The funding for this study was provided by the CHS foundation. We acknowledge the protein crystallization platform within the excellence cluster CellNetworks of the University of Heidelberg for crystal screening and the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities.

1. P Domain Cloning
<ol>
	<li>Determine the P domain coding region by sequence alignment of norovirus strains (e.g., GII.10 strain, GenBank: AF504671, pdb-ID: 3ONU)6. Moreover, remove the flexible region at the C-terminal end of the P domain (Figure 2A). Codon-optimize the DNA for E. coli expression and include BamHI (N-terminal) and NotI (C-terminal) restriction sites in order to sub-clone the P domain coding region into the pMalc2x expression vector6,7. 
	Note: The P domain coding region is optimized and synthesized by a commercial service. The P domain coding region (insert) is approximately 1 kb in length and delivered in a standard transfer vector.</li>
	<li>Digest 2 &#181;g of the transfer vector with each 1 &#181;l BamHI (20,000 U/ml) and NotI (10,000 U/ml) restriction enzymes for 1 hr at 37 &#176;C with manufacturer supplied buffers.</li>
	<li>Separate the digested insert on a 1% agarose gel for 20 min at 135 V and purify the insert DNA from the gel using a commercial kit.</li>
	<li>Prepare the pMalc2x expression vector by digesting 2 &#181;g of this vector with each 1 &#181;l BamHI (20,000 U/ml) and NotI (10,000 U/ml) restriction enzymes for 1 hr at 37 &#176;C. Purify the vector from an agarose gel as described above (1.3). Note: Both samples (1.2 and 1.4) can be stored at -20 &#176;C.</li>
	<li>Ligate the purified insert into the digested pMalc2x vector at the BamHI and NotI restriction sites with 1 &#181;l T4-DNA ligase (400,000 U/ml) for 15 min at room temperature (RT) (Figure 2B and 2C). Use at least 20 ng of the pMalc2x vector and a vector:insert ratio 1:3 (molecular weight). The ligation mix is usually ~ 20 &#181;l.</li>
	<li>Transform 2 &#181;l of the ligation mix into 50 &#181;l chemically competent E. coli DH5&#945; bacterial cells using a standard transformation protocol (10 min on ice, heat shock 45 sec at 42 &#176;C) and grow in 600 &#181;l S.O.C. medium for 1 hr at 37 &#176;C. Centrifuge the transformed cells for 3 min at 1,000 x g, discard the supernatant, and resuspend the pellet in 30 &#181;l of S.O.C. medium.
	<ol>
		<li>Plate the transformation mix on LB-Agar plates, containing 100 &#181;g/ml ampicillin for selection, and grow overnight at 37 &#176;C. Select at least five colonies.</li>
	</ol>
	</li>
	<li>For each of the five colonies, inoculate 2-3 ml culture of LB-medium supplemented with 50 &#181;g/ml ampicillin (LB-amp) and grow by shaking overnight at 160 rpm at 37 &#176;C.</li>
	<li>Extract the plasmids from the overnight culture using a commercial kit. Verify the presence of the P domain insert by sequencing with a pMalc2x forward primer (5&#39;-TCAGACTGTCGATGAAGC-3&#39;) and reverse primer (5&#39;-GATGTGCTGCAAGGCGAT-3&#39;).</li>
</ol>
2. P Domain Expression
<ol>
	<li>Transform 1 &#956;l (150 ng/&#956;l - 400 ng/&#956;l) of the pMalc2x vector coding for the MBP-His-P domain fusion protein into 50 &#956;l of competent E. coli BL21 cells using a standard transformation protocol (10 min on ice, heat shock 45 sec at 42 &#176;C) and grow in 600 &#956;l S.O.C. medium for 1&#160;hr at 37 &#176;C. Subculture into 120 ml of LB-amp overnight at 160 rpm and 37 &#176;C.</li>
	<li>Inoculate nine liters (e.g., 6 x 5 L flasks with 1.5 L medium each) of LB-amp with the subculture (1:100). Grow the cells shaking at 160 rpm and 37 &#176;C until the OD600 reaches 0.4 - 0.6. Subsequently, lower the temperature to 22 &#176;C for ~ 1 hr and then induce the protein expression with 0.66 mM of isopropyl-&#946;-D-thiogalactopyranoside (IPTG)8. Grow the cells overnight at 22 &#176;C (~ 18 hr). 
	Note: The temperature can be varied, but we recommend to use 22 &#176;C or lower.</li>
	<li>Harvest the cells by centrifugation (10,543 x g, 15 min, 4 &#176;C). Discard the supernatant and freeze the cell pellet at -20 &#176;C.</li>
</ol>
3. 1st Purification Step and Protease Cleavage
<ol>
	<li>Prepare buffers that are used during the protein purification steps from stock solutions to guarantee reproducibility and stability of the experiments. Prepare four different buffers for the immobilized metal ion affinity chromatography (IMAC), each containing a different concentration of imidazole (10 mM, 20 mM, 50 mM, and 250 mM). For the SEC, prepare a gel-filtration buffer (GFB) with a higher salt concentration, but without imidazole. Use deionized water and filter all buffers before use with a pore size of 0.45 &#956;m. 
	Note: For a detailed buffer preparation scheme, refer to Table 1.</li>
	<li>Thaw the cell pellet from the nine liter culture and dissolve in 150 ml PBS at 4 &#176;C. Sonicate the cell suspension three times for 2 min (power 130 W, amplitude 20%, pulse frequency 50%) to disrupt the cells. Keep the cell suspension on ice during sonication.</li>
	<li>Centrifuge the sonicated cell suspension (43,667 x g, 30 min, 4 &#176;C) to separate cell debris from the supernatant containing expressed protein. Collect the supernatant and discard the pellet.</li>
