Name: formulation and characterization of bioactive agent containing nanodisks
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This work was supported by a grant from the National Institutes of Health (R37 HL-64159).

1. Transformation, expression, and purification of scaffold protein component
<ol>
	<li>BL21 bacterial transformation with apoE4-NT containing plasmid
	<ol>
		<li>Thaw a tube of BL21 (DE3) competent cells on ice for 10 min.</li>
		<li>Once all the ice has melted, mix gently and carefully pipette 50 &#181;L of the cells into a transformation tube on ice.</li>
		<li>Add 5 &#181;L containing 50 ng of plasmid DNA (for sequence, see Supplemental Table 1) to the cell mixture. Carefully flick...

<ol>
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O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanodisks:+hydrophobic+drug+delivery+vehicles.">Nanodisks: hydrophobic drug delivery vehicles.</a> Expert Opinion on Drug Delivery. 5 (3), 343-351 (2008).</li><li>Oda, M. N., 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=Reconstituted+high+density+lipoprotein+enriched+with+the+polyene+antibiotic+amphotericin+B.">Reconstituted high density lipoprotein enriched with the polyene antibiotic amphotericin B.</a> Journal of Lipid Research. 47 (2), 260-267 (2006).</li><li>Redmond, K. A., Nguyen, T. S., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=All-trans-retinoic+acid+nanodisks.">All-trans-retinoic acid nanodisks.</a> International Journal of Pharmaceutics. 339 (1-2), 246-250 (2007).</li><li>Ghosh, 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=Curcumin+nanodisks:+formulation+and+characterization.">Curcumin nanodisks: formulation and characterization.</a> Nanomedicine. 7 (2), 162-167 (2011).</li><li>Yuan, 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=Synthetic+high-density+lipoproteins+for+delivery+of+10-hydroxycamptothecin.">Synthetic high-density lipoproteins for delivery of 10-hydroxycamptothecin.</a> International Journal of Nanomedicine. 11, 6229-6238 (2016).</li><li>Zhao, P., 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=Sphingadienes+show+therapeutic+efficacy+in+neuroblastoma+in+vitro+and+in+vivo+by+targeting+the+AKT+signaling+pathway.">Sphingadienes show therapeutic efficacy in neuroblastoma in vitro and in vivo by targeting the AKT signaling pathway.</a> Investigational New Drugs. 36 (5), 743-754 (2018).</li><li>Moschetti, A., 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=Assembly+and+characterization+of+biocompatible+coenzyme+Q10+enriched+lipid+nanoparticles.">Assembly and characterization of biocompatible coenzyme Q10 enriched lipid nanoparticles.</a> Lipids. 55 (2), 141-149 (2020).</li><li>Krishnamoorthy, A., Witkowski, A., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nutlin-3a+nanodisks+induce+p53+stabilization+and+apoptosis+in+a+subset+of+cultured+glioblastoma+cells.">Nutlin-3a nanodisks induce p53 stabilization and apoptosis in a subset of cultured glioblastoma cells.</a> Journal of Nanomedicine and Nanotechnology. 8 (4), 454 (2017).</li><li>Moschetti, A., Fox, C. A., McGowen, S., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lutein+nanodisks+protect+retinal+pigment+epithelial+cells+from+UV+light+induced+damage.">Lutein nanodisks protect retinal pigment epithelial cells from UV light induced damage.</a> Frontiers in Nanotechnology. 4, 955022 (2022).</li><li>Scheetz, L. 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=Synthetic+HDL+nanoparticles+delivering+docetaxel+and+CpG+for+chemoimmunotherapy+of+colon+adenocarcinoma.">Synthetic HDL nanoparticles delivering docetaxel and CpG for chemoimmunotherapy of colon adenocarcinoma.</a> International Journal of Molecular Sciences. 21 (5), 1777 (2020).</li><li>Duivenvoorden, 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=A+statin-loaded+reconstituted+high-density+lipoprotein+nanoparticle+inhibits+atherosclerotic+plaque+inflammation.">A statin-loaded reconstituted high-density lipoprotein nanoparticle inhibits atherosclerotic plaque inflammation.</a> Nature Communications. 5, 3065 (2014).</li><li>Hargreaves, P. L., Nguyen, T. S., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spectroscopic+studies+of+amphotericin+B+solubilized+in+nanoscale+bilayer+membranes.">Spectroscopic studies of amphotericin B solubilized in nanoscale bilayer membranes.</a> Biochimica et Biophysica Acta. 1758 (1), 38-44 (2006).</li><li>Tufteland, M., Pesavento, J. B., Bermingham, R. L., Hoeprich Jr, P. D., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Peptide+stabilized+amphotericin+B+nanodisks.">Peptide stabilized amphotericin B nanodisks.</a> Peptides. 28 (4), 741-746 (2007).</li><li>Tufteland, M., Ren, G., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanodisks+derived+from+amphotericin+B+lipid+complex.">Nanodisks derived from amphotericin B lipid complex.</a> Journal of Pharmaceutical Sciences. 97 (10), 4425-4432 (2008).</li><li>Nguyen, T. S., 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=Amphotericin+B+induces+interdigitation+of+apolipoprotein+stabilized+nanodisk+bilayers.">Amphotericin B induces interdigitation of apolipoprotein stabilized nanodisk bilayers.</a> Biochimica et Biophysica Acta. 1778 (1), 303-312 (2008).</li><li>Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanobiotechnology+applications+of+reconstituted+high+density+lipoprotein.">Nanobiotechnology applications of reconstituted high density lipoprotein.</a> Journal of Nanobiotechnology. 8, 28 (2010).</li><li>Lalefar, N. R., Witkowski, A., Simonsen, J. B., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wnt3a+nanodisks+promote+ex+vivo+expansion+of+hematopoietic+stem+and+progenitor+cells.">Wnt3a nanodisks promote ex vivo expansion of hematopoietic stem and progenitor cells.</a> Journal of Nanobiotechnology. 14 (1), 66 (2016).</li><li>Crosby, N. 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=Anti-CD20+single+chain+variable+antibody+fragment-apolipoprotein+A-I+chimera+containing+nanodisks+promote+targeted+bioactive+agent+delivery+to+CD20-positive+lymphomas.">Anti-CD20 single chain variable antibody fragment-apolipoprotein A-I chimera containing nanodisks promote targeted bioactive agent delivery to CD20-positive lymphomas.</a> Biochemistry and Cell Biology. 93 (4), 343-350 (2015).</li><li>Ghosh, M., Ren, G., Simonsen, J. B., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cationic+lipid+nanodisks+as+an+siRNA+delivery+vehicle.">Cationic lipid nanodisks as an siRNA delivery vehicle.</a> Biochemistry and Cell Biology. 92 (3), 200-205 (2014).</li><li>Fox, C. A., Ellison, P., Ikon, N., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calcium-induced+transformation+of+cardiolipin+nanodisks.">Calcium-induced transformation of cardiolipin nanodisks.</a> Biochimica et Biophysica Acta. Biomembranes. 1861 (5), 1030-1036 (2019).</li><li>Fox, C. A., Lethcoe, K., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calcium-induced+release+of+cytochrome+c+from+cardiolipin+nanodisks:+Implications+for+apoptosis.">Calcium-induced release of cytochrome c from cardiolipin nanodisks: Implications for apoptosis.</a> Biochimica et Biophysica Acta Biomembranes. 1861 (12), 183722 (2021).</li><li>Fox, C. A., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dye+binding+assay+reveals+doxorubicin+preference+for+DNA+versus+cardiolipin.">Dye binding assay reveals doxorubicin preference for DNA versus cardiolipin.</a> Analytical Biochemistry. 594, 113617 (2020).</li><li>Fox, C. A., Romenskaia, I., Dagda, R. K., Ryan, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cardiolipin+nanodisks+confer+protection+against+doxorubicin-induced+mitochondrial+dysfunction.">Cardiolipin nanodisks confer protection against doxorubicin-induced mitochondrial dysfunction.</a> Biochimica et Biophysica Acta Biomembranes. 1864 (10), 183984 (2022).</li></ol>

