This work was funded by the Ministry of Education ERC CZ grant LL1205, the Grant Agency of Czech Republic grant 18-17529S, and by ERDF/ESF project Centre for research of pathogenicity and virulence of parasites (No. CZ.02.1.01/0.0/0.0/16_019/0000759).

1. Buffers and Solutions
<ol>
	<li>Prepare the solutions listed below. Degas all buffers for liquid chromatography. Add ADP, benzamidine, and protease inhibitors just before use.
	<ol>
		<li>Prepare buffer A: 50 mM Tris buffer with hydrochloric acid (Tris-HCl) pH 8.0, 0.25 M sucrose, 5 mM benzamidine, 5 mM aminocaproic acid (ACA), and protease inhibitors (10 &#181;M amastatin, 50 &#181;M bestatin, 50 &#181;M pepstatin, 50 &#181;M leupeptin, and 50 &#181;M diprotin A).</li>
		<li>Prepare buffer B: 50 mM Tris-HCl pH 8.0,...

<ol>
	<li>Walker, J. E., Wikstr&#246;m, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure,+mechanism+and+regulation+of+ATP+synthases.">Structure, mechanism and regulation of ATP synthases.</a> Mechanisms of Primary Energy Transduction in Biology. , 338-373 (2017).</li><li>Pullman, M. E., Penefsky, H. S., Datta, A., Racker, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Partial+resolution+of+the+enzymes+catalyzing+oxidative+phosphorylation.+I.+Purification+and+properties+of+soluble+dinitrophenol-stimulated+adenosine+triphosphatase.">Partial resolution of the enzymes catalyzing oxidative phosphorylation. I. Purification and properties of soluble dinitrophenol-stimulated adenosine triphosphatase.</a> The Journal of Biological Chemistry. 235, 3322-3329 (1960).</li><li>Schatz, G., Penefsky, H. S., Racker, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Partial+resolution+of+the+enzymes+catalyzing+oxidative+phosphorylation.">Partial resolution of the enzymes catalyzing oxidative phosphorylation.</a> XIV. The Journal of Biological Chemistry. 242 (10), 2552-2560 (1967).</li><li>Racker, E., Horstman, L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Partial+resolution+of+the+enzymes+catalyzing+oxidative+phosphorylation.+13.+Structure+and+function+of+submitochondrial+particles+completely+resolved+with+respect+to+coupling+factor.">Partial resolution of the enzymes catalyzing oxidative phosphorylation. 13. Structure and function of submitochondrial particles completely resolved with respect to coupling factor.</a> The Journal of Biological Chemistry. 242 (10), 2547-2551 (1967).</li><li>Senior, A. E., Brooks, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studies+on+the+mitochondrial+oligomycin-insensitive+ATPase.+I.+An+improved+method+of+purification+and+the+behavior+of+the+enzyme+in+solutions+of+various+depolymerizing+agents.">Studies on the mitochondrial oligomycin-insensitive ATPase. I. An improved method of purification and the behavior of the enzyme in solutions of various depolymerizing agents.</a> Archives of Biochemistry and Biophysics. 140 (1), 257-266 (1970).</li><li>Tzagoloff, A., Meagher, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assembly+of+the+mitochondrial+membrane+system.+V.+Properties+of+a+dispersed+preparation+of+the+rutamycin-sensitive+adenosine+triphosphatase+of+yeast+mitochondria.">Assembly of the mitochondrial membrane system. V. Properties of a dispersed preparation of the rutamycin-sensitive adenosine triphosphatase of yeast mitochondria.</a> The Journal of Biological Chemistry. 246 (23), 7328-7336 (1971).</li><li>Beechey, R. B., Hubbard, S. A., Linnett, P. E., Mitchell, A. D., Munn, 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=A+simple+and+rapid+method+for+the+preparation+of+adenosine+triphosphatase+from+submitochondrial+particles.">A simple and rapid method for the preparation of adenosine triphosphatase from submitochondrial particles.</a> Biochemical Journal. 148 (3), 533-537 (1975).</li><li>Tyler, D. D., Webb, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+and+properties+of+the+adenosine+triphosphatase+released+from+the+liver+mitochondrial+membrane+by+chloroform.">Purification and properties of the adenosine triphosphatase released from the liver mitochondrial membrane by chloroform.</a> Biochemical Journal. 178 (2), 289-297 (1979).</li><li>Hack, E., Leaver, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+alpha-subunit+of+the+maize+F1-ATPase+is+synthesised+in+the+mitochondrion.">The alpha-subunit of the maize F1-ATPase is synthesised in the mitochondrion.</a> The EMBO Journal. 2 (10), 1783-1789 (1983).</li><li>Dunn, P. P., Slabas, A. R., Moore, 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=Purification+of+F1-ATPase+from+cuckoo-pint+(Arum+maculatum)+mitochondria.+A+comparison+of+subunit+composition+with+that+of+rat+liver+F1-ATPase.">Purification of F1-ATPase from cuckoo-pint (Arum maculatum) mitochondria. A comparison of subunit composition with that of rat liver F1-ATPase.</a> Biochemical Journal. 225 (3), 821-824 (1985).</li><li>Satre, M., Bof, M., Vignais, P. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interaction+of+Escherichia+coli+adenosine+triphosphatase+with+aurovertin+and+citreoviridin:+inhibition+and+fluorescence+studies.">Interaction of Escherichia coli adenosine triphosphatase with aurovertin and citreoviridin: inhibition and fluorescence studies.</a> Journal of Bacteriology. 142 (3), 768-776 (1980).</li><li>Abrahams, J. P., Leslie, A. G., Lutter, R., Walker, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+at+2.8+&#197;+resolution+of+F1ATPase+from+bovine+heart+mitochondria.">Structure at 2.8 &#197; resolution of F1ATPase from bovine heart mitochondria.</a> Nature. 370 (6491), 621-628 (1994).</li><li>Lutter, R., 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=Crystallization+of+F1-ATPase+from+bovine+heart+mitochondria.">Crystallization of F1-ATPase from bovine heart mitochondria.</a> Journal of Molecular Biology. 229 (3), 787-790 (1993).</li><li>Kabaleeswaran, V., Puri, N., Walker, J. E., Leslie, A. G., Mueller, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+features+of+the+rotary+catalytic+mechanism+revealed+in+the+structure+of+yeast+F1-ATPase.">Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1-ATPase.</a> The EMBO Journal. 25 (22), 5433-5442 (2006).</li><li>Shirakihara, Y., 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+of+a+thermophilic+F1-ATPase+inhibited+by+an+epsilon-subunit:+deeper+insight+into+the+epsilon-inhibition+mechanism.">Structure of a thermophilic F1-ATPase inhibited by an epsilon-subunit: deeper insight into the epsilon-inhibition mechanism.