Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies

Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1A and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryo-electron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.

The solution structure of the human IgG2 subclass is distinct from those for human IgG1 and IgG4 providing an explanation for their discrete functions

Human IgG2 antibody displays distinct therapeutically-useful properties compared with the IgG1, IgG3, and IgG4 antibody subclasses. IgG2 is the second most abundant IgG subclass, being able to bind human FcγRII/FcγRIII but not to FcγRI or complement C1q. Structural information on IgG2 is limited by the absence of a full-length crystal structure for this. To this end, we determined the solution structure of human myeloma IgG2 by atomistic X-ray and neutron-scattering modeling. Analytical ultracentrifugation disclosed that IgG2 is monomeric with a sedimentation coefficient (s20, w0) of 7.2 S. IgG2 dimer formation was ≤5% and independent of the buffer conditions. Small-angle X-ray scattering in a range of NaCl concentrations and in light and heavy water revealed that the X-ray radius of gyration (Rg ) is 5.2-5.4 nm, after allowing for radiation damage at higher concentrations, and that the neutron Rg value of 5.0 nm remained unchanged in all conditions. The X-ray and neutron distance distribution curves (P(r)) revealed two peaks, M1 and M2, that were unchanged in different buffers. The creation of >123,000 physically-realistic atomistic models by Monte Carlo simulations for joint X-ray and neutron-scattering curve fits, constrained by the requirement of correct disulfide bridges in the hinge, resulted in the determination of symmetric Y-shaped IgG2 structures. These molecular structures were distinct from those for asymmetric IgG1 and asymmetric and symmetric IgG4 and were attributable to the four hinge disulfides. Our IgG2 structures rationalize the existence of the human IgG1, IgG2, and IgG4 subclasses and explain the receptor-binding functions of IgG2.

Immunoglobulin G Expression in Human Sperm and Possible Functional Significance

Immunoglobulin G (IgG), the major molecule of the immune system, which was traditionally thought to be produced by differentiated B-lymphocytes, had recently been found in non-immune cells including spermatozoa of rabbit testis. To study if human sperms could produce IgG that might play a role in fertilization, we employed immunofluorescent staining, Western blot, in situ hybridization, RT-PCR (reverse transcription polymerase chain reaction) and immunoelectron microscope and found that human sperms were capable of synthesizing IgG. IgG protein and mRNA were detected in the cytoplasm, mainly the neck region of the sperm and IgG immunoreactivity was found to cover the entire sperm cell. The essential enzymes necessary for IgG synthesis and class switching, RAG1 (recombination activating gene 1), RAG2 (recombination activating gene 2) and AID (activation-induced cytidine deaminase), were also detected in the sperm cells. Furthermore, we found that anti-IgG antibody could inhibit sperm from penetrating Zona-free hamster egg with statistical significance. These discoveries suggested that immunoglobulin G could be produced by human sperms and it might play a role during fertilization.

Proteomic Investigation on Grp94-IgG Complexes Circulating in Plasma of Type 1 Diabetic Subjects

The glucose-regulated protein94 (Grp94) has been found in complexes with IgG in plasma of Type 1 (T1) diabetic subjects; however, the pathogenetic meaning of Grp94-IgG complexes has not yet been elucidated. To shed light on the nature and structure of these complexes in vivo, we conducted a proteomic analysis on plasma of both T1 diabetic subjects and healthy control subjects. IgG purified from plasma was submitted to 2D PAGE followed by Western blotting and mass analysis. Grp94 was detected in plasma of all diabetic but not control subjects and found linked with its N-terminus to the IgG heavy chain. Mass analysis of heavy chain of IgG that binds Grp94 also in vitro, forming stable complexes with characteristics similar to those of native ones, permitted identifying CH2 and CH3 regions as those involved in binding Grp94. At the electron microscopy, IgG from diabetic plasma appeared as fibrils of various lengthes and dimensions, suggestive of elevated aggregating tendency conferred to IgG by Grp94. The nonimmune nature of complexes turned out to be responsible for the particular stability and structure adopted by complexes in plasma of diabetic subjects. Results are of relevance to understanding the pathogenetic mechanisms underlying diabetes and its complications.

