Name: native cell membrane nanoparticles system for membrane protein-protein interaction analysis
Uploaded: 2020-07-16T13:30:00
Description: Watch this Scientific Journal Video about Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis at JoVE.com

This research was supported by VCU startup fund (to Y.G.) and the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number R01GM132329 (to Y.G.) The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. We thank Montserrat Samso and Kevin McRoberts for their generous support for video recording.

1. Protein expression
<ol>
	<li>Inoculate 15 mL of Terrific Broth (TB) media with antibiotics specific to plasmids with BL21(DE3) pLysS cells containing the AcrB expressing plasmids in 50 mL tubes overnight at 37 &#176;C with shaking at 250 rpm.</li>
	<li>Check the optical density of the overnight culture at 600 nm (OD600) and ensure that it is over 2.0.</li>
	<li>Dilute 5 mL of cell culture into 1 L of TB media containing antibiotics specific to plasmids and incubate at 37 &#176;C with shaking until OD...

<ol>
	<li>Berggard, T., Linse, S., James, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+for+the+detection+and+analysis+of+protein-protein+interactions.">Methods for the detection and analysis of protein-protein interactions.</a> Proteomics. 7 (16), 2833-2842 (2007).</li><li>Huang, H., Bader, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Precision+and+recall+estimates+for+two-hybrid+screens.">Precision and recall estimates for two-hybrid screens.</a> Bioinformatics. 25 (3), 372-378 (2009).</li><li>Serebriiskii, I. G., Golemis, E. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two-hybrid+system+and+false+positives.+Approaches+to+detection+and+elimination.">Two-hybrid system and false positives. Approaches to detection and elimination.</a> Methods in Molecular Biology. 177, 123-134 (2001).</li><li>Gingras, A. C., Gstaiger, M., Raught, B., Aebersold, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+protein+complexes+using+mass+spectrometry.">Analysis of protein complexes using mass spectrometry.</a> Nature Reviews in Molecular Cell Biology. 8 (8), 645-654 (2007).</li><li>Ngounou Wetie, A. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Investigation+of+stable+and+transient+protein-protein+interactions:+Past,+present,+and+future.">Investigation of stable and transient protein-protein interactions: Past, present, and future.</a> Proteomics. 13 (3-4), 538-557 (2013).</li><li>Schaufele, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Maximizing+the+quantitative+accuracy+and+reproducibility+of+Forster+resonance+energy+transfer+measurement+for+screening+by+high+throughput+widefield+microscopy.">Maximizing the quantitative accuracy and reproducibility of Forster resonance energy transfer measurement for screening by high throughput widefield microscopy.</a> Methods. 66 (2), 188-199 (2014).</li><li>Berney, C., Danuser, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FRET+or+no+FRET:+a+quantitative+comparison.">FRET or no FRET: a quantitative comparison.</a> Biophysical Journal. 84 (6), 3992-4010 (2003).</li><li>Almen, M. S., Nordstrom, K. J., Fredriksson, R., Schioth, H. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+the+human+membrane+proteome:+a+majority+of+the+human+membrane+proteins+can+be+classified+according+to+function+and+evolutionary+origin.">Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin.</a> BMC Biology. 7, 50 (2009).</li><li>Overington, J. P., Al-Lazikani, B., Hopkins, A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+many+drug+targets+are+there.">How many drug targets are there.</a> Nature Reviews in Drug Discovery. 5 (12), 993-996 (2006).</li><li>Berman, H. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Protein+Data+Bank.">The Protein Data Bank.</a> Nucleic Acids Research. 28 (1), 235-242 (2000).</li><li>Overduin, M., Esmaili, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Memtein:+The+fundamental+unit+of+membrane-protein+structure+and+function.">Memtein: The fundamental unit of membrane-protein structure and function.</a> Chemistry and Physics of Lipids. 218, 73-84 (2019).</li><li>Qiu, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+and+activity+of+lipid+bilayer+within+a+membrane-protein+transporter.">Structure and activity of lipid bilayer within a membrane-protein transporter.</a> Proceedings of the National Academy of Sciences U. S. A. 115 (51), 12985-12990 (2018).</li><li>Knowles, T. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane+proteins+solubilized+intact+in+lipid+containing+nanoparticles+bounded+by+styrene+maleic+acid+copolymer.">Membrane proteins solubilized intact in lipid containing nanoparticles bounded by styrene maleic acid copolymer.