</a> The FEBS Journal. 282 (15), 2895-2913 (2015).</li><li>Stocker, A., Keis, S., Cook, G. M., Dimroth, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification,+crystallization,+and+properties+of+F1-ATPase+complexes+from+the+thermoalkaliphilic+Bacillus+sp.+strain+TA2.A1.">Purification, crystallization, and properties of F1-ATPase complexes from the thermoalkaliphilic Bacillus sp. strain TA2.A1.</a> Journal of Structural Biology. 152 (2), 140-145 (2005).</li><li>Ferguson, S. A., Cook, G. M., Montgomery, M. G., Leslie, A. G., Walker, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+the+thermoalkaliphilic+F1-ATPase+from+Caldalkalibacillus+thermarum.">Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum.</a> Proceedings of the National Academy of Sciences of the United States of America. 113 (39), 10860-10865 (2016).</li><li>Cataldi de Flombaum, M. A., Frasch, A. C. C., Stoppani, A. O. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adenosine+triphosphatase+from+Trypanosoma+cruzi:+purification+and+properties.">Adenosine triphosphatase from Trypanosoma cruzi: purification and properties.</a> Comparative Biochemistry and Physiology Part B: Comparative Biochemistry. 65 (1), 103-109 (1980).</li><li>Williams, N., Frank, P. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mitochondrial+ATP+synthase+of+Trypanosoma+brucei:+isolation+and+characterization+of+the+intact+F1+moiety.">The mitochondrial ATP synthase of Trypanosoma brucei: isolation and characterization of the intact F1 moiety.</a> Molecular and Biochemical Parasitology. 43 (1), 125-132 (1990).</li><li>Higa, A. I., Cazzulo, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mg2+-activated+adenosine+triphosphatase+from+Crithidia+fasciculata:+purification+and+inhibition+by+suramin+and+efrapeptin.">Mg2+-activated adenosine triphosphatase from Crithidia fasciculata: purification and inhibition by suramin and efrapeptin.</a> Molecular and Biochemical Parasitology. 3 (6), 357-367 (1981).</li><li>Walker, J. E., 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=Primary+structure+and+subunit+stoichiometry+of+F1-ATPase+from+bovine+mitochondria.">Primary structure and subunit stoichiometry of F1-ATPase from bovine mitochondria.</a> Journal of Molecular Biology. 184 (4), 677-701 (1985).</li><li>Mueller, D. 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=Ni-chelate-affinity+purification+and+crystallization+of+the+yeast+mitochondrial+F1-ATPase.">Ni-chelate-affinity purification and crystallization of the yeast mitochondrial F1-ATPase.</a> Protein Expression and Purification. 37 (2), 479-485 (2004).</li><li>Gahura, 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=The+F1-ATPase+from+Trypanosoma+brucei+is+elaborated+by+three+copies+of+an+additional+p18-subunit.">The F1-ATPase from Trypanosoma brucei is elaborated by three copies of an additional p18-subunit.</a> The FEBS Journal. 285 (3), 614-628 (2018).</li><li>Montgomery, M. G., Gahura, O., Leslie, A. G. W., Zikova, A., Walker, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ATP+synthase+from+Trypanosoma+brucei+has+an+elaborated+canonical+F1-domain+and+conventional+catalytic+sites.">ATP synthase from Trypanosoma brucei has an elaborated canonical F1-domain and conventional catalytic sites.</a> Proceedings of the National Academy of Sciences of the United States of America. 115 (9), 2102-2107 (2018).</li><li>Schneider, A., Charriere, F., Pusnik, M., Horn, E. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+mitochondria+from+procyclic+Trypanosoma+brucei.">Isolation of mitochondria from procyclic Trypanosoma brucei.</a> Methods in Molecular Biology. 372, 67-80 (2007).</li><li>Smith, P. K., 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=Measurement+of+protein+using+bicinchoninic+acid.">Measurement of protein using bicinchoninic acid.</a> Analytical Biochemistry. 150 (1), 76-85 (1985).</li><li>Wirtz, E., Leal, S., Ochatt, C., Cross, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+tightly+regulated+inducible+expression+system+for+conditional+gene+knock-outs+and+dominant-negative+genetics+in+Trypanosoma+brucei.">A tightly regulated inducible expression system for conditional gene knock-outs and dominant-negative genetics in Trypanosoma brucei.</a> Molecular and Biochemical Parasitology. 99 (1), 89-101 (1999).</li><li>Speijer, D., 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=Characterization+of+the+respiratory+chain+from+cultured+Crithidia+fasciculata.">Characterization of the respiratory chain from cultured Crithidia fasciculata.</a> Molecular and Biochemical Parasitology. 85 (2), 171-186 (1997).</li><li>Nelson, R. E., Aphasizheva, I., Falick, A. M., Nebohacova, M., Simpson, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+I-complex+in+Leishmania+tarentolae+is+an+uniquely-structured+F1-ATPase.">The I-complex in Leishmania tarentolae is an uniquely-structured F1-ATPase.</a> Molecular and Biochemical Parasitology. 135 (2), 221-224 (2004).</li><li>Carbajo, R. 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=How+the+N-terminal+domain+of+the+OSCP+subunit+of+bovine+F1Fo-ATP+synthase+interacts+with+the+N-terminal+region+of+an+alpha+subunit.">How the N-terminal domain of the OSCP subunit of bovine F1Fo-ATP synthase interacts with the N-terminal region of an alpha subunit.</a> Journal of Molecular Biology. 368 (2), 310-318 (2007).</li><li>Bowler, M. W., Montgomery, M. G., Leslie, A. G., Walker, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ground+state+structure+of+F1-ATPase+from+bovine+heart+mitochondria+at+1.9+&#197;+resolution.">Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 &#197; resolution.</a> The Journal of Biological Chemistry. 282 (19), 14238-14242 (2007).</li></ol>

The protocol for F1-ATPase purification from T. brucei was developed based on previously published methods for the isolation of F1-ATPase complexes from other species13,14. The method does not require any genetic modification (e.g., tagging) and yields a fully active complex with all subunits present. The crucial step is the chloroform-facilitated release of the F1-ATPase from the membrane-attached part of the en...

