X-ray diffraction experiments described in this paper were performed using beamlines 08-ID and 08-BM at the Canadian Light Source, which is supported by the Canada Foundation for Innovation, Natural Sciences and Engineering Research Council of Canada, the University of Saskatchewan, the Government of Saskatchewan, Western Economic Diversification Canada, the National Research Council Canada, and the Canadian Institutes of Health Research. We would like to acknowledge the Structural &#38; Biophysical Core Facility, The Hospital for Sick Children, for access to the ITC and BLI instruments. J.E.O. was supported by Banting Postdoctoral Fellowship BPF-144483 from the Canadian Institutes of Health Research. T.S. is a recipient of a Canada Graduate Scholarship Master&#39;s Award and a Vanier Canada Graduate Scholarship&#160;from the Canadian Institutes of Health Research. This work was supported by operating grant PJT-148811 (J.-P.J.) from the Canadian Institutes of Health Research. This research was undertaken, in part, thanks to funding from the Canada Research Chairs program (J.-P.J.).

The authors declare no competing interests.

Membrane-anchored glycoproteins are critical for cell function and are attractive therapeutic targets. Here, we present a protocol for the structural and biophysical characterization of the ECD of membrane glycoproteins, both alone and in complex with small molecule ligands and Fab fragments. We have successfully used this protocol to determine the crystal structure of the three N-terminal-most Ig domains of the extracellular portion of human CD2228, a critical co-receptor on B cells involved in keeping humoral immunity in check79. We have also characterized the binding site of CD22 with its natural ligand &#945;2-6 sialyllactose, and defined the mode of recognition of a therapeutic antibody towards human CD22. These results provide insights into the structure-function relationship of a key member of the Siglecs family that has restricted expression on B cells, and a molecular roadmap towards the development of new CD22 targeted small molecule and antibody-based therapeutics. While this protocol was used successfully for an Ig-containing B cell receptor, we propose that our approach can be applied for the structural and biophysical characterization of any membrane glycoprotein with a distinct domain organization. In such cases, construct design and combinatorial N-linked glycan mutations (either to Gln or Ala) can be evaluated to find a construct suitable for crystal growth and high-resolution diffraction.
Obtaining a homogeneous and pure glycoprotein sample is of critical importance for crystal growth and X-ray diffraction, as well as for downstream biophysical characterization. N-linked glycans present on glycoproteins are inherently heterogeneous, and can cause conformational and chemical heterogeneity within the glycoprotein that can deter crystal formation. To reduce this micro-heterogeneity, strategies that introduce point mutations to remove Asn residues predicted to harbor N-linked glycans, or using mutant cell lines (such as HEK293S) followed by treatment with endoglycosidases (such as EndoH) can considerably improve crystallization success15,21,22. In this protocol, we discuss the purification of soluble glycoproteins and Fabs that are secreted into the cell supernatant. Glycoprotein secretion provides a relatively simple route towards purity, without the need for cell lysis or the addition of harsh chemicals or detergents. The cell supernatant, obtained following cell harvesting is then run directly over a column that has affinity for the protein of interest (e.g., Ni-NTA for His-tagged glycoproteins, or LC affinity for Fab fragments). However, depending on the column of use and the conditions of the cell supernatant (e.g., pH), the binding capability of the protein of interest to the column may be affected. If this is the case, it may be necessary to concentrate and buffer exchange the cell supernatant to improve binding to the column. Furthermore, it is strongly recommended that quality control steps during purification be employed to help assess protein purity. Running an SDS-PAGE gel or Western blot of all samples (before, during and after purification steps) can yield insights into whether the proposed purification scheme is suitable for the protein of interest. If contaminating bands are visible on SDS-PAGE, or if several species are obtained during purification (e.g., several peaks on size exclusion), additional purification steps should be considered, e.g., ion exchange chromatography, to gain in purity and increase chances of downstream crystallization80.
For macromolecular crystallization, it is often critical to obtain high yields of the protein of interest to allow for the screening of a large number of potential crystallization conditions at high protein concentrations to find suitable crystal hits. Generally, the HEK293 cell lines discussed here (HEK293F and HEK293S) are robust expression systems, and can be easily scaled up to produce more sample as necessary. However, it is possible that the protein of interest may not express sufficiently within these cell lines. In these cases, other cell lines, such as Expi293 cells81,82, have been found to show superior levels of protein expression and should be considered as an alternative.
If well-ordered, diffracting crystals are not obtained following testing of several constructs of the protein of interest despite high purity, it may be necessary to expand crystallization techniques to promote crystal formation. It has been shown that Fab fragments of antibodies and nanobodies can be&#160;excellent crystallization enhancers, and promote well-ordered crystal packing83,84,85. These fragments can be expressed and purified to homogeneity, and used in a complex with the protein of interest to promote crystallization. Importantly, Fab fragments produced as described in Section 10 can have a tendency to form non-functional LC dimers86. These dimers are contaminants and should be removed during purification. In our experience, LC dimers often have a different retention volume on size exclusion, or elute as a distinct peak on ion exchange chromatography, and thus can be removed from the Fab purification - however this is not always the case. If these techniques are insufficient to remove LC dimers from the Fab purification, additional purification methods, such as Protein G affinity purification, can be employed to improve purity.
Alternative to co-complexation with Fab fragments, well-documented techniques such as random matrix microseeding can improve chances of obtaining well-ordered crystals63,70. This method involves the addition of small amounts of crushed, suboptimal crystals into the crystallization condition, providing a crystal nucleate to promote crystal growth. This can be performed using crystals of the protein of interest, or ones with similar domain architecture and tertiary structure. Furthermore, random matrix microseeding can&#160;be performed in attempts to crystallize the protein alone, or in complex with a Fab fragment or small molecule of interest. Recent advances in cryo-electron microscopy also make this technique an attractive alternative to X-ray crystallography for obtaining high-resolution structural information for molecules with appropriate features87,88,89,90,91.
When phasing of X-ray diffraction datasets fails by MR, HA soaking may be needed to solve the phase problem by anomalous dispersion or isomorphous replacement. Inspection of the amino acid sequence of the protein can provide clues about the strategy for HA derivatization, including optimum pH for binding. In particular, unpaired cysteines within the protein can specifically bind HA compounds that contain mercury. Soaking native crystals with HA compounds is an iterative process to determine the identity of the optimal HA compound, its concentration, and the required incubation time. If initial soaking attempts do not yield well-diffracting crystals containing a HA suitable for phasing, it may be necessary to introduce amino acid substitutions to improve the probability of HA binding and improve anomalous signal. Examples include mutations to include a free cysteine residue to efficiently bind Hg, Au, Pt or Pb. Expression of proteins for anomalous phasing in a seleno-methionine supplemented media in E. coli is extensively used for anomalous phasing, however an equivalent system that reliably incorporates seleno-methionine is not readily available for mammalian cells in suspension92,93, and is an area of future development.
Once the unliganded structure of the glycoprotein of interest is obtained, soaking the crystals with small molecule ligands can be performed to obtain a structure of the immune receptor-ligand complex. These data provide a blueprint for the rational design of more specific and high-affinity ligands that can be used as small-molecule therapeutics as well as provides high resolution insights into the biological function of the glycoprotein. When attempting to soak glycoprotein crystals with small molecule ligands of interest, inspection of the unliganded crystal structure can indicate whether soaking should be possible. If close crystal-packing contacts are found around the ligand-binding site or around regions expected to undergo conformational changes upon ligand binding, soaking will likely be problematic. In this case, other methods such as co-crystallization of the protein-ligand complex should be performed.