Formulation of a bioactive agent containing nanodisks provide&#160;a convenient method to solubilize otherwise insoluble hydrophobic compounds. Because the product bioactive agent nanodisks are fully soluble in aqueous media, they provide a useful delivery method for a wide range of hydrophobic molecules (Table 1). These include small molecules, natural and synthetic drugs, phytonutrients, hormones, etc. The formulation strategy usually follows a standard protocol that must take into consideration the so...

Nascent discoidal high density lipoproteins (HDLs) are naturally occurring progenitors of the far more abundant spherical HDL present in the human circulatory system. These nascent particles, also referred to as pre-&#223; HDL, possess unique and distinctive structural properties1. Indeed, rather than existing as a spheroidal particle, nascent HDLs are disk-shaped. Extensive structural characterization studies on natural and reconstituted discoidal HDLs have revealed that they are comprised of a phospholipid bilayer whose perimeter is circumscribed by an amphipathic exchangeable apolipoprotein (apo), such as apoA-I. In human lipoprotein metabolism, circulating nascent HDLs accrue lipids from peripheral cells and mature into spherical HDLs in a process that is dependent upon key protein mediators, including the ATP binding cassette transporter A1 and lecithin:cholesterol acyltransferse2. This process represents a critical component of the reverse cholesterol transport pathway that is considered to be protective against heart disease. Armed with this knowledge and the ability to reconstitute discoidal HDLs, researchers have employed these particles as a therapeutic intervention to treat atherosclerosis3. In essence, the infusion of reconstituted HDL (rHDL) into patients promotes cholesterol efflux from plaque deposits and returns it to the liver for conversion to bile acids and excretion from the body. Several biotechnology/pharmaceutical companies are pursuing this treatment strategy4.
At the same time, the ability to generate these particles in the laboratory has sparked a flurry of research activities that has led to novel applications and new technologies. One prominent application involves the use of rHDL particles as a miniature membrane to house transmembrane proteins in a native-like environment5. To date, hundreds of proteins have been successfully incorporated into discoidal rHDL, and research has demonstrated that these proteins retain both native conformation and biological activity as receptors, enzymes, transporters, etc. These particles, referred to as &#34;nanodiscs&#34;, have also been shown to be amenable to structural characterization, often at high resolution6. This approach to investigations of transmembrane proteins is recognized as superior to studies with detergent micelles or liposomes and, as a result, is rapidly advancing. It is important to recognize that two distinct methods have been reported that are capable of forming an rHDL. The &#34;cholate dialysis&#34; method13 is popular for applications related to the incorporation of transmembrane proteins in the rHDL bilayer5. Essentially, this method of formulation involves mixing a bilayer forming phospholipid, a scaffold protein, and the transmembrane protein of interest in a buffer containing the detergent sodium cholate (or sodium deoxycholate; micelle molecular weight [MW] of 4,200 Da). The detergent effectively solubilizes the different reaction components, permitting the sample to be dialyzed against buffer lacking detergent. During the dialysis step, as the detergent is removed from the sample, an rHDL spontaneously forms. When this approach is used to entrap a transmembrane protein of interest, the product particles have been termed nanodiscs5. Attempts to use this method to incorporate small molecule hydrophobic bioactive agents (MW &#60;1,000 Da), however, have been largely unsuccessful. Unlike transmembrane proteins, small molecule bioactive agents are able to escape from the dialysis bag along with the detergent, greatly decreasing their incorporation efficiency into rHDLs. This problem was solved by omitting detergents from the formulation mixture14. Instead, the components are added to an aqueous buffer sequentially, beginning with the bilayer forming lipid, forming a stable bioactive agent containing rHDL, referred to as a nanodisk. Others have used rHDL for the incorporation and transport of in vivo imaging agents7. More recently, specialized rHDL comprised of an apolipoprotein scaffold and the anionic glycerophospholipid, cardiolipin, have been employed in ligand binding studies. These particles provide a platform for studies of the interaction of cardiolipin with various water soluble ligands, including calcium, cytochrome c, and the anticancer agent doxorubicin8.
The focus of the present study is on the formulation of rHDL that possess a stably incorporated hydrophobic bioactive agent (i.e. nanodisk). The ability of these agents to integrate into the lipid milieu of discoidal rHDL particles effectively confers them with aqueous solubility. As such, nanodisks have the potential for in vivo therapeutic applications. When formulating nanodisks, specific incubation/reaction conditions are required to successfully incorporate discrete hydrophobic bioactive agents into the product particle, and the goal of this report is to provide detailed practical information that can be used as a foundational template for creating novel nanodisk particles for specific applications. Thus, in the context of this manuscript the terms nanodisc and nanodisk are not interchangeable. Whereas nanodisc refers to an rHDL formulated to contain a transmembrane protein embedded in its lipid bilayer5, the term nanodisk refers to an rHDL formulated to incorporate low molecular weight (&#60; 1,000 Da) hydrophobic bioactive agents, such as amphotericin B14.