The F-type ATP synthases are membrane-bound rotating multiprotein complexes that couple proton translocation across energy-transducing membranes of bacteria, mitochondria, and chloroplasts with the formation of ATP. Molecular details of the rotational mechanism of ATP synthesis are known mainly because of structural studies of purified bacterial and mitochondrial ATP synthases and their subcomplexes1. F-type ATP synthase is organized into membrane-intrinsic and membrane-extrinsic moieties. The membrane-extrinsic part, known as F1-ATPase, contains three catalytic sites, where the phosphorylation of adenosine diphosphate (ADP) to ATP or the reverse reaction occurs. F1-ATPase can be released experimentally from the membrane-intrinsic moiety while retaining its ability to hydrolyze, but not synthesize, ATP. The membrane-bound sector, called Fo, mediates protein translocation, which drives the rotation of the central part of the enzyme. The F1 and Fo sectors are connected by the&#160;central and peripheral stalks.
The first attempts to purify the F1-ATPase from budding yeast and bovine heart mitochondria date back to the 1960s. These protocols used extracted mitochondria, which were disrupted by sonication, fractionated by ammonium or protamine sulfate precipitation, followed by optional chromatography step(s) and heat treatment2,3,4,5,6. The purification was greatly improved and simplified by the use of chloroform, which readily releases the F1-ATPase from the mitochondrial membrane fragments7. The chloroform extraction was then used to extract F1-ATPases from various animal, plant, and bacterial sources (e.g., rat liver8, corn9, Arum maculatum10, and Escherichia coli11). Further purification of the chloroform-released F1-ATPase by affinity or size-exclusion chromatography (SEC) yielded a highly pure protein complex, which was suitable for high-resolution structure determination by X-ray crystallography, as documented by the structures of F1-ATPase from bovine heart12,13 and Saccharomyces cerevisiae14. F1-ATPase structures were also determined from organisms that are difficult to cultivate and, thus, the amount of the initial biological material was limited. In this case, the F1-ATPase subunits were artificially expressed and assembled into the complex in E. coli, and the whole heterologous enzyme was purified by affinity chromatography via a tagged subunit. Such approach led to the determination of F1-ATPase structures from two thermophilic bacterial species, Geobacillus stearothermophilus15 and Caldalkalibacillus thermarum16,17. However, this methodology is rather unsuitable for eukaryotic F1-ATPases since it relies on the prokaryotic protheosynthetic apparatus, posttranslational processing, and complex assembly.
The chloroform-based extraction was previously used to isolate F1-ATPases from unicellular digenetic parasites Trypanosoma cruzi18 and T. brucei19, important mammalian pathogens causing American and African trypanosomiases, respectively, and from monogenic insect parasite Crithidia fasciculata20. These purifications led only to a simple description of the F1-ATPases, since no downstream applications were used to fully characterize the composition, structure, and enzymatic properties of the complex. This article describes an optimized method for F1-ATPase purification from the cultured insect life cycle stage of T. brucei. The method is developed based on the established protocols for isolation of bovine and yeast F1-ATPases21,22. The procedure yields highly pure and homogeneous enzyme suitable for in vitro enzymatic and inhibitory assays, detailed proteomic characterization by mass spectrometry23, and structure determination24. The purification protocol and the knowledge of the F1-ATPase structure at the atomic level opens a possibility to design screens to identify small-molecule inhibitors, and aid in the development of new drugs against African trypanosomiases. Moreover, the protocol can be adapted to purify F1-ATPase from other organisms.

<table>
	<tbody>
		<tr>
			<td>Chemicals</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Adenosin Diphosphate Disodium Salt (ADP)</td>
			<td>Applichem</td>
			<td>A0948</td>
			<td></td>
		</tr>
		<tr>
			<td>Amastatin Hydrochloride</td>
			<td>Glantham Life Sciences</td>
			<td>GA1330</td>
			<td></td>
		</tr>
		<tr>
			<td>Aminocaproic Acid</td>
			<td>Applichem</td>
			<td>A2266</td>
			<td></td>
		</tr>
		<tr>
			<td>BCA Protein Assay Kit</td>
			<td>ThermoFischer Scientific/Pierce</td>
			<td>23225</td>
			<td></td>
		</tr>
		<tr>
			<td>Benzamidine Hydrochloride</td>
			<td>Calbiochem</td>
			<td>199001</td>
			<td></td>
		</tr>
		<tr>
			<td>Bestatin Hydrochloride</td>
			<td>Sigma Aldrich/Merck</td>
			<td>B8385</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>cOmplete Tablets, Mini EDTA-free</td>
			<td>Roche</td>
			<td>4693159001</td>
			<td>Protease inhibitor cocktail tablets</td>
		</tr>
		<tr>
			<td>Ethylenediaminetetraacetic Acid (EDTA)</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric Acid</td>
			<td>Any supplier</td>
			<td></td>
			<td>For pH adjustment</td>
		</tr>
		<tr>
			<td>Ile-Pro-Ile</td>
			<td>Sigma Aldrich/Merck</td>
			<td>I9759</td>
			<td>Alias Diprotin A</td>
		</tr>
		<tr>
			<td>Leupeptin</td>
			<td>Sigma Aldrich/Merck</td>
			<td>L2884</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium Sulfate Heptahydrate</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Pepstatin A</td>
			<td>Sigma Aldrich/Merck</td>
			<td>P5318</td>
			<td></td>
		</tr>
		<tr>
			<td>Protein Electrophoresis System</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Consumables</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge Tubes for SW60Ti, Polyallomer</td>
			<td>Beckman Coulture</td>
			<td>328874</td>
			<td></td>
		</tr>
		<tr>
			<td>DounceTissues Homogenizer 2 mL</td>
			<td>Any supplier</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Glass Vacuum Filtration Device</td>
			<td>Sartorius</td>
			<td>516-7017</td>
			<td>Degasing solutions for liquid chromatography</td>
		</tr>
		<tr>
			<td>HiTrap Q HP, 5 mL</td>
			<td>GE Healthcare Life Sciences</td>
			<td>17115401</td>
			<td>Anion exchange chromatography column</td>
		</tr>
		<tr>
			<td>Regenaretad Cellulose Membrane Filters, pore size 0.45 &#956;m, diameter 47 mm</td>
			<td>Sartorius</td>
			<td>18406--47------N</td>
			<td>Degasing solutions for liquid chromatography</td>
		</tr>
		<tr>
			<td>Superdex 200 Increase 10/300 GL</td>
			<td>GE Healthcare Life Sciences</td>
			<td>29091596</td>
			<td>Size-exclusion chromatography column</td>
		</tr>
		<tr>
			<td>Vivaspin 6 MWCO 100 kDa PES</td>
			<td>Sartorius</td>
			<td>VS0641</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>AKTA Pure 25</td>
			<td>GE Healthcare Life Sciences</td>
			<td>29018224</td>
			<td>Or similar FPLC system</td>
		</tr>
		<tr>
			<td>Spectrophotometer Shimadzu UV-1601</td>
			<td>Shimadzu</td>
			<td></td>
			<td>Or similar spectrophotometer with kinetic assay mode</td>
		</tr>
		<tr>
			<td>Ultracentrifuge Beckman Optima with SW60Ti Rotor</td>
			<td>Beckman Coulture</td>
			<td></td>
			<td>Or similar ultracentrifuge and rotor</td>
		</tr>
		<tr>
			<td>Ultrasonic Homogenizer with Thin Probe, Model 3000</td>
			<td>BioLogics</td>
			<td>0-127-0001</td>
			<td>Or similar ultrasonic homogenizer</td>
		</tr>
	</tbody>
</table>

