Name: a high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease pcsk9
Uploaded: 2018-08-28T15:00:00
Description: Watch this Scientific Journal Video about A High-Throughput Luciferase Assay to Evaluate Proteolysis of the Single-Turnover Protease PCSK9 at JoVE.com

The authors thank the generous funding support from the NHLBI/NIH (K08 HL124068 and LRP HMOT1243), NCATS/NIH through the UCSF Clinical and Translational Science Institute Catalyst Program (UL1 TR000004), the UCSF Academic Senate, the Hellman Foundation, a Gilead Sciences Research Scholar Award, a Pfizer ASPIRE Cardiovascular Award (all to John S. Chorba) and the Howard Hughes Medical Institute (to Adri M. Galvan and Kevan M. Shokat).

1. Site-directed Mutagenesis of Protease Vector
<ol>
	<li>Design and order custom-synthesized oligonucleotides to install a mutation of interest using a modification of standard site-directed mutagenesis protocols12. Standard desalted primers (without additional purification) are perfectly acceptable. 
	Note: A general approach to primer designs involves creating partially overlapping primers as indicated in Table 1, using a melting temperature (Tm) calculator sp...

<ol>
	<li>Park, S. W., Moon, Y. A., Horton, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Post-transcriptional+regulation+of+low+density+lipoprotein+receptor+protein+by+proprotein+convertase+subtilisin/kexin+type+9a+in+mouse+liver.">Post-transcriptional regulation of low density lipoprotein receptor protein by proprotein convertase subtilisin/kexin type 9a in mouse liver.</a> Journal of Biological Chemistry. 279 (48), 50630-50638 (2004).</li><li>Cohen, J. C., Boerwinkle, E., Mosley, T. H., Hobbs, H. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sequence+variations+in+PCSK9,+low+LDL,+and+protection+against+coronary+heart+disease.">Sequence variations in PCSK9, low LDL, and protection against coronary heart disease.</a> New England Journal of Medicine. 354 (12), 1264-1272 (2006).</li><li>Ridker, P. 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=Cardiovascular+Efficacy+and+Safety+of+Bococizumab+in+High-Risk+Patients.">Cardiovascular Efficacy and Safety of Bococizumab in High-Risk Patients.</a> New England Journal of Medicine. 376 (16), 1527-1539 (2017).</li><li>Sabatine, M. 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=Evolocumab+and+Clinical+Outcomes+in+Patients+with+Cardiovascular+Disease.">Evolocumab and Clinical Outcomes in Patients with Cardiovascular Disease.</a> New England Journal of Medicine. 376 (18), 1713-1722 (2017).</li><li>Kazi, D. 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=Cost-effectiveness+of+PCSK9+Inhibitor+Therapy+in+Patients+With+Heterozygous+Familial+Hypercholesterolemia+or+Atherosclerotic+Cardiovascular+Disease.">Cost-effectiveness of PCSK9 Inhibitor Therapy in Patients With Heterozygous Familial Hypercholesterolemia or Atherosclerotic Cardiovascular Disease.</a> Journal of the American Medical Association. 316 (7), 743-753 (2016).</li><li>Kazi, D. 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=Updated+Cost-effectiveness+Analysis+of+PCSK9+Inhibitors+Based+on+the+Results+of+the+FOURIER+Trial.">Updated Cost-effectiveness Analysis of PCSK9 Inhibitors Based on the Results of the FOURIER Trial.</a> Journal of the American Medical Association. 318 (8), (2017).</li><li>Pettersen, D., Fjellstr&#246;m, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+molecule+modulators+of+PCSK9+-+A+literature+and+patent+overview.">Small molecule modulators of PCSK9 - A literature and patent overview.</a> Bioorganic &amp; Medicinal Chemistry Letters. 28 (7), 1155-1160 (2018).</li><li>Chorba, J. S., Galvan, A. M., Shokat, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stepwise+processing+analyses+of+the+single-turnover+PCSK9+protease+reveal+its+substrate+sequence+specificity+and+link+clinical+genotype+to+lipid+phenotype.">Stepwise processing analyses of the single-turnover PCSK9 protease reveal its substrate sequence specificity and link clinical genotype to lipid phenotype.</a> Journal of Biological Chemistry. 293 (6), 1875-1886 (2018).