	<li>Wash and equilibrate 10 ml (=1 column volume [CV]) slurry of Nickel (Ni)-NTA agarose beads with 10 mM imidazole buffer in a chromatography column. Add the equilibrated Ni beads to the supernatant from step 3.3 containing expressed MBP-His-P domain fusion protein and incubate for 30 min at 4 &#176;C with slow rotation.</li>
	<li>After incubation, apply the entire Ni-bead-protein mixture to a chromatography column. Wash the column slowly with each 5 CVs of 10 mM, 20 mM, and 50 mM imidazole buffers, starting with 10 mM, then 20 mM and last 50 mM (Figure 3A).</li>
	<li>Elute the MBP-His-P domain fusion protein using 250 mM imidazole buffer (Figure 3A). During elution, check the OD280nm to verify the elution of the fusion protein (the rise in OD280nm). Continue elution until the OD280nm drops to ~ 0.1. Wash the beads with excessive amounts of 250 mM imidazole buffer (at least 10 CVs), followed by at least 10 CVs of 10 mM imidazole buffer. Save the beads for the second purification step (section 4).</li>
	<li>Verify the presence of the MBP-His-P domain fusion protein with SDS-PAGE using a 12% SDS-polyacrylamide gel (10 x 8 cm)9 (Figure 3A). Perform gel electrophoresis at 45 A and 200 V for 45 min.</li>
	<li>Concentrate (e.g., using a commercial concentrator) the eluted MBP-His-P domain fusion protein to a final concentration of ~ 3 mg/ml. Cleave the MBP-His-P domain fusion with HRV-3C protease during dialysis against 2 L of 10 mM imidazole buffer (~ 1:100) overnight at 4 &#176;C (Figure 3A). Depending on the final volume of concentrated protein, perform dialysis in a dialysis cassette or dialysis tubing. 
	Note: The amount of HRV-3C protease for protein cleavage is calculated according to the specific protease activity (2 U/&#181;l, 1 U is sufficient to cleave 100 &#181;g of protein) and amount of eluted fusion protein that varies on the expression level and can be estimated from the SDS-PAGE result (3.7).</li>
</ol>
4. 2nd Purification Step
<ol>
	<li>Equilibrate the Ni-beads from step 3.6 in 10 mM imidazole buffer.</li>
	<li>Incubate the dialyzed protein from step 3.7 (containing cleaved P domain, MBP protein, and HRV-protease) with the equilibrated Ni-beads (4.1) for 30 min at 4 &#176;C with slow rotation.</li>
	<li>Apply the Ni-bead mixture to a column and collect the flow-through (cleaved P domain) (Figure 3B). Measure the concentration of protein as it comes off the column until the OD280nm reaches ~ 0.1. 
	Note: The MBP-His should remain bound to the Ni-beads (Figure 3B).</li>
	<li>Check the presence of cleaved P domain using SDS-PAGE with a 12% gel as described above (Figure 3B). Concentrate the eluted P domain to ~ 3 mg/ml and dialyze overnight at 4 &#176;C against GFB for subsequent SEC purification.</li>
</ol>
5. 3rd Purification Step
<ol>
	<li>Wash pumps and pipes of the HPLC purification system and pre-equilibrate the SEC-column (see Materials List) with GFB.</li>
	<li>Inject the P domain to the column at a flow-rate of 1 ml/min using a superloop (up to 12 ml) or loop (up to 3 ml), depending on the volume of the concentrated sample. After the injection is finished, increase the flow rate to 2.5 ml/min.</li>
	<li>As the OD increases and the P domain comes off the column, collect fractions of 1.5 ml. Check fractions using SDS-PAGE with a 12% gel (Figure 4A and 4B). Pool only the purest fractions and concentrate to ~ 3 mg/ml and ~ 8 mg/ml. 
	Note: After ~110 ml (void volume) most impurities are eluted from a SEC column with 320 ml bed volume. The P domain is usually eluted as a dimer. Elution time/volume of the P domain dimer is dependent on the prep grade (pg) of the SEC column.</li>
</ol>
6. Crystallization of the P Domain
<ol>
	<li>Use the P domain at ~ 3 mg/ml and 8 mg/ml for initial crystallization screening. Prepare at least 100 &#181;l of P domain per concentration for initial screens with 384 commercially available screening conditions. Perform screening at 18 &#176;C in a 96-well plate format, where the reservoir contains 100 &#181;l of mother solution and a drop is composed of 0.2 &#181;l mother solution and 0.2 &#181;l protein.</li>
	<li>Repeat and optimize successful crystallization conditions. Therefore, use 15-well plates that contain 3 rows. Set up the first row with 100% mother solution, the second row with 90% mother solution and 10% water, and the third row with 80% mother solution and 20% water. Use a drop size of 2 &#181;l (1 &#181;l protein + 1 &#181;l mother solution) and 500 &#181;l of mother solution as a reservoir volume.</li>
	<li>Use optimized crystal conditions for co-crystallizing the P domain with ligands. Prepare plates as described in 6.2. Instead of 2 &#181;l drop size, set up drops containing 1 &#181;l mother solution, 1 &#181;l protein, and 1 &#181;l of ligand at a concentration of 1 mg/ml.</li>
	<li>Collect data sets of single crystals using synchrotron radiation. Perform molecular replacement using published P domain structures with a high sequence similarity as initial search model6,10-13. 
	Note: Presence of a ligand shows up as un-modeled blob of electron density.</li>
</ol>