Self-assembled proteinticle nanostructures for 3-dimensional display of antibodies

"Proteinticle" is a nano-scale protein particle that is self-assembled inside cells with constant 3D structure and surface topology. The binding of IgG to the B domain of Staphylococcal protein A (SPA(B)) molecules that are genetically inserted on the surface of proteinticle enables the variable domains of bound IgG to be well oriented to effectively capture antigens, accordingly forming a highly sensitive 3D IgG probe. The five different proteinticles that originate from humans, bacteria, and virus and totally differ in size, shape, and surface structure were used for the surface display of SPA(B). The dissociation constant (K(D)) in the binding of IgG to SPA(B) on the proteinticle surface was estimated based on the Langmuir adsorption isotherm model: K(D) was 1-3 orders-of-magnitude lower compared to the previously reported K(D) in the binding of IgG to Staphylococcal protein A. The surface density and distribution of SPA(B) and especially the existence of hot (or highly congested) spots of SPA(B), which depend on the surface structure and the number of subunits as well as size and shape of proteinticle, is of crucial importance for the effective binding of IgG to SPA(B) on proteinticles. Although the five different proteinticles were demonstrated as proof-of-concept here, SPA(B)-mediated immobilization of IgG on the other proteinticles would be very useful for the fabrication of sensitive 3D immunoassay platforms.

Three-dimensional structure of the human myeloma IgG2

Human immunoglobulin G, subclass 2 (hIgG2), plays an important role in immunity to bacterial pathogens and in numerous pathological conditions. However, there is a lack of information regarding the three-dimensional (3D) structure of the hIgG2 molecule. We used electron microscopy (EM), differential scanning microcalorimetry (DSC) and fluorescence for structural analysis of the hIgG2. DSC and fluorescence indicated two types of interaction between C_H1 domain of Fab (antigen-binding fragment/subunit) and C_H2 domain of Fc (complement fixation fragment/subunit) simultaneously present in the sample: close interaction, which increases the thermostability of both, C_H1 and C_H2 domains, and weak (or no) interaction, which is typical for most IgGs but not hIgG2. Thermodynamics could not determine if both types of interactions are present within a single molecule. To address this question, EM was used. We employed a single-particle reconstruction and negative staining approach to reveal the three-dimensional structure of the hIgG2. A three-dimensional model of hIgG2 was created at 1.78 nm resolution. The hIgG2 is asymmetrical: one Fab subunit is in close proximity to the upper portion of the Fc subunit (C_H2 domain) and the other Fab is distant from Fc. The plane of Fab subunits is nearly perpendicular to Fc. EM structure of the hIgG2 is in good agreement with thermodynamic data: a Fab distant from Fc should exhibit a lower melting temperature while a Fab interacting with Fc should exhibit a higher melting temperature. Both types of Fab subunits exist within one molecule resembling an A/B hIgG2 isoform introduced earlier on physicochemical level by Dillon et al. (2008). In such an arrangement, the access to the upper portion of Fc subunit is partially blocked by a Fab subunit. That might explain for instance why hIgG2 mildly activates complement and binds poorly to Fc receptors. Understanding of the three-dimensional structure of the hIgG2 should lead to better design of antibody-based therapeutics.

Immunoglobulin G locus events in soft tissue sarcoma cell lines

Recently immunoglobulins (Igs) have been found to be expressed by cells other than B lymphocytes, including various human carcinoma cells. Sarcomas are derived from mesenchyme, and the knowledge about the occurrence of Ig production in sarcoma cells is very limited. Here we investigated the phenomenon of immunoglobulin G (IgG) expression and its molecular basis in 3 sarcoma cell lines. The mRNA transcripts of IgG heavy chain and kappa light chain were detected by RT-PCR. In addition, the expression of IgG proteins was confirmed by Western blot and immunofluorescence. Immuno-electron microscopy localized IgG to the cell membrane and rough endoplasmic reticulum. The essential enzymes required for gene rearrangement and class switch recombination, and IgG germ-line transcripts were also identified in these sarcoma cells. Chromatin immunoprecipitation results demonstrated histone H3 acetylation of both the recombination activating gene and Ig heavy chain regulatory elements. Collectively, these results confirmed IgG expression in sarcoma cells, the mechanism of which is very similar to that regulating IgG expression in B lymphocytes.