</li><li>Maxwell, K. N., Breslow, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adenoviral-mediated+expression+of+Pcsk9+in+mice+results+in+a+low-density+lipoprotein+receptor+knockout+phenotype.">Adenoviral-mediated expression of Pcsk9 in mice results in a low-density lipoprotein receptor knockout phenotype.</a> Proceedings of the National Academy of Sciences of the United States of America. 101 (18), 7100-7105 (2004).</li><li>Benjannet, 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=NARC-1/PCSK9+and+its+natural+mutants:+zymogen+cleavage+and+effects+on+the+low+density+lipoprotein+(LDL)+receptor+and+LDL+cholesterol.">NARC-1/PCSK9 and its natural mutants: zymogen cleavage and effects on the low density lipoprotein (LDL) receptor and LDL cholesterol.</a> Journal of Biological Chemistry. 279 (47), 48865-48875 (2004).</li><li>Cunningham, 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=Structural+and+biophysical+studies+of+PCSK9+and+its+mutants+linked+to+familial+hypercholesterolemia.">Structural and biophysical studies of PCSK9 and its mutants linked to familial hypercholesterolemia.</a> Nature Structural &amp; Molecular Biology. 14 (5), 413-419 (2007).</li><li>Liu, H., Naismith, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+efficient+one-step+site-directed+deletion,+insertion,+single+and+multiple-site+plasmid+mutagenesis+protocol.">An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol.</a> BMC Biotechnology. 8, 91 (2008).</li><li>Zhang, J., Chung, T., Oldenburg, K. <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+Statistical+Parameter+for+Use+in+Evaluation+and+Validation+of+High+Throughput+Screening+Assays.">A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays.</a> Journal of Biomolecular Screening. 4 (2), 67-73 (1999).</li><li>Hall, M. 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=Engineered+luciferase+reporter+from+a+deep+sea+shrimp+utilizing+a+novel+imidazopyrazinone+substrate.">Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate.</a> ACS Chemical Biology. 7 (11), 1848-1857 (2012).</li><li>McNutt, M. C., Lagace, T. A., Horton, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Catalytic+activity+is+not+required+for+secreted+PCSK9+to+reduce+low+density+lipoprotein+receptors+in+HepG2+cells.">Catalytic activity is not required for secreted PCSK9 to reduce low density lipoprotein receptors in HepG2 cells.</a> Journal of Biological Chemistry. 282 (29), 20799-20803 (2007).</li><li>Chorba, J. S., Shokat, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+proprotein+convertase+subtilisin/kexin+type+9+(PCSK9)+active+site+and+cleavage+sequence+differentially+regulate+protein+secretion+from+proteolysis.">The proprotein convertase subtilisin/kexin type 9 (PCSK9) active site and cleavage sequence differentially regulate protein secretion from proteolysis.</a> Journal of Biological Chemistry. 289 (42), 29030-29043 (2014).</li><li>Benjannet, S., Rhainds, D., Hamelin, J., Nassoury, N., Seidah, N. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+proprotein+convertase+(PC)+PCSK9+is+inactivated+by+furin+and/or+PC5/6A:+functional+consequences+of+natural+mutations+and+post-translational+modifications.">The proprotein convertase (PC) PCSK9 is inactivated by furin and/or PC5/6A: functional consequences of natural mutations and post-translational modifications.</a> Journal of Biological Chemistry. 281 (41), 30561-30572 (2006).</li><li>Zhao, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+characterization+of+loss-of-function+mutations+in+PCSK9+and+identification+of+a+compound+heterozygote.">Molecular characterization of loss-of-function mutations in PCSK9 and identification of a compound heterozygote.</a> American Journal of Human Genetics. 79 (3), 514-523 (2006).</li></ol>

The experimental procedures described above present a method to overcome the intrinsically low activity of the single-turnover protease PCSK9 and evaluate its proteolytic function in a robust manner. The key concept of the assay relies upon converting a single-turnover event into an enzymatically amplified readout. The strengths of the assay include the relatively short time-frame and ease of use of the luciferase reporter, as well as its scalability to high-throughput approaches. In addition, the assay evaluates proteol...