</a> Journal of the American Chemical Society. 131 (22), 7484-7485 (2009).</li><li>Xue, M., Cheng, L., Faustino, I., Guo, W., Marrink, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+Mechanism+of+Lipid+Nanodisk+Formation+by+Styrene-Maleic+Acid+Copolymers.">Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers.</a> Biophysical Journal. 115 (3), 494-502 (2018).</li><li>Parmar, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+a+SMALP+platform+to+determine+a+sub-nm+single+particle+cryo-EM+membrane+protein+structure.">Using a SMALP platform to determine a sub-nm single particle cryo-EM membrane protein structure.</a> Biochimica and Biophysica Acta Biomembrames. 1860 (2), 378-383 (2018).</li><li>Yu, L., Lu, W., Wei, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AcrB+trimer+stability+and+efflux+activity,+insight+from+mutagenesis+studies.">AcrB trimer stability and efflux activity, insight from mutagenesis studies.</a> PLoS One. 6 (12), 28390 (2011).</li><li>Broussard, J. A., Rappaz, B., Webb, D. J., Brown, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+resonance+energy+transfer+microscopy+as+demonstrated+by+measuring+the+activation+of+the+serine/threonine+kinase+Akt.">Fluorescence resonance energy transfer microscopy as demonstrated by measuring the activation of the serine/threonine kinase Akt.</a> Nature Protocols. 8 (2), 265-281 (2013).</li><li>Ma, L., Yang, F., Zheng, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Application+of+fluorescence+resonance+energy+transfer+in+protein+studies.">Application of fluorescence resonance energy transfer in protein studies.</a> Journal of Molecular Structure. 1077, 87-100 (2014).</li><li>Sachl, R., Humpolickova, J., Stefl, M., Johansson, L. B., Hof, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Limitations+of+electronic+energy+transfer+in+the+determination+of+lipid+nanodomain+sizes.">Limitations of electronic energy transfer in the determination of lipid nanodomain sizes.</a> Biophysical Journal. 101 (11), 60-62 (2011).</li><li>Woehler, A., Wlodarczyk, J., Neher, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signal/noise+analysis+of+FRET-based+sensors.">Signal/noise analysis of FRET-based sensors.</a> Biophysical Journal. 99 (7), 2344-2354 (2010).</li><li>Wang, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+in+vitro+and+in+vivo+oligomeric+states+of+a+wild+type+and+mutant+trimeric+inner+membrane+multidrug+transporter.">Comparison of in vitro and in vivo oligomeric states of a wild type and mutant trimeric inner membrane multidrug transporter.</a> Biochemical and Biophysical Reports. 16, 122-129 (2018).</li><li>Scarff, C. A., Fuller, M. J. G., Thompson, R. F., Iadaza, M. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Variations+on+Negative+Stain+Electron+Microscopy+Methods:+Tools+for+Tackling+Challenging+Systems.">Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems.</a> Journal of Visualized Experiments. (132), e57199 (2018).</li><li>Lu, W., Zhong, M., Wei, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+of+AcrB+Subunit+Precedes+Trimerization.">Folding of AcrB Subunit Precedes Trimerization.</a> Journal of Molecular Biology. 411 (1), 264-274 (2011).</li><li>Lebon, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Structure and Function of GPCRs. , 229-230 (2019).</li><li>Rames, M., Yu, Y., Ren, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimized+negative+staining:+a+high-throughput+protocol+for+examining+small+and+asymmetric+protein+structure+by+electron+microscopy.">Optimized negative staining: a high-throughput protocol for examining small and asymmetric protein structure by electron microscopy.</a> Journal of Visualized Experiments. (90), e51087 (2014).</li><li>Lee, S. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+method+for+detergent-free+isolation+of+membrane+proteins+in+their+local+lipid+environment.">A method for detergent-free isolation of membrane proteins in their local lipid environment.</a> Nature Protocols. 11 (7), 1149-1162 (2016).</li><li>Hall, S. C. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+acid-compatible+co-polymer+for+the+solubilization+of+membranes+and+proteins+into+lipid+bilayer-containing+nanoparticles.">An acid-compatible co-polymer for the solubilization of membranes and proteins into lipid bilayer-containing nanoparticles.</a> Nanoscale. 10 (22), 10609-10619 (2018).</li><li>Oluwole, A. O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Solubilization+of+Membrane+Proteins+into+Functional+Lipid-Bilayer+Nanodiscs+Using+a+Diisobutylene/Maleic+Acid+Copolymer.">Solubilization of Membrane Proteins into Functional Lipid-Bilayer Nanodiscs Using a Diisobutylene/Maleic Acid Copolymer.</a> Angewandte Chemie International Edition England. 56 (7), 1919-1924 (2017).</li></ol>