A variety of methods are available for the acquisition of suitable scaffold proteins. It is possible to purchase scaffold proteins from manufacturers [e.g. apoA-I (SRP4693) or apoE4 (A3234)], however, the cost may be a limiting factor. A preferred approach is to express recombinant scaffold proteins in Escherichia coli. Protocols are published for human apoA-I9, apoE410, as well as the insect hemolymph protein apolipophorin-III11. For the purpose of the experiments described herein, recombinant human apoE4 N-terminal (NT) domain (amino acids 1-183) was used. The nucleotide sequence encoding human apoE4-NT was synthesized and inserted into a pET-22b (+) expression vector directly adjacent to the vector-encoded pelB leader sequence. This construct leads to the expression of a pelB leader sequence-apoE4-NT fusion protein. Following protein synthesis, the bacterial pelB leader sequence directs the newly synthesized protein to the periplasmic space where leader peptidase cleaves the pelB sequence. The resultant apoE4-NT protein, with no sequence tags or tails, subsequently escapes the bacteria and accumulates in the culture medium11,12, simplifying downstream processing.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Amphotericin B</td>
			<td>Cayman Chemical Company</td>
			<td>11636</td>
			<td>ND Formulation &#38; Standard Preparation</td>
		</tr>
		<tr>
			<td>Ampicillin</td>
			<td>Fisher Scientific</td>
			<td>BP17925</td>
			<td>Transformation &#38; Expansion</td>
		</tr>
		<tr>
			<td>ApoE4-NT Plasmid</td>
			<td>GenScript</td>
			<td>N/A</td>
			<td>Transformation</td>
		</tr>
		<tr>
			<td>Baffled Flask</td>
			<td>New Brunswick Scientific</td>
			<td>N/A</td>
			<td>Expansion &#38; Expression</td>
		</tr>
		<tr>
			<td>BL21 competent E coli</td>
			<td>New England Biolabs</td>
			<td>C2527I</td>
			<td>Transformation</td>
		</tr>
		<tr>
			<td>Centrifuge bottles</td>
			<td>Nalgene</td>
			<td>3140-0250</td>
			<td>Expression</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Fisher Scientific</td>
			<td>G607-4</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Sigma Aldrich</td>
			<td>472301</td>
			<td>Standard Prepartation</td>
		</tr>
		<tr>
			<td>Dymyristoylphosphatidylcholine</td>
			<td>Avanti Lipids</td>
			<td>850345P</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>Erlenmeyer flask</td>
			<td>Bellco Biotechnology</td>
			<td>N/A</td>
			<td>Expansion &#38; Expression</td>
		</tr>
		<tr>
			<td>Falcon Tubes</td>
			<td>Sarstedt Ag &#38; Co</td>
			<td>D51588</td>
			<td>Yeast Viability Assay</td>
		</tr>
		<tr>
			<td>Glass borosilicate tubes</td>
			<td>VWR</td>
			<td>47729-570</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>GraphPad (Software)</td>
			<td>Dotmatics</td>
			<td>N/A</td>
			<td>Yeast Viability Assay</td>
		</tr>
		<tr>
			<td>Heated Sonication Bath</td>
			<td>VWR</td>
			<td>N/A</td>
			<td>ND Formulaton</td>
		</tr>
		<tr>
			<td>Heating and Nitrogen module</td>
			<td>Thermo Scientific</td>
			<td>TS-18822</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>HiTrap Heparin HP (5 mL)</td>
			<td>GE Healthcare</td>
			<td>17-0407-03</td>
			<td>Purification</td>
		</tr>
		<tr>
			<td>Isopropyl &#946;-D-1-thiogalactopyranoside&#160;</td>
			<td>Fisher Scientific</td>
			<td>BP1755</td>
			<td>Expression</td>
		</tr>
		<tr>
			<td>J-25 Centrifuge</td>
			<td>Beckman Coulter</td>
			<td>J325-IM-2</td>
			<td>Expression</td>
		</tr>
		<tr>
			<td>JA-14 Rotor</td>
			<td>Beckman Coulter</td>
			<td>339247</td>
			<td>Expression</td>
		</tr>
		<tr>
			<td>Lyophilizer</td>
			<td>Labconco</td>
			<td>7755030</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Fisher Scientific</td>
			<td>A452-4</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>Nitrogen gas</td>
			<td>Praxair</td>
			<td>UN1066</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>NZCYM media</td>
			<td>RPI Research Products</td>
			<td>N7200-1000.0</td>
			<td>Expansion &#38; Expression</td>
		</tr>
		<tr>
			<td>Pet-22B vector</td>
			<td>GenScript</td>
			<td>N/A</td>
			<td>Transformation</td>
		</tr>
		<tr>
			<td>Petri dish</td>
			<td>Fisher Scientific</td>
			<td>FB0875718</td>
			<td>Transformation &#38; Expansion</td>
		</tr>
		<tr>
			<td>Quartz Cuvettes</td>
			<td>Fisher Brand</td>
			<td>14385 928A</td>
			<td>Spectral Analysis</td>
		</tr>
		<tr>
			<td>Shaking Incubator</td>
			<td>New Brunswick Scientific</td>
			<td>M1344-0004</td>
			<td>Transformation, Expansion, &#38; Expression</td>
		</tr>
		<tr>
			<td>Slide-A-Lyzer Buoys</td>
			<td>Thermo Scientific</td>
			<td>66430</td>
			<td>Purification</td>
		</tr>
		<tr>
			<td>SnakeSkin Dialysis Tubing</td>
			<td>Thermo Scientific</td>
			<td>68100</td>
			<td>Purification</td>
		</tr>
		<tr>
			<td>SnakeSkin Dialysis Tubing</td>
			<td>Thermo Scientific</td>
			<td>88243</td>
			<td>Purification</td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>Fisher Scientific</td>
			<td>S271</td>
			<td>Purification</td>
		</tr>
		<tr>
			<td>Sodium Phosphate dibasic</td>
			<td>Fisher Scientific</td>
			<td>S374-500</td>
			<td>Purification</td>
		</tr>
		<tr>
			<td>Sodium Phosphate monobasic</td>
			<td>Fisher Scientific</td>
			<td>BP329-500</td>
			<td>Purification</td>
		</tr>
		<tr>
			<td>Spectra/POR Weighted Closures</td>
			<td>Spectrum Medical Industries</td>
			<td>132736</td>
			<td>Purification</td>
		</tr>
		<tr>
			<td>Spectrophotometer</td>
			<td>Shimadzu UV-1800</td>
			<td>220-92961-01</td>
			<td>spectral analysis</td>
		</tr>
		<tr>
			<td>Tabletop Centrifuge</td>
			<td>Beckman Coulter</td>
			<td>366816</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>UVProbe 2.61 (Software)</td>
			<td>Shimadzu</td>
			<td>N/A</td>
			<td>Spectral Analysis</td>
		</tr>
		<tr>
			<td>Vacuum filter</td>
			<td>Millipore</td>
			<td>9004-70-0</td>
			<td>Expression &#38; Purification</td>
		</tr>
		<tr>
			<td>Vacuum pump</td>
			<td>GAST Manufacturing Inc</td>
			<td>DOA-P704-AA</td>
			<td>Expression &#38; Purification</td>
		</tr>
		<tr>
			<td>Vortex</td>
			<td>Fisher Scientific</td>
			<td>12-812</td>
			<td>ND Formulation</td>
		</tr>
		<tr>
			<td>Yeast</td>
			<td>N/A</td>
			<td>BY4741</td>
			<td>Yeast Viability Assay</td>
		</tr>
		<tr>
			<td>Yeast Extract-Peptone-Dextrose</td>
			<td>BD</td>
			<td>242820</td>
			<td>Yeast Viability Assay</td>
		</tr>
	</tbody>
</table>