isolation of f1-atpase from the parasitic protist trypanosoma brucei

F1-ATPase is a membrane-extrinsic catalytic subcomplex of F-type ATP synthase, an enzyme that uses the proton motive force across biological membranes to produce adenosine triphosphate (ATP). The isolation of the intact F1-ATPase from its native source is an essential prerequisite to characterize the enzyme&#39;s protein composition, kinetic parameters, and sensitivity to inhibitors. A highly pure and homogeneous F1-ATPase can be used for structural studies, which provide insight into molecular mechanisms of ATP synthesis and hydrolysis. This article describes a procedure for the purification of the F1-ATPase from Trypanosoma brucei, the causative agent of African trypanosomiases. The F1-ATPase is isolated from mitochondrial vesicles, which are obtained by hypotonic lysis from in vitro cultured trypanosomes. The vesicles are mechanically fragmented by sonication and the F1-ATPase is released from the inner mitochondrial membrane by the chloroform extraction. The enzymatic complex is further purified by consecutive anion exchange and size-exclusion chromatography. Sensitive mass spectrometry techniques showed that the purified complex is devoid of virtually any protein contaminants and, therefore, represents suitable material for structure determination by X-ray crystallography or cryo-electron microscopy. The isolated F1-ATPase exhibits ATP hydrolytic activity, which can be inhibited fully by sodium azide, a potent inhibitor of F-type ATP synthases. The purified complex remains stable and active for at least three days at room temperature. Precipitation by ammonium sulfate is used for long-term storage. Similar procedures have been used for the purification of F1-ATPases from mammalian and plant tissues, yeasts, or bacteria. Thus, the presented protocol can serve as a guideline for the F1-ATPase isolation from other organisms.

A typical purification (Figure 1) starts with mitochondrial vesicles (mitoplasts) isolated on the Percoll gradient from hypotonically lysed 1 x 1011 to 2 x 1011 procyclic T. brucei cells25 cultured in standard glucose-rich SDM-79 medium27. The mitoplasts are fragmented by sonication, spun, and the matrix-containing supernatant is discarded. Mitochondrial membranes are treated with ...

Watch this Scientific Journal Video about Isolation of F1-ATPase from the Parasitic Protist Trypanosoma brucei at JoVE.com

Isolation of F1-ATPase from the Parasitic Protist Trypanosoma brucei

This protocol describes the purification of F1-ATPase from the cultured insect stage of Trypanosoma brucei. The procedure yields a highly pure, homogeneous, and active complex suitable for structural and enzymatic studies.

Isolation of F1-ATPase from the Parasitic Protist Trypanosoma brucei

F1-ATPase is a membrane-extrinsic catalytic subcomplex of F-type ATP synthase, an enzyme that uses the proton motive force across biological membranes to ...