Protein-protein interactions are important for the integrity of the structure and function of membrane proteins. Many approaches have been developed to investigate protein-protein interactions. When compared with soluble proteins, membrane proteins and their PPIs are more difficult to study due to the unique intrinsic properties of membrane proteins. This difficulty mainly comes from the requirement of membrane proteins to be embedded in a native lipid bilayer environment for structural stability and functionality. This ...

Protein-protein interactions (PPI) play pivotal roles throughout biology, from the maintenance of the structure and function of proteins to the regulation of entire systems. PPIs come in many different forms and can be categorized based on what types of interactions they form. One such categorization is homooligomeric or heterooligomeric, based on whether the interactions are between identical subunits or different proteins acting as subunits. Another categorization is based on the strength of the interaction if the interactions leads to the formation of stable complexes or transient complex states. Structural information about the PPIs between proteins is crucial in understanding the mechanism by which proteins carry out their function. It has been estimated that over 80% of proteins rely on complex formation in order to carry out their functional roles1. Given the percentage of proteins observed to be reliant on PPIs for proper innate functioning their significance in biology is readily apparent, yet being able to properly investigate the proteins that engage in these interactions has remained challenging due to limitations in the techniques available to experimentally observe when proteins are forming PPIs.
There is a high degree of disagreement between the results for many experimentally determined PPIs due to the high amount of noise, false positives, and false negatives that are derived from many of the currently available PPI determining techniques. This is particularly so for the yeast two-hybrid (Y2H) system, tandem affinity purification-mass spectrometry (TAP-MS), and fluorescence resonance energy transfer (FRET), which represent three of the most commonly used methods for PPI determination2,3,4,5,6,7. In comparison, protein structural biology techniques, such as nuclear magnetic resonance (NMR), X-ray crystallography and electron microscopy (EM), can be used to gain high-resolution structural information about protein-protein interactions down to the atomic level and allow for the direct visual confirmation of the interactions occurring for a target protein of interest. All of the currently available non-structure based PPI determining research techniques (e.g., Y2H, TAP-MS, and FRET) lack this ability and additionally suffer from having difficulty in identifying weak and transient interactions between proteins5. These shortcomings are further enhanced when studying membrane proteins due to the added complexity brought on by the additional variable of the lipid environment that influences the formation of proper quaternary structure and heteromeric complex assembly.
Membrane proteins make up a large portion of the proteome and are known to play many crucial roles in proper cell functioning within all living organisms. Despite the fact that membrane proteins are estimated to make up 27% of the human genome and constitute ~60% of all current drug targets there is a major anomaly in the number of solved models for membrane proteins which make up only ~2.2% of all published protein structures8,9,10. The primary cause of the discrepancy in the availability of structural information lies in the intrinsic properties of membrane proteins themselves. Due to their poor solubility, reliance on interactions with a lipid environment for maintaining native structure and function, and various physicochemical properties of the lipid membrane itself, membrane proteins continue to represent a substantial problem when implementing structural biology techniques to study them. Of these intrinsic properties, the most important for obtaining accurate structural information is the requirement of having interactions with their natural lipid environment for them to maintain their native structure and function. The lipid environment is such an integral part of the structure and function of membrane proteins that the concept of memtein (a combination of the words membrane and protein) has been proposed as the fundamental unit of membrane-protein structure and function11. Despite the importance of lipid-protein interactions the currently available structure-based PPI determination techniques often require that the proteins being studied be soluble or be solubilized with detergents. Exposure to harsh detergents can denature the proteins or cause false positives and negatives due to delipidation, which can induce aggregation, denaturation of protein, dissociation of non-covalent interactions, and formation of artificial oligomeric states. Due to the necessity of maintaining a natural lipid environment for accurate determination of the native oligomeric state of membrane proteins we have developed a Native Cell Membrane Nanoparticles system (NCMNs)12 based on the previously reported Styrene Maleic Acid Lipid Particles (SMALP)13 method.