PCSK9 targets the LDL receptor (LDL-R) for degradation, raising LDL cholesterol (LDL-C) and driving atherosclerotic heart disease1,2. Therapeutics targeting PCSK9 robustly lower LDL-C and improve cardiovascular outcomes for patients, even when added to an aggressive lipid-lowering therapy with statins3,4. Currently approved therapies are limited to antibody-based approaches, however, and suffer from a lack of cost-effectiveness5,6. To solve this problem, less costly therapeutic alternatives, a means to identify patients likely to gain greater benefits, or both, are needed.
Small-molecule approaches could target intracellular PCSK9, provide an improved route of administration, and reduce costs, making them the &#34;Holy Grail&#34; in this area7. However, PCSK9 has proven difficult to drug by small molecules. As a protease, targeting PCSK9&#39;s proteolytic function is an attractive strategy, as self-proteolysis is the rate-limiting step of PCSK9 maturation8 and is required for its maximal effect on the LDL-R9. To date, however, this strategy has not been successful, likely due to PCSK9&#39;s unique biochemistry: PCSK9 cleaves only itself10, performing a single-turnover reaction, and after self-cleavage, the PCSK9 prodomain remains bound in the active site as an auto-inhibitor11, preventing the readout of any further protease activity.
This article presents a method to evaluate PCSK9 proteolytic function in high-throughput fashion8. Through site-directed mutagenesis, investigators can use this assay to probe the effects of coding SNPs found in the clinic to assess them for effects on proteolysis, the rate-limiting step of PCSK9 maturation. Additionally, this method will be useful in the design of high-throughput screens to identify modulators of PCSK9 proteolysis, which are anticipated to ultimately disrupt the presentation of PCSK9 to the LDL-R (and modulate PCSK9&#39;s hypercholesterolemic effect). Lastly, this protocol can be adapted to other proteases with intrinsically low activity, provided that i) a specific substrate-protease pair can be found, and ii) a suitable intracellular anchor can be established for the substrate.

