td>69450</td>
			<td>Protein overexpression</td>
		</tr>
		<tr>
			<td>Experiment models</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>D.melanogaster: W1118 strain</td>
			<td>Bloomington Drosophila Stock Center</td>
			<td>BDSC:3605</td>
			<td>Drosophila head preparation</td>
		</tr>
		<tr>
			<td>Material</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>20/30/40 mesh stainless steel sieves</td>
			<td>Jiufeng metal mesh company</td>
			<td>GB/T6003.1</td>
			<td>Drosophila head preparation</td>
		</tr>
		<tr>
			<td>30% Acrylamide-N,N&#8242;-Methylenebisacrylamide(29:1)</td>
			<td>Lablead</td>
			<td>A3291</td>
			<td>SDS-PAGE gel preparation</td>
		</tr>
		<tr>
			<td>Ammonium Persulfate</td>
			<td>Invitrogen</td>
			<td>HC2005</td>
			<td>SDS-PAGE gel preparation</td>
		</tr>
		<tr>
			<td>Cocktail protease inhibitor</td>
			<td>Roche</td>
			<td>05892953001</td>
			<td>Protease inhibitor</td>
		</tr>
		<tr>
			<td>Coomassie brilliant blue R-250</td>
			<td>Sangon Biotech</td>
			<td>A100472-0025</td>
			<td>SDS-PAGE gel staining</td>
		</tr>
		<tr>
			<td>DL-Dithiothreitol (DTT)</td>
			<td>Sangon Biotech</td>
			<td>A620058-0100</td>
			<td>Size-exclusion column buffer preparation</td>
		</tr>
		<tr>
			<td>Ethylenediaminetetraacetic acid disodium salt (EDTA)</td>
			<td>Sangon Biotech</td>
			<td>A500838-0500</td>
			<td>Size-exclusion column buffer preparation</td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sangon Biotech</td>
			<td>A610235-0005</td>
			<td>SDS-PAGE buffer preparation</td>
		</tr>
		<tr>
			<td>Glutathione Sepharose 4 Fast Flow beads</td>
			<td>Cytiva</td>
			<td>17513202</td>
			<td>Affinity chromatography</td>
		</tr>
		<tr>
			<td>Imidazole</td>
			<td>Sangon Biotech</td>
			<td>A500529-0001</td>
			<td>Elution buffer preparation for Ni-column</td>
		</tr>
		<tr>
			<td>Isopropyl-beta-D-thiogalactopyranoside (IPTG)</td>
			<td>Sangon Biotech</td>
			<td>A600168-0025</td>
			<td>Induction of protein overexpression</td>
		</tr>
		<tr>
			<td>LB Broth Powder</td>
			<td>Sangon Biotech</td>
			<td>A507002-0250</td>
			<td>E.coli. cell culture</td>
		</tr>
		<tr>
			<td>L-Glutathione reduced (GSH)</td>
			<td>Sigma-aldrich</td>
			<td>G4251-100G</td>
			<td>Elution buffer preparation for Glutathione beads</td>
		</tr>
		<tr>
			<td>Ni-Sepharose excel beads</td>
			<td>Cytiva</td>
			<td>17371202</td>
			<td>Affinity chromatography</td>
		</tr>
		<tr>
			<td>N-Dodecyl beta-D-maltoside (DDM)</td>
			<td>Sangon Biotech</td>
			<td>A610424-001</td>
			<td>Detergent for protein purification</td>
		</tr>
		<tr>
			<td>N,N,N&#39;,N&#39;-Tetramethylethylenediamine (TEMED)</td>
			<td>Sigma-aldrich</td>
			<td>T9281-100ML</td>
			<td>SDS-PAGE gel preparation</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Sangon Biotech</td>
			<td>E607008-0500</td>
			<td>Homogenization buffer for E.coli. cell</td>
		</tr>
		<tr>
			<td>PMSF</td>
			<td>Lablead</td>
			<td>P0754-25G</td>
			<td>Protease inhibitor</td>
		</tr>
		<tr>
			<td>Prestained protein marker</td>
			<td>Thermo Scientific</td>
			<td>26619/26616</td>