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V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+resolution+structural+characterization+of+recognition+of+histo-blood+group+antigens+by+Norwalk+virus.">Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus.</a> Proc. Natl. Acad. Sci. U.S.A. 105, 9175-9180 (2008).</li><li>Marionneau, 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=Norwalk+virus+binds+to+histo-blood+group+antigens+present+on+gastroduodenal+epithelial+cells+of+secretor+individuals.">Norwalk virus binds to histo-blood group antigens present on gastroduodenal epithelial cells of secretor individuals.</a> Gastroenterology. 122, 1967-1977 (2002).</li><li>Jones, M. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enteric+bacteria+promote+human+and+mouse+norovirus+infection+of+B+cells.">Enteric bacteria promote human and mouse norovirus infection of B cells.</a> Science. 346, 755-759 (2014).</li><li>Hansman, G. 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=Crystal+structures+of+GII.10+and+GII.12+norovirus+protruding+domains+in+complex+with+histo-blood+group+antigens+reveal+details+for+a+potential+site+of+vulnerability.">Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability.</a> J. Virol. 85, 6687-6701 (2011).</li><li>Fath, 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=Multiparameter+RNA+and+codon+optimization:+a+standardized+tool+to+assess+and+enhance+autologous+mammalian+gene+expression.">Multiparameter RNA and codon optimization: a standardized tool to assess and enhance autologous mammalian gene expression.</a> PLoS One. 6 (e17596), (2011).</li><li>Jacob, F., Monod, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+regulatory+mechanisms+in+the+synthesis+of+proteins.">Genetic regulatory mechanisms in the synthesis of proteins.</a> J. Mol. Biol. 3, 318-356 (1961).</li><li>Laemmli, U. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cleavage+of+structural+proteins+during+the+assembly+of+the+head+of+bacteriophage+T4.">Cleavage of structural proteins during the assembly of the head of bacteriophage T4.</a> Nature. 227, 680-685 (1970).</li><li>Kabsch, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automatic+Processing+of+Rotation+Diffraction+Data+from+Crystals+of+Initially+Unknown+Symmetry+and+Cell+Constants.">Automatic Processing of Rotation Diffraction Data from Crystals of Initially Unknown Symmetry and Cell Constants.</a> J. Appl. Crystallogr. 26, 795-800 (1993).</li><li>Mccoy, A. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phaser+crystallographic+software.">Phaser crystallographic software.</a> J. Appl. Crystallogr. 40, 658-674 (2007).</li><li>Emsley, P., Lohkamp, B., Scott, W. G., Cowtan, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Features+and+development+of+Coot.">Features and development of Coot.</a> Acta Crystallogr. Sect. D-Biol. Crystallogr. 66, 486-501 (2010).</li><li>Adams, P. 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=PHENIX:+a+comprehensive+Python-based+system+for+macromolecular+structure+solution.">PHENIX: a comprehensive Python-based system for macromolecular structure solution.</a> Acta Crystallogr. Sect. D-Biol. Crystallogr. 66, 213-221 (2010).</li><li>Koromyslova, A. D., Hansman, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanobody+binding+to+a+conserved+epitope+promotes+norovirus+particle+disassembly.">Nanobody binding to a conserved epitope promotes norovirus particle disassembly.</a> J. Virol. 89, 2718-2730 (2015).</li><li>Hansman, G. 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=Structural+basis+for+broad+detection+of+genogroup+II+noroviruses+by+a+monoclonal+antibody+that+binds+to+a+site+occluded+in+the+viral+particle.">Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle.</a> J. Virol. 86, 3635-3646 (2012).</li><li>Singh, B. K., Leuthold, M. M., Hansman, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+noroviruses'+fondness+for+histo-blood+group+antigens.">Human noroviruses' fondness for histo-blood group antigens.</a> J. Virol. 89, 2024-2040 (2015).</li><li>Leuthold, M. M., Dalton, K. P., Hansman, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+analysis+of+a+rabbit+hemorrhagic+disease+virus+binding+to+histo-blood+group+antigens.">Structural analysis of a rabbit hemorrhagic disease virus binding to histo-blood group antigens.</a> J. Virol. 89, 2378-2387 (2015).</li></ol>

The authors have nothing to disclose.

Here, we describe a protocol for the expression and purification of norovirus P domains in high quality and quantity. Noroviruses are not well studied and structural data are continuously needed. To our knowledge, P domain production using other protocols (e.g., GST-tagged P domains) has been problematic, so far, and sufficient structural data on norovirus-host interaction have been missing. With the method described here, we have recently contributed significantly to the understanding of the molecular details o...