<table>
	<tbody>
		<tr>
			<td>PCR Tubes</td>
			<td>USA Scientific</td>
			<td>1402-2900</td>
			<td>For PCR</td>
		</tr>
		<tr>
			<td>Q5 Hot Start</td>
			<td>New England Biolabs</td>
			<td>M0493L</td>
			<td>High-fidelity DNA Polymerase</td>
		</tr>
		<tr>
			<td>Deoxynucleotide Solution Mix</td>
			<td>New England Biolabs</td>
			<td>N0447L</td>
			<td>dNTPs (for PCR)</td>
		</tr>
		<tr>
			<td>pPCSK9-NLucProteaseAssay-WT</td>
			<td>Authors</td>
			<td>n/a</td>
			<td>Available from authors</td>
		</tr>
		<tr>
			<td>pPCSK9-NLucProteaseAssay-S386A</td>
			<td>Authors</td>
			<td>n/a</td>
			<td>Available from authors</td>
		</tr>
		<tr>
			<td>Agarose LE</td>
			<td>Gold Biotechnology</td>
			<td>A-201-100</td>
			<td>For DNA gels</td>
		</tr>
		<tr>
			<td>E-Gel Imager System with Blue Light Base</td>
			<td>ThermoFisher Scientific</td>
			<td>4466612</td>
			<td>For imaging DNA gels</td>
		</tr>
		<tr>
			<td>SYBR Safe DNA Gel Stain</td>
			<td>ThermoFisher Scientific</td>
			<td>S33102</td>
			<td>For DNA gels</td>
		</tr>
		<tr>
			<td>Tris Base</td>
			<td>ThermoFisher Scientific</td>
			<td>BP152-1</td>
			<td>For DNA gel running buffer</td>
		</tr>
		<tr>
			<td>Glacial acetic acid</td>
			<td>ThermoFisher Scientific</td>
			<td>A38-500</td>
			<td>For DNA gel running buffer</td>
		</tr>
		<tr>
			<td>Ethylenediaminetetraacetic acid solution</td>
			<td>Millipore Sigma</td>
			<td>3690</td>
			<td>EDTA, for DNA gel running buffer</td>
		</tr>
		<tr>
			<td>1 kb DNA ladder</td>
			<td>Gold Biotechnology</td>
			<td>D010</td>
			<td>DNA ladder</td>
		</tr>
		<tr>
			<td>DpnI</td>
			<td>New England Biolabs</td>
			<td>R0176S</td>
			<td>Restriction enzyme</td>
		</tr>
		<tr>
			<td>LB Agar plates with 100 &#181;g/mL carbenicillin</td>
			<td>Teknova</td>
			<td>L1010</td>
			<td>LB-Carb plates</td>
		</tr>
		<tr>
			<td>One Shot Mach1 T Phage-Resistent Chemically Competent E. coli</td>
			<td>ThermoFisher Scientific</td>
			<td>C862003</td>
			<td>Chemically competent cells</td>
		</tr>
		<tr>
			<td>LB Broth, Miller</td>
			<td>ThermoFisher Scientific</td>
			<td>BP1426-2</td>
			<td>LB</td>
		</tr>
		<tr>
			<td>Carbenicillin</td>
			<td>Gold Biotechnology</td>
			<td>C-103-5</td>
			<td>Selective antibiotic</td>
		</tr>
		<tr>
			<td>E.Z.N.A. Plasmid Mini Kit I</td>
			<td>Omega BioTek</td>
			<td>D6942-02</td>
			<td>DNA Purification Miniprep kit</td>
		</tr>
		<tr>
			<td>NanoDrop 2000 Spectrophotomer</td>
			<td>ThermoFisher Scientific</td>
			<td>ND-2000C</td>
			<td>Spectrophotometer</td>
		</tr>
		<tr>
			<td>293T Cells</td>
			<td>American Tissue Culture Collection (ATCC)</td>
			<td>CRL-3216</td>
			<td>HEK 293T cells</td>
		</tr>
		<tr>
			<td>DMEM, high glucose, pyruvate</td>
			<td>ThermoFisher Scientific</td>
			<td>11995065</td>
			<td>DMEM, mammalian cell media</td>
		</tr>
		<tr>
			<td>Fetal Bovine Sera</td>
			<td>Axenia Biologix</td>
			<td>F001</td>
			<td>FBS</td>
		</tr>
		<tr>
			<td>Trypsin-EDTA (0.05%), phenol red</td>
			<td>ThermoFisher Scientific</td>
			<td>25300062</td>
			<td>Trypsin, for cell dissociation</td>
		</tr>
		<tr>
			<td>Phosphate buffered saline (PBS)</td>
			<td>ThermoFisher Scientific</td>
			<td>10010023</td>
			<td>PBS</td>
		</tr>
		<tr>