Surface proteins play critical roles in cellular function. Through their extracellular domains, these membrane proteins can modulate cell-cell interactions, adhesion, transport and signalling1,2. The extracellular localization of these proteins makes them attractive targets for the development of therapeutics for the treatment of a wide range of diseases, including cancer and autoimmune diseases3,4,5,6,7. One of the most common folds of human membrane protein ectodomains is the immunoglobulin-like (Ig) fold, which is formed by seven or more &#946;-strands arranged into two &#946;-sheets8,9. Typically, Ig-containing glycoproteins are multi-domain structures with Ig domains sequentially arranged on the extracellular portion of the membrane protein10. Post-translational modifications of these cell-surface proteins, particularly N- and O-linked glycosylation, have been shown to play essential roles in their regulation, folding, secretion and function11. To improve our understanding of their function and to better design therapeutics that can target them, techniques are required that allow for their detailed molecular characterization. Here, we present a combination of techniques that allow for the biophysical (biolayer interferometry (BLI) and isothermal titration calorimetry (ITC)) and structural (X-ray crystallography) characterization of the extracellular domain of Ig-containing membrane glycoproteins, alone and&#160; in complex with their biologically relevant ligands and therapeutic molecules (Figure 1).
N-linked glycosylation is one of the most common post-translation modifications on mammalian proteins, and occurs during protein maturation within the endoplasmic reticulum and Golgi12,13. Cell lines, such as human embryonic kidney (HEK) 293 cells, have been developed for the recombinant expression of large quantities of glycosylated mammalian proteins14,15. This cell line has been developed in a suspension format, which allows for the ease of scaling up protein production to larger quantities&#160;in comparison to adherent cell lines. Here, we utilize two HEK293 cell lines: HEK293F and HEK293 Gnt I-/- (HEK293S), which differ by the absence of N-acetylglucosaminyl transferase I (Gnt I) in the latter. In turn, production of complex glycans (as seen in HEK293F) is not possible and instead high mannose-type glycans (predominantly Man5GlcNAc2) reside at&#160;N-linked glycan sites18,19,20. Using these two cell lines in parallel allows studying the effect of glycan size and complexity on biological function and therapeutic targeting. Indeed, glycoproteins produced in HEK293F cells will have larger, more complex glycans compared to the same glycoprotein produced in HEK293S cells. Glycoproteins produced in HEK293S cells are more amenable to crystallization, because of the reduced chemical and conformational heterogeneity of their N-linked glycans. To further improve crystallizability, glycoproteins produced in HEK293S (but not HEK293F) cells can be treated with the enzyme endoglycosidase H (Endo H), which results in the cleavage of high mannose glycans such that only a single N-acetylglucosamine (GlcNAc) moiety remains at each N-linked glycosylation site21,22. Other methods can also be used to limit N-glycan processing within the cells, such as the addition of glycosyltransferase inhibitors during glycoprotein expression, including kifunensine23. Alternative approaches involve the expression of native glycoproteins (in HEK293F cells) followed by enzymatic deglycosylation using peptide N-glycosidase F (PNGaseF). However, deglycosylation with PNGaseF has been shown to be less effective under native conditions and increases aggregation in some proteins; in cases when the protein remains soluble after treatment, it acquires negative charges on its surface due to the deamidation of the asparagine residue to aspartic acid24, which might be detrimental for its crystallization. Predicted N-glycosylation sites can also be mutated, most often to alanine or glutamine residues, to prevent N-linked glycosylation at these sites and to generate glycoprotein samples of high homogeneity. Alternatively, glycoproteins can be produced in other eukaryotic cell cultures, including yeast, insect, and plant systems, or other mammalian cell lines such as Chinese hamster ovarian (CHO) cells16,17.
Many mammalian expression vectors, including pHLsec, allow for the secretion of recombinant glycoprotein ectodomains into the cell medium25. Secretion of glycoproteins from HEK293 cells allows for rapid and easy purification without the need for cell lysis. Addition of purification tags (e.g., His-tag, Strep-tag, Flag-tag, Myc-tag, HA-tag) to the N or C terminus of the target glycoprotein allows purification by a single-step affinity chromatography. Subsequently, size exclusion chromatography can be used to yield a monodisperse sample for biophysical and structural characterization.
A highly pure and homogeneous glycoprotein sample under appropriate conditions can result in well-diffracting crystals. Once a full X-ray diffraction dataset has been obtained from such crystals, initial phases need to be determined to calculate the electron density of the glycoprotein. Thanks to an ever increasing number of structures in the Protein Data Bank (PDB), the most commonly used method for phasing has by far become molecular replacement (MR), which uses a related protein structure to obtain initial phases26. However, when MR fails to solve the phase problem, as has occasionally been the case for multi-Ig domain glycoproteins27,28,29, alternative methods are required. In this article, we detail a method to soak crystals with heavy atoms (HA) for phasing, which was required for solving the structure of the CD22 ectodomain28. Identifying the right HA for phasing is an iterative process that depends on HA reactivity, available atoms in the glycoprotein in a given crystal lattice, and the crystallization solution30,31. Alternatively, natural sulfur atoms in cysteine and methionine residues can be used for phasing if present at a high enough ratio to other atoms in the glycoprotein, and if X-ray diffraction data can be collected with high enough redundancy32,33.
The biological function of membrane glycoproteins is often mediated by protein-protein interactions or protein-ligand interactions, such as with carbohydrates. When the ligand is small enough to diffuse from the solution to the glycoprotein binding site in the crystal lattice, soaking experiments can be successful to obtain a glycoprotein-ligand co-crystal structure to better understand ligand recognition.
The protocols presented here are also relevant for understanding the interactions of surface glycoproteins with synthetic therapeutic ligands34,35 and antibody therapeutics36,37. When combined with structural information, binding kinetics and thermodynamics can be powerful to understand and improve their mechanisms of action. One technique that allows for the kinetic analysis of therapeutic antibodies binding to a glycoprotein is BLI38,39. BLI uses biosensors with an immobilized ligand to measure the association and dissociation kinetics with a binding partner, ultimately determining an equilibrium dissociation constant (KD). BLI is an attractive approach because small amounts of glycoproteins are required (&#60;100 &#181;g), experiment time is fast (~10-15 min per run), and it can be automated. ITC is also useful for studying affinities between glycoproteins and binding partners40,41,42,43. While ITC is more time and reagent intensive, valuable information can be obtained regarding the thermodynamics of the interaction (&#916;G, &#916;H, &#916;S, and stoichiometry). ITC is also very useful for studying weak interactions that are often associated with the transient binding of surface glycoproteins to ligands. Furthermore, these techniques can be used in conjunction to evaluate the binding of various constructs and assess the effect of different N-linked glycoforms obtained from expressing the glycoprotein in different cell lines. Performing BLI and ITC with glycoproteins produced in HEK293F, HEK293S and treated with Endo H can provide an in-depth view of the role of glycans in biological activity and therapeutic engagement.
We successfully applied these protocols to characterize the extracellular domain (ECD) of human CD2228, a glycoprotein member of the sialic acid-binding Ig-like lectins (Siglecs) family that is essential for maintaining B-cell homeostasis44. We performed in-depth construct design to facilitate crystallization and phased the X-ray dataset by HA soaking with Hg. We also soaked CD22 crystals with its ligand sialic acid (&#945;2-6 sialyllactose) to obtain a structure of the immune receptor-ligand complex and thus provided the blueprints for the structure-guided design of glycan mimetics45,46. In addition, we generated the fragment antigen binding (Fab) of the anti-CD22 therapeutic antibody epratuzumab - a therapeutic candidate currently in phase III clinical trials for non-Hodgkin&#39;s lymphoma47- to determine its binding affinity by BLI and ITC to differentially glycosylated CD22 ECD constructs. These studies revealed a critical role for N-linked glycosylation in epratuzumab engagement, with potential implications for CD22 recognition on dysfunctional B cells.