			<td>Prestained protein ladder</td>
		</tr>
		<tr>
			<td>Size exclusion column (preparation grade)</td>
			<td>Cytiva</td>
			<td>28989336</td>
			<td>HiLoad 26/60 Superdex 200 PG column</td>
		</tr>
		<tr>
			<td>Size exclusion column (analytical grade)</td>
			<td>Cytiva</td>
			<td>29091596</td>
			<td>Superose 6 Increase 10/300 GL column</td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Sangon Biotech</td>
			<td>A501218-0001</td>
			<td>Protein purification buffer preparation</td>
		</tr>
		<tr>
			<td>Sodium dodecyl sulfate (SDS)</td>
			<td>Sangon Biotech</td>
			<td>A500228-0001</td>
			<td>SDS-PAGE gel/buffer preparation</td>
		</tr>
		<tr>
			<td>Tris base</td>
			<td>Sigma-aldrich</td>
			<td>T1503-10KG</td>
			<td>Protein purification buffer preparation</td>
		</tr>
		<tr>
			<td>Ultrafiltration spin column</td>
			<td>Millipore</td>
			<td>UFC901096/801096</td>
			<td>Protein concentration</td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Analytical Balance</td>
			<td>DENVER</td>
			<td>APX-60</td>
			<td>Metage of Drosophila head</td>
		</tr>
		<tr>
			<td>Desk-top high-speed refrigerated centrifuge for 15mL and 50mL conical centrifugation tubes</td>
			<td>Eppendorf</td>
			<td>5810R</td>
			<td>Protein concentration</td>
		</tr>
		<tr>
			<td>Desk-top high-speed refrigerated centrifuge 1.5mL centrifugation tubes</td>
			<td>Eppendorf</td>
			<td>5417R</td>
			<td>Centrifugation of Drosophila head lysate after homogenization</td>
		</tr>
		<tr>
			<td>Empty gravity flow column (Inner Diameter=1.0cm)</td>
			<td>Bio-Rad</td>
			<td>738-0015</td>
			<td>TRP protein purification</td>
		</tr>
		<tr>
			<td>Empty gravity flow column (Inner Diameter=2.5cm)</td>
			<td>Bio-Rad</td>
			<td>738-0017</td>
			<td>Bait and competitor protein purification from E.coli.</td>
		</tr>
		<tr>
			<td>Gel Documentation System</td>
			<td>Bio-Rad</td>
			<td>Universal Hood II Gel Doc XR System</td>
			<td>SDS-PAGE imaging</td>
		</tr>
		<tr>
			<td>High-speed refrigerated centrifuge</td>
			<td>Beckman coulter</td>
			<td>Avanti J-26 XP</td>
			<td>Centrifugation of E.coli. cells/cell lysate</td>
		</tr>
		<tr>
			<td>High pressure homogenizer</td>
			<td>UNION-BIOTECH</td>
			<td>UH-05</td>
			<td>Homogenization of E.coli. cells</td>
		</tr>
		<tr>
			<td>Liquid nitrogen tank</td>
			<td>Taylor-Wharton</td>
			<td>CX-100</td>
			<td>Drosophila head preparation</td>
		</tr>
		<tr>
			<td>Protein purification system</td>
			<td>Cytiva</td>
			<td>AKTA purifier</td>
			<td>Protein purification</td>
		</tr>
		<tr>
			<td>Refrigerator (-80&#176;C)</td>
			<td>Thermo</td>
			<td>900GP</td>
			<td>Drosophila head preparation</td>
		</tr>
		<tr>
			<td>Spectrophotometer</td>
			<td>MAPADA</td>
			<td>UV-1200</td>
			<td>OD600 measurement of E.coli. cells</td>
		</tr>
		<tr>
			<td>Spectrophotometer</td>
			<td>Thermo Scientific</td>
			<td>NanoDrop 2000c</td>
			<td>Determination of protein concentration</td>
		</tr>
		<tr>
			<td>Ultracentrifuge</td>
			<td>Beckman coulter</td>
			<td>Optima XPN-100 Ultracentrifuge</td>
			<td>Ultracentrifugation</td>
		</tr>
	</tbody>
</table>