The purification of F1-ATPase is based on a classical biochemical methods which proved to be crucial for our understanding of the mechanism of ATP production by other ATP synthases. The main advantage of this technique is that it produces a highly pure enzyme suitable for structure determination by X-ray crystallography or cryo-electron microscopy. Although this protocol is optimized for the isolation of F1-ATPase from trypanosomes, it can be adapted to other sources, such as tissue or culture cells, and to various pathogenic protists.This technique may lead to the identification of new drugs to treat severe human diseases. For example, Mycobacterium tuberculosis F-ATPase is an authenticated drug target for the treatment of tuberculosis. To begin the protocol, thaw and gently resuspend mitochondrial vesicles, also known as mitoplasts, previously isolated by hypotonic lysis from one times 10 to the 11 to two times 10 to the 11 cells of procyclic Trypanosoma brucei in five milliliters of ice-cold Buffer A.Keep the sample chilled.Next, determine the protein concentration in the suspension by the bicinchoninic acid, or BCA, protein assay according to the manufacturer's instructions. Perform a BSA dilution series in ultra pure water to construct the standard curve. Dilute a small amount of the sample 20 to 100 times with ultra pure water to fit into the range of the BSA standards.After calculating the total protein amount in the sample, bring the protein concentration to 16 milligrams per milliliter by diluting it with additional Buffer A.Then fragment the mitoplasts into inverted vesicles and membrane pieces by sonication seven times for 15 seconds each, with a total energy of 70 to 100 joules per impulse with a microtip with a diameter of 3.9 millimeters. While fragmenting, incubate the sample on ice for 30 seconds between impulses. After the sonication, the suspension might appear slightly darker.Sediment the membrane fragments by ultracentrifugation at 54, 000 g for 16 hours or at 98, 000 g for five hours at four degrees Celsius. Decant the supernatant and proceed with the chloroform extraction. Calculate the volume of Buffer B based on the total amount of Buffer A used.Transfer the frozen sediment from the centrifuge tube into the homogenizer. Resuspend the pellet of mitochondrial membranes in Buffer B with the aid of a small Dounce homogenizer. Transfer the suspension to a 50 milliliter conical tube.Remove the sample from ice, and keep the sample and all the solutions at room temperature for the remaining steps. Then add chloroform saturated with two molar tris adjusted with HCl to pH 8.5, one to one. Close the cap tightly, and shake the sample vigorously for exactly 20 seconds.Immediately centrifuge the mixture at 8, 400 g for five minutes at room temperature. Next, transfer the upper, cloudy aqueous phase to 1.6 milliliter microtubes. Add protease inhibitors to the sample to replace the inhibitors removed by the chloroform treatment.Centrifuge the samples at 13, 000 g for 30 minutes at room temperature. After the spin, transfer the supernatant to fresh microtubes, and repeat the centrifugation to remove any remaining insoluble material. Equilibrate the five milliliter anion exchange Q column attached to a fast protein liquid chromatography system with 50 milliliters of Q column buffer at a flow rate of five milliliters per minute until the absorbance at 280 nanometers and the conductivity stabilize.Load the supernatant on the equilibrated column at a flow rate of one milliliter per minute. Wait until the absorbance at 280 nanometers stabilizes at the background. Apply a 25 milliliter linear gradient of the Q column elution buffer from 0%to 100%at a flow rate of 0.5 milliliters per minute and collect one milliliter fractions.Assay 10 microliters of each individual fraction corresponding to the major elution peak for ATP hydrolytic activity per on milliliter of reaction mixture by the Pullman ATPase assay at pH 8.0. Pool the fractions that exhibit ATPase activity. Concentrate the pooled sample by membrane ultrafiltration using a spin column with a 100, 000 molecular weight cutoff PES filter to 200 to 500 microliters.Then proceed to size exclusion chromatography. Equilibrate the Superose 6 Increase column attached to a liquid chromatography system with at least 48 milliliters of SEC buffer at a flow rate of 0.5 milliliters per minute. Apply the sample to the column.Run the chromatography at a flow rate of 0.25 milliliters per minute, while collecting 0.25 milliliter fractions. Next, run 10 microliters of the fractions that correspond to the peaks of the UV 280 nanometer absorbance trace on SDS-PAGE. Then stain the samples with Coomassie Blue.Assay the fractions corresponding to the first major peak containing the F1 peak for the ATP hydrolytic activity and azide sensitivity by the Pullman ATPase assay. Then perform a BCA assay to determine the protein concentration. Finally, keep the purified F1-ATPase at room temperature, and use it within three days after purification for downstream applications.This elution profile of an anion exchange chromatography displays the UV absorbance at 280 nanometers and concentration of sodium chloride in the elution buffer. The selected fractions were separated on the SDS-PAGE gel and stained with Coomassie Blue dye. The fractions that correspond to the major elution peak from anion exchange chromatography and contain the F1-ATPase were pooled, concentrated, and used as the input for size-exclusion chromatography.The major contaminant is dihydrolipoyl dehydrogenase, which elutes from the size-exclusion chromatography column as a discrete peak. The F1-ATPase elutes in the first dominant, largely symmetric peak. The Coomassie Blue staining of a typical band pattern after the separation of the purified F1-ATPase via SDS-PAGE shows sporadic weak bands visible above the beta subunit, which represent subcomplexes of the alpha three beta three headpiece, dimers and oligomers of the alpha and beta subunits, and are devoid of any contaminants detectable by mass spectrometry.While performing the chloroform extraction, the critical step of the protocol, it is essential to shake the sample vigorously and proceed to the centrifugal separation of the organic and aqueous phases immediately. Following this procedure, the isolated F1-ATPase can be characterized in detail by mass spectrometry. Further, it can be used in activity assays or for structural studies, either on its own or in the presence of various inhibitors or substrate analogs.

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7.1K Views.  Czech Academy of Science, Institute of Parasitology. The purification of F1-ATPase is based on a classical biochemical methods which proved to be crucial for our understanding of the mechanism of ATP production by other ATP synthases. The main advantage of this technique is that it produces a highly pure enzyme suitable for structure determination by X-ray crystallography or cryo-electron microscopy. Although this protocol is optimized for the isolation of F1-ATPase from trypanosomes, it can be adapted to other sources, such as tissue or cultur...

Video: Isolation of F1-ATPase from the Parasitic Protist Trypanosoma brucei

This protocol describes the purification of F1-ATPase from the cultured insect stage of Trypanosoma brucei. The procedure yields a highly pure, homogeneous, and active complex suitable for structural and enzymatic...

high-throughput gene tagging in trypanosoma brucei

High-throughput Gene Tagging in Trypanosoma brucei

Addition of a tag to a protein is a powerful way of gaining insight into its function. Here, we describe a protocol to endogenously tag hundreds of Trypanosoma brucei proteins in parallel such that genome scale tagging is...

High-throughput Gene Tagging in Trypanosoma brucei

measuring dynamic glycosomal ph changes in living trypanosoma brucei

Author Spotlight: Advancements in Glycosomal pH Monitoring in &lt;i&gt;Trypanosoma brucei&lt;/i&gt; Using pHluorin2 Biosensor

We describe a method to study how pH responds to environmental cues in the glycosomes of the bloodstream form of African trypanosomes. This approach involves a pH-sensitive heritable protein sensor in combination with flow cytometry to measure pH dynamics, both as a time-course assay and in a high-throughput screen...

Development of pHluorin2-Based Sensor for Glycosomal pH in &lt;i&gt;Trypanosoma brucei&lt;/i&gt;

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Measuring Dynamic Glycosomal pH Changes in Living Trypanosoma brucei

examination of the telomere g-overhang structure in trypanosoma brucei

Examination of the Telomere G-overhang Structure in Trypanosoma brucei

Telomeres are essential for chromosome stability and the telomere G-overhang structure is essential for telomerase-mediated telomere maintenance. We have recently adopted two methods for detecting the telomere G-overhang structure in Trypanosoma brucei, which are native in-gel hybridization and ligation-mediated primer extension, which will be...

Examination of the Telomere G-overhang Structure in Trypanosoma brucei

detection of trypanosoma brucei variant surface glycoprotein switching by magnetic activated cell sorting and flow cytometry

Detection of Trypanosoma brucei Variant Surface Glycoprotein Switching by Magnetic Activated Cell Sorting and Flow Cytometry

African trypanosomes grown in vitro undergo antigenic variation at a low rate, such that populations are made up of parasites expressing a dominant variant surface glycoprotein (VSG) type and a small population of "switched" variants.  This protocol describes a fast method for detecting and quantifying these...