Human noroviruses are the major cause of acute gastroenteritis worldwide1. These viruses belong to the Caliciviridae family, of which there are at least five genera, including Norovirus, Sapovirus, Lagovirus, Vesivirus, and Nebovirus. Despite their high impact on the healthcare system and wide distribution, the study of human noroviruses is hampered by the lack of a robust cell culture system. To date, there are no approved vaccines or antiviral strategies available.
The norovirus major capsid protein, termed VP1, can be divided into a shell (S) domain and a protruding (P) domain2. The P domain is connected to the S domain by a flexible hinge (H) region. The S domain forms a scaffold around the viral RNA, whereas the P domain forms the outmost part of the viral capsid. The P domain assembles into biologically relevant dimers when expressed in bacteria. The P dimer interacts with carbohydrate structures, termed histo-blood group antigens (HBGAs) that are present as soluble antigens in saliva and found on certain host cells3. The P domain-HBGA interaction is thought to be important for infection4. Indeed, a recent report revealed the importance of synthetic HBGAs or HBGA-expressing bacteria for human norovirus infection in vitro5.
Current studies regarding the host cell attachment of noroviruses are mainly performed with virus-like particles (VLPs) that can be expressed in insect cells or with recombinant P domains expressed in Escherichia coli (E. coli). To understand the P domain-HBGA interactions at atomic resolution, P domain-HBGA complex structures can be solved using X-ray crystallography. Here, we describe a protocol for P domain expression and purification that allows production of P domain in high quantity and quality to be used for X-ray crystallography. Moreover, this method can be applied for other calicivirus P domains and non-structural proteins.
The P domain is codon-optimized for E. coli expression and cloned into a standard transfer vector. The P domain is then re-cloned into an expression vector that encodes a polyhistidine (His) tag and a mannose-binding protein (MBP) that are followed by a protease cleavage site. The MBP-His-P domain fusion protein is expressed in E. coli, followed by three purification steps. The MBP-His-P domain fusion protein is purified using immobilized metal ion affinity chromatography (IMAC). Next, the fusion protein is cleaved with human rhinovirus (HRV)-3C protease and the P domain is separated from the MBP-His by an additional IMAC purification step. Lastly, the P domain is purified using size exclusion chromatography (SEC). The purified P domain can then be used for X-ray crystallography. Screening of protein crystallization conditions is performed with commercially available screening kits using different P domain protein concentrations. Crystal growth is observed and the most promising conditions are optimized.
With the methods described here, it is possible to go from gene to protein to structure within less than four weeks. Therefore, our method of P domain expression, purification, and crystallization is suitable to study norovirus-host interaction at the molecular level and provide important data to assist in up-to-date vaccine design and drug screening.

<table><tbody><tr><td>P domain DNA</td><td>Life Technologies</td><td></td><td>GeneArt Gene Synthesis</td></tr><tr><td>pMalc2x&amp;nbsp; vector</td><td>On request</td><td></td><td></td></tr><tr><td>BamHI</td><td>New England Biolabs</td><td>R0136L</td><td></td></tr><tr><td>NotI</td><td>New England Biolabs</td><td>R0189L</td><td></td></tr><tr><td>T4 DNA Ligase</td><td>New England Biolabs</td><td>M0202S</td><td></td></tr><tr><td>QIAquick Gel Extraction Kit</td><td>Qiagen</td><td>28704</td><td></td></tr><tr><td>QIAprep Spin Miniprep Kit</td><td>Qiagen</td><td>27104</td><td></td></tr><tr><td>S.O.C. Medium</td><td>Life Technologies</td><td>15544-034</td><td></td></tr><tr><td>Econo-Column Chromatography Column</td><td>Bio-Rad</td><td>7372512</td><td>2.5 x 10 cm, possible to use other size</td></tr><tr><td>Ni-NTA Agarose</td><td>Qiagen</td><td>30210</td><td></td></tr><tr><td>Vivaspin 20</td><td>GE Healthcare</td><td>various</td><td>cutoff of 10 kDa, 30 kDa and 50 kDa used</td></tr><tr><td>Subcloning Efficiency DH5&amp;alpha; Competent Cells</td><td>Life Technologies</td><td>18265-017</td><td></td></tr><tr><td>One Shot BL21(DE3) Chemically Competent &lt;em&gt;E. coli&lt;/em&gt;</td><td>Life Technologies</td><td>C6000-03</td><td></td></tr><tr><td>HRV 3C Protease</td><td>Merck Millipore</td><td>71493</td><td></td></tr><tr><td>HiLoad 26/600 Superdex 75 PG</td><td>GE Healthcare</td><td>28-9893-34</td><td>SEC column</td></tr><tr><td>JCSG Core suites</td><td>Qiagen</td><td>various</td><td>4 screens with each 96 wells</td></tr><tr><td>Carbohydrates</td><td>Dextra Laboratories, UK</td><td>various</td><td>Blood group products</td></tr></tbody></table>

production of human norovirus protruding domains in e. coli for x-ray crystallography

The norovirus capsid is composed of a single major structural protein, termed VP1. VP1 is subdivided into a shell (S) domain and a protruding (P) domain. The S domain forms a contiguous scaffold around the viral RNA, whereas the P domain forms viral spikes on the S domain and contains determinants for antigenicity and host-cell interactions. The P domain binds carbohydrate structures, i.e., histo-blood group antigens, which are thought to be important for norovirus infections. In this protocol, we describe a method for producing high quality norovirus P domains in high yields. These proteins can then be used for X-ray crystallography and ELISA in order to study antigenicity and host-cell interactions.
The P domain is firstly cloned into an expression vector and then expressed in bacteria. The protein is purified using three steps that involve immobilized metal-ion affinity chromatography and size exclusion chromatography. In principle, it is possible to clone, express, purify, and crystallize proteins in less than four weeks, which makes this protocol a rapid system for analyzing newly emerging norovirus strains.