Competitive protein adsorption--multilayer adsorption and surface induced protein aggregation

In this study, competitive adsorption of albumin and IgG (immunoglobulin G) from human serum solutions and protein mixtures onto polymer surfaces is studied by means of radioactive labeling. By using two different radiolabels (125I and 131I), albumin and IgG adsorption to polymer surfaces is monitored simultaneously and the influence from the presence of other human serum proteins on albumin and IgG adsorption, as well as their mutual influence during adsorption processes, is investigated. Exploring protein adsorption by combining analysis of competitive adsorption from complex solutions of high concentration with investigation of single protein adsorption and interdependent adsorption between two specific proteins enables us to map protein adsorption sequences during competitive protein adsorption. Our study shows that proteins can adsorb in a multilayer fashion onto the polymer surfaces and that the outcome of IgG adsorption is much more sensitive to surface characteristics than the outcome of albumin adsorption. Using high concentrations of protein solution and hydrophobic polymer surfaces during adsorption can induce IgG aggregation, which is observed as extremely high IgG adsorptions. Besides using a more hydrophilic substrate, surface-induced IgG aggregation can be inhibited by changing the adsorption sequence of albumin and IgG.

[Preparation and identification of antibody against Cecropin-XJ]

AIM

To prepare the mouse antibody against Cecropin-XJ, identify its specificity and use it in cellular localization of Cecropin-XJ in vitro.

METHODS

The cDNA sequence of Cecropin-XJ with signal peptide sequence was subcloned into the eukaryotic expression vector pcDNA3. The recombinant plasmid was named pcDNA3-Cecropin-XJ, which was used as an antigen to immune the Kunming white mouse. Meanwhile, the cDNA sequence was subcloned into the fusion expression vector and the fusion protein was expressed as a test antigen.

RESULTS

Indirect ELISA showed that the fifth immunity's titer was highest. The immune gold-conjugated experiment showed that the prepared antibody was clearly and efficiently localized in prokaryotic cells where the Cecropin-XJ worked.

CONCLUSION

The antibody against Cecropin-XJ has high immune reactivity and specificity, which is beneficial to further study on Cecropin-XJ function and antibody preparation of small peptides.

Solution conformation of wild-type and mutant IgG3 and IgG4 immunoglobulins using crystallohydrodynamics: possible implications for complement activation

We have employed the recently described crystallohydrodynamic approach to compare the time-averaged domain orientation of human chimeric IgG3wt (wild-type) and IgG4wt as well as two hinge mutants of IgG3 and an IgG4S331P (mutation from serine to proline at position 331, EU numbering) mutant of IgG4. The approach involves combination of the known shape of the Fab and Fc regions from crystallography with hydrodynamic data for the Fab and Fc fragments and hydrodynamic and small angle x-ray scattering data for the intact IgG structures. In this way, ad hoc assumptions over hydration can be avoided and model degeneracy (uniqueness problems) can be minimized. The best fit model for the solution structure of IgG3wt demonstrated that the Fab regions are directed away from the plane of the Fc region and with a long extended hinge region in between. The best fit model of the IgG3m15 mutant with a short hinge (and enhanced complement activation activity) showed a more open, but asymmetric structure. The IgG3HM5 mutant devoid of a hinge region (and also devoid of complement-activation activity) could not be distinguished at the low-resolution level from the structure of the enhanced complement-activating mutant IgG3m15. The lack of inter-heavy-chain disulphide bond rather than a significantly different domain orientation may be the reason for the lack of complement-activating activity of the IgG3HM5 mutant. With IgG4, there are significant and interesting conformational differences between the wild-type IgG4, which shows a symmetric structure, and the IgG4S331P mutant, which shows a highly asymmetric structure. This structural difference may explain the ability of the IgG4S331P mutant to activate complement in stark contrast to the wild-type IgG4 molecule which is devoid of this activity.

A novel approach to the micropatterning of proteins using dewetting of polymer bilayers

The ability to control protein and cell positioning on a microscopic scale is crucial in many biomedical and bioengineering applications, such as tissue engineering and the development of biosensors. We propose here a novel, simple, and versatile method for the micropatterning of proteins. Micropatterned substrates are produced by the dewetting of a metastable polymer film on top of another polymer film. Selective adsorption, or micropatterning, of proteins can be achieved on such substrates by choosing pairs of polymers which differ in protein affinity. In this study, patterns were produced in bilayers of poly(methylmethacrylate) (PMMA) and polystyrene (PS), and of PMMA and octadecyltrichlorosilane (OTS). Fluorescence microscopy and atomic force microscopy (AFM) provide evidence that model proteins adsorb preferentially on isolated bio-adhesive (PS and OTS) micropatches in a protein-resistant (PMMA) matrix. "Inverse" protein patterns, containing non-adhesive (PMMA) islands in a protein-adhesive (PS) matrix can also be produced. Such micropatterned substrates could potentially be used in the development of biosensors and bioassays, and in the study of cell growth and motility.