Detection of Trypanosoma brucei Variant Surface Glycoprotein Switching by Magnetic Activated Cell Sorting and Flow Cytometry

analysis of flow cytometry data to measure the relative ph of the glycosome in living trypanosoma brucei

Analysis of Flow Cytometry Data to Measure the Relative pH of the Glycosome in Living Trypanosoma brucei

flow cytometry procedure to measure relative ph of the glycosome in living trypanosoma brucei

Flow Cytometry Procedure to Measure Relative pH of the Glycosome in Living Trypanosoma brucei

sample preparation for flow cytometry to measure phluorin2 fluorescence in living trypanosoma brucei

Sample Preparation for Flow Cytometry to Measure pHluorin2 Fluorescence in Living Trypanosoma brucei

experimental infection of mice with the parasitic nematode strongyloides ratti

Author Spotlight: Sex-Dependent Intestinal Immunity and Site-Specific Immune Responses in Strongyloides ratti Infection

Strongyloides ratti is a parasitic nematode that causes transient infections in laboratory mice, displaying tissue-migrating and intestinal life stages. Here, we present a protocol for the maintenance of the parasite cycle in rats and experimental infection of mice, including parasite quantification in the head, lung, and intestine.

Experimental Infection of Mice with the Parasitic Nematode Strongyloides ratti

detection of extravascular trypanosoma parasites by fine needle aspiration

Detection of Extravascular Trypanosoma Parasites by Fine Needle Aspiration

Fine Needle Aspiration is a technique, whereby cells are obtained from a lesion or organ using a thin needle. Aspirated material is smeared, stained and examined under a microscope for diagnosis or used for molecular biology, cytometry or in vitro analysis. It is cheap, simple, quick and causes minimal...

Detection of Extravascular Trypanosoma Parasites by Fine Needle Aspiration

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An Introduction to Parasitic Wasps of Drosophila and the Antiparasite Immune Response

Parasitoid (parasitic) wasps constitute a major class of natural enemies of many insects including Drosophila melanogaster. We will introduce the techniques to propagate these parasites in Drosophila spp. and demonstrate how to analyze their effects on immune tissues of Drosophila...

An Introduction to Parasitic Wasps of Drosophila and the Antiparasite Immune Response

ultrastructural expansion microscopy in three in vitro life cycle stages of trypanosoma cruzi

Author Spotlight: Imaging &lt;i&gt;Trypanosoma cruzi &lt;/i&gt; at the Nanoscale Using Ultrastructure Expansion Microscopy

This study shows a detailed protocol to perform ultrastructure expansion microscopy in three in vitro life cycle stages of Trypanosoma cruzi, the pathogen responsible for Chagas disease. We include the optimized technique for cytoskeletal proteins and pan-proteome labeling.

Ultrastructural Expansion Microscopy in In Vitro Life Cycle of &lt;i&gt;Trypanosoma cruzi &lt;/i&gt;

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ready-to-use qpcr for detection of dna from trypanosoma cruzi or other pathogenic organisms

Ready-To-Use qPCR for Detection of DNA from Trypanosoma cruzi or Other Pathogenic Organisms

The present work describes the steps for producing ready-to-use qPCR for T. cruzi DNA detection that can be pre-loaded on the reaction vessel and stored in the refrigerator for several...

Ready-To-Use qPCR for Detection of DNA from Trypanosoma cruzi or Other Pathogenic Organisms

establishment of larval zebrafish as an animal model to investigate trypanosoma cruzi motility in vivo

Establishment of Larval Zebrafish as an Animal Model to Investigate Trypanosoma cruzi Motility In Vivo

In this protocol, fluorescently labeled T. cruzi&#160;were injected into transparent zebrafish larvae, and parasite motility was observed in vivo using light sheet fluorescence...

Establishment of Larval Zebrafish as an Animal Model to Investigate Trypanosoma cruzi Motility In Vivo

culturing and screening the plant parasitic nematode ditylenchus dipsaci

Culturing and Screening the Plant Parasitic Nematode Ditylenchus dipsaci

The present protocol describes a reliable and straightforward method for culturing, collecting, and screening Ditylenchus dipsaci.

Culturing and Screening the Plant Parasitic Nematode Ditylenchus dipsaci

introducing a gene knockout directly into the amastigote stage of trypanosoma cruzi using the crispr/cas9 system

Introducing a Gene Knockout Directly Into the Amastigote Stage of Trypanosoma cruzi Using the CRISPR/Cas9 System

Here, we describe a protocol to introduce a gene knockout into the extracellular amastigote of Trypanosoma cruzi, using the CRISPR/Cas9 system. The growth phenotype can be followed up either by cell counting of axenic amastigote culture or by proliferation of intracellular amastigotes after host cell...

Introducing a Gene Knockout Directly Into the Amastigote Stage of Trypanosoma cruzi Using the CRISPR/Cas9 System

measuring in vitro atpase activity for enzymatic characterization

Measuring In Vitro ATPase Activity for Enzymatic Characterization

We describe a basic protocol for quantitating in vitro ATPase activity. This protocol can be optimized based on the level of activity and requirements for a given purified...

Measuring In Vitro ATPase Activity for Enzymatic Characterization

electronic von frey associated with the mouse grimace scale to assess allodynia and pain in trypanosoma evansi-infected mice

Author Spotlight: Assessing Pain and Promoting Animal Welfare in Laboratory Animals Infected with &lt;em&gt;Trypanosoma evansi&lt;/em&gt;

Here, we present a protocol to evaluate nociception in mice infected with Trypanosoma evansi, using the electronic von Frey apparatus as a tool, measuring mechanical thresholds of the hind paw and...

Assessing Pain and Allodynia in &lt;em&gt;T. evansi&lt;/em&gt;-Infected Animals

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leveraging micro-ct scanning to analyze parasitic plant-host interactions

Leveraging Micro-CT Scanning to Analyze Parasitic Plant-Host Interactions

Micro-CT is a non-destructive tool that can analyze plant structures in three dimensions. The present protocol describes the sample preparation to leverage micro-CT to analyze parasitic plant structure and function. Different species are used to highlight the advantages of this method when coupled with specific preparations.

Isolation of Cognate RNA-protein Complexes from Cells Using Oligonucleotide-directed Elution

Ribonucleoprotein particles direct the biogenesis and post-transcriptional regulation of all mRNAs through distinct combinations of RNA binding proteins. They are composed of position-dependent, cis-acting RNA elements and unique combinations of RNA binding proteins. Defining the composition of a specific RNP is essential to achieving a fundamental understanding of gene regulation. The isolation of a select RNP is akin to finding a needle in a haystack. Here, we demonstrate an approach to isolate RNPs associated at the 5' untranslated region of a select mRNA in asynchronous, transfected cells. This cognate RNP has been demonstrated to be necessary for the translation of select viruses and cellular stress-response genes.
The demonstrated RNA-protein co-precipitation protocol is suitable for the downstream analysis of protein components through proteomic analyses, immunoblots, or suitable biochemical identification assays. This experimental protocol demonstrates that DHX9/RNA helicase A is enriched at the 5' terminus of cognate retroviral RNA and provides preliminary information for the identification of its association with cell stress-associated huR and junD cognate mRNAs.

