Name: Fully Processed Recombinant KRAS4b: Isolating and Characterizing the Farnesylated and Methylated Protein (Video) | JoVE Journal
Uploaded: 2020-01-16T14:00:00.000+00:00
Duration: 7 min 8 s
Description: Learn to isolate fully processed KRAS4b with authentic farnesylation and carboxymethylation for cancer research. This high-yield protocol enables biophysical and structural biology experiments.

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We acknowledge cloning and expression support from Carissa Grose, Jen Melhalko, and Matt Drew in the Protein Expression Laboratory, Frederick National Laboratory for Cancer Research. This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government

<ol><li>Cox, A. D., Der, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Protein+prenylation%3A+more+than+just+glue%5BTitle%5D)+AND+%22Current+Opinion+in+Cell+Biology%22%5BJournal%5D)">Protein prenylation: more than just glue.</a> Current Opinion in Cell Biology. 4 (6), 1008-1016 (1992).</li>
<li>Zhang, F. L., Casey, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Protein+Prenylation%3A+Molecular+Mechanisms+and+Functional+Consequences%5BTitle%5D)+AND+%22Annual+Review+of+Biochemistry%22%5BJournal%5D)">Protein Prenylation: Molecular Mechanisms and Functional Consequences.</a> Annual Review of Biochemistry. 65, 241-269 (1996).</li>
<li>Hottman, D. A., Li, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Protein+prenylation+and+synaptic+plasticity%3A+implications+for+Alzheimer%27s+disease%5BTitle%5D)+AND+%22Molecular+Neurobiology%22%5BJournal%5D)">Protein prenylation and synaptic plasticity: implications for Alzheimer's disease.</a> Molecular Neurobiology. 50 (1), 177-185 (2014).</li>
<li>Hottman, D. A., Chernick, D., Cheng, S., Wang, Z., Li, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((HDL+and+cognition+in+neurodegenerative+disorders%5BTitle%5D)+AND+%22Neurobiology+of+Disease%22%5BJournal%5D)">HDL and cognition in neurodegenerative disorders.</a> Neurobiology of Disease. 72, Pt A 22-36 (2014).</li>
<li>Nakagami, H., Jensen, K. S., Liao, J. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+novel+pleiotropic+effect+of+statins%3A+prevention+of+cardiac+hypertrophy+by+cholesterol-independent+mechanisms%5BTitle%5D)+AND+%22Annals+of+Medicine%22%5BJournal%5D)">A novel pleiotropic effect of statins: prevention of cardiac hypertrophy by cholesterol-independent mechanisms.</a> Annals of Medicine. 35 (6), 398-403 (2003).</li>
<li>Kohnke, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Rab+GTPase+prenylation+hierarchy+and+its+potential+role+in+choroideremia+disease%5BTitle%5D)+AND+%22PLoS+One%22%5BJournal%5D)">Rab GTPase prenylation hierarchy and its potential role in choroideremia disease.</a> PLoS One. 8 (12), 81758(2013).</li>
<li>Berndt, N., Hamilton, A. D., Sebti, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Targeting+protein+prenylation+for+cancer+therapy%5BTitle%5D)+AND+%22Nature+Reviews+Cancer%22%5BJournal%5D)">Targeting protein prenylation for cancer therapy.</a> Nature Reviews Cancer. 11 (11), 775-791 (2011).</li>
<li>Kho, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+tagging-via-substrate+technology+for+detection+and+proteomics+of+farnesylated+proteins%5BTitle%5D)+AND+%22Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America%22%5BJournal%5D)">A tagging-via-substrate technology for detection and proteomics of farnesylated proteins.</a> Proceedings of the National Academy of Sciences of the United States of America. 101 (34), 12479-12484 (2004).</li>
<li>Armstrong, S. A., Hannah, V. C., Goldstein, J. L., Brown, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((CAAX+geranylgeranyl+transferase+transfers+farnesyl+as+efficiently+as+geranylgeranyl+to+RhoB%5BTitle%5D)+AND+%22Journal+of+Biological+Chemistry%22%5BJournal%5D)">CAAX geranylgeranyl transferase transfers farnesyl as efficiently as geranylgeranyl to RhoB.</a> Journal of Biological Chemistry. 270 (14), 7864-7868 (1995).</li>
<li>Stephen, A. G., Esposito, D., Bagni, R. K., McCormick, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Dragging+ras+back+in+the+ring%5BTitle%5D)+AND+%22Cancer+Cell%22%5BJournal%5D)">Dragging ras back in the ring.</a> Cancer Cell. 25 (3), 272-281 (2014).</li>
<li>Denisov, I. G., Sligar, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Nanodiscs+in+Membrane+Biochemistry+and+Biophysics%5BTitle%5D)+AND+%22Chemical+Reviews%22%5BJournal%5D)">Nanodiscs in Membrane Biochemistry and Biophysics.</a> Chemical Reviews. 117 (6), 4669-4713 (2017).</li>