formulation and characterization of bioactive agent containing nanodisks

The term nanodisk refers to a discrete type of nanoparticle comprised of a bilayer forming lipid, a scaffold protein, and an integrated bioactive agent. Nanodisks are organized as a disk-shaped lipid bilayer whose perimeter is circumscribed by the scaffold protein, usually a member of the exchangeable apolipoprotein family. Numerous hydrophobic bioactive agents have been efficiently solubilized in nanodisks by their integration into the hydrophobic milieu of the particle&#39;s lipid bilayer, yielding a largely homogenous population of particles in the range of 10-20 nm in diameter. The formulation of nanodisks requires a precise ratio of individual components, an appropriate sequential addition of each component, followed by bath sonication of the formulation mixture. The amphipathic scaffold protein spontaneously contacts and reorganizes the dispersed bilayer forming lipid/bioactive agent mixture to form a discrete, homogeneous population of nanodisk&#160;particles. During this process, the reaction mixture transitions from an opaque, turbid appearance to a clarified sample that, when fully optimized, yields no precipitate upon centrifugation. Characterization studies involve the determination of bioactive agent solubilization efficiency, electron microscopy, gel filtration chromatography, ultraviolet visible (UV/Vis) absorbance spectroscopy, and/or fluorescence spectroscopy. This is normally followed by an investigation of biological activity using cultured cells or mice. In the case of nanodisks harboring an antibiotic (i.e., the macrolide polyene antibiotic amphotericin B), their ability to inhibit the growth of yeast or fungi as a function of concentration or time can be measured. The relative ease of formulation, versatility with respect to component parts, nanoscale particle size, inherent stability, and aqueous solubility permits myriad in vitro and in vivo applications of nanodisk technology. In the present article, we describe a general methodology to formulate and characterize nanodisks containing amphotericin&#160;B as the hydrophobic bioactive agent.