The schematic of the described protocol is depicted in Figure 1. The protocol covers 6 major parts that include cloning of the target gene, expression, a three-step purification, and crystallization. Figure 2 illustrates the design of the expression construct (EC) and characteristics of the pMalc2x expression vector. The sequence of the multiple cloning site (MCS) of the pMalc2x vector shows restriction and protease cleavage sites. Figure 3</stron...

Watch this Scientific Journal Video about Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography at JoVE.com

Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography

Here, we describe a method to express and purify high quality norovirus protruding (P) domains in E. coli for use in X-ray crystallography studies. This method can be applied to other calicivirus P domains, as well as non-structural proteins, i.e., viral protein genome-linked (VPg), protease, and RNA dependent RNA polymerase (RdRp).

Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography

The norovirus capsid is composed of a single major structural protein, termed VP1. VP1 is subdivided into a shell (S) domain and a protruding (P) domain. ...

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8.6K Views.  University of Heidelberg and the German Cancer Research Center. Here, we describe a method to express and purify high quality norovirus protruding (P) domains in E. coli for use in X-ray crystallography studies. This method can be applied to other calicivirus P domains, as well as non-structural proteins, i.e., viral protein genome-linked (VPg), protease, and RNA dependent RNA polymerase (RdRp).

Video: Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

New therapies are needed to treat Clostridium difficile infections that are a major threat to human health. The C. difficile metalloprotease PPEP-1 is a target for future development of inhibitors to decrease the virulence of the pathogen. To perform biophysical and structural characterization as well as inhibitor screening, large amounts of pure and active protein will be needed. We have developed a protocol for efficient production and purification of PPEP-1 by the use of E. coli as the expression host yielding sufficient amounts and purity of protein for crystallization and structure determination. Additionally, using microseeding, highly intergrown crystals of PPEP-1 can be grown to well-ordered crystals suitable for X-ray diffraction analysis. The methods could also be used to produce other recombinant proteins and to study the structures of other proteins producing intergrown crystals.

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Proline-proline endopeptidase-1 (PPEP-1) is a secreted metalloprotease and promising drug-target from the human pathogen Clostridium difficile. Here we describe all methods necessary for the production and structure determination of this protein.

New therapies are needed to treat Clostridium difficile infections that are a major threat to human health. The C. difficile metalloprotease PPEP-1 is a ...

Biochemistry

From Constructs to Crystals &#8211; Towards Structure Determination of &#946;-barrel Outer Membrane Proteins

Membrane proteins serve important functions in cells such as nutrient transport, motility, signaling, survival and virulence, yet constitute only ~1% percent of known structures. There are two types of membrane proteins, &#945;-helical and &#946;-barrel. While &#945;-helical membrane proteins can be found in nearly all cellular membranes, &#946;-barrel membrane proteins can only be found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. One common bottleneck in structural studies of membrane proteins in general is getting enough pure sample for analysis. In hopes of assisting those interested in solving the structure of their favorite &#946;-barrel outer membrane protein (OMP), general protocols are presented for the production of target &#946;-barrel OMPs at levels useful for structure determination by either X-ray crystallography and/or NMR spectroscopy. Here, we outline construct design for both native expression and for expression into inclusion bodies, purification using an affinity tag, and crystallization using detergent screening, bicelle, and lipidic cubic phase techniques. These protocols have been tested and found to work for most OMPs from Gram-negative bacteria; however, there are some targets, particularly for mitochondria and chloroplasts that may require other methods for expression and purification. As such, the methods here should be applicable for most projects that involve OMPs from Gram-negative bacteria, yet the expression levels and amount of purified sample will vary depending on the target OMP.

&#946;-barrel outer membrane proteins (OMPs) serve many functions within the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. Here, we hope to alleviate a known bottleneck in structural studies by presenting protocols for the production of &#946;-barrel OMPs in sufficient quantities for structure determination by X-ray crystallography or NMR spectroscopy.

Membrane proteins serve important functions in cells such as nutrient transport, motility, signaling, survival and virulence, yet constitute only ~1% ...

Chemistry

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Determination of the full-length structure of ribosome assembly factor Nsa1 from Saccharomyces cerevisiae (S. cerevisiae) is challenging because of the disordered and protease labile C-terminus of the protein. This manuscript describes the methods to purify recombinant Nsa1 from S. cerevisiae for structural analysis by both X-ray crystallography and SAXS. X-ray crystallography was utilized to solve the structure of the well-ordered N-terminal WD40 domain of Nsa1, and then SAXS was used to resolve the structure of the C-terminus of Nsa1 in solution. Solution scattering data was collected from full-length Nsa1 in solution. The theoretical scattering amplitudes were calculated from the high-resolution crystal structure of the WD40 domain, and then a combination of rigid body and ab initio modeling revealed the C-terminus of Nsa1. Through this hybrid approach the quaternary structure of the entire protein was reconstructed. The methods presented here should be generally applicable for the hybrid structural determination of other proteins composed of a mix of structured and unstructured domains.

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

This method describes the cloning, expression, and purification of recombinant Nsa1 for structural determination by X-ray crystallography and small-angle X-ray scattering (SAXS), and is applicable for the hybrid structural analysis of other proteins containing both ordered and disordered domains.

Determination of the full-length structure of ribosome assembly factor Nsa1 from Saccharomyces cerevisiae (S. cerevisiae) is challenging because of the ...