A smart membrane based on an antigen-responsive hydrogel

Hydrogel membranes have been fabricated that incorporate antibody/antigen moieties. The permeability of large solutes through these membranes is dependent on the presence of soluble antigen that can compete with the internal interactions between antibody and antigen leading to an increase in gel mesh size. Specifically, the membrane's structure is based on a dextran backbone grafted with a fluorescein isothiocyanate (FITC) antigen and a sheep anti-FITC IgG antibody. The backbone is covalently cross-linked by conjugated divinyl sulfone (DVS) groups. The gel structure is additionally stabilized by affinity crosslinks formed by biospecific interactions between the bound IgG and FITC. FTIR spectra of the gel are consistent with formation of covalent bonds between cysteine groups in the IgG and DVS groups in the dextran. Results obtained using isothermal titration calorimetry (ITC) confirmed the competitive interaction binding between IgG-FITC-dextran and free sodium fluorescein at pH 5.0. Scanning electron microscopy (SEM) of samples prepared using cryofixation and cryofracturing techniques showed that observed changes in permeability correlate with free fluorescein-dependent structural changes in the gel. Three-dimensional images obtained from confocal laser scanning microscopy show that these changes occur throughout the gel and indicate that SEM results are not artifacts of sample preparation. The permeability of these gels, as shown by blue-dextran (12 kDa) diffusion, increases in response to the presence of free fluorescein of the external medium, which causes competitive displacement of the affinity cross-links. Sequential addition and removal of sodium fluorescein showed that these permeability changes are reversible.

Crystallohydrodynamics of protein assemblies: Combining sedimentation, viscometry, and x-ray scattering

Crystallohydrodynamics describes the domain orientation in solution of antibodies and other multidomain protein assemblies where the crystal structures may be known for the domains but not the intact structure. The approach removes the necessity for an ad hoc assumed value for protein hydration. Previous studies have involved only the sedimentation coefficient leading to considerable degeneracy or multiplicity of possible models for the conformation of a given protein assembly, all agreeing with the experimental data. This degeneracy can be considerably reduced by using additional solution parameters. Conformation charts are generated for the three universal (i.e., size-independent) shape parameters P (obtained from the sedimentation coefficient or translational diffusion coefficient), nu (from the intrinsic viscosity), and G (from the radius of gyration), and calculated for a wide range of plausible orientations of the domains (represented as bead-shell ellipsoidal models derived from their crystal structures) and after allowance for any linker or hinge regions. Matches are then sought with the set of functions P, nu, and G calculated from experimental data (allowing for experimental error). The number of solutions can be further reduced by the employment of the D max parameter (maximum particle dimension) from x-ray scattering data. Using this approach we are able to reduce the degeneracy of possible solution models for IgG3 to a possible representative structure in which the Fab domains are directed away from the plane of the Fc domain, a structure in accord with the recognition that IgG3 is the most efficient complement activator among human IgG subclasses.

The substructure of immunoglobulin G resolved to 25kDa using amplitude modulation AFM in air

Amplitude modulation (or tapping-mode) atomic force microscopy (AM AFM or TM AFM) in air can reveal sub-molecular details of isolated multi-subunit proteins, such as immunoglobulin G (IgG) antibodies, on atomically flat support surfaces such as mica [A. San Paulo, R. Garcia, Biophys. J. 78(3) (2000) 1599]. This is achieved by controlling the microscope imaging parameters (e.g. cantilever drive frequency and set-point amplitude) to keep the AFM tip predominantly in the attractive force regime. Under these conditions, the 50 kDa F(c) and F(ab) subunits can be resolved when the molecule has the appropriate orientation on the surface. The presence of a water layer on hydrophilic mica is an important factor affecting imaging contrast, a consequence of capillary neck formation between tip and surface [L. Zitzler, S. Herminghaus, F. Mugele, Phys. Rev. B 66(15) (2002) 155436]. Desiccation of samples to remove surface bound water layers can yield reproducible imaging of the IgG substructure [N.H. Thomson, J. Microsc. (Oxford) 217(3) (2004) 193]. This approach has also given higher resolution than previously achieved, down to about 25 kDa, and these data are detailed here. These subdomains are formed as two immunoglobulin folds from the light and heavy peptide chains of the IgG crossover. This result has been validated by comparing the AFM images with X-ray crystallography data from the protein data bank. These data show that the AFM can obtain 25 kDa resolution on isolated protein molecules with commercially available silicon tips, but, as expected for a local probe technique, resolution is highly dependent on the macromolecular orientation on the support surface.