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			<td height="21" style="height:21px;width:345px;">0.22 &#956;m Steritop filter</td>
			<td style="width:163px;">EMD Millipore</td>
			<td style="width:155px;">SCGPS02RE</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">10 well 4-15% gradient SDS-PAGE gel</td>
			<td>Bio-Rad</td>
			<td>4561084</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">10x glycobuffer 3</td>
			<td style="width:163px;">New England Biolabs</td>
			<td style="width:155px;">P0702S</td>
			<td>Comes with Endo H reagent</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">10x Kinetics Buffer</td>
			<td>PALL Fort&#233;Bio</td>
			<td style="width:155px;">18-1092</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">10x Tris/Glycine/SDS Buffer</td>
			<td>Bio-Rad</td>
			<td>1610732</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">1 mL round bottom 96 well block</td>
			<td style="width:163px;">ThermoFisher</td>
			<td style="width:155px;">260251</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">22 mm cover slip</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR3-231</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">4x Laemmli Sample Buffer</td>
			<td>Bio-Rad</td>
			<td>1610747</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:345px;">96-3 well INTELLIPLATE&#160; low volume reservior</td>
			<td style="width:163px;">Art Robbins Instruments</td>
			<td style="width:155px;">102-0001-03</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">AgeI</td>
			<td>New England Biolabs</td>
			<td>R0552S</td>
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		<tr height="21">
			<td height="21" style="height:21px;width:345px;">&#196;KTA Pure</td>
			<td style="width:163px;">GE Healthcare</td>
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			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:345px;">&#196;KTA Start&#160;</td>
			<td style="width:163px;">GE Healthcare</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Amicon Ultra 15 centrifugal filtration device 10KDa MWCO</td>
			<td style="width:163px;">Millipore</td>
			<td style="width:155px;">UFC901008</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Amicon Ultra 4 centrifugal filtration device 10KDa MWCO</td>
			<td style="width:163px;">Millipore</td>
			<td style="width:155px;">UFC801008</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Auto-iTC200</td>
			<td style="width:163px;">Malvern</td>
			<td style="width:155px;"></td>
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			<td height="21" style="height:21px;">Axygen MaxyClear Snaplock 1.5 mL microtubes</td>
			<td>Fisher Scientific</td>
			<td>MCT150C</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Countess Cell Counting Chamber Slides</td>
			<td>Thermo Fisher Scientific</td>
			<td>C10228</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">CryoLoop 18 x 0.05-0.1 mm</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR4-945</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:345px;">CryoLoop 18 x 0.1-0.2 mm</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR4-947</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">CryoLoop 18 x 0.2-0.3 mm</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR4-970</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Digital Dry Bath</td>
			<td>Bio-Rad</td>
			<td>1660562EDU</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">E. coli DH5&#945;</td>
			<td>Invitrogen</td>
			<td>18258012</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Endo H</td>
			<td style="width:163px;">New England Biolabs</td>
			<td style="width:155px;">P0702S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Erlenmeyer flask (baffled base), polycarbonate, sterile, 500 mL, DuoCAP</td>
			<td>TriForest Labware</td>
			<td>FBC05000S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Erlenmeyer flask 125 mL (baffled base), polycarbonate, sterile, 125 mL with vented cap</td>
			<td>VWR</td>
			<td>89095-258</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Falcon Disposable sterile serological pipet, non-pyrogenic, 10 mL</td>
			<td>Greiner Bio-One</td>
			<td>607180</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Falcon Disposable sterile serological pipet, non-pyrogenic, 25 mL</td>
			<td>Greiner Bio-One</td>
			<td>760180</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Falcon Disposable sterile serological pipet, non-pyrogenic, 5 mL</td>
			<td>Greiner Bio-One</td>
			<td>606180</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Falcon Disposable sterile serological pipet, non-pyrogenic, 50 mL</td>
			<td>Greiner Bio-One</td>
			<td>768180</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">FectoPRO DNA Transfection Reagent, Polyplus</td>
			<td>VWR</td>
			<td>10118-842</td>
			<td></td>
		</tr>
		<tr height="18">
			<td height="18" style="height:19px;">Freestyle 293F cells</td>
			<td>Thermo Fisher Scientific</td>
			<td>R79007</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Freestyle Expression medium</td>
			<td>Thermo Fisher Scientific</td>
			<td>12338001</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Heavy Atom Screens Au</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR2-444</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Heavy Atom Screens Hg</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR2-446</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Heavy Atom Screens M1</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR2-448</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Heavy Atom Screens M2</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR2-450</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Heavy Atom Screens Pt</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR2-442</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HEK 293S</td>
			<td>ATCC</td>
			<td>ATCC CRL-3022</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HisTrap Affinity Column</td>
			<td>GE Healthcare</td>
			<td>17525501</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">HiTrap KappaSelect Affinity Columns</td>
			<td style="width:163px;">GE Healthcare</td>
			<td style="width:155px;">17545811</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">HiTrap LambdaSelect Affinity Columns</td>
			<td style="width:163px;">GE Healthcare</td>
			<td style="width:155px;">17548211</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">KpnI</td>
			<td>New England Biolabs</td>
			<td>R0142S</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">MCSG-1 Crystal Screen 1.7 mL block</td>
			<td style="width:163px;">Anatrace</td>
			<td style="width:155px;">MCSG-1</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">MCSG-2 Crystal Screen 1.7 mL block</td>
			<td style="width:163px;">Anatrace</td>
			<td style="width:155px;">MCSG-2</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">MCSG-3 Crystal Screen 1.7 mL block</td>
			<td style="width:163px;">Anatrace</td>
			<td style="width:155px;">MCSG-3</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">MCSG-4 Crystal Screen 1.7 mL block</td>
			<td style="width:163px;">Anatrace</td>
			<td style="width:155px;">MCSG-4</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Mercuric chloride</td>
			<td style="width:163px;">Sigma</td>
			<td style="width:155px;">1044170100</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Microplate, 96 well, polypropelene, flat bottom, black&#160;</td>
			<td style="width:163px;">Greiner Bio-One</td>
			<td style="width:155px;">655209</td>
			<td style="width:197px;"></td>
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			<td height="21" style="height:21px;width:345px;">Minstrel DT UV</td>
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			<td height="21" style="height:21px;">Multitron Pro shaker</td>
			<td>Infors HT</td>
			<td>MP25-TA-CO2HB</td>
			<td style="width:197px;"></td>
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		<tr height="42">
			<td height="42" style="height:42px;width:345px;">Nanodrop 2000/2000c Spectrophotometer</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
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			<td style="width:197px;"></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Nanosep 3K Omega centrifugal device</td>
			<td style="width:163px;">PALL Life Science</td>
			<td style="width:155px;">OD003C33</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ni-NTA biosensors</td>
			<td>PALL Fort&#233;Bio</td>
			<td>18-5102</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Octet RED96</td>
			<td style="width:163px;">PALL ForteBio</td>
			<td style="width:155px;"></td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Oryx 4 crystallizaiton robot</td>
			<td style="width:163px;">Douglas Instrument</td>
			<td style="width:155px;">ORY-4/1</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Platinum chloride</td>
			<td style="width:163px;">Sigma</td>
			<td style="width:155px;">520632-1g</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Precision Plus Protein Standard</td>
			<td>Bio-Rad</td>
			<td>161-0374</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PureLink HiPure Plasmid Maxiprep Kit</td>
			<td>Invitrogen</td>
			<td>K210006</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Quick Coomassie Stain</td>
			<td>Protein Ark</td>
			<td>GEN-QC-STAIN-1L</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Steriflip Sterile 50 mL Disposable Vacuum Filtration System 0.22 &#181;m Millipore Express</td>
			<td>EMD Millipore</td>
			<td>SCGP00525</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Superdex 200 Increase 10/300 GL</td>
			<td style="width:163px;">GE Healthcare</td>
			<td style="width:155px;">28990944</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Superose 6 10/300 GL</td>
			<td style="width:163px;">GE Healthcare</td>
			<td style="width:155px;">17517201</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Tantalum bromide cluster</td>
			<td style="width:163px;">Jena bioscience</td>
			<td style="width:155px;">PK-103</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">Top96 Crystallization Screen</td>
			<td style="width:163px;">Rigaku Reagents</td>
			<td style="width:155px;">1009846</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tryphan Blue</td>
			<td>Thermo Fisher Scientific</td>
			<td>T10282</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">VDX 24-well with sealant</td>
			<td style="width:163px;">Hampton research</td>
			<td style="width:155px;">HR3-172</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:345px;">&#945;2-6 sialyllactose</td>
			<td style="width:163px;">Sigma Aldrich</td>
			<td style="width:155px;">A8556-1mg</td>
			<td style="width:197px;"></td>
		</tr>
	</tbody>
</table>