This manuscript describes an approach to isolate select cognate RNPs formed in eukaryotic cells via a specific oligonucleotide-directed enrichment. We demonstrate the applicability of this approach by isolating a cognate RNP bound to the retroviral 5' untranslated region that is composed of DHX9/RNA helicase A.

Ribonucleoprotein particles direct the biogenesis and post-transcriptional regulation of all mRNAs through distinct combinations of RNA binding proteins. ...

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as industrial materials. Gene expression profiles are powerful tools for investigating metabolic regulation in plant cells. Therefore, detailed, accurate gene expression profiles during seed development are required for crop breeding. Acquiring highly purified RNA is essential for producing these profiles. Efficient methods are needed to isolate highly purified RNA from seeds. Here, we describe a method for isolating RNA from seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method enables highly purified RNA to be obtained from seeds without the use of phenol, chloroform, or additional processes for RNA purification. This method is applicable to Arabidopsis, rapeseed, and soybean seeds. Our method will be useful for monitoring the expression patterns of low level transcripts in developing and mature seeds.

We have succeeded in establishing a method for RNA isolation from plant seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method is suitable for monitoring the expression of genes with low level transcripts in seeds.

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as ...

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 ...

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

Mitochondria are essential organelles involved in numerous metabolic pathways in plants, most notably the production of adenosine triphosphate (ATP) from the oxidation of reduced compounds such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADH2). The complete annotation of the Arabidopsis thaliana genome has established it as the most widely used plant model system, and thus the need to purify mitochondria from a variety of organs (leaf, root, or flower) is necessary to fully utilize the tools that are now available for Arabidopsis to study mitochondrial biology. Mitochondria are isolated by homogenization of the tissue using a variety of approaches, followed by a series of differential centrifugation steps producing a crude mitochondrial pellet that is further purified using continuous colloidal density gradient centrifugation. The colloidal density material is subsequently removed by multiple centrifugation steps. Starting from 100 g of fresh leaf tissue, 2 - 3 mg of mitochondria can be routinely obtained. Respiratory experiments on these mitochondria display typical rates of 100 - 250 nmol O2 min-1 mg total mitochondrial protein-1 (NADH-dependent rate) with the ability to use various substrates and inhibitors to determine which substrates are being oxidized and the capacity of the alternative and cytochrome terminal oxidases. This protocol describes an isolation method of mitochondria from Arabidopsis thaliana leaves using continuous colloidal density gradients and an efficient respiratory measurements of purified plant mitochondria.

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

As mitochondria are only a small percentage of the plant cell, they need to be purified for a range of studies. Mitochondria can be isolated from a variety of plant organs by homogenization, followed by differential and density gradient centrifugation to obtain a highly purified mitochondrial fraction.

Mitochondria are essential organelles involved in numerous metabolic pathways in plants, most notably the production of adenosine triphosphate (ATP) from ...

Protein Digestion, Ultrafiltration, and Size Exclusion Chromatography to Optimize the Isolation of Exosomes from Human Blood Plasma and Serum

Exosomes, a type of nanovesicle released from all cell types, can be isolated from any bodily fluid. The contents of exosomes, including proteins and RNAs, are unique to the cells from which they are derived and can be used as indicators of disease. Several common enrichment protocols, including ultracentrifugation, yield exosomes laden with soluble protein contaminants. Specifically, we have found that the most abundant proteins within blood often co-purify with exosomes and can confound downstream proteomic studies, thwarting the identification of low abundance biomarker candidates. Of additional concern is irreproducibility of exosome protein quantification due to inconsistent representation of non-exosomal protein levels. The protocol detailed here was developed to remove non-exosomal proteins that co-purify along with exosomes, adding rigor to the exosome purification process. Five methods were compared using paired blood plasma and serum from five donors. Analysis using nanoparticle tracking analysis and micro bicinchoninic acid protein assay revealed that a combined protocol utilizing ultrafiltration and size exclusion chromatography yielded the optimal vesicle enrichment and soluble protein removal. Western blotting was used to verify that the expected abundant blood proteins, including albumin and apolipoproteins, were depleted.

Here, we present a protocol to purify exosomes from both plasma and serum with reduced co-purification of non-exosomal blood proteins. The optimized protocol includes ultrafiltration, protease treatment, and size exclusion chromatography. Enhanced purification of exosomes benefits downstream analyses, including more accurate quantification of vesicles and proteomic characterization.

Exosomes, a type of nanovesicle released from all cell types, can be isolated from any bodily fluid. The contents of exosomes, including proteins and ...

Rapid Isolation of the Mitoribosome from HEK Cells

The human mitochondria possess a dedicated set of ribosomes (mitoribosomes) that translate 13 essential protein components of the oxidative phosphorylation complexes encoded by the mitochondrial genome. Since all proteins synthesized by human mitoribosomes are integral membrane proteins, human mitoribosomes are tethered to the mitochondrial inner membrane during translation. Compared to the cytosolic ribosome the mitoribosome has a sedimentation coefficient of 55S, half the rRNA content, no 5S rRNA and 36 additional proteins. Therefore, a higher protein-to-RNA ratio and an atypical structure make the human mitoribosome substantially distinct from its cytosolic counterpart.
Despite the central importance of the mitoribosome to life, no protocols were available to purify the intact complex from human cell lines. Traditionally, mitoribosomes were isolated from mitochondria-rich animal tissues that required kilograms of starting material. We reasoned that mitochondria in dividing HEK293-derived human cells grown in nutrient-rich expression medium would have an active mitochondrial translation, and, therefore, could be a suitable source of material for the structural and biochemical studies of the mitoribosome. To investigate its structure, we developed a protocol for large-scale purification of intact mitoribosomes from HEK cells. Herein, we introduce nitrogen cavitation method as a faster, less labor-intensive and more efficient alternative to traditional mechanical shear-based methods for cell lysis. This resulted in preparations of the mitoribosome that allowed for its structural determination to high resolution, revealing the composition of the intact human mitoribosome and its assembly intermediates. Here, we follow up on this work and present an optimized and more cost-effective method requiring only ~1010 cultured HEK cells. The method can be employed to purify human mitoribosomal translating complexes, mutants, quality control assemblies and mitoribosomal subunits intermediates. The purification can be linearly scaled up tenfold if needed, and also applied to other types of cells.