<li>Bao, H., Duong, F., Chan, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+Step-by-step+Method+for+the+Reconstitution+of+an+ABC+Transporter+into+Nanodisc+Lipid+Particles%5BTitle%5D)+AND+%22Journal+of+Visualized+Experiments%22%5BJournal%5D)">A Step-by-step Method for the Reconstitution of an ABC Transporter into Nanodisc Lipid Particles.</a> Journal of Visualized Experiments. (66), e3910(2012).</li>
<li>Dementiev, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((K-Ras4B+lipoprotein+synthesis%3A+biochemical+characterization%2C+functional+properties%2C+and+dimer+formation%5BTitle%5D)+AND+%22Protein+Expression+and+Purification%22%5BJournal%5D)">K-Ras4B lipoprotein synthesis: biochemical characterization, functional properties, and dimer formation.</a> Protein Expression and Purification. 84 (1), 86-93 (2012).</li>
<li>Lowe, P. N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Characterization+of+recombinant+human+Kirsten-ras+%284B%29+p21+produced+at+high+levels+in+Escherichia+coli+and+insect+baculovirus+expression+systems%5BTitle%5D)+AND+%22Journal+of+Biological+Chemistry%22%5BJournal%5D)">Characterization of recombinant human Kirsten-ras (4B) p21 produced at high levels in Escherichia coli and insect baculovirus expression systems.</a> Journal of Biological Chemistry. 266 (3), 1672-1678 (1991).</li>
<li>Gillette, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Production+of+Farnesylated+and+Methylated+Proteins+in+an+Engineered+Insect+Cell+System%5BTitle%5D)+AND+%22Methods+in+Molecular+Biology%22%5BJournal%5D)">Production of Farnesylated and Methylated Proteins in an Engineered Insect Cell System.</a> Methods in Molecular Biology. 2009, 259-277 (2019).</li>
<li>Agamasu, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((KRAS+Prenylation+Is+Required+for+Bivalent+Binding+with+Calmodulin+in+a+Nucleotide-Independent+Manner%5BTitle%5D)+AND+%22Biophysical+Journal%22%5BJournal%5D)">KRAS Prenylation Is Required for Bivalent Binding with Calmodulin in a Nucleotide-Independent Manner.</a> Biophysical Journal. 116 (6), 1049-1063 (2019).</li>
<li>Talsania, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Genome+Assembly+and+Annotation+of+the+Trichoplusia+ni+Tni-FNL+Insect+Cell+Line+Enabled+by+Long-Read+Technologies%5BTitle%5D)+AND+%22Genes%22%5BJournal%5D)">Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies.</a> Genes. 10 (2), 79(2019).</li>
<li>Spencer-Smith, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Inhibition+of+RAS+function+through+targeting+an+allosteric+regulatory+site%5BTitle%5D)+AND+%22Nature+Chemical+Biology%22%5BJournal%5D)">Inhibition of RAS function through targeting an allosteric regulatory site.</a> Nature Chemical Biology. 13 (1), 62-68 (2016).</li>
<li>Lowe, P. N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Expression+of+polyisoprenylated+Ras+proteins+in+the+insect%2Fbaculovirus+system%5BTitle%5D)+AND+%22Biochemical+Society+Transactions%22%5BJournal%5D)">Expression of polyisoprenylated Ras proteins in the insect/baculovirus system.</a> Biochemical Society Transactions. 20 (2), 484-487 (1992).</li>
<li>Dharmaiaha, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Structural+basis+of+recognition+of+farnesylated+and+methylated+KRAS4b+by+PDE%CE%B4%5BTitle%5D)+AND+%22Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America%22%5BJournal%5D)">Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.</a> Proceedings of the National Academy of Sciences of the United States of America. 113 (44), 6766-6775 (2016).</li>
<li>Abdiche, Y. N., Myszka, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Probing+the+mechanism+of+drug%2FLipid+membrane+interactions+using+Biacore%5BTitle%5D)+AND+%22Analytical+Biochemistry%22%5BJournal%5D)">Probing the mechanism of drug/Lipid membrane interactions using Biacore.</a> Analytical Biochemistry. 328 (2), 233-243 (2004).</li>
<li>Fisher, R. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Complex+interactions+of+HIV-1+nucleocapsid+protein+with+oligonucleotides%5BTitle%5D)+AND+%22Nucleic+Acids+Research%22%5BJournal%5D)">Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides.</a> Nucleic Acids Research. 34 (2), 472-484 (2006).</li>
<li>Lakshman, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Quantitative+biophysical+analysis+defines+key+components+modulating+recruitment+of+the+GTPase+KRAS+to+the+plasma+membrane%5BTitle%5D)+AND+%22Journal+of+Biological+Chemistry%22%5BJournal%5D)">Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane.</a> Journal of Biological Chemistry. 294, 2193-2207 (2019).</li>
</ol>