SMALP uses styrene maleic acid copolymer as a membrane active polymer to extract and solubilize membrane proteins. Poly(Styrene-co-Maleic Acid) (SMA) is a unique amphiphilic polymer due to its hydrophobic styrene moiety and diametrically opposing hydrophilic maleic acid moiety. It forms nanoparticles by adsorbing to, destabilizing, and disrupting the cell membrane in a pH-dependent mechanism14. This functional activity of SMA is what allows it to be utilized as a detergent-free system for membrane protein extraction and solubilization. The NCMN system is distinct from the SMALP system in several aspects. The most unique feature of the NCMN system is that it has a membrane active polymer library with a multitude of polymers that have unique properties that make them suitable for the isolation of many different membrane proteins that require different conditions for stability and native functioning. The NCMN system also has different protocols compared to the SMALP method when it comes to preparing the nanoparticles. One such example is that NCMNs use a single-step nickel affinity column purification for high-resolution structure determination; the effect of these different protocols can be observed when comparing the NCMNs protocol, which generated 3.2 and 3.0 &#197; cryo-EM AcrB structures, with a similar study using the SMALP method, which resulted in a cryo-EM AcrB structure at an 8.8 &#197; resolution12,15. These unique features of the NCMN system are the improvements made on the previously established SMALP method and make it an ideal candidate for the study of PPIs.
The multidrug efflux transporter AcrB exists as functional homotrimer in E. coli12. A mutagenic analysis suggested that a single P223G point mutation, located on a loop that is responsible for the stability of the AcrB trimer, destabilizes the trimer state and yields an AcrB monomer when prepared with the detergent DDM, which could be detected with native blue gel electrophoresis16. However, the FRET analysis of the AcrB-P223G mutant suggested that when in the native cell membrane lipid bilayer environment, the majority of mutant AcrB-P223G still existed as a trimer and that the expression levels for both wild type AcrB and AcrB-P223G are similar. Yet despite the FRET analysis results, an activity assay for the mutant transporter showed that activity dramatically decreased when compared to the wild type16. Although FRET technology has been popularly used for the analysis of protein-protein interactions, research has shown that it can frequently give false positives17,18,19,20.
Recently, high-resolution cryo-EM structures of the AcrB trimer were determined which showed the interaction of AcrB with its associated native cell membrane lipid bilayer through the use of the NCMNs12. In principle, the NCMNs can readily be utilized for the analysis of protein-protein interactions found on the native cell membrane. In a test of this system, experiments were carried out to directly observe the oligomeric state of AcrB-P223G with the use of native cell membrane nanoparticles and negative staining electron microscopy. In order to compare with the wild type AcrB nanoparticles, we used the same membrane active polymer (SMA2000 made in our laboratory, which is indexed as NCMNP1-1 in the NCMN library) used for high-resolution cryo-EM structure determination of AcrB and alternative polymers found in the NCMNs library12. Based on the previously reported results, it was expected that the majority of the AcrB-P223G mutant would exist in the form of trimeric native cell membrane nanoparticles21. However, no AcrB trimers were found present in the sample, such as the ones that were observed with the wild type AcrB. This suggests the majority of AcrB-P223G does not form trimers on the native cell membrane as previously suggested.
Here we report a detailed analysis of the mutant E. coli AcrB-P223G in a comparison with the wild type E. coli AcrB using the NCMNs. This case study of AcrB suggests NCMNs is a good system for protein-protein interaction analysis.