Histopathological atlas of renal diseases: anti-glomerular basement membrane antibody disease

The main diagnostic feature of anti-glomerular basement membrane (anti-GBM) antibody disease is represented by the immunofluorescence pattern of intense and diffuse linear IgG deposition along the glomerular basement membrane. By light microscopy several histological patterns can be observed.

Imaging the substructure of antibodies with tapping-mode AFM in air: the importance of a water layer on mica

Monoclonal antibodies (immunoglobulin G; IgG) against the N-terminal domain of the A subunit of DNA gyrase have been imaged using tapping-mode atomic force microscopy under ambient conditions on hydrophilic mica surfaces. The familiar tri-nodal submolecular resolution of IgG (i.e. 50-kDa resolution) has been achieved when operating the microscope with the tip predominantly in the attractive force regime. Under common laboratory conditions of about 40% relative humidity, the resolution of this substructure was not achieved owing to motion of the antibodies on the surface and/or image distortion from tip-sample instabilities. Reproducible imaging of the tri-nodal antibody substructure was achieved by desiccating the samples for extended periods of time (1 week or more) before imaging. This effect is attributed to the presence of a humidity-dependent thin water layer (a few molecules or nanometres thick), which has been observed previously using the surface force apparatus and scanning polarization force microscopy. Desiccation of the mica surfaces allowed enough water to be removed from the mica surface to prevent this effect. Degradation in the image quality over the imaging period of an hour or two was observed, owing to re-adsorption of water under the ambient laboratory conditions.

Research on double-probe, double- and triple-tip effects during atomic force microscopy scanning

Information obtained by atomic force microscopy (AFM) depends strongly on the kind of probe or tip used; therefore, probe and tip effects have to be taken into account when verifying or interpreting the data acquired. In many papers, double-tip effects have been mentioned while other research was done; however, there are only a few special reports on double- or triple-tip effects, especially double-probe effects. In our paper, metaphase chromosomes of Chinese hamster ovary (CHO) cells, aggregates of pectin molecules, membrane surface of mouse embryonic stem cells, and R-phycoerythrin-conjugated immunoglobulin G complexes were imaged by AFM with high-quality probes, double-probe cantilever, and double-tip and triple-tip probes, respectively, in order to determine double-probe, double-tip, and triple-tip effects during AFM scanning. We found that the double-probe, double-tip, and triple-tip effects share the same principle, and that these effects correlate with distance and height differences between probes of double-probe cantilever or tips of double-tip or multiple-tip probes. Since many other factors influence double-probe or double-tip effects, more in-depth studies must be undertaken. However, this initial research will make all users of AFM techniques aware of double-probe and double-tip or triple-tip effects during AFM scanning and aid in verifying or interpreting the data acquired.

Surface structural characterization of protein- and polymer-modified polystyrene microspheres by infrared-visible sum frequency generation vibrational spectroscopy and scanning force microscopy

Structural investigations of bare and surface-modified polystyrene microspheres (beads) have been carried out by infrared-visible sum frequency generation (SFG) vibrational spectroscopy and scanning force microscopy (SFM). Bead surfaces have been modified by either the covalent linking of immunoglobulin G (IgG) and bovine serum albumin (BSA) or the nonspecific adsorption of a Pluronic surfactant. After surface modification with protein, SFG signals in the aliphatic CH-stretch region are detected at both the buffer/bead and air/bead interfaces, indicating that some amino acid residues in proteins adopt preferred orientations. SFG results indicate that the hydrophobic poly(propylene glycol) moieties in the Pluronic order when adsorbed onto the bead, at both the buffer/bead and air/bead interfaces, whereas hydrophilic poly(ethylene glycol) groups align to a lesser extent. SFG spectra also show that the phenyl rings of bare polystyrene beads in contact with air or buffer are ordered, with a dipole component directed along the surface normal, but become less ordered after the adsorption of either proteins or the polymer. Molecular orientation and ordering at the bead surface affect its hydrophobicity and aggregation behavior. SFM results reveal the formation of nonuniform islands when bare beads with more hydrophobic character are spun-cast onto a silica substrate. In the presence of adsorbed protein, a hexagonal packing of beads, with some defects, is observed, depending on the bulk pH and the type of attached protein. Adsorbed Pluronic causes the beads to aggregate in a disordered fashion, as compared to the behavior of bare and protein-modified beads.