purification of endogenous drosophila transient receptor potential channels

Drosophila phototransduction is one of the fastest known G protein-coupled signaling pathways. To ensure the specificity and efficiency of this cascade, the calcium (Ca2+)-permeable cation channel, transient receptor potential (TRP), binds tightly to the scaffold protein, inactivation-no-after-potential D (INAD), and forms a large signaling protein complex with eye-specific protein kinase C (ePKC) and phospholipase C&#946;/No receptor potential A (PLC&#946;/NORPA). However, the biochemical properties of the Drosophila TRP channel remain unclear. Based on the assembling mechanism of INAD protein complex, a modified affinity purification plus competition strategy was developed to purify the endogenous TRP channel. First, the purified histidine (His)-tagged NORPA 863-1095 fragment was bound to Ni-beads and used as bait to pull down the endogenous INAD protein complex from Drosophila head homogenates. Then, excessive purified glutathione S-transferase (GST)-tagged TRP 1261-1275 fragment was added to the Ni-beads to compete with the TRP channel. Finally, the TRP channel in the supernatant was separated from the excessive TRP 1261-1275 peptide by size-exclusion chromatography. This method makes it possible to study the gating mechanism of the Drosophila TRP channel from both biochemical and structural angles. The electrophysiology properties of purified Drosophila TRP channels can also be measured in the future.

In this article, a protein purification method is demonstrated to purify endogenous Drosophila TRP channel (Figure 1).
First, recombinant protein expression and purification are applied to obtain the bait and competitor proteins. Then, a GST-tagged TRP 1261-1275 fragment is expressed in E. coli BL21 (DE3) cells in LB medium and purified using glutathione beads and a size-exclusion column (Figure 2). The samples were ...

Watch this Scientific Journal Video about Purification of Endogenous Drosophila Transient Receptor Potential Channels at JoVE.com

Purification of Endogenous Drosophila Transient Receptor Potential Channels

Based on the assembling mechanism of the INAD protein complex, in this protocol, a modified affinity purification plus competition strategy was developed to purify the endogenous Drosophila TRP channel.

Purification of Endogenous Drosophila Transient Receptor Potential Channels

Drosophila phototransduction is one of the fastest known G protein-coupled signaling pathways. To ensure the specificity and efficiency of this cascade, ...

purification-endogenous-drosophila-transient-receptor-potential

Research

JoVE Journal

Biochemistry

1.6K Views.  Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center. Based on the assembling mechanism of the INAD protein complex, in this protocol, a modified affinity purification plus competition strategy was developed to purify the endogenous Drosophila TRP channel.

Video: Purification of Endogenous Drosophila Transient Receptor Potential Channels

Tandem Affinity Purification of Protein Complexes from Eukaryotic Cells

The purification of active protein-protein and protein-nucleic acid complexes is crucial for the characterization of enzymatic activities and de novo identification of novel subunits and post-translational modifications. Bacterial systems allow for the expression and purification of a wide variety of single polypeptides and protein complexes. However, this system does not enable the purification of protein subunits that contain post-translational modifications (e.g., phosphorylation and acetylation), and the identification of novel regulatory subunits that are only present/expressed in the eukaryotic system. Here, we provide a detailed description of a novel, robust, and efficient tandem affinity purification (TAP) method using STREP- and FLAG-tagged proteins that facilitates the purification of protein complexes with transiently or stably expressed epitope-tagged proteins from eukaryotic cells. This protocol can be applied to characterize protein complex functionality, to discover post-translational modifications on complex subunits, and to identify novel regulatory complex components by mass spectrometry. Notably, this TAP method can be applied to study protein complexes formed by eukaryotic or pathogenic (viral and bacterial) components, thus yielding a wide array of downstream experimental opportunities. We propose that researchers working with protein complexes could utilize this approach in many different ways.

We describe here a novel, robust, and efficient tandem affinity purification (TAP) method for the expression, isolation, and characterization of protein complexes from eukaryotic cells. This protocol could be utilized for the biochemical characterization of discrete complexes as well as the identification of novel interactors and post-translational modifications that regulate their function.

The purification of active protein-protein and protein-nucleic acid complexes is crucial for the characterization of enzymatic activities and de novo ...

Expression, Purification, and Antimicrobial Activity of S100A12

Calgranulin proteins are important mediators of innate immunity and are members of the S100 class of the EF-hand family of calcium binding proteins. Some S100 proteins have the capacity to bind transition metals with high affinity and effectively sequester them away from invading microbial pathogens in a process that is termed "nutritional immunity". S100A12 (EN-RAGE) binds both zinc and copper and is highly abundant in innate immune cells such as macrophages and neutrophils. We report a refined method for the expression, enrichment and purification of S100A12 in its active, metal-binding configuration. Utilization of this protein in bacterial growth and viability analyses reveals that S100A12 has antimicrobial activity against the bacterial pathogen, Helicobacter pylori. The antimicrobial activity is predicated on the zinc-binding activity of S100A12, which chelates nutrient zinc, thereby starving H. pylori which requires zinc for growth and proliferation.