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

NEMO is a scaffolding protein which plays an essential role in the NF-&#954;B pathway by assembling the IKK-complex with the kinases IKK&#945; and IKK&#946;. Upon activation, the IKK complex phosphorylates the I&#954;B molecules leading to NF-&#954;B nuclear translocation and activation of target genes. Inhibition of the NEMO/IKK interaction is an attractive therapeutic paradigm for the modulation of NF-&#954;B pathway activity, making NEMO a target for inhibitors design and discovery. To facilitate the process of discovery and optimization of NEMO inhibitors, we engineered an improved construct of the IKK-binding domain of NEMO that would allow for structure determination of the protein in the apo form and while bound to small molecular weight inhibitors. Here, we present the strategy utilized for the design, expression and structural characterization of the IKK-binding domain of NEMO. The protein is expressed in E. coli cells, solubilized under denaturing conditions and purified through three chromatographic steps. We discuss the protocols for obtaining crystals for structure determination and describe data acquisition and analysis strategies. The protocols will find wide applicability to the structure determination of complexes of NEMO and small molecule inhibitors.

We describe protocols for the structure determination of the IKK-binding domain of NEMO by X-ray crystallography. The methods include protein expression, purification and characterization as well as strategies for successful crystal optimization and structure determination of the protein in its unbound form.

NEMO is a scaffolding protein which plays an essential role in the NF-&#954;B pathway by assembling the IKK-complex with the kinases IKK&#945; and ...

Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography

Cryo-electron tomography (Cryo-ET) is a powerful three-dimensional (3-D) imaging technique for visualizing macromolecular complexes in their native context at a molecular level. The technique involves initially preserving the sample in its native state by rapidly freezing the specimen in vitreous ice, then collecting a series of micrographs from different angles at high magnification, and finally computationally reconstructing a 3-D density map. The frozen-hydrated specimen is extremely sensitive to the electron beam and so micrographs are collected at very low electron doses to limit the radiation damage. As a result, the raw cryo-tomogram has a very low signal to noise ratio characterized by an intrinsically noisy image. To better visualize subjects of interest, conventional imaging analysis and sub-tomogram averaging in which sub-tomograms of the subject are extracted from the initial tomogram and aligned and averaged are utilized to improve both contrast and resolution. Large datasets of tilt-series are essential to understanding and resolving the complexes at different states, conditions, or mutations as well as obtaining a large enough collection of sub-tomograms for averaging and classification. Collecting and processing this data can be a major obstacle preventing further analysis. Here we describe a high-throughput cryo-ET protocol based on a computer-controlled 300kV cryo-electron microscope, a direct detection device (DDD) camera and a highly effective, semi-automated image-processing pipeline software wrapper library tomoauto developed in-house. This protocol has been effectively utilized to visualize the intact type III secretion system (T3SS) in Shigella flexneri minicells. It can be applicable to any project suitable for cryo-ET.

We present a protocol on how to utilize high-throughput cryo-electron tomography to determine high resolution in situ structures of molecular machines. The protocol permits large amounts of data to be processed, avoids common bottlenecks and reduces resource downtime, allowing the user to focus on important biological questions.

Cryo-electron tomography (Cryo-ET) is a powerful three-dimensional (3-D) imaging technique for visualizing macromolecular complexes in their native ...

Bioengineering

Swab Sampling Method for the Detection of Human Norovirus on Surfaces

Human noroviruses are a leading cause of epidemic and sporadic gastroenteritis worldwide. Because most infections are either spread directly via the person-to-person route or indirectly through environmental surfaces or food, contaminated fomites and inanimate surfaces are important vehicles for the spread of the virus during norovirus outbreaks.
We developed and evaluated a protocol using macrofoam swabs for the detection and typing of human noroviruses from hard surfaces. Compared with fiber-tipped swabs or antistatic wipes, macrofoam swabs allow virus recovery (range 1.2-33.6%) from toilet seat surfaces of up to 700 cm2. The protocol includes steps for the extraction of the virus from the swabs and further concentration of the viral RNA using spin columns. In total, 127 (58.5%) of 217 swab samples that had been collected from surfaces in cruise ships and long-term care facilities where norovirus gastroenteritis had been reported tested positive for GII norovirus by RT-qPCR. Of these 29 (22.8%) could be successfully genotyped. In conclusion, detection of norovirus on environmental surfaces using the protocol we developed may assist in determining the level of environmental contamination during outbreaks as well as detection of virus when clinical samples are not available; it may also facilitate monitoring of effectiveness of remediation strategies.

A macrofoam based sampling methodology was developed and evaluated for the detection and quantification of norovirus on environmental hard surfaces.

Human noroviruses are a leading cause of epidemic and sporadic gastroenteritis worldwide. Because most infections are either spread directly via the ...