A general model for amyloid fibril assembly based on morphological studies using atomic force microscopy

Based on atomic force microscopy analysis of the morphology of fibrillar species formed during fibrillation of alpha-synuclein, insulin, and the B1 domain of protein G, a previously described model for the assembly of amyloid fibrils of immunoglobulin light-chain variable domains is proposed as a general model for the assembly of protein fibrils. For all of the proteins studied, we observed two or three fibrillar species that vary in diameter. The smallest, protofilaments, have a uniform height, whereas the larger species, protofibrils and fibrils, have morphologies that are indicative of multiple protofilaments intertwining. In all cases, protofilaments intertwine to form protofibrils, and protofibrils intertwine to form fibrils. We propose that the hierarchical assembly model describes a general mechanism of assembly for all amyloid fibrils.

A practical technique for differentiation of subepidermal bullous diseases: localization of in vivo-bound IgG by laser scanning confocal microscopy

OBJECTIVE

To develop a practical technique to distinguish autoimmune subepidermal bullous diseases.

DESIGN

A prospective study.

SETTING

Academic referral center-the Department of Dermatology, Medical University of Warsaw. Patients Forty-two patients fulfilling clinical, immunological, and/or immunoelectron microscopic criteria for bullous pemphigoid (n = 31), mucous membrane pemphigoid (n = 6), or epidermolysis bullosa acquisita (n = 5), diagnosed as having disease and treated from January 1, 1997, to December 31, 2002.

MAIN OUTCOME MEASURES

We applied laser scanning confocal microscopy to determine the localization of in vivo-bound IgG at the basement membrane zone in biopsy specimens taken from patients' skin to compare the localization of basement membrane zone markers: antibody against beta4 integrin, antibody against laminin 5, and antibody against type IV collagen. In vivo-bound IgG was visualized by labeling with fluorescein isothiocyanate-conjugated anti-human IgG antibody, whereas basement membrane zone markers were labeled with anti-mouse Cy5-conjugated antibodies.

RESULTS

In patients with bullous pemphigoid, in vivo-bound IgG was localized on the epidermal side of laminin 5 and co-localized with beta4 integrin. In patients with mucous membrane pemphigoid, IgG was in vivo bound to the dermal-epidermal junction between localization of laminin 5 and type IV collagen. In patients with epidermolysis bullosa acquisita, in vivo-bound IgG was present on the dermal side of type IV collagen.

CONCLUSIONS

Laser scanning confocal microscopy allows precise localization of in vivo-bound IgG in patients' skin and, thus, it is a rapid method for the differentiation of mucous membrane pemphigoid from bullous pemphigoid and epidermolysis bullosa acquisita. This tool is suitable for the routine diagnosis of individual patients and for retrospective studies. This method is of special value in those patients in whom circulating autoantibodies are not detectable.

Intracytoplasmic filamentous inclusions in the peripheral blood of a patient with chronic lymphocytic leukemia. A bright-field, electron microscopic, immunofluorescent, and flow cytometric study

Intracellular inclusions in lymphoproliferative disorders are not common. Multiple different types of inclusions have been reported in chronic lymphocytic leukemia (CLL), including vacuoles, crystals, and pseudocrystals. Most of the reported cases were seen in the bone marrow lymphocytes, and the majority of these on electron microscopy. We report a case of long-standing CLL with no therapy that had filamentous cytoplasmic inclusions in the peripheral blood that were readily seen by light microscopy. Electron microscopy demonstrated dilated cisternae of the rough endoplasmic reticulum filled with amorphous electron-dense material. By immunofluorescence, the material proved to be immunoglobulin G-lambda deposits. The immunophenotype had the typical CLL pattern with positive staining with CD19, CD5, and CD23, and low-density CD20 staining; however, it also had unusual staining with CD25 and intermediate-intensity staining with CD22.

Membranous glomerulonephritis associated with follicular B-cell lymphoma and subepithelial deposition of IgG1-kappa paraprotein

A case is described of B-cell lymphoma/chronic lymphocytic leukaemia associated with membranous glomerulonephritis in which the subepithelial deposits of immunoglobulin showed kappa light chain restriction by immunofluorescence. Surface IgG-kappa immunoglobulin was demonstrated on the malignant B cells, and a monoclonal protein of the same type was eluted from kidney. The mechanism of membranous glomerulonephritis in this type of lymphoid malignancy is clearly different from that in epithelial malignancies.