Here, we present a method to express and purify S100A12 (calgranulin C). We describe a protocol to measure its antimicrobial activity against the human pathogen H. pylori.

Calgranulin proteins are important mediators of innate immunity and are members of the S100 class of the EF-hand family of calcium binding proteins. Some ...

Purification and Reconstitution of TRPV1 for Spectroscopic Analysis

Polymodal ion channels transduce multiple stimuli of different natures into allosteric changes; these dynamic conformations are challenging to determine and remain largely unknown. With recent advances in single-particle cryo-electron microscopy (cryo-EM) shedding light on the structural features of agonist binding sites and the activation mechanism of several ion channels, the stage is set for an in-depth dynamic analysis of their gating mechanisms using spectroscopic approaches. Spectroscopic techniques such as electron paramagnetic resonance (EPR) and double electron-electron resonance (DEER) have been mainly restricted to the study of prokaryotic ion channels that can be purified in large quantities. The requirement for large amounts of functional and stable membrane proteins has hampered the study of mammalian ion channels using these approaches. EPR and DEER offer many advantages, including determination of the structure and dynamic changes of mobile protein regions, albeit at low resolution, that might be difficult to obtain by X-ray crystallography or cryo-EM, and monitoring reversible gating transition (i.e., closed, open, sensitized, and desensitized). Here, we provide protocols for obtaining milligrams of functional detergent-solubilized transient receptor potential cation channel subfamily V member 1 (TRPV1) that can be labeled for EPR and DEER spectroscopy.

This article describes specific methods to obtain biochemical quantities of detergent-solubilized TRPV1 for spectroscopic analysis. The combined protocols provide biochemical and biophysical tools that can be adapted to facilitate structural and functional studies for mammalian ion channels in a membrane-controlled environment.

Polymodal ion channels transduce multiple stimuli of different natures into allosteric changes; these dynamic conformations are challenging to determine ...

Expression and Purification of Mammalian Bestrophin Ion Channels

The human genome encodes four bestrophin paralogs, namely BEST1, BEST2, BEST3, and BEST4. BEST1, encoded by the BEST1 gene, is a Ca2+-activated Cl- channel (CaCC) predominantly expressed in retinal pigment epithelium (RPE). The physiological and pathological significance of BEST1 is highlighted by the fact that over 200 distinct mutations in the BEST1 gene have been genetically linked to a spectrum of at least five retinal degenerative disorders, such as Best vitelliform macular dystrophy (Best disease). Therefore, understanding the biophysics of bestrophin channels at the single-molecule level holds tremendous significance. However, obtaining purified mammalian ion channels is often a challenging task. Here, we report a protocol for the expression of mammalian bestrophin proteins with the BacMam baculovirus gene transfer system and their purification by affinity and size-exclusion chromatography. The purified proteins have the potential to be utilized in subsequent functional and structural analyses, such as electrophysiological recording in lipid bilayers and crystallography. Importantly, this pipeline can be adapted to study the functions and structures of other ion channels.

The purification of ion channels is often challenging, but once achieved, it can potentially allow in vitro investigations of the functions and structures of the channels. Here, we describe the stepwise procedures for the expression and purification of mammalian bestrophin proteins, a family of Ca2+-activated Cl- channels.

The human genome encodes four bestrophin paralogs, namely BEST1, BEST2, BEST3, and BEST4. BEST1, encoded by the BEST1 gene, is a Ca2+-activated Cl- ...

Transient Expression in Nicotiana Benthamiana Leaves for Triterpene Production at a Preparative Scale