<table>
	<tbody>
		<tr>
			<td>Chemicals</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>30% Acrylamide/BIS SOL (37.5:1)</td>
			<td>Bio-Rad</td>
			<td>161-0158</td>
			<td></td>
		</tr>
		<tr>
			<td>4x Laemmli Sample Buffer (Loading Buffer)</td>
			<td>Bio-Rad</td>
			<td>1610747</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic Acid Glacial</td>
			<td>ThermoFisher Scientific</td>
			<td>A38S-212</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium Persulfate (APS)</td>
			<td>Bio-Rad</td>
			<td>161-0700</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloramphenicol</td>
			<td>Goldbio</td>
			<td>C-105-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Coomassie Brilliant Blue R-250 protein stain powder</td>
			<td>Bio-Rad</td>
			<td>161-0400</td>
			<td></td>
		</tr>
		<tr>
			<td>DTT (Dithiothreitol) (&#62; 99% pure) Protease free</td>
			<td>Goldbio</td>
			<td>DTT10</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>ThermoFisher Scientific</td>
			<td>G33-4</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>ThermoFisher Scientific</td>
			<td>BP310-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Imidazole</td>
			<td>Affymetrix</td>
			<td>17525 1 KG</td>
			<td></td>
		</tr>
		<tr>
			<td>IPTG</td>
			<td>Goldbio</td>
			<td>I2481C100</td>
			<td></td>
		</tr>
		<tr>
			<td>Kanamycin</td>
			<td>Goldbio</td>
			<td>K-120-25</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium chloride hexahydrate</td>
			<td>ThermoFisher Scientific</td>
			<td>AA3622636</td>
			<td></td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>ThermoFisher Scientific</td>
			<td>A412-4</td>
			<td></td>
		</tr>
		<tr>
			<td>N,N-dimethylethylenediamine (EDTA)</td>
			<td>Merck</td>
			<td>8.03779.0100</td>
			<td></td>
		</tr>
		<tr>
			<td>NCMNS-P5-2</td>
			<td>Not commercially available yet</td>
			<td>Submit request for obtaining to corresponding author</td>
			<td></td>
		</tr>
		<tr>
			<td>Precision Plus Protein Dual Color Standard</td>
			<td>Bio-Rad</td>
			<td>161-0374</td>
			<td></td>
		</tr>
		<tr>
			<td>SDS (Sodium Dodecyl Sulfate)</td>
			<td>Bio-Rad</td>
			<td>161-0301</td>
			<td></td>
		</tr>
		<tr>
			<td>SMA2000</td>
			<td>Cray Valley</td>
			<td>Submit request for obtaining to corresponding author</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>ThermoFisher Scientific</td>
			<td>S271-10</td>
			<td></td>
		</tr>
		<tr>
			<td>TCEP-HCl</td>
			<td>Goldbio</td>
			<td>TCEP25</td>
			<td></td>
		</tr>
		<tr>
			<td>TEMED</td>
			<td>Bio-Rad</td>
			<td>161-0800</td>
			<td></td>
		</tr>
		<tr>
			<td>Terrific Broth Media</td>
			<td>Affymetrix</td>
			<td>75856 1 KG</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris Base</td>
			<td>Bio-Rad</td>
			<td>161-0719</td>
			<td></td>
		</tr>
		<tr>
			<td>Uranyl Acetate</td>
			<td>Ambinter</td>
			<td>Amb22348393</td>
			<td></td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Avanti J-26S XPI</td>
			<td>Beckman Coulter</td>
			<td>B14538</td>
			<td></td>
		</tr>
		<tr>
			<td>Avanti JXN-30</td>
			<td>Beckman Coulter</td>
			<td>B34193</td>
			<td></td>
		</tr>
		<tr>
			<td>Carbon Electron Microscope Grids (10 nm)</td>
			<td>Electron Microscopy Sciences</td>
			<td>CF300-Cu-TH</td>
			<td></td>
		</tr>
		<tr>
			<td>Con-Torque Tissue Homogenizer</td>
			<td>Eberbach</td>
			<td>E7265</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning LSE Mini Microcentrifuge</td>
			<td>ThermoFisher Scientific</td>
			<td>07-203-954</td>
			<td></td>
		</tr>
		<tr>
			<td>EmulsiFlex-C3</td>
			<td>Avestin</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fraction Collector F9-R</td>
			<td>GE Healthcare Life Sciences</td>
			<td>29003875</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini-PROTEAN Tetra Vertical Electrophoresis Cell</td>
			<td>Bio-Rad</td>
			<td>165-8004</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoDrop 2000 Spectrophotometer</td>
			<td>ThermoFisher Scientific</td>
			<td>ND-2000</td>
			<td></td>
		</tr>
		<tr>
			<td>Optima L-90K Ultracentrifuge</td>
			<td>Beckman Coulter</td>
			<td>PN LL-IM-12AB</td>
			<td></td>
		</tr>
		<tr>
			<td>PELCO easiGlow Glow Discharge Cleaning System</td>
			<td>Ted Pella</td>
			<td>91000S-230</td>
			<td></td>
		</tr>
		<tr>
			<td>Potter-Elvehjem Safe Grind Tissue Grinder</td>
			<td>Wheaton</td>
			<td>358013</td>
			<td></td>
		</tr>
		<tr>
			<td>PowerPac Basic Power Supply</td>
			<td>Bio-Rad</td>
			<td>164-5050</td>
			<td></td>
		</tr>
		<tr>
			<td>Razel R99-E Variable Speed Syringe Pump</td>
			<td>Razel Scientific Instruments</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Superdex 200 Increase 10/300 GL</td>
			<td>GE Healthcare Life Sciences</td>
			<td>28990944</td>
			<td></td>
		</tr>
		<tr>
			<td>Tecnai F20 200kV</td>
			<td>FEI</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Type 70 Ti Fixed-Angle Rotor</td>
			<td>Beckman Coulter</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>General Materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 ml Microcentrifuge Tubes</td>
			<td>ThermoFisher Scientific</td>
			<td>05-408-129</td>
			<td></td>
		</tr>
		<tr>
			<td>4 ml Amicon Ultra-4 30 kDa</td>
			<td>Millipore Sigma</td>
			<td>UFC803024</td>
			<td></td>
		</tr>
		<tr>
			<td>AKTA pure 25 L1 FPLC</td>
			<td>GE Healthcare Life Sciences</td>
			<td>29018225</td>
			<td></td>
		</tr>
		<tr>
			<td>BL21(DE3)pLysS Cells</td>
			<td>ThermoFisher Scientific</td>
			<td>C606003</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon 50 ml Conical Centrifuge Tube</td>
			<td>ThermoFisher Scientific</td>
			<td>14-959-49A</td>
			<td></td>
		</tr>
		<tr>
			<td>HisTrap HP 5 ml Column</td>
			<td>GE Healthcare Life Sciences</td>
			<td>17524802</td>
			<td></td>
		</tr>
		<tr>
			<td>pET-24a</td>
			<td>EMD Biosciences</td>
			<td>69749-3</td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