Investigating specific antigen/antibody binding with the atomic force microscope

The aim of this work is to detect immune complexes without any kind of labelling of each of the immunological species, with a view to create a very sensitive biosensor. This is achieved by using the atomic force microscopy. We have proceeded by imaging the antibody (anti-rabbit IgG) or anti-rabbit IgG moieties adsorbed onto mica surface, before and after incubation of two kinds of antigens: a specific (rabbit IgG) and a non-specific one (sheep IgG). The analysis using the height histograms reveals many interesting features. We propose a general framework for interpreting these analysis, which enables the discrimination between specific and non-specific complexes.

Expression of functionally active FcRn and the differentiated bidirectional transport of IgG in human placental endothelial cells

The mechanism of selective transport of the immunoglobulins G from the placental stroma to the lumen of the fetal blood vessels has not been elucidated yet. It was postulated that the specific transport as well as the regulation of IgG level in the blood, involves the MHC class I related receptor FcRn for the Fc domain of IgG. We questioned whether human placental endothelial cells (HPEC) express FcRn and, if present, whether it is in a functionally active form. The experiments were performed on cultured HPEC and as positive control, human trophoblastic (JEG3) and mouse endothelial cells (SVEC) were used. Expression of FcRn, was demonstrated by indirect immunofluorescence and RT-PCR. The role of FcRn was assessed by quantifying the transcellular transport of [(125)I]-hIgG or [(125)I]-rF(ab')(2) fragments from the apical to basolateral surface, and in the reverse direction of HPEC grown on filters in a double chamber system. The intracellular pathway of FcRn or IgG was examined by electron microscopy using the proteins adsorbed to 5 nm and 20 nm colloidal gold particles, respectively. The results showed that: (a) FcRn is expressed by human placental endothelial cells, in a functionally active form; (b) transcytosis of IgG in HPEC is a time-dependent process that takes place preferentially from the basolateral to the apical compartment; and (c) both IgG and FcRn colocalize in an intracellular endocytic compartment, chloroquine sensitive. Together these data suggest that the regulation of IgG level by endothelial cells may result from interplay between salvaging, exocytosis, and transcytosis of the molecules. One can assume that IgG that does not bind to FcRn may be destined for destruction, and this would explain the mechanism by which IgG homeostasis is maintained.

Chimeric human-simian anti-CD4 antibodies form crystalline high symmetry particles

A chimeric human-simian IgG, antigen specific for CD4, when exposed to 0.5 M SO(=)(4) containing 0.4% polyethylene glycol or Jeffamine, self-assembles into discreet, roughly spherical particles 23 nm in diameter. Increasing SO(=)(4) to 1.55 M induces the IgG particles to crystallize in either a hexagonal or a monoclinic form. From X-ray diffraction, the former crystal is of space group P622, with one IgG particle in the unit cell; thus the particle itself must have 622 point group symmetry. Both crystal forms have been imaged using atomic force microscopy. Detailed features of the duodecamer were evident, including the symmetry and a large solvent channel along the sixfold axis. The particles in some ways resemble the hexameric IgG aggregates believed to activate compliment upon antigen binding and, therefore, may have physiological relevance. Investigation of seven other IgGs of diverse origins and subclasses indicates that many, if not most, IgGs form similar particles. To our knowledge, this is the first observation of the assembly of IgG into high symmetry aggregates in the absence of antigen or their crystallization.

Carbon nanotube atomic force microscopy tips: direct growth by chemical vapor deposition and application to high-resolution imaging

Carbon nanotubes are potentially ideal atomic force microscopy probes because they can have diameters as small as one nanometer, have robust mechanical properties, and can be specifically functionalized with chemical and biological probes at the tip ends. This communication describes methods for the direct growth of carbon nanotube tips by chemical vapor deposition (CVD) using ethylene and iron catalysts deposited on commercial silicon-cantilever-tip assemblies. Scanning electron microscopy and transmission electron microscopy measurements demonstrate that multiwalled nanotube and single-walled nanotube tips can be grown by predictable variations in the CVD growth conditions. Force-displacement measurements made on the tips show that they buckle elastically and have very small (</= 100 pN) nonspecific adhesion on mica surfaces in air. Analysis of images recorded on gold nanoparticle standards shows that these multi- and single-walled carbon nanotube tips have radii of curvature of 3-6 and 2-4 nm, respectively. Moreover, the nanotube tip radii determined from the nanoparticle images are consistent with those determined directly by transmission electron microscopy imaging of the nanotube ends. These molecular-scale CVD nanotube probes have been used to image isolated IgG and GroES proteins at high-resolution.