Immunology and Infection

Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Human norovirus exacts considerable public health and economic losses worldwide. Emerging in vitro cultivation advances are not yet applicable for routine detection of the virus. The current detection and quantification techniques, which rely primarily on nucleic acid amplification, do not discriminate infectious from non-infectious viral particles. The purpose of this article is to present specific details on recent advances in techniques used together in order to acquire further information on the infectivity status of viral particles. One technique involves assessing binding of a norovirus ssDNA aptamer to capsids. Aptamers have the advantage of being easily synthesized and modified, and are inexpensive and stable. Another technique, dynamic light scattering (DLS), has the advantage of observing capsid behavior in solution. Electron microscopy allows for visualization of the structural integrity of the viral capsids. Although promising, there are some drawbacks to each technique, such as non-specific aptamer binding to positively-charged molecules from sample matrices, requirement of purified capsid for DLS, and poor sensitivity for electron microscopy. Nonetheless, when these techniques are used in combination, the body of data produced provides more comprehensive information on norovirus capsid integrity that can be used to infer infectivity, information which is essential for accurate evaluation of inactivation methods or interpretation of virus detection. This article provides protocols for using these methods to discriminate infectious human norovirus particles.

Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Routine detection methods utilizing viral genome amplification are limited by their inability to discriminate infectious from non-infectious particles. The purpose of this article is to provide detailed protocols for alternative methods to aid in discrimination of infectious norovirus particles using aptamer binding, dynamic light scattering, and transmission electron microscopy.

Human norovirus exacts considerable public health and economic losses worldwide. Emerging in vitro cultivation advances are not yet applicable for routine ...

Quantifying Human Norovirus Virus-like Particles Binding to Commensal Bacteria Using Flow Cytometry

Commensal bacteria are well established to impact infection of eukaryotic viruses. Direct binding between the pathogen and the host microbiome is responsible for altering infection for many of these viruses. Thus, characterizing the nature of virus-bacteria binding is a foundational step needed for elucidating the mechanism(s) by which bacteria alter viral infection. For human norovirus, commensal bacteria enhance B cell infection. The virus directly binds to these bacteria, indicating that this direct interaction is involved in the mechanism of infection enhancement. A variety of techniques can be used to quantify interactions between bacteria and viruses including scintillation counting of radiolabeled viruses and polymerase chain reaction (PCR). Both methods require the use of live virus, which may need to be generated in the laboratory. Currently, none of the established in vitro culture systems available for human norovirus are robust enough to allow for generation of highly concentrated viral stocks. In lieu of live virus, virus-like particles (VLPs) have been used to characterize the interactions between norovirus and bacteria. Herein a flow cytometry method is described with uses virus specific antibodies to quantify VLP binding to gram-negative and gram-positive bacteria. Inclusion of both bacteria only and isotype controls allowed for optimization of the assay to reduce background antibody binding and accurate quantification of VLP attachment to the bacteria tested. High VLP:bacterium ratios result in VLPs binding to large percentages of the bacterial population. However, when VLP quantities are decreased, the percent of bacteria bound also decreases. Ultimately, this method can be employed in future experiments elucidating the specific conditions and structural components that regulate norovirus:bacterial interactions.

The goal of this protocol is to quantify binding of the eukaryotic pathogen human norovirus to bacteria. After performing an initial virus-bacterium attachment assay, flow cytometry is used to detect virally-bound bacteria within the population.

Commensal bacteria are well established to impact infection of eukaryotic viruses. Direct binding between the pathogen and the host microbiome is ...

Calcium Imaging of Virus-Infected Human Intestinal Organoid Monolayers

Live Calcium Imaging of Virus-Infected Human Intestinal Organoid Monolayers Using Genetically Encoded Calcium Indicators

Calcium signaling is an integral regulator of nearly every tissue. Within the intestinal epithelium, calcium is involved in the regulation of secretory activity, actin dynamics, inflammatory responses, stem cell proliferation, and many other uncharacterized cellular functions. As such, mapping calcium signaling dynamics within the intestinal epithelium can provide insight into homeostatic cellular processes and unveil unique responses to various stimuli. Human intestinal organoids (HIOs) are a high-throughput, human-derived model to study the intestinal epithelium and thus represent a useful system to investigate calcium dynamics. This paper describes a protocol to stably transduce HIOs with genetically encoded calcium indicators (GECIs), perform live fluorescence microscopy, and analyze imaging data to meaningfully characterize calcium signals. As a representative example, 3-dimensional HIOs were transduced with lentivirus to stably express GCaMP6s, a green fluorescent protein-based cytosolic GECI. The engineered HIOs were then dispersed into a single-cell suspension and seeded as monolayers. After differentiation, the HIO monolayers were infected with rotavirus and/or treated with drugs known to stimulate a calcium response. An epifluorescence microscope fitted with a temperature-controlled, humidified live-imaging chamber allowed for long-term imaging of infected or drug-treated monolayers. Following imaging, acquired images were analyzed using the freely available analysis software, ImageJ. Overall, this work establishes an adaptable pipeline for characterizing cellular signaling in HIOs.

Author Spotlight: Investigating Viral Disruption of Intestinal Epithelial Signaling &#8211; Research Insights and Future Directions 

This protocol describes an approach for performing calcium imaging in virus-infected human intestinal organoids and offers an approach to analysis.

Calcium signaling is an integral regulator of nearly every tissue. Within the intestinal epithelium, calcium is involved in the regulation of secretory ...