Bioactive agent nanodisk formulation process 
In the ampB-nanodisk formulation procedure described, the reaction is considered complete when the sample appearance transitions from turbid to clear (Figure 1). This change indicates that nanodisks have formed and that the bioactive agent has been solubilized. Oftentimes, bioactive agents absorb light in the visible wavelength region (e.g., ampB, curcumin, lutein, coenzyme Q10) and, in these cases, the sample ado...

Watch this Scientific Journal Video about Formulation and Characterization of Bioactive Agent Containing Nanodisks at JoVE.com

Formulation and Characterization of Bioactive Agent Containing Nanodisks

Here, we describe the production and characterization of bioactive agents containing nanodisks. Amphotericin B nanodisks are taken as an example to describe the protocol in a stepwise manner.

The term nanodisk refers to a discrete type of nanoparticle comprised of a bilayer forming lipid, a scaffold protein, and an integrated bioactive agent. ...

This protocol provides practical knowledge, useful for formulating nanoscale particles, i.e. nanodisks, that stably incorporate a wide range of hydrophobic bioactive molecules. This method has many practical applications.The ability to confer aqueous solubility to otherwise insoluble bioactive compounds permits the use of nanodisks in drug delivery applications. The method described is straightforward. It is preferred to conduct studies at the scale described, five milligrams phospholipid, two milligrams scaffold protein, so that the formation of nanodisks is readily monitored by visual inspection.Demonstrating the procedure will be Michael Karo and Matthew Swackhammer, undergraduate student researchers in the Ryan lab. To prepare a phospholipid aliquot, weigh five milligrams of DMPC and transfer it to a glass test tube. Dissolve the phospholipid by adding 300 microliters of chloroform and 100 microliters of methanol for a ratio of three to one.Evaporate the organic solvent by placing the glass test tube under a gentle stream of nitrogen gas for 10 to 15 minutes, such that a thin film of dried phospholipid forms along the walls of the bottom portion of the tube. To formulate amphotericin B or AmpB-Nanodisks, pipette 450 microliters of PBS to the lyophilized phospholipid aliquot, and vortex for 30 seconds to disperse the lipid. Pipette 50 microliters of 20 milligrams per milliliter stock AmpB solution into the dispersed phospholipid sample and vortex.Add 500 microliters of four milligrams per milliliter ApoE4 NT scaffold protein to the glass test tube containing the dispersed phospholipid and AmpB. Bath sonicate the sample at 24 degrees Celsius until the solution clarifies. For AmpB-Nanodisk dialysis, prepare a section of dialysis tubing by thoroughly soaking it in distilled deionized water for 10 minutes.Using a dialysis tubing clamp, clamp one end of the soaked dialysis tubing, ensuring no liquid can escape. Insert a narrow neck funnel into the open end of the dialysis tubing and transfer the AmpB-Nanodisk sample into the dialysis tubing. Remove the funnel, and clamp the end of the dialysis tubing with another dialysis tube clamp.Place a foam dialysis float onto one of the sealed ends of the dialysis tubing, and place the assembled dialysis tubing into the beaker containing freshly prepared one liter PBS buffer. Place a magnetic stir bar into the bottom of the beaker and adjust the stirring control to low, ensuring not to produce a vortex. Allow dialysis to continue overnight at four degrees Celsius.Turn on the spectrophotometer by flipping the power switch and connect to a corresponding support computer by pressing PC control. On the support computer, open the software labeled UVProbe 2.61, and connect to the spectrophotometer by clicking connect"in the bottom left corner. Click on the spectrum, then click method"in the top toolbar.Click on the measurement tab and input 500 into the start"text box located under wavelength range, and 300 into the end"text box. Click the dropdown menu next to the tab labeled scan speed"and set it to medium. Prepare a sample blank by transferring one milliliter of DMSO into two quartz cuvettes.Load both cuvettes into the respective sample ports of the spectrophotometer. Click auto blank"and record a spectrum from 300 to 500 nanometers by clicking start"in the bottom left corner. For AmpB standard spectral analysis, remove the cuvette from the front sample port and add 20 microliters of one milligram per milliliter AmpB stock solution.Load the cuvette back into the sample board and click start"to record the sample absorbance. After recording sample absorbance, remove the cuvette and decant the liquid contents into a waste container. Thoroughly rinse the cuvette with three washes of deionized water, followed by three washes with 70%ethanol.For spectral analysis of disrupted AmpB-Nanodisk, prepare the sample by pipetting 20 microliters of one milligram per milliliter AmpB-Nanodisk stock into one milliliter of DMSO, and incubate for one minute before recording the spectrum. Load the cuvette into the front sample port and click start"to record the sample absorbance. For spectral analysis of a PBS buffer blank, prepare a blank by transferring one milliliter of PBS into two quartz cuvettes.Load the cuvettes into the sample port. Click auto blank"and record the spectrum from 300 to 500 nanometers. For spectral analysis of a non-disrupted AmpB-Nanodisk sample, remove the cuvette from the front sample port and add 20 microliters of a one milligram per milliliter AmpB-Nanodisk sample into the PBS buffer.Load the cuvette back into the sample board. Click start"and record the sample spectrum. The AmpB-Nanodisk formulation reaction is considered complete when the sample appearance transitions from turbid to clear.UV visible absorption spectroscopy of AmpB samples in DMSO and PBS is shown. In DMSO, three distinctive absorbance maxima at 372, 392, and 415 nanometers, peaks indicative of AmpB, were observed. The absorbance spectra of AmpB-Nanodisks in PBS showed a single major absorbance peak at a shorter wavelength.In comparison, the absorbance spectra of AmpB-Nanodisks in DMSO appeared similar to the spectra of stock AmpB. Biological activity of AmpB-Nanodisks was performed by assessing yeast growth inhibition assays. Control samples like PBS, DMSO, and reconstituted high density lipoproteins demonstrated that nanodisks components other than AmpB have no discernible effect on yeast growth.The positive control confirmed that AmpB is an efficient inhibitor of yeast growth. In the case of AmpB-Nanodisks, concentration-dependent growth inhibition activity was observed. Not all nanodisk preparations are the same.Some may require more time, different lipids, or different scaffold proteins. They only indistinct}is the clarification of the nanodisk sample. This technique has led to novel nanoparticles used to study Doxorubicin-induced cardiotoxicity, apoptosis, ligand interactions, and delivered numerous aqueous insoluble bioactive molecules, including lutein and curcumin.