characterization of glycoproteins with the immunoglobulin fold by x-ray crystallography and biophysical techniques

Glycoproteins on the surface of cells play critical roles in cellular function, including signalling, adhesion and transport. On leukocytes, several of these glycoproteins possess immunoglobulin (Ig) folds and are central to immune recognition and regulation. Here, we present a platform for the design, expression and biophysical characterization of the extracellular domain of human B cell receptor CD22. We propose that these approaches are broadly applicable to the characterization of mammalian glycoprotein ectodomains containing Ig domains. Two suspension human embryonic kidney (HEK) cell lines, HEK293F and HEK293S, are used to express glycoproteins harbouring complex and high-mannose glycans, respectively. These recombinant glycoproteins with different glycoforms allow investigating the effect of glycan size and composition on ligand binding. We discuss protocols for studying the kinetics and thermodynamics of glycoprotein binding to biologically relevant ligands and therapeutic antibody candidates. Recombinant glycoproteins produced in HEK293S cells are amenable to crystallization due to glycan homogeneity, reduced flexibility and susceptibility to endoglycosidase H treatment. We present methods for soaking glycoprotein crystals with heavy atoms and small molecules for phase determination and analysis of ligand binding, respectively. The experimental protocols discussed here hold promise for the characterization of mammalian glycoproteins to give insight into their function and investigate the mechanism of action of therapeutics.