			<td>Countess automated cell counter</td>
			<td>ThermoFisher Scientific</td>
			<td>C10227</td>
			<td>Automated cell counting</td>
		</tr>
		<tr>
			<td>Countess cell counting chamber slides</td>
			<td>ThermoFisher Scientific</td>
			<td>C10228</td>
			<td>Slides for cell counting</td>
		</tr>
		<tr>
			<td>CELLSTAR Tissue Culture Plates, White, White-Bottom, with Lid</td>
			<td>Grenier Bio-One</td>
			<td>655083</td>
			<td>White, white-bottom 96 well plate</td>
		</tr>
		<tr>
			<td>TempPlate non-skirted 96-well PCR plate, natural</td>
			<td>USA Scientific</td>
			<td>1402-9596</td>
			<td>96 well plate for master plasmid plate</td>
		</tr>
		<tr>
			<td>Nunc 2.0mL DeepWell Plates</td>
			<td>ThermoFisher Scientific</td>
			<td>278743</td>
			<td>96 well deep well plate</td>
		</tr>
		<tr>
			<td>Lipofectamine 3000</td>
			<td>ThermoFisher Scientific</td>
			<td>L3000008</td>
			<td>Lipid transfection reagent, Lf3K</td>
		</tr>
		<tr>
			<td>P3000 Reagent</td>
			<td>ThermoFisher Scientific</td>
			<td>L3000008</td>
			<td>DNA pre-complexation reagent, provided with Lf3K</td>
		</tr>
		<tr>
			<td>OptiMEM I Reduced Serum Medium</td>
			<td>ThermoFisher Scientific</td>
			<td>31985062</td>
			<td>Reduced serum medium for transfection</td>
		</tr>
		<tr>
			<td>(+)-Sodium L-ascorbate</td>
			<td>Millipore Sigma</td>
			<td>A4034</td>
			<td>Sodium ascorbate</td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Millipore Sigma</td>
			<td>S9888</td>
			<td>NaCl</td>
		</tr>
		<tr>
			<td>Albumin, Bovine Serum, Fraction V, Low Heavy Metals</td>
			<td>Millipore Sigma</td>
			<td>12659</td>
			<td>BSA</td>
		</tr>
		<tr>
			<td>Methanol (HPLC)</td>
			<td>ThermoFisher Scientific</td>
			<td>A4524</td>
			<td>MeOH</td>
		</tr>
		<tr>
			<td>Hydrochloric acid</td>
			<td>VWR</td>
			<td>JT9535-2</td>
			<td>Concentrated HCl</td>
		</tr>
		<tr>
			<td>Coelenterazine</td>
			<td>Gold Biotechnology</td>
			<td>CZ2.5</td>
			<td>Luciferase substrate</td>
		</tr>
		<tr>
			<td>Syringe Filter, Sterile</td>
			<td>ThermoFisher Scientific</td>
			<td>09-720-3</td>
			<td>Sterile filter, PVDF, 0.22 &#181;m pore</td>
		</tr>
		<tr>
			<td>Pipet-Lite Multi Pipette L12-200XLS+</td>
			<td>Rainin</td>
			<td>17013810</td>
			<td>Multichannel pipette</td>
		</tr>
		<tr>
			<td>Pipet-Lite Multi Pipette L12-20XLS+</td>
			<td>Rainin</td>
			<td>17013808</td>
			<td>Multichannel pipette</td>
		</tr>
		<tr>
			<td>Pipet-Lite Multi Pipette L12-10XLS+</td>
			<td>Rainin</td>
			<td>17013807</td>
			<td>Multichannel pipette</td>
		</tr>
		<tr>
			<td>Reagent reservoir</td>
			<td>Corning</td>
			<td>4870</td>
			<td>Trough for reagents</td>
		</tr>
		<tr>
			<td>Centrifuge tubes, 15 mL</td>
			<td>ThermoFisher Scientific</td>
			<td>05-539-12</td>
			<td>15 mL tubes</td>
		</tr>
		<tr>
			<td>Centrifuge tubes, 50 mL</td>
			<td>Corning</td>
			<td>430829</td>
			<td>50 mL tubes</td>
		</tr>
		<tr>
			<td>Spark Microplate Reader</td>
			<td>Tecan</td>
			<td>N/a</td>
			<td>Plate Reader</td>
		</tr>
		<tr>
			<td>Excel</td>
			<td>Microsoft</td>
			<td>2016 for Mac</td>
			<td>Spreadsheet software</td>
		</tr>
		<tr>
			<td>Prism</td>
			<td>GraphPad Software</td>
			<td>v7</td>
			<td>Scientific data analysis software</td>
		</tr>
	</tbody>
</table>