Mitochondria have specialized ribosomes that diverged from their bacterial and cytoplasmic counterparts. Here we show how mitoribosomes can be obtained from their native compartment in HEK cells. The method involves isolation of mitochondria from suspension cells and consequent purification of mitoribosomes.

The human mitochondria possess a dedicated set of ribosomes (mitoribosomes) that translate 13 essential protein components of the oxidative ...

Isolation of Tissue Extracellular Vesicles from the Liver

Extracellular vesicles (EVs) can be released from many different cell types and detected in most, if not all, body fluids. EVs can participate in cell-to-cell communication by shuttling bioactive molecules such as RNA or protein from one cell to another. Most studies of EVs have been performed in cell culture models or in EVs isolated from body fluids. There is emerging interest in the isolation of EVs from tissues to study their contribution to physiological processes and how they are altered in disease. The isolation of EVs with sufficient yield from tissues is technically challenging because of the need for tissue dissociation without cellular damage. This method describes a procedure for the isolation of EVs from mouse liver tissue. The method involves a two-step process starting with in situ collagenase digestion followed by differential ultra-centrifugation. Tissue perfusion using collagenase provides an advantage over mechanical cutting or homogenization of liver tissue due to its increased yield of obtained EVs. The use of this two-step process to isolate EVs from the liver will be useful for the study of tissue EVs.

This is a protocol to isolate tissue extracellular vesicles (EVs) from the liver. The protocol describes a two-step process involving collagenase perfusion followed by differential ultracentrifugation to isolate liver tissue EVs.

Extracellular vesicles (EVs) can be released from many different cell types and detected in most, if not all, body fluids. EVs can participate in ...

Isolation of Lipoprotein Particles from Chicken Egg Yolk for the Study of Bacterial Pathogen Fatty Acid Incorporation into Membrane Phospholipids

Staphylococcus aureus and other Gram-positive pathogens incorporate fatty acids from the environment into membrane phospholipids. During infection, the majority of exogenous fatty acids are present within host lipoprotein particles. Uncertainty remains as to the reservoirs of host fatty acids and the mechanisms by which bacteria extract fatty acids from the lipoprotein particles. In this work, we describe protocols for enrichment of low-density lipoprotein (LDL) particles from chicken egg yolk and determining whether LDLs serve as fatty acid reservoirs for S. aureus. This method exploits unbiased lipidomic analysis and chicken LDLs, an effective and economical model for the exploration of interactions between LDLs and bacteria. The analysis of S. aureus integration of exogenous fatty acids from LDLs is performed using high-resolution/accurate mass spectrometry and tandem mass spectrometry, enabling the characterization of the fatty acid composition of the bacterial membrane and unbiased identification of novel combinations of fatty acids that arise in bacterial membrane lipids upon exposure to LDLs. These advanced mass spectrometry techniques offer an unparalleled perspective of fatty acid incorporation by revealing the specific exogenous fatty acids incorporated into the phospholipids. The methods outlined here are adaptable to the study of other bacterial pathogens and alternative sources of complex fatty acids.

This method provides a framework for studying incorporation of exogenous fatty acids from complex host sources into bacterial membranes, particularly Staphylococcus aureus. To achieve this, protocols for the enrichment of lipoprotein particles from chicken egg yolk and subsequent fatty acid profiling of bacterial phospholipids utilizing mass spectrometry are described.

Staphylococcus aureus and other Gram-positive pathogens incorporate fatty acids from the environment into membrane phospholipids. During infection, the ...

Translating Ribosome Affinity Purification (TRAP) for RNA Isolation from Endothelial Cells In Vivo

Many studies have been limited to using in vitro cellular assays and whole tissues or isolating of specific cell types from animals for in vitro analysis of transcriptome and gene expression by qPCR and RNA sequencing. Comprehensive transcriptome and gene expression analysis of specific cell types in complex tissues and organs will be critical to understand cellular and molecular mechanisms by which genes are regulated and their association with tissue homeostasis and organ functions. In this article, we demonstrate the methodology for isolation of ribosome-bound RNA directly in vivo in the vascular endothelia of animal lungs as an example. The specific materials and procedures for tissue processing and RNA purification will be described, including the assessment of RNA quality and yield as well as real time qPCR for arteriogenic gene assays. This approach, known as translating ribosome affinity purification (TRAP) technique, can be utilized for characterization of gene expression and transcriptome analysis of certain cell types directly in vivo in any specific type in complex tissues.

Translating Ribosome Affinity Purification TRAP for RNA Isolation from Endothelial Cells In Vivo

We present an approach to purify ribosome-bound mRNA from vascular endothelial cells (ECs) directly in mouse brain, lung and heart tissues via EC-specific genetic tag of enhanced green fluorescence protein (EGFP)in ribosomes in combination with RNA purification.

Many studies have been limited to using in vitro cellular assays and whole tissues or isolating of specific cell types from animals for in vitro analysis ...

Real-time PCR (qPCR) is a remarkably sensitive and precise technique&#160;that allows for amplifying&#160;minute amounts of nucleic acid targets from a multitude of samples. It has been extensively used in many research areas and achieved industrial application in fields such as human diagnostics and trait selection in crops of genetically modified organisms (GMO) crops. However, qPCR is not an error-proof technique. Mixing all reagents into a single master mix subsequently distributed onto 96 wells of a regular qPCR plate might lead to operator mistakes such as incorrect mixing of reagents or inaccurate dispensing into the wells. Here, a technique called gelification is presented, whereby most of the water present in the master mix is substituted by reagents that form a sol-gel mixture when submitted to a vacuum. As a result, qPCR reagents are effectively preserved for a few weeks at room temperature or a few months at 2-8 oC. Details of preparing each solution are shown here along with the expected aspect of a gelified reaction designed to detect&#160;T. cruzi satellite DNA (satDNA). A similar procedure can be applied to detect other organisms. Starting a gelified qPCR run is as simple as removing the plate from the refrigerator, adding the samples to their respective wells, and starting the run, thus decreasing the setup time of a full-plate reaction to the time it takes to load the samples. Additionally, gelified PCR reactions can be produced and controlled for quality in batches, saving time and avoiding common operator mistakes while running routine PCR reactions.

The present work describes the steps for producing ready-to-use qPCR for T. cruzi DNA detection that can be pre-loaded on the reaction vessel and stored in the refrigerator for several months.

Real-time PCR (qPCR) is a remarkably sensitive and precise technique&#160;that allows for amplifying&#160;minute amounts of nucleic acid targets from a ...