The triterpenes are one of the largest and most structurally diverse families of plant natural products. Many triterpene derivatives have been shown to possess medicinally relevant biological activity. However, thus far this potential has not translated into a plethora of triterpene-derived drugs in the clinic. This is arguably (at least partially) a consequence of limited practical synthetic access to this class of compound, a problem that can stifle the exploration of structure-activity relationships and development of lead candidates by traditional medicinal chemistry workflows. Despite their immense diversity, triterpenes are all derived from a single linear precursor, 2,3-oxidosqualene. Transient heterologous expression of biosynthetic enzymes in N. benthamiana can divert endogenous supplies of 2,3-oxidosqualene towards the production of new high-value triterpene products that are not naturally produced by this host. Agro-infiltration is an efficient and simple means of achieving transient expression in N. benthamiana. The process involves infiltration of plant leaves with a suspension of Agrobacterium tumefaciens carrying the expression construct(s) of interest. Co-infiltration of an additional A. tumefaciens strain carrying an expression construct encoding an enzyme that boosts precursor supply significantly increases yields. After a period of five days, the infiltrated leaf material can be harvested and processed to extract and isolate the resulting triterpene product(s). This is a process that is linearly and reliably scalable, simply by increasing the number of plants used in the experiment. Herein is described a protocol for rapid preparative-scale production of triterpenes utilizing this plant-based platform. The protocol utilizes an easily replicable vacuum infiltration apparatus, which allows the simultaneous infiltration of up to four plants, enabling batch-wise infiltration of hundreds of plants in a short period of time.

Transient Expression in Nicotiana Benthamiana Leaves for Triterpene Production at a Preparative Scale

Transient heterologous expression of biosynthetic enzymes in Nicotiana benthamiana leaves can divert endogenous supplies of 2,3-oxidosqualene towards the production of new high-value triterpene products. Herein is described a detailed protocol for rapid (5 days) preparative-scale production of triterpenes and analogs utilizing this powerful plant-based platform.

The triterpenes are one of the largest and most structurally diverse families of plant natural products. Many triterpene derivatives have been shown to ...

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 ...

Expression, Solubilization, and Purification of Eukaryotic Borate Transporters

The Solute Carrier 4 (SLC4) family of proteins is called the bicarbonate transporters and includes the archetypal protein Anion Exchanger 1 (AE1, also known as Band 3), the most abundant membrane protein in the red blood cells. The SLC4 family is homologous with borate transporters, which have been characterized in plants and fungi. It remains a significant technical challenge to express and purify membrane transport proteins to homogeneity in quantities suitable for&#160;structural or functional studies. Here we describe detailed procedures for the overexpression of borate transporters in Saccharomyces cerevisiae, isolation of yeast membranes, solubilization of protein by detergent, and purification of borate transporter homologs from S. cerevisiae, Arabidopsis thaliana, and Oryza sativa. We also detail a glutaraldehyde cross-linking experiment to assay multimerization of homomeric transporters. Our generalized procedures can be applied to all three proteins and have been optimized for efficacy. Many of the strategies developed here can be utilized for the study of other challenging membrane proteins.

Here we present a protocol to express, solubilize, and purify several eukaryotic borate transporters with homology to the SLC4 transporter family using yeast. We also describe a chemical cross-linking assay to assess the purified homomeric proteins for multimeric assembly. These protocols can be adapted for other challenging membrane proteins.

The Solute Carrier 4 (SLC4) family of proteins is called the bicarbonate transporters and includes the archetypal protein Anion Exchanger 1 (AE1, also ...

Spectrophotometric Screening for Potential Inhibitors of Cytosolic Glutathione S-Transferases

Glutathione S-transferases (GSTs) are metabolic enzymes responsible for the elimination of endogenous or exogenous electrophilic compounds by glutathione (GSH) conjugation. In addition, GSTs are regulators of mitogen-activated protein kinases (MAPKs) involved in apoptotic pathways. Overexpression of GSTs is correlated with decreased therapeutic efficacy among patients undergoing chemotherapy with electrophilic alkylating agents. Using GST inhibitors may be a potential solution to reverse this tendency and augment treatment potency. Achieving this goal requires the discovery of such compounds, with an accurate, quick, and easy enzyme assay. A spectrophotometric protocol using 1-chloro-2,4-dinitrobenzene (CDNB) as the substrate is the most employed method in the literature. However, already described GST inhibition experiments do not provide a protocol detailing each stage of an optimal inhibition assay, such as the measurement of the Michaelis-Menten constant (Km) for CDNB or indication of the employed enzyme concentration, crucial parameters to assess the inhibition potency of a tested compound. Hence, with this protocol, we describe each step of an optimized spectrophotometric GST enzyme assay, to screen libraries of potential inhibitors. We explain the calculation of both the half-maximal inhibitory concentration (IC50) and the constant of inhibition (Ki)&#8212;two characteristics used to measure the potency of an enzyme inhibitor. The method described can be implemented using a pool of GSTs extracted from cells or pure recombinant human GSTs, namely GST alpha 1 (GSTA1), GST mu 1 (GSTM1) or GST pi 1 (GSTP1). However, this protocol cannot be applied to GST theta 1 (GSTT1), as CDNB is not a substrate for this isoform. This method was used to test the inhibition potency of curcumin using GSTs from equine liver. Curcumin is a molecule exhibiting anti-cancer properties and showed affinity towards GST isoforms after in silico docking predictions. We demonstrated that curcumin is a potent competitive GST inhibitor, with an IC50 of 31.6 &#177; 3.6 &#181;M and a Ki of 23.2 &#177; 3.2 &#181;M. Curcumin has potential to be combined with electrophilic chemotherapy medication to improve its efficacy.