a high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease pcsk9

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a single-turnover protease which regulates serum low-density lipoprotein (LDL) levels and, consequently, cardiovascular disease. Although PCSK9 proteolysis is required for its full hypercholesterolemic effect, the evaluation of its proteolytic function is challenging: PCSK9 is only known to cleave itself, undergoes only a single turnover, and after proteolysis, retains its substrate in its active site as an auto-inhibitor. The methods presented here describe an assay which overcomes these challenges. The assay focuses on intermolecular proteolysis in a cell-based context and links successful cleavage to the secreted luciferase activity, which can be easily read out in the conditioned medium. Via sequential steps of mutagenesis, transient transfection, and a luciferase readout, the assay can probe PCSK9 proteolysis under conditions of either genetic or molecular perturbation in a high-throughput manner. This system is well suited for both the biochemical evaluation of clinically discovered missense single-nucleotide polymorphisms (SNPs), as well as for the screening of small-molecule inhibitors of PCSK9 proteolysis.

The high-throughput proteolysis assay relies upon overcoming three major challenges. First, to overcome the intrinsically low output of a single-turnover PCSK9 protease, a PCSK9 protease lacking the inhibitory prodomain is used, with the cleavage sequence at the tail of the prodomain linked to a luciferase that can be secreted14. Second, to satisfy the need for the protease to fold in complex with its inhibitory prodomain, the two polypeptides are coexpressed i...

Watch this Scientific Journal Video about A High-Throughput Luciferase Assay to Evaluate Proteolysis of the Single-Turnover Protease PCSK9 at JoVE.com

A High-Throughput Luciferase Assay to Evaluate Proteolysis of the Single-Turnover Protease PCSK9

This protocol presents a method to evaluate the proteolytic activity of an intrinsically low-activity, single turnover protease in a cellular context. Specifically, this method is applied to evaluate the proteolytic activity of PCSK9, a key driver of lipid metabolism whose proteolytic activity is required for its ultimate hypercholesterolemic function.

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a single-turnover protease which regulates serum low-density lipoprotein (LDL) levels and, ...

This method can help answer key questions in the PCSK9 Biochemistry Field such as which drugs or genetic changes affect PCSK9's Proteolytic Function. The main advantage of this technique is that it allows a rapid and amplifiable readout of an intrinsically low frequency biochemical event. The implications of this technique extend towards Atherosclerotic Heart Disease because PCSK9 Proteolytic Function is required for its ultimate effect on Serum cholesterol levels.Though this method can provide insight into PCSK9 itself, it can also be applied to other biochemical systems such as other Proteases with intrinsically low Proteolytic activity. To begin, aspirate Medium from each HEK293 T cells. Wash with PBS, and treat with the minimal volume of 0.5%Trypsin-EDTA.And incubate at 37 degrees Celsius for two to five minutes to dissociate the cells from the parent flask. Add two volumes of DMEM supplemented with 10%FBS to inactivate the Trypsin-EDTA. Then pipette the liquid in the flask up and down several times, dislodging the adherent cells and transfer the cells to a sterile tube.Next, remove a small aliquot of cells. Stain with an equal volume of Trypan Blue and transfer the stained cells to a slide, and use an automated cell counter to count the cells. Centrifuge the tube at 500 times G for five minutes to recover the cells.After this, aspirate the Medium and reconstitute the cells and Culture Medium to the desired concentration. Using a multi-channel pipette and a sterile trough, transfer 100 micrometers of the cells in each well to a white 96 Well Plate. Next, incubate the cells at 37 degrees Celsius with 5%carbon dioxide for 24 hours.Then, prepare the plate of Plasmids to the desired concentration for transfection, including four wells each for the positive control Plasmid, negative control Plasmid, and Plasmid-free Buffer. First, prepare a Master Mix of Diluted Lipid Transfection Reagent and a Master Mix of DNA Pre-complexation Reagent. Then, using a multi-channel pipette and a sterile trough, aliquot 16.8 microliters of the Diluted DNA Pre-complexation Reagent into each well of a Deep Well Plate.After this, use the multi-channel pipette to transfer 3.2 microliters of each Plasmid from the Master Plate to each well of the Deep Well Plate. Then, use the pipette to add 20 microliters of the Diluted Lipid Transfection Reagent Mixture to each well of the plate and mix thoroughly. Cover the plates and let them sit at room temperature for 10 to 15 minutes to form Lipid DNA Complexes.After this, use the multi-channel pipette to gently remove the Medium from the 293 T cells in the 96 Well plate. Then, replace the Medium with 95 microliters of DMEM supplemented with 10%FBS. Next, use the multi-channel pipette to add 10 microliters of the Transfection Mixture to each appropriate well.Next, incubate the cells at 37 degrees Celsius with 5%Carbon Dioxide for 24 hours. First, prepare the Stock Solutions required to make the Double-Strength Coelenterazine Assay Reagent, including three molar sodium ascorbate in PBS, five molar sodium chloride in distilled water, 10 milligrams per milliliter of BSA in PBS, and two millimolar Coelenterazine in acidified methanol. Next, prepare sufficient Coelenterazine Reagents for the Luciferase readout.With a separate reagent each for the cells in the Medium. Then, mix all of the reagents expect for the Coelenterazine. Filter the mixture through a 0.22 micrometer syringe filter.And then after filtration, add the Coelenterazine. Remove the cells from the incubator 24 hours after the transfection. Then, use the multi-channel pipette to transfer 50 microliters of Conditioned Medium from each well to a fresh white 96-Well Plate.Use the multi-channel pipette to add 50 microliters of Double-Strength Non-lytic Coelenterazine Reagent to the plate containing only Conditioned Medium. Then, gently shake the plate in the dark for five to 10 minutes at room temperature. Then, repeat this step by adding the Double-Strength Lytic Coelenterazine Reagent to the plate containing the cells.After the incubations, measure the luminescence of the Medium-only plate and the Cell-containing plate in a Plate Reader. Finally, discard the plates and save the files for further data analysis. It is important to incubate the Luciferase Reagent with the Medium-only Plate and the Cell-containing Plate for the same amount of time because the data for these plates are directly compared.In this protocol, the Cleavage Sequence Specificity of the PCSK9 Protease at Substrate Sites P6 through P6 Prime was evaluated by a Luciferase Assay. The changes in the Cleavage Sequence at positions P6 and P4 through P1 Prime are poorly tolerated by the Protease. But positions P5 and P2 Prime through P6 Prime are more flexible to change.Additionally, the results show that the optimal Cleavage Sequences are essentially the same as the Wild type Sequence. The relative Cleavage Activity of a library of missent snips found in the clinic was compared to the Wild type Protease. Of the 84 snips evaluated, over half demonstrated significant changes in activity compared to the Wild type Protease, suggesting that alterations in Protease Activity are frequently observed in the clinical population.Following this procedure, other methods, such as flow cytometry or Cholesterol Uptake Assays in hepatocytes can be performed to evaluate alterations in PCSK9 Proteolytic Ability on PCSK9's effect on the LDL Receptor.