formulation-characterization-bioactive-agent-containing

Research

JoVE Journal

Biochemistry

Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins

Obtaining crystals for structure determination can be a difficult and time consuming proposition for any protein. Coiled-coil proteins and domains are found throughout nature, however, because of their physical properties and tendency to aggregate, they are traditionally viewed as being especially difficult to crystallize. Here, we utilize a variety of quick and simple techniques designed to identify a series of possible domain boundaries for a given coiled-coil protein, and then quickly characterize the behavior of these proteins in solution. With the addition of a strongly fluorescent tag (mRuby2), protein characterization is simple and straightforward. The target protein can be readily visualized under normal lighting and can be quantified with the use of an appropriate imager. The goal is to quickly identify candidates that can be removed from the crystallization pipeline because they are unlikely to succeed, affording more time for the best candidates and fewer funds expended on proteins that do not produce crystals. This process can be iterated to incorporate information gained from initial screening efforts, can be adapted for high-throughput expression and purification procedures, and is augmented by robotic screening for crystallization.

We describe a framework incorporating straightforward biochemical and computational analysis to guide the characterization and crystallization of large coiled-coil domains. This framework can be adapted for globular proteins or extended to incorporate a variety of high-throughput techniques.

Obtaining crystals for structure determination can be a difficult and time consuming proposition for any protein. Coiled-coil proteins and domains are ...

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Development of new antimicrobials and vaccines for Streptococcus pneumoniae (pneumococcus) are necessary to halt the rapid rise in multiple resistant strains. Carbohydrate substrate binding proteins (SBPs) represent viable targets for the development of protein-based vaccines and new antimicrobials because of their extracellular localization and the centrality of carbohydrate import for pneumococcal metabolism, respectively. Described here is a rationalized integrated protocol to carry out a comprehensive characterization of SP0092, which can be extended to other carbohydrate SBPs from the pneumococcus and other bacteria. This procedure can aid the structure-based design of inhibitors for this class of proteins. Presented in the first part of this manuscript are protocols for biochemical analysis by thermal shift assay, multi angle light scattering (MALS), and size exclusion chromatography (SEC), which optimize the stability and homogeneity of the sample directed to crystallization trials and so enhance the probability of success. The second part of this procedure describes the characterization of the SBP crystals using a tunable wavelength anomalous diffraction synchrotron beamline, and data collection protocols for measuring data that can be used to resolve the crystallized protein structure.

A streamlined protocol for performing an extensive biochemical and structural characterization of a carbohydrate substrate binding protein from Streptococcus pneumoniae is presented.

Development of new antimicrobials and vaccines for Streptococcus pneumoniae (pneumococcus) are necessary to halt the rapid rise in multiple resistant ...

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.

A protocol for the structural analysis of polysaccharides by gel electrophoresis (PACE), using mannan as an example, is described.

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts ...

Simultaneous Measurement of Superoxide/Hydrogen Peroxide and NADH Production by Flavin-containing Mitochondrial Dehydrogenases

It has been reported that mitochondria can contain up to 12 enzymatic sources of reactive oxygen species (ROS). A majority of these sites include flavin-dependent respiratory complexes and dehydrogenases that produce a mixture of superoxide (O2&#9679;-) and hydrogen peroxide (H2O2). Accurate quantification of the ROS-producing potential of individual sites in isolated mitochondria can be challenging due to the presence of antioxidant defense systems&#160;and side reactions that also form O2&#9679;-/H2O2. Use&#160;of nonspecific inhibitors that can disrupt mitochondrial bioenergetics can also compromise measurements by altering&#160;ROS release from other sites of production. Here, we present an easy method for the simultaneous measurement of H2O2 release and nicotinamide adenine dinucleotide (NADH) production by purified flavin-linked dehydrogenases. For our purposes here, we have used purified pyruvate dehydrogenase complex (PDHC) and &#945;-ketoglutarate dehydrogenase complex (KGDHC) of porcine heart origin as examples. This method allows for an accurate measure of native H2O2 release rates by individual sites of production by eliminating other potential sources of ROS and antioxidant systems. In addition, this method allows for a direct comparison of the relationship between H2O2 release and enzyme activity and the screening of the effectiveness and selectivity of inhibitors for ROS production. Overall, this approach can allow for the in-depth assessment of native rates of ROS release for individual enzymes prior to conducting more sophisticated experiments with isolated mitochondria or permeabilized muscle fiber.