The authors have nothing to disclose.

As noted in the Representative Results section, the most critical step during the purification is the handling of the sample during the time it is in lower salt. Limiting the time that the sample is exposed to less than 200 mM NaCl will help reduce precipitation and increase sample yield. Interpretation of the results of the CEX can be difficult if the profile does not match the expectations (see Figure 2). Until the protocol has become routine, it is advised that the CEX elution fractions t...

Posttranslational modifications play a key role in defining the functional activity of proteins. Modifications such as phosphorylation and glycosylation are well established. Lipid modifications are less well characterized, however. It is estimated that as much as 0.5% of all cellular proteins may be prenylated1. Prenylation is the transfer of a 15-carbon farnesyl or a 20-carbon geranylgeranyl lipid chain to an acceptor protein containing the CAAX motif2. Prenylated proteins have been implicated in the progression of several human diseases including premature aging3, Alzheimer&#39;s4, cardiac dysfunction5, choroideremia6, and cancer7. The small GTPases, HRAS, NRAS, and KRAS1, nuclear laminins, and the kinetochores CENP-E and F are farnesylated proteins under the basal condition. Other small GTPases, namely RhoA, RhoC, Rac1, cdc-42, and RRAS are geranylgeranylated8, whereas RhoB can be farnesylated or geranylgeranylated9.
The small GTPase KRAS4b functions as a molecular switch, essentially transmitting extracellular growth factor signaling to intracellular signal transduction pathways that stimulate cell growth and proliferation, via multiple protein-protein interactions. There are two key aspects of KRAS4b biochemistry that are essential for its activity. First, the protein cycles between an inactive GDP and an active GTP bound state whereby it actively engages with effectors. Second, a C-terminal poly-lysine region and a farnesylated and carboxymethylated cysteine direct the protein to the plasma membrane, enabling recruitment and activation of downstream effectors. Mutant KRAS4b is an oncogenic driver in pancreatic, colorectal, and lung cancer10, and as such, therapeutic intervention would have a huge clinical benefit. Production of authentically modified recombinant protein that is farnesylated and carboxymethylated would enable biochemical screening using KRAS4b in combination with membrane surrogates such as liposomes or lipid nanodiscs11,12.
Farnesyl transferase (FNT) catalyzes the addition of farnesyl pyrophosphate to the C-terminal cysteine in the CAAX motif in KRAS4b. After prenylation, the protein is trafficked to the endoplasmic reticulum (ER) where the Ras converting enzyme (RCE1) cleaves the three C-terminal residues. The final step in processing is methylation of the new C-terminal farnesylcysteine residue by the ER membrane protein, isoprenylcysteine carboxyl methyltransferase (ICMT). Expression of recombinant KRAS4b in E. coli results in the production of an unmodified protein. Previous attempts to produce processed KRAS4b have been limited due to insufficient yields for structural or drug screening experiments or have failed to recapitulate the native full-length mature protein13,14. The protocol presented here utilizes an engineered baculovirus-based insect cell expression system and purification method that generates highly purified, fully processed KRAS4b at yields of 5 mg/L of cell culture.
Careful protein characterization is essential to validate the quality of recombinant proteins prior to embarking on structural biology or drug screening studies. Two key parameters of fully processed KRAS4b are validation of the correct prenyl modification and the availability of the farnesylated and carboxymethylated C-terminus (FMe) for interaction with membrane substitutes or lipids. Electrospray ionization mass spectrometry (ESI-MS) of the KRAS4b-FMe was used to measure the molecular weight and confirm the presence of the farnesyl and carboxymethyl modifications. Native mass spectrometry, where samples are sprayed with nondenaturing solvents, was used to demonstrate that KRAS4b-FMe was also bound to its GDP cofactor. Finally, surface plasmon resonance spectroscopy was used to measure the direct binding of KRAS4b-FMe with immobilized liposomes.