Research

JoVE Journal

Biochemistry

High-throughput Screening of Carbohydrate-degrading Enzymes Using Novel Insoluble Chromogenic Substrate Assay Kits

Carbohydrates active enzymes (CAZymes) have multiple roles in vivo and are widely used for industrial processing in the biofuel, textile, detergent, paper ...

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

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

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

We describe a simple, robust and high throughput single molecule flow-stretching assay for studying 1D diffusion of molecules along DNA. In this assay, ...

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages ...

Use of Recombinant Fusion Proteins in a Fluorescent Protease Assay Platform and Their In-gel Renaturation

Proteases are intensively studied enzymes due to their essential roles in several biological pathways of living organisms and in pathogenesis; therefore, ...

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

DNA primase synthesizes short RNA primers that initiate DNA synthesis of Okazaki fragments on the lagging strand by DNA polymerase during DNA replication. ...

A Semi-High-Throughput Adaptation of the NADH-Coupled ATPase Assay for Screening Small Molecule Inhibitors

ATPase enzymes utilize the free energy stored in adenosine triphosphate to catalyze a wide variety of endergonic biochemical processes in vivo that would ...

High-Throughput Total Internal Reflection Fluorescence and Direct Stochastic Optical Reconstruction Microscopy Using a Photonic Chip

Total internal reflection fluorescence (TIRF) is commonly used in single molecule localization based super-resolution microscopy as it gives enhanced ...

Click-Chemistry Based Fluorometric Assay for Apolipoprotein N-acyltransferase from Enzyme Characterization to High-Throughput Screening

Lipoproteins from proteobacteria are posttranslationally modified by fatty acids derived from membrane phospholipids by the action of three integral ...

A High-Throughput Enzyme-Coupled Activity Assay to Probe Small Molecule Interaction with the dNTPase SAMHD1

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a pivotal regulator of intracellular deoxynucleoside triphosphate (dNTP) pools, as this ...