Several constructs of CD22 ECD were successfully cloned into the pHLsec expression vector and overexpressed in mammalian HEK293F and HEK293S cell lines (Figure&#160;2 and 3A). All constructs were purified to size homogeneity by size exclusion chromatography and yielded a highly pure sample for crystallization studies (Figure&#160;3B and 3C). The CD22 construct that led to well-diffracting crystals was the d1-d3 truncation (residues 20-330), with&#160;five&#160;of the six predicted N-linked glycosylation sites mutated from Asn to Ala (N67A, N112A, N135A, N164A and N231A), produced in HEK293S cells, such that only the glycosylation site at position N101 was retained (this construct is named CD2220-330, 5A). Crystals were obtained in several conditions of the MCSG-1 sparse-matrix screen, but the best crystals were from a condition containing 30% (w/v) polyethylene glycol 4000, 0.2 M lithium chloride and 0.1 M Tris, pH 8.5. These native crystals diffracted to 2.1 &#197; resolution; using known structures of Ig domains of related Siglec proteins did not yield any solutions in MR searches.
To acquire phasing information, we soaked native crystals with a panel of HA compounds that included Hg, Pt, Os, Ta, and Br at concentrations ranging from 1-20 mM of HA compound for an incubation time from 5 min to 1 d (Figure 4). We monitored crystals for changes in morphology, and found that crystals soaked with HA compound at 20 mM resulted in the rapid cracking and dissolving of the crystal. We froze a total of 63 crystals that retained their shape following set incubation times that were soaked with tantalum bromide cluster, platinum chloride, mercuric acetate and mercuric chloride. Crystals soaked with 7 mM of mercuric chloride for 30 min showed anomalous signal on a fluorescence scan at the Canadian Light Source (CLS) 08-BM beamline (Saskatoon, Canada) and allowed for multi-wavelength anomalous dispersion X-ray data collection on a single crystal. These datasets allowed us to solve the mercury substructure of CD2220-330, 5A, which revealed a single mercury atom bound to a free cysteine at position C308 and ultimately allowed us to build the structure of CD2220-330, 5A into the phased electron density map using AutoBuild78.
Once the unliganded structure was solved, we were interested in solving the structure of CD22 bound to its ligand, &#945;2-6 siallylactose. We first calculated the affinity of CD22 towards &#945;2-6 sialyllactose using ITC to characterize the binding thermodynamics of the interaction. We observed an affinity of ~280 &#181;M and used this information to identify an initial concentration (~ 100 x KD) of ligand to use for soaking of our native CD2220-330,5A crystals. We soaked the CD2220-330, 5A crystals with 25 mM siallylactose for 5 min, 2 h, 14 h, 40 h and 5 d and monitored for changes in crystal morphology. A total of ~75 crystals were frozen from various time points and sent to the CLS synchrotron beamline 08-ID (Saskatoon, Canada) for remote data collection. A total of six X-ray datasets were collected from well-diffracting crystals. The structure from each X-ray dataset was solved by MR&#160;using the unliganded CD2220-330, 5A structure as an initial search model. The resulting electron density for all datasets was then inspected for positive density in the Fo-Fc map that would correspond to bound &#945;2-6 sialyllactose within the binding site of CD22. Remarkably, all datasets collected, even those from crystals soaked after only 5 min of incubation time, contained positive density corresponding to the ligand in the binding site. Overall structures of the unliganded and liganded CD22 were highly similar with minimal conformational changes, which might explain the success of soaking experiments with &#945;2-6 sialyllactose.
We next characterized the antigenic surface of CD22 recognized by therapeutic antibody epratuzumab in BLI and ITC experiments (Figure 5). Kinetics and thermodynamics profiles of epratuzumab Fab binding to CD22 constructs with different glycoforms revealed an increasing affinity to CD22 with reduced N-linked glycan size, with up to a 14-fold improvement in affinity for smaller glycans (327 nM vs 24 nM in BLI; 188 nM vs 58 nM in ITC). The CD22 N-linked glycan restricting access of the antibody to its epitope was identified by BLI using single-point mutants of CD22 and by solving the epratuzumab Fab-CD22 d1-d3 co-crystal structure28.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/57750/57750fig1.jpg" /> 
Figure 1. Overview of glycoprotein characterization from construct design to biophysical and structural characterization. (1) Primary sequence analysis of representative glycoprotein. In grey, the extracellular domain (ECD); in green, the transmembrane (TM) segment; and in blue, the cytosolic domain of the glycoprotein. Predicted N-linked glycans are labeled. (2) Cloning of ECD constructs. (3) Expression of ECD constructs in mammalian cells. (4) Glycoprotein purification. While proteins expressed in HEK293F will contain complex glycans, proteins expressed in HEK293S will have high mannose glycans. Enzymatic treatment of glycoproteins produced in HEK293S cells with Endo H results in glycoproteins with only a GlcNAc moiety at N-linked glycosylation sites. (5a) Glycoproteins are tested for their binding to antibodies by biolayer interferometry (BLI) and isothermal titration calorimetry (ITC). Affinity to small ligands can also be measured by ITC. (5b) Crystallization trials of glycoproteins with homogeneous N-linked glycans, such as those expressed in HEK293S and deglycosylated with Endo H. (6) In some cases, mutation of N-linked glycosylation sites is necessary to obtain crystals. <a href="https://www.jove.com/files/ftp_upload/57750/57750fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/57750/57750fig2.jpg" /> 
Figure 2. Design of CD22 ectodomain DNA constructs for expression in mammalian cells.&#160;A) Representation of the pHLsec plasmid used for transient transfection of CD22 ECD constructs. AgeI and KpnI sites used for cloning are indicated with red boxes. B) The CD22 ECD contains seven Ig domains (d1-d7) and 12 predicted N-linked glycosylation sites (in blue). Four constructs were designed from the CD22 ECD. C) 1% agarose gel showing PCR amplicons of CD22 ECD constructs for cloning into the pHLsec mammalian expression vector. First lane contains 1 kb DNA marker. <a href="https://www.jove.com/files/ftp_upload/57750/57750fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/57750/57750fig3.jpg" /> 
Figure 3. Expression and purification of glycoproteins.&#160;A) Effect of cell density on expression yields. Glycoprotein expression in small-scale 25 mL culture of HEK293F suspension cells transfected using three different starting densities of cells (0.5 x 106 cells mL-1, 1.0 x 106 cells mL-1, and 1.5 x 106 cells mL-1). Quantification performed by densitometry from SDS-PAGE in left panel and by quantitative BLI in right panel. Values are representative of one glycoprotein preparation. B) Chromatogram of the first purification step for construct CD2220-330, 5A from 600 mL of supernatant using a Ni-NTA affinity column. The glycoprotein was eluted using a gradient of imidazole (grey line), where 100% corresponds to the elution buffer, which contains 500 mM imidazole. Pooled fractions are depicted with vertical lines. C) Size-exclusion chromatogram for construct CD2220-330,5A using a high-performance gel filtration column. Pooled fractions from the elution peak are depicted with vertical lines. Inset: Coomassie-stained SDS-PAGE gel showing the purity of the glycoprotein. <a href="https://www.jove.com/files/ftp_upload/57750/57750fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/57750/57750fig4.jpg" /> 
Figure 4. Crystal soaking with heavy atoms. A) Sample workstation for soaking native crystals with HA compounds. All required tools are labeled. B) Steps followed to soak crystals of construct CD2220-330, 5A with HA compounds. Step 1, Open well containing crystals, and transfer crystals using a loop to a 0.2 &#181;L drop on a cover slip containing HA solution diluted in the crystallization condition such that the final concentration of HA ranges from 1-10 mM. Step 2, seal the drop in the crystallization plate and incubate crystals with the HA compound for different periods of time. Step 3, mount the soaked crystal in the loop and back-soak for 30 s in three consecutive 0.2 &#181;l drops containing the mother liquor solution supplemented with 20% (v/v) glycerol dispensed on a cover slip. Step 4, flash freeze the crystal mounted on a loop with liquid nitrogen and place it in a puck for shipment to the synchrotron beamline. <a href="https://www.jove.com/files/ftp_upload/57750/57750fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/57750/57750fig5.jpg" /> 
Figure 5. Biolayer interferometry and isothermal titration calorimetry measurements. A) Representative BLI experiment. Top panel: example of plate setup for a kinetics experiment, where the following are labeled: 1x kinetics buffer (B), His6x-tagged glycoprotein loading (L), representative Fab concentrations (500, 250, 125,&#160; 62.5&#160;nM), PBS + 500 mM regeneration buffer (R), and 1x kinetics neutralization buffer (B). Each well contains 200 &#181;L of solution. Step number for the kinetics experiment is indicated at the top of the plate. Middle panel: Representative raw data of BLI experiment performed using Ni-NTA biosensors and the plate described in the top panel. Step numbers correspond to baseline (1), His6x glycoprotein loading (2), baseline (3), association in serial dilution of Fab (4) and dissociation (5). Regeneration steps are not represented (Steps 6-7). Bottom panel: Representative analyzed data showing raw association and dissociation (blue line) with the corresponding 1:1 fit (red line). B)&#160;Top panel: Representative plate setup for a single ITC run on an automated ITC instrument with seven experiments in a 96-well round bottom block. Each experiment is comprised of three wells. The first well (red) corresponds to sample for the cell (400 &#181;L), the second well (green) corresponds to sample for the syringe (120 &#181;L). The third well is left empty, and the mixed samples will be returned to this well following experiment completion. Experiments 1, 2, and 7 are buffer into buffer controls. Experiments 3-5 represent triplicate experiments with glycoprotein (P) in the cell and Fab or ligand (L) in the syringe. Experiment 6 represents a ligand heat of dilution control and should be subtracted from experiments 3-5 during data analysis. Bottom panel: Representative raw (top) and processed (bottom) ITC data showing Fab (epratuzumab) binding to CD22 ECD produced in HEK293F cells. <a href="https://www.jove.com/files/ftp_upload/57750/57750fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques at JoVE.com

Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques

We present approaches for the biophysical and structural characterization of glycoproteins with the immunoglobulin fold by biolayer interferometry, isothermal titration calorimetry, and X-ray crystallography.

Glycoproteins on the surface of cells play critical roles in cellular function, including signalling, adhesion and transport. On leukocytes, several of ...

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12.5K Views.  The Hospital for Sick Children Research Institute. We present approaches for the biophysical and structural characterization of glycoproteins with the immunoglobulin fold by biolayer interferometry, isothermal titration calorimetry, and X-ray crystallography.

Video: Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques

Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography

Membrane proteins (MPs) are essential components of cellular membranes and primary drug targets. Rational drug design relies on precise structural information, typically obtained by crystallography; however MPs are difficult to crystallize. Recent progress in MP structural determination has benefited greatly from the development of lipidic cubic phase (LCP) crystallization methods, which typically yield well-diffracting, but often small crystals that suffer from radiation damage during traditional crystallographic data collection at synchrotron sources. The development of new-generation X-ray free-electron laser (XFEL) sources that produce extremely bright femtosecond pulses has enabled room temperature data collection from microcrystals with no or negligible radiation damage. Our recent efforts in combining LCP technology with serial femtosecond crystallography (LCP-SFX) have resulted in high-resolution structures of several human G protein-coupled receptors, which represent a notoriously difficult target for structure determination. In the LCP-SFX technique, LCP is recruited as a matrix for both growth and delivery of MP microcrystals to the intersection of the injector stream with an XFEL beam for crystallographic data collection. It has been demonstrated that LCP-SFX can substantially improve the diffraction resolution when only sub-10 &#181;m crystals are available, or when the use of smaller crystals at room temperature can overcome various problems associated with larger cryocooled crystals, such as accumulation of defects, high mosaicity and cryocooling artifacts. Future advancements in X-ray sources and detector technologies should make serial crystallography highly attractive and practicable for implementation not only at XFELs, but also at more accessible synchrotron beamlines. Here we present detailed visual protocols for the preparation, characterization and delivery of microcrystals in LCP for serial crystallography experiments. These protocols include methods for conducting crystallization experiments in syringes, detecting and characterizing the crystal samples, optimizing crystal density, loading microcrystal laden LCP into the injector device and delivering the sample to the beam for data collection.