<table><tbody><tr><td>1.8 mL Safe-Lock Tubes, Natural</td><td>Eppendorf</td><td>22363204</td><td></td></tr><tr><td>11 mm Cl SS Interlocked Insert Autosampler Vials</td><td>Thermo Scientific</td><td>30211SS-1232</td><td></td></tr><tr><td>1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC)</td><td>AVANTI POLAR LIPIDS</td><td>850457</td><td>purchase as liquid stocks in chloroform</td></tr><tr><td>1-palmitoyl-2-oleoyl-glycero-3-phospho-L-serine (POPS)</td><td>AVANTI POLAR LIPIDS</td><td>840034</td><td>purchase as liquid stocks in chloroform</td></tr><tr><td>5427R Centrifuge</td><td>Eppendorf</td><td></td><td></td></tr><tr><td>Acetonitrile, HPLC Grade</td><td>Fisher Chemical</td><td>A998-1 1L</td><td></td></tr><tr><td>Ammonium Acetate</td><td>Sigma-Aldrich</td><td>09689-250g</td><td></td></tr><tr><td>Argon gas</td><td>Airgas</td><td>ARUP</td><td></td></tr><tr><td>Assay Plate 384</td><td>CORNING</td><td>3544</td><td></td></tr><tr><td>Biacore T200 Instrument</td><td>GE Healthcare</td><td></td><td></td></tr><tr><td>Blue Snap-It Seals, T/S</td><td>Thermo Scientific</td><td>C4011-54B</td><td></td></tr><tr><td>Branson Ultrasonic Bath</td><td>Thermo Fisher</td><td>15-336-1000</td><td></td></tr><tr><td>Cation Exchange Chromatography (CEX) column</td><td>GE Healthcare Life Sciences</td><td>29018183</td><td>HiPrep SP Sepharose High Performance</td></tr><tr><td>CHAPS</td><td>Sigma</td><td>C3023</td><td></td></tr><tr><td>Dyna Pro Plate Reader</td><td>Wyatt Technologies</td><td></td><td></td></tr><tr><td>Exactive Plus EMR Mass Spectrometer</td><td>Thermo Scientific</td><td></td><td></td></tr><tr><td>Formic Acid</td><td>Sigma-Aldrich</td><td>F0507-500Ml</td><td>Use Reagent Grade or better</td></tr><tr><td>Gilson vials 7x14 mm Tubes</td><td>GE Healthcare</td><td>BR-1002-12</td><td></td></tr><tr><td>Glass screw thread vials with PTFE foam liners</td><td>Scientific Specialities</td><td>B69302</td><td></td></tr><tr><td>High speed/benchtop centrifuge</td><td>Thermo Fischer Scientific</td><td>05-112-114D</td><td>capable of up to 4,000 xg</td></tr><tr><td>His6-Tobacco Etch Virus (TEV) protease</td><td>Addgene</td><td>92414</td><td>Purified as per Raran-Kurussi et al. (2017) Removal of Affinity Tags with TEV Protease. In: Burgess-Brown N. (eds) Heterologous Gene Expression in E.coli. Methods in Molecular Biology, vol 1586. Humana Press, New York, NY</td></tr><tr><td>Immobilized Metal Affinity Chromatography (IMAC) column</td><td>GE Healthcare Life Sciences</td><td>28-9365-51</td><td>HisPrep FF 16/10</td></tr><tr><td>In-House Water Supply, Arium Advance</td><td>Sartorius Stedim</td><td></td><td>Resistivity of 18 M&amp;Omega;0-cm</td></tr><tr><td>Lipid extruder set with holder</td><td>AVANTI POLAR LIPIDS</td><td>610023</td><td></td></tr><tr><td>Liquid nitrogen</td><td>Airgas</td><td>NI-DEWAR</td><td></td></tr><tr><td>M110-EH microfluidizer</td><td>Microfluidics</td><td></td><td></td></tr><tr><td>MabPac RP UHPLC Column, 4 um, 3.0 x 50 mm</td><td>Thermo Scientific</td><td>088645</td><td></td></tr><tr><td>MabPac SEC-1 Column, 5 um, 300 &amp;Aring;, 2.1 x 150 mm</td><td>Thermo Scientific</td><td>088790</td><td></td></tr><tr><td>MagTran software</td><td>Thermo Scientific</td><td></td><td></td></tr><tr><td>Methanol, HPLC Grade</td><td>VWR Chemicals</td><td>BDH20864.400</td><td></td></tr><tr><td>NGC Chromatography System</td><td>BioRad</td><td>78880002</td><td>NGC QuestTM 100 Chromatography system</td></tr><tr><td>Protease Inhibitor Cocktail without EDTA or other chelators</td><td>Millipore Sigma</td><td>P8849</td><td></td></tr><tr><td>Rubber Caps type 3</td><td>GE Healthcare</td><td>BR-1005-02</td><td></td></tr><tr><td>Series S Sensor Chip L1</td><td>GE Healthcare</td><td>29104993</td><td></td></tr><tr><td>Spectrophotometer</td><td>Thermo Fischer Scientific</td><td>13-400-519</td><td>Absorbace at 280nm</td></tr><tr><td>Ultra-15 Centrifugal Filter Units, 10K NMWL</td><td>Millipore Sigma</td><td>UFC901008</td><td>PES membrane</td></tr><tr><td>Ultracel 10K MWCO Ultra 0.5 mL Centrifuge Filters</td><td>Amicon</td><td>UFC501024</td><td></td></tr><tr><td>Ultracentrifuge</td><td>Beckman Coulter</td><td>Optima - L80K</td><td>capable of 100,000 xg</td></tr><tr><td>Vanquish UHPLC (Pump, Column Hearter, and LC System)</td><td>Thermo Scientific</td><td></td><td></td></tr><tr><td>Vortex Genie 2</td><td>Fisher</td><td>12-812</td><td></td></tr><tr><td>Water, HPLC Grade</td><td>Sigma-Aldrich</td><td>270733-1L</td><td>May use in-house water source (see below)</td></tr><tr><td>Whatman GD/XP PES 0.45 mm syringe filter</td><td>GE Healthcare - Whatman</td><td>6994-2504</td><td></td></tr><tr><td>Xcalibur QualBrowser</td><td>Thermo Scientific</td><td></td><td>proteomics software</td></tr></tbody></table>