Mitochondria contain several flavin-dependent enzymes that can produce reactive oxygen species (ROS). Monitoring ROS release from individual sites in mitochondria is challenging due to unwanted side reactions. We present an easy, inexpensive method for direct assessment of native rates for ROS release using purified flavoenzymes and microplate fluorometry.

It has been reported that mitochondria can contain up to 12 enzymatic sources of reactive oxygen species (ROS). A majority of these sites include ...

Functional Characterization of Carboxylesterases in Insecticide Resistant House Flies, Musca Domestica

Carboxylesterase-mediated metabolism is thought to play a major role in insecticide resistance in various insects. Several carboxylesterase genes were found up-regulated in the resistant house fly strain, whereas their roles in conferring insecticide resistance remained to be explored. Here, we designed a protocol for the functional characterization of carboxylesterases. Three example experiments are presented: (1) expression and isolation of carboxylesterase proteins through a baculovirus-mediated insect Spodoptera frugiperda (Sf9) cell expression system; (2) a cell-based MTT (3-[4, 5-dimethykthiazol-2-yl]-2, 5-diphenyltetrazolium bromide) cytotoxicity assay to measure the tolerance of insect cells to different permethrin treatments; and (3) in vitro metabolic studies to explore the metabolic capabilities of carboxylesterases toward permethrin. The carboxylesterase gene Md&#945;E7 was cloned from a resistant house fly strain ALHF and used to construct a recombinant baculovirus for Sf9 cells infection. The cell viabilities against different permethrin treatments were measured with the MTT assay. The enhanced cell tolerance of the experimental group (Md&#945;E7-recombinant baculovirus infected cells) compared with those of the control groups (CAT-recombinant baculovirus infected cells and GFP-recombinant baculovirus infected cells) to permethrin treatments suggested the capabilities of Md&#945;E7 in metabolizing insecticides, thereby protecting cells from chemical damages. Besides that, carboxylesterase proteins were expressed in insect Sf9 cells and isolated to conduct an in vitro metabolic study. Our results indicated a significant in vitro metabolic efficiency of Md&#945;E7 toward permethrin, directly indicating the involvement of carboxylesterases in metabolizing insecticides and thus conferring insecticide resistance in house flies.

Functional Characterization of Carboxylesterases in Insecticide Resistant House Flies, Musca Domestica

Here, we present a protocol to produce house fly carboxylesterase proteins in vitro with a baculovirus mediated insect cell expression system and later functionally characterize their roles in metabolizing permethrin, thereby, conferring pyrethroid resistance by conducting cell-based MTT assay and in vitro metabolic studies.

Carboxylesterase-mediated metabolism is thought to play a major role in insecticide resistance in various insects. Several carboxylesterase genes were ...

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

High-brilliance X-ray beams coupled with automation have&#160;led to the use of synchrotron-based macromolecular X-ray crystallography (MX) beamlines for even the most challenging projects in structural biology. However, most facilities still require the presence of a scientist on site to perform the experiments. A new generation of automated beamlines dedicated to the fully automatic characterization of, and data collection from, crystals of biological macromolecules has recently been developed. These beamlines represent a new tool for structural biologists to screen the results of initial crystallization trials and/or the collection of large numbers of diffraction data sets, without users having to control the beamline themselves. Here we show how to set up an experiment for automatic screening and data collection, how an experiment is performed at the beamline, how the resulting data sets are processed, and how, when possible, the crystal structure of the biological macromolecule is solved.

Here, we describe how to use the automated screening and data collection options available at some synchrotron beamlines. Scientists send cryocooled samples to the synchrotron, and the diffraction properties are screened, the data sets are collected and processed and, where possible, a structure solution is carried out&#8212;all without human intervention.

High-brilliance X-ray beams coupled with automation have&#160;led to the use of synchrotron-based macromolecular X-ray crystallography (MX) beamlines for ...

Expression, Purification, Crystallization, and Enzyme Assays of Fumarylacetoacetate Hydrolase Domain-Containing Proteins

Fumarylacetoacetate hydrolase (FAH) domain-containing proteins (FAHD) are identified members of the FAH superfamily in eukaryotes. Enzymes of this superfamily generally display multi-functionality, involving mainly hydrolase and decarboxylase mechanisms. This article presents a series of consecutive methods for the expression and purification of FAHD proteins, mainly FAHD protein 1 (FAHD1) orthologues among species (human, mouse, nematodes, plants, etc.). Covered methods are protein expression in E. coli, affinity chromatography, ion exchange chromatography, preparative and analytical gel filtration, crystallization, X-ray diffraction, and photometric assays. Concentrated protein of high levels of purity (&#62;98%) may be employed for crystallization or antibody production. Proteins of similar or lower quality may be employed in enzyme assays or used as antigens in detection systems (Western-Blot, ELISA). In the discussion of this work, the identified enzymatic mechanisms of FAHD1 are outlined to describe its hydrolase and decarboxylase bi-functionality in more detail.