Using the procedures presented here, samples of E. coli AcrB wild type and E. coli mutant AcrB-P223G were purified. The samples were then adsorbed to carbon negative stain electron microscopy grids and stained using uranyl acetate with the side blotting method22. Negative stain images were collected using transmission electron microscopy. The negative stain image for the AcrB wild type sample purified with DDM reveals a homogenous solution of monodispersed particles with the prot...

Watch this Scientific Journal Video about Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis at JoVE.com

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

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 ...

Research

JoVE Journal

Biochemistry

Method for Identifying Small Molecule Inhibitors of the Protein-protein Interaction Between HCN1 and TRIP8b

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are expressed ubiquitously throughout the brain, where they function to regulate the ...

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating ...

High Precision FRET at Single-molecule Level for Biomolecule Structure Determination

A protocol on how to perform high-precision interdye distance measurements using F&#246;rster resonance energy transfer (FRET) at the single-molecule ...

A Modified Yeast-one Hybrid System for Heteromeric Protein Complex-DNA Interaction Studies

Over the years, the yeast one-hybrid assay has proven to be an important technique for the identification and validation of physical interactions between ...

Analysis of Thylakoid Membrane Protein Complexes by Blue Native Gel Electrophoresis

Photosynthetic electron transfer chain (ETC) converts solar energy to chemical energy in the form of NADPH and ATP. Four large protein complexes embedded ...

A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts

A variety of biological processes involves cell-cell interactions, typically mediated by proteins that interact at the interface between neighboring ...

Evaluation of Protein&#8211;Protein Interactions using an On-Membrane Digestion Technique

Evaluation of ProteinÃƒÂ¢Ã¢â€šÂ¬Ã¢â‚¬Å“Protein Interactions using an On-Membrane Digestion Technique

Numerous intracellular proteins physically interact in accordance with their intracellular and extracellular circumstances. Indeed, cellular functions ...

Characterization of Membrane Transporters by Heterologous Expression in E. coli and Production of Membrane Vesicles

Characterization of Membrane Transporters by Heterologous Expression in E. coli and Production of Membrane Vesicles

Several methods have been developed to functionally characterize novel membrane transporters. Polyamines are ubiquitous in all organisms, but polyamine ...

Screening for Thermotoga maritima Membrane-Bound Pyrophosphatase Inhibitors

Screening for Thermotoga maritima Membrane-Bound Pyrophosphatase Inhibitors

Membrane-bound pyrophosphatases (mPPases) are dimeric enzymes that occur in bacteria, archaea, plants, and protist parasites. These proteins cleave ...

A Model Membrane Platform for Reconstituting Mitochondrial Membrane Dynamics

Mitochondrial dynamics is essential for the organelle&#8217;s diverse functions and cellular responses. The crowded, spatially complex, mitochondrial ...