Protein Crystallization

Protein crystallization, obtaining a solid lattice of biomolecules, elucidates protein structure and enables the study of protein function. Crystallization involves drying purified protein under a combination of many factors, including pH, temperature, ionic strength, and protein concentration. Once crystals are obtained, the protein structure can be elucidated by x-ray diffraction and computation of an electron density model.
This video introduces protein crystallization and shows a general procedure. Protein expression and purification, crystallization, and x-ray diffraction are covered in the procedure. Applications of protein crystallization include in silico drug design, binding site determination, and membrane protein structure analysis.
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Protein crystallization is the process of obtaining a latticed solid form of a protein. These crystals are especially valuable to structural biologists, assisting in the study of protein function. Other techniques, such as mass spec or SDS-PAGE, can only provide information on the one-dimensional structure of proteins. Protein crystallization is complemented by the techniques of recombinant protein expression and x-ray diffraction. This video will show the principles of protein crystallization, a general laboratory procedure, and several of its applications in the biochemical field.
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The first step required in the process is to obtain milligram quantities of very pure protein, typically using recombinant protein expression. The gene corresponding to the protein of interest is cloned into an expression vector, and the expressed protein is fused to an affinity tag, such as poly-histidine, to assist in the purification by affinity chromatography. To learn more, see this collection&#39;s video on affinity chromatography.
Formation of the purified protein into crystals is dependent on the proper combination of many factors, including pH, ionic strength, concentrations of precipitant and protein, temperature, and rate of equilibration. The most common method used is vapor diffusion, of which there are two categories: hanging drop and sitting drop. A droplet containing pure protein, buffer, and precipitant, which is an ionic solid that binds water molecules, reducing water availability for the protein and mimicking higher protein concentration, is in an enclosed microwell with a reservoir with a more highly concentrated mixture of the same buffer and precipitant. At the beginning, the concentrations of protein and precipitant are too low to cause crystallization. During the course of the experiment, water vaporizes from the droplet and collects in the reservoir; a decrease in the amount of water in the droplet causes the system to become supersaturated, and nucleation, followed by crystallization, can occur. The net transfer of water from the droplet is in equilibrium, and the system is maintained until the process is complete.
To visualize the 3D structure, x-ray diffraction is used. To obtain x-ray data from a crystal, it is placed in a monochromatic x-ray beam, where it is exposed to the beam at all angles. Each exposure provides an image, where each spot is a diffracted x-ray, which emerges from the crystal and is registered by a detector. The data are combined to produce a model of the arrangement of atoms within the crystal. The resulting crystal structure demonstrates the 3-dimensional placement of the atoms, with a typical resolution of 2 angstroms.

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Now that we have covered the principles of protein crystallization, let us look at a generalized protocol.
To begin the procedure an expression vector containing the gene of interest is transformed into cells. The cells are incubated and at mid-log phase, expression is initiated by adding an inducer, such as IPTG, which triggers transcription of the gene&#39;s mRNA. After protein expression, the crude material is suspended in lysis buffer, and then clarified by centrifugation.
The clarified lysate is then loaded onto a nickel column, and the polyhistidine-tagged protein binds to the column while all other biomolecules are washed away.
Once several milligrams of pure protein have been obtained, it is ready for crystallization by vapor diffusion. A 24-well hanging/sitting drop tray is filled with varying concentrations of sodium chloride and sodium acetate buffer solutions. For the sitting drop method, equal volumes of protein and reservoir solution are pipetted onto the shelf above each well, and then the tray is covered with transparent tape. The tray is then placed in an incubation chamber, and the wells are monitored for growth the following day, then every few days.
Once a proper crystal has been obtained it is ready for x-ray diffraction analysis. The crystal is mounted on a goniometer to position the crystal at selected orientations. The crystal is illuminated with a monochromatic beam of x-rays at all angles, producing a diffraction pattern. The software converts the two-dimensional images, taken at different orientations, to a three-dimensional model of the density of electrons within the crystal by determining the positions of the atoms in the crystal.
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Now that we have reviewed a procedure, let&#39;s review some useful applications of protein crystallization, and another crystallization technique.
Protein crystallization may be used for in silico drug design. The three-dimensional structure of Influenza virus&#39;s polymerase basic protein 2, which has been linked to viral infection in mammals, was determined by crystallization and x-ray diffraction. Potential binding sites in the protein are visualized, and with the use of a docking program, a three-dimensional molecule was designed that would insert into a cleft in the protein.
Co-crystallization of protein-DNA complexes is also a useful technique. DNA-binding proteins modulate a wide variety of biological functions such as transcription and DNA polymerization and DNA repair; and crystal structures of these complexes can provide insight into protein function, mechanism, and the nature of the specific interaction. The E. coli protein SeqA, a negative regulator of DNA replication, was co-crystallized with hemimethylated DNA.
Integral membrane proteins such as G-protein coupled receptors, or GCPRs, are difficult to crystallize due to their limited amount of polar surface area available for forming crystal lattice contacts, which has led to the development of fusion-protein-assisted protein crystallization. Genes encoding &#946;2 adrenergic receptor, a GCPR, and a lysozyme were inserted into an expression vector. The crystallization of the &#946;2AR- lysozyme fusion protein was achieved due to the increased extracellular hydrophilic surface over the naturally hydrophobic &#946;2AR, provided by the lysozyme, necessary for forming packing interactions in the crystal lattice.
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You&#39;ve just watched JoVE&#39;s video on protein crystallization. This video described its principles, a generalized protocol, and some its uses in the biomedical field. Thanks for watching!
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Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography

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Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography

Swab Sampling Method for the Detection of Human Norovirus on Surfaces

Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Quantifying Human Norovirus Virus-like Particles Binding to Commensal Bacteria Using Flow Cytometry

Live Calcium Imaging of Virus-Infected Human Intestinal Organoid Monolayers Using Genetically Encoded Calcium Indicators

Protein Crystallization