Glutathione S-transferases (GSTs) are detoxification enzymes involved in the metabolism of numerous chemotherapeutic drugs. Overexpression of GSTs is correlated with cancer chemotherapy resistance. One way to counter this phenotype is to use inhibitors. This protocol describes a method using a spectrophotometric assay to screen for potential GST inhibitors.

Glutathione S-transferases (GSTs) are metabolic enzymes responsible for the elimination of endogenous or exogenous electrophilic compounds by glutathione ...

Removal and Replacement of Endogenous Ligands from Lipid-Bound Proteins and Allergens

Many major allergens bind to hydrophobic lipid-like molecules, including Mus m 1, Bet v 1, Der p 2, and Fel d 1. These ligands are strongly retained and have the potential to influence the sensitization process either through directly stimulating the immune system or altering the biophysical properties of the allergenic protein. In order to control for these variables, techniques are required for the removal of endogenously bound ligands and, if necessary, replacement with lipids of known composition. The cockroach allergen Bla g 1 encloses a large hydrophobic cavity which binds a heterogeneous mixture of endogenous lipids when purified using traditional techniques. Here, we describe a method through which these lipids are removed using reverse-phase HPLC followed by thermal annealing to yield Bla g 1 in either its Apo-form or reloaded with a user-defined mixture of fatty acid or phospholipid cargoes. Coupling this protocol with biochemical assays reveal that fatty acid cargoes significantly alter the thermostability and proteolytic resistance of Bla g 1, with downstream implications for the rate of T-cell epitope generation and allergenicity. These results highlight the importance of lipid removal/reloading protocols such as the one described herein when studying allergens from both recombinant and natural sources. The protocol is generalizable to other allergen families including lipocalins (Mus m 1), PR-10 (Bet v 1), MD-2 (Der p 2) and Uteroglobin (Fel d 1), providing a valuable tool to study the role of lipids in the allergic response.

This protocol describes the removal of endogenous lipids from allergens, and their replacement with user-specified ligands through reverse-phase HPLC coupled with thermal annealing. 31P-NMR and circular dichroism allow for the rapid confirmation of ligand removal/loading, and the recovery of native allergen structure.

Many major allergens bind to hydrophobic lipid-like molecules, including Mus m 1, Bet v 1, Der p 2, and Fel d 1. These ligands are strongly retained and ...

Utilization of Grafix for the Detection of Transient Interactors of Saccharomyces cerevisiae Spliceosome Subcomplexes

Pre-mRNA splicing is a very dynamic process that involves many molecular rearrangements of the spliceosome subcomplexes during assembly, RNA processing, and release of the complex components. Glycerol gradient centrifugation has been used for the separation of protein or RNP (RiboNucleoProtein) complexes for functional and structural studies. Here, we describe the utilization of Grafix (Gradient Fixation), which was first developed to purify and stabilize macromolecular complexes for single particle cryo-electron microscopy, to identify interactions between splicing factors that bind transiently to the spliceosome complex. This method is based on the centrifugation of samples into an increasing concentration of a fixation reagent to stabilize complexes. After centrifugation of yeast total extracts loaded on glycerol gradients, recovered fractions are analyzed by dot blot for the identification of the spliceosome sub-complexes and determination of the presence of individual splicing factors.

Utilization of Grafix for the Detection of Transient Interactors of Saccharomyces cerevisiae Spliceosome Subcomplexes

Here, we describe the utilization of Grafix (Gradient Fixation), a glycerol gradient centrifugation in the presence of a crosslinker, to identify interactions between splicing factors that bind transiently to the spliceosome complex.

Pre-mRNA splicing is a very dynamic process that involves many molecular rearrangements of the spliceosome subcomplexes during assembly, RNA processing, ...