We describe procedures for the preparation and delivery of membrane protein microcrystals in lipidic cubic phase for serial crystallography at X-ray free-electron lasers and synchrotron sources. These protocols can also be applied for incorporation and delivery of soluble protein microcrystals, leading to substantially reduced sample consumption compared to liquid injection.

Membrane proteins (MPs) are essential components of cellular membranes and primary drug targets. Rational drug design relies on precise structural ...

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 ...

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Protein-protein interactions involving proteins with multiple globular domains present technical challenges for determining how such complexes form and how the domains are oriented/positioned. Here, a protocol with the potential for elucidating which specific domains mediate interactions in multicomponent system through ab initio modeling is described. A method for calculating solution structures of macromolecules and their assemblies is provided that involves integrating data from small angle X-ray scattering (SAXS), chromatography, and atomic resolution structures together in a hybrid approach. A specific example is that of the complex of full-length nidogen-1, which assembles extracellular matrix proteins and forms an extended, curved nanostructure. One of its globular domains attaches to laminin &#947;-1, which structures the basement membrane. This provides a basis for determining accurate structures of flexible multidomain protein complexes and is enabled by synchrotron sources coupled with automation robotics and size exclusion chromatography systems. This combination allows rapid analysis in which multiple oligomeric states are separated just prior to SAXS data collection. The analysis yields information on the radius of gyration, particle dimension, molecular shape and interdomain pairing. The protocol for generating 3D models of complexes by fitting high-resolution structures of the component proteins is also given.

Here, we present how Small Angle X-Ray Scattering (SAXS) can be utilized to obtain information on low-resolution envelopes representing the macromolecular structures. When used in conjunction with high-resolution structural techniques such as X-Ray Crystallography and Nuclear Magnetic Resonance, SAXS can provide detailed insights into multidomain proteins and macromolecular complexes in-solution.

Protein-protein interactions involving proteins with multiple globular domains present technical challenges for determining how such complexes form and ...

Characterization of Proteins by Size-Exclusion Chromatography Coupled to Multi-Angle Light Scattering (SEC-MALS)

Analytical size-exclusion chromatography (SEC), commonly used for the determination of the molecular weight of proteins and protein-protein complexes in solution, is a relative technique that relies on the elution volume of the analyte to estimate molecular weight. When the protein is not globular or undergoes non-ideal column interactions, the calibration curve based on protein standards is invalid, and the molecular weight determined from elution volume is incorrect. Multi-angle light scattering (MALS) is an absolute technique that determines the molecular weight of an analyte in solution from basic physical equations. The combination of SEC for separation with MALS for analysis constitutes a versatile, reliable means for characterizing solutions of one or more protein species including monomers, native oligomers or aggregates, and heterocomplexes. Since the measurement is performed at each elution volume, SEC-MALS can determine if an eluting peak is homogeneous or heterogeneous and distinguish between a fixed molecular weight distribution versus dynamic equilibrium. Analysis of modified proteins such as glycoproteins or lipoproteins, or conjugates such as detergent-solubilized membrane proteins, is also possible. Hence, SEC-MALS is a critical tool for the protein chemist who must confirm the biophysical properties and solution behavior of molecules produced for biological or biotechnological research. This protocol for SEC-MALS analyzes the molecular weight and size of pure protein monomers and aggregates. The data acquired serve as a foundation for further SEC-MALS analyses including those of complexes, glycoproteins and surfactant-bound membrane proteins.

Characterization of Proteins by Size-Exclusion Chromatography Coupled to Multi-Angle Light Scattering SEC-MALS

This protocol describes the combination of size exclusion chromatography with multi-angle light scattering (SEC-MALS) for absolute characterization of proteins and complexes in solution. SEC-MALS determines the molecular weight and size of pure proteins, native oligomers, heterocomplexes and modified proteins such as glycoproteins.

Analytical size-exclusion chromatography (SEC), commonly used for the determination of the molecular weight of proteins and protein-protein complexes in ...

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. A prerequisite for the method is that highly ordered crystalline specimen need to be grown from the macromolecule to be studied, which then need to be prepared for the diffraction experiment. This preparation procedure typically involves removal of the crystal from the solution, in which it was grown, soaking of the crystal in ligand solution or cryo-protectant solution and then immobilizing the crystal on a mount suitable for the experiment. A serious problem for this procedure is that macromolecular crystals are often mechanically unstable and rather fragile. Consequently, the handling of such fragile crystals can easily become a bottleneck in a structure determination attempt. Any mechanical force applied to such delicate crystals may disturb the regular packing of the molecules and may lead to a loss of diffraction power of the crystals. Here, we present a novel all-in-one sample holder, which has been developed in order to minimize the handling steps of crystals and hence to maximize the success rate of the structure determination experiment. The sample holder supports the setup of crystal drops by replacing the commonly used microscope cover slips. Further, it allows in-place crystal manipulation such as ligand soaking, cryo-protection and complex formation without any opening of the crystallization cavity and without crystal handling. Finally, the sample holder has been designed in order to enable the collection of in situ X-ray diffraction data at both, ambient and cryogenic temperature. By using this sample holder, the chances to damage the crystal on its way from crystallization to diffraction data collection are considerably reduced since direct crystal handling is no longer required.

A novel sample holder for macromolecular X-ray crystallography along with a suitable handling protocol is presented. The system allows crystal growth, crystal soaking and in situ diffraction data collection at both, ambient and cryogenic temperature without the need of any crystal manipulation or mounting.

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. ...

Cell Culture on Silicon Nitride Membranes and Cryopreparation for Synchrotron X-ray Fluorescence Nano-analysis

Very little is known about the distribution of metal ions at the subcellular level. However, those chemical elements have essential regulatory functions and their disturbed homeostasis is involved in various diseases. State-of-the-art synchrotron X-ray fluorescence nanoprobes provide the required sensitivity and spatial resolution to elucidate the two-dimensional (2D) and three-dimensional (3D) distribution and concentration of metals inside entire cells at the organelle level. This opens new exciting scientific fields of investigation on the role of metals in the physiopathology of the cell. The cellular preparation is a key and often complex procedure, particularly for basic analysis. Although X-ray fluorescence techniques are now widespread and various preparation methods have been used, very few studies have investigated the preservation of the elemental content of cells at best, and no stepwise detailed protocol for the cryopreparation of adherent cells for X-ray fluorescence nanoprobes has been released so far. This is a description of a protocol that provides the stepwise cellular preparation for fast cryofixation to enable synchrotron X-ray fluorescence nano-analysis of cells in a frozen hydrated state when a cryogenic environment and transfer is available. In case nano-analysis has to be performed at room temperature, an additional procedure for freeze-drying the cryofixed adherent cellular preparation is provided. The proposed protocols have been successfully used in previous works, most recently in studying the 2D and 3D intracellular distribution of an organometallic compound in breast cancer cells.