fully processed recombinant kras4b: isolating and characterizing the farnesylated and methylated protein

Fully Processed Recombinant KRAS4b: Isolating and Characterizing the Farnesylated and Methylated Protein

Protein prenylation is a key modification that is responsible for targeting proteins to intracellular membranes. KRAS4b, which is mutated in 22% of human cancers, is processed by farnesylation and carboxymethylation due to the presence of a &#39;CAAX&#39; box motif at the C-terminus. An engineered baculovirus system was used to express farnesylated and carboxymethylated KRAS4b in insect cells and has been described previously. Here, we describe the detailed, practical purification and biochemical characterization of the protein. Specifically, affinity and ion exchange chromatography were used to purify the protein to homogeneity. Intact and native mass spectrometry was used to validate the correct modification of KRAS4b and to verify nucleotide binding. Finally, membrane association of farnesylated and carboxymethylated KRAS4b to liposomes was measured using surface plasmon resonance spectroscopy.

One of the largest variables in the protocol is the amount of expressed target protein (His6-MBP-tev-KRAS4b). This protocol was developed using an isolate from a Trichoplusia ni cell line, Tni-FNL17, adapted for suspension growth and weaned from serum. Given the wide range of results reported across the various insect cell lines with the baculovirus expression system, it is advisable that Tni-FNL be used, at least initially, to produced KRAS4b-FMe.
A dark prote...

Prenylation is an important modification on peripheral membrane binding proteins. Insect cells can be manipulated to produce farnesylated and carboxymethylated KRAS4b in quantities that enable biophysical measurements of protein-protein and protein-lipid interactions

Protein prenylation is a key modification that is responsible for targeting proteins to intracellular membranes. KRAS4b, which is mutated in 22% of human ...

fully-processed-recombinant-kras4b-isolating-characterizing

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Learn to isolate fully processed KRAS4b with authentic farnesylation and carboxymethylation for cancer research. This high-yield protocol enables biophysical and structural biology experiments.

Fully Processed Recombinant KRAS4b: Isolating and Characterizing the Farnesylated and Methylated Protein

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