Expression and purification of fumarylacetoacetate hydrolase domain-containing proteins is described with examples (expression in E. coli, FPLC). Purified proteins are used for crystallization and antibody production and employed for enzyme assays. Selected photometric assays are presented to display the multi-functionality of FAHD1 as oxaloacetate decarboxylase and acylpyruvate hydrolase.

Fumarylacetoacetate hydrolase (FAH) domain-containing proteins (FAHD) are identified members of the FAH superfamily in eukaryotes. Enzymes of this ...

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

In addition to linear mRNAs, many eukaryotic genes generate circular RNAs. Most circular RNAs are generated by joining a 5&#39; splice site with an upstream 3&#39; splice site within a pre-mRNA, a process called back-splicing. This circularization is likely aided by secondary structures in the pre-mRNA that bring the splice sites into close proximity. In human genes, Alu elements are thought to promote these secondary RNA structures, as Alu elements are abundant and exhibit base complementarities with each other when present in opposite directions in the pre-mRNA. Here, we describe the generation and analysis of large, Alu element containing reporter genes that form circular RNAs. Through optimization of cloning protocols, reporter genes with up to 20 kb insert length can be generated. Their analysis in co-transfection experiments allows the identification of regulatory factors. Thus, this method can identify RNA sequences and cellular components involved in circular RNA formation.

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

We clone and analyze reporter genes generating circular RNAs. These reporter genes are larger than constructs to analyze linear splicing and contain Alu elements. To investigate the circular RNAs, the constructs are transfected into cells and resulting RNA is analyzed using RT-PCR after removal of linear RNA.

In addition to linear mRNAs, many eukaryotic genes generate circular RNAs. Most circular RNAs are generated by joining a 5&#39; splice site with an ...

Quantification of Humic and Fulvic Acids in Humate Ores, DOC, Humified Materials and Humic Substance-Containing Commercial Products

The purpose of this method is to provide an accurate and precise concentration of humic (HA) and/or fulvic acids (FA) in soft coals, humic ores and shales, peats, composts and humic substance-containing commercial products. The method is based on the alkaline extraction of test materials, using 0.1 N NaOH as an extractant, and separation of the alkaline soluble humic substances (HS) from nonsoluble products by centrifugation. The pH of the centrifuged alkaline extract is then adjusted to pH 1 with conc. HCl, which results in precipitation of the HA. The precipitated HA are separated from the fulvic fraction (FF) (the fraction of HS that remains in solution,) by centrifugation. The HA is then oven or freeze dried and the ash content of the dried HA determined. The weight of the pure (i.e., ash-free) HA is then divided by the weight of the sample and the resulting fraction multiplied by 100 to determine the % HA in the sample. To determine the FA content, the FF is loaded onto a hydrophobic DAX-8 resin, which adsorbs the FA fraction also referred to as the hydrophobic fulvic acid (HFA). The remaining non-fulvic acid fraction, also called the hydrophilic fulvic fraction (HyFF) is then removed by washing the resin with deionized H2O until all nonabsorbed material is completely removed. The FA is then desorbed with 0.1 N NaOH. The resulting Na-fulvate is then protonated by passing it over a strong H+-exchange resin. The resulting FA is oven or freeze dried, the ash content determined and the concentration in the sample calculated as described above for HA.

This method provides a gravimetric quantification of humic substances (e.g., humic and fulvic acids) on an ash-free basis, in dry and liquid materials from soft coals (i.e., oxidized and non-oxidized lignite and sub-bituminous coal), humate ores and shales, peats, composts and commercial fertilizers and soil amendments.

The purpose of this method is to provide an accurate and precise concentration of humic (HA) and/or fulvic acids (FA) in soft coals, humic ores and ...

In Vitro Characterization of Histone Chaperones using Analytical, Pull-Down and Chaperoning Assays

Histone proteins associate with DNA to form the eukaryotic chromatin. The basic unit of chromatin is a nucleosome, made up of a histone octamer consisting of two copies of the core histones H2A, H2B, H3, and H4, wrapped around by the DNA. The octamer is composed of two copies of an H2A/H2B dimer and a single copy of an H3/H4 tetramer. The highly charged core histones are prone to non-specific interactions with several proteins in the cellular cytoplasm and the nucleus. Histone chaperones form a diverse class of proteins that shuttle histones from the cytoplasm into the nucleus and aid their deposition onto the DNA, thus assisting the nucleosome assembly process. Some histone chaperones are specific for either H2A/H2B or H3/H4, and some function as chaperones for both. This protocol describes how in vitro laboratory techniques such as pull-down assays, analytical size-exclusion chromatography, analytical ultra-centrifugation, and histone chaperoning assay could be used in tandem to confirm whether a given protein is functional as a histone chaperone.

In Vitro Characterization of Histone Chaperones using Analytical, Pull-Down and Chaperoning Assays

This protocol describes a battery of methods that includes analytical size-exclusion chromatography to study histone chaperone oligomerization and stability, pull-down assay to unravel histone chaperone-histone interactions, AUC to analyze the stoichiometry of the protein complexes, and histone chaperoning assay to functionally characterize a putative histone chaperone in vitro.

Histone proteins associate with DNA to form the eukaryotic chromatin. The basic unit of chromatin is a nucleosome, made up of a histone octamer consisting ...