Presented here is a protocol for cell culture on silicon nitride membranes and plunge-freezing prior to X-ray fluorescence imaging with a synchrotron cryogenic X-ray nanoprobe. When only room temperature nano-analysis is provided, the frozen samples can be further freeze-dried. These are critical steps to obtain information on the intracellular elemental composition.

Very little is known about the distribution of metal ions at the subcellular level. However, those chemical elements have essential regulatory functions ...

Visualization of Estrogen Receptors in Colons of Mice with TNBS-Induced Crohn's Disease using Immunofluorescence

Crohn&#39;s disease is the most diagnosed type of inflammatory bowel disease. Chronic inflammation developing in the intestine leads to peristalsis disorder and damage of intestinal mucosa and seems to be associated with an increased risk of colon neoplastic transformation. Accumulating evidence indicates that estrogens and estrogen receptors affect not only hormone-sensitive tissues, but also other tissues not directly related to estrogens, such as the lungs or colon. Here, we describe the protocol for the successful immunofluorescence staining of estrogen receptors in colon obtained from a murine model of TNBS-induced Crohn&#39;s disease. A detailed protocol for the induction of Crohn&#39;s disease in mice and intestine preparation is provided as well as a step-by-step immunohistochemical procedure using formalin-fixed paraffin-embedded intestine sections. The described methods are not only useful for estrogen receptor detection and estrogen signaling investigation in vivo but can also be applied to for other proteins which may be involved in the development of colitis.

The protocol presents a complete validated TNBS-induced murine model of Crohn&#39;s disease and methods for visualization of estrogen receptors by immunohistochemistry using immunofluorescence of formalin-fixed colon sections embedded in paraffin.

Crohn&#39;s disease is the most diagnosed type of inflammatory bowel disease. Chronic inflammation developing in the intestine leads to peristalsis ...

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

The M42 aminopeptidases form functionally active complexes made of 12 subunits. Their assembly process appears to be regulated by their metal ion cofactors triggering a dimer-dodecamer transition. Upon metal ion binding, several structural modifications occur in the active site and at the interaction interface, shaping dimers to promote the self-assembly. To observe such modifications, stable oligomers must be isolated prior to structural study. Reported here is a method that allows the purification of stable dodecamers and dimers of TmPep1050, an M42 aminopeptidase of T. maritima, and their structure determination by X-ray crystallography. Dimers were prepared from dodecamers by removing metal ions with a chelating agent. Without their&#160;cofactor, dodecamers became less stable and were fully dissociated upon heating. The oligomeric structures were solved by the straightforward molecular replacement approach. To illustrate the methodology, the structure of a TmPep1050 variant, totally impaired in metal ion binding, is presented showing no further breakdown of dimers to monomers.

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

This protocol has been developed to study the dimer-dodecamer transition of TmPep1050, an M42 aminopeptidase, at the structural level. It is a straightforward pipeline starting from protein purification to X-ray data processing. Crystallogenesis, data set indexation, and molecular replacement have been emphasized through a case of study, TmPep1050H60A H307A variant.

The M42 aminopeptidases form functionally active complexes made of 12 subunits. Their assembly process appears to be regulated by their metal ion ...

Optimizing the Growth of Endothiapepsin Crystals for Serial Crystallography Experiments

Here, a protocol is presented to facilitate the creation of large volumes (&#62; 100 &#181;L) of micro-crystalline slurries suitable for serial crystallography experiments at both synchrotrons and XFELs. The method is based upon an understanding of the protein crystal phase diagram, and how that knowledge can be utilized. The method is divided into three stages: (1) optimizing crystal morphology, (2) transitioning to batch, and (3) scaling. Stage 1 involves finding well diffracting, single crystals, hopefully but not necessarily, presenting in a cube-like morphology. In Stage 2, the Stage 1 condition is optimized by crystal growth time. This strategy can transform crystals grown by vapor diffusion to batch. Once crystal growth can occur within approximately 24 h, a morphogram of the protein and precipitant mixture can be plotted and used as the basis for a scaling strategy (Stage 3). When crystals can be grown in batch, scaling can be attempted, and the crystal size and concentration optimized as the volume is increased. Endothiapepsin has been used as a demonstration protein for this protocol. Some of the decisions presented are specific to endothiapepsin. However, it is hoped that the way they have been applied will inspire a way of thinking about this procedure that others can adapt to their own projects.

The aim of this article is to give the viewer a solid understanding of how to transform their small-volume, vapor-diffusion protocol, for growing large, single protein crystals, into a large-volume batch micro-crystallization method for serial crystallography.

Here, a protocol is presented to facilitate the creation of large volumes (&#62; 100 &#181;L) of micro-crystalline slurries suitable for serial ...

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

The preparation of well diffracting crystals and their handling before their X-ray analysis are two critical steps of biocrystallographic studies. We describe a versatile microfluidic chip that enables the production of crystals by the efficient method of counter-diffusion. The convection-free environment provided by the microfluidic channels is ideal for crystal growth and useful to diffuse a substrate into the active site of the crystalline enzyme. Here we applied this approach to the CCA-adding enzyme of the psychrophilic bacterium Planococcus halocryophilus in the presented example. After crystallization and substrate diffusion/soaking, the crystal structure of the enzyme:substrate complex was determined at room temperature by serial crystallography and the analysis of multiple crystals directly inside the chip. The whole procedure preserves the genuine diffraction properties of the samples because it requires no crystal handling.

A versatile microfluidic device is described that enables the crystallization of an enzyme using the counter-diffusion method, the introduction of a substrate in the crystals by soaking, and the 3D structure determination of the enzyme:substrate complex by a serial analysis of crystals inside the chip at room temperature.

The preparation of well diffracting crystals and their handling before their X-ray analysis are two critical steps of biocrystallographic studies. We ...