Monomeric complement-activating IgG paraproteins

Three patients presented a unique syndrome of recurrent panniculitis with an IgGkappa paraprotein and depletion of the early components of the classical pathway of complement. The IgGkappa paraproteins were monomers with a normal structure, and with no evidence for aggregation, as assessed by electron microscopy and ultracentrifugation. Both heavy and light chains were of normal molecular size (SDS-PAGE), and the paraproteins were not heavily glycosylated. However, the paraproteins from all three patients had unusual features that included abnormal behavior on gel filtration chromatography and a heavy chain of high pI. When analyzed by fast protein liquid chromatography (Superdex 200), elution of the paraproteins was retarded, particularly when the ionic strength was increased. This retardation was partially reversed in 20% alcohol, and fully reversed in 6 M guanidine-HCl. Neither anti-C1 inhibitor nor anti-C1q autoantibodies were found in any of the patients' sera. However, the paraproteins bound to the globular heads of C1q at normal ionic strength. They activated C4 in normal human serum, but not in C1q-deficient serum. Activation led to the formation of C1s-C1 inhibitor complexes. Taken together, the data suggest that the unusual paraproteins have the capacity to bind C1q, which then leads to activation of C1. The ability of these paraproteins to activate C1, in spite of their being soluble monomers, is likely to be related to their unique physicochemical features.

Formation of helical protein assemblies of IgG and transducin on varied lipid tubules

Helical protein arrays on lipid tubules are valuable assemblies for studying protein structure and protein-lipid interactions through electron microscopy and crystallography. We describe conditions for forming such arrays from two proteins, IgG and transducin, the photoreceptor G protein, using a variety of lipid surfaces. Anti-dinitrophenyl (DNP) IgG arrays formed on DNP-phosphatidylethanolamine (DNP-PE) mixed with either galactosyl-ceramide lipids or phosphatidylcholine (PC) display different pH sensitivities and dimensions, yet have similar helical symmetries. DNP-PE/PC mixtures formed small crystals and large well-ordered flattened tubules. The peripheral membrane protein transducin (G(t)) formed helical arrays either on a mixture of cationic and neutral lipids or on residual photoreceptor lipids. Despite differences in lipid composition, the G(t) arrays have similar structures and show similar sensitivity to activation and variations in ionic environment. G(t) activation causes the helical assemblies to collapse to small vesicles, a process resembling the vesiculation of activated dynamin-lipid tubules. In a preliminary three-dimensional reconstruction, the hapten-bound IgG appears to make two contacts to the central lipid tubule, presumably via the F(ab) domains. The ability to generate a three-dimensional reconstruction without tilts illustrates one advantage of helical structures for two-dimensional crystallography, especially for visualizing protein-lipid interactions.

Immunoglobulin structure and function as revealed by electron microscopy

Electron-microscopic (EM) analysis preceded crystallographic analysis [1,2] of Igs by over a decade and was for a time the only direct way of analyzing their 3-D molecular structure. Once the X-ray structures were deduced, the role of EM gradually shifted from gross structural analysis to the addressing of more sophisticated structural and functional questions. EM remains a vital adjunct to the many physicochemical, biochemical, and serological tools brought to bear on these remarkable molecules as we try to relate form to function. In this review I will highlight some of the many contributions that have been made possible by virtue of being able to 'see' Ig molecules and immune complexes.

Visualising intraparticle protein transport in porous adsorbents by confocal microscopy

Confocal scanning microscopy was used to study protein uptake to porous adsorbents during batch experiments in a finite bath. By coupling of a fluorescent dye to the protein molecules the penetration of single adsorbent particles at different times during batch uptake could be observed visually. Intensity profiles of the protein distribution within a single particle were obtained by horizontal scanning. After integration of the profiles the overall fluorescence within a bead could be calculated. Relating the overall fluorescence at different incubation times to the value at equilibrium allowed the construction of the fractional approach to equilibrium versus time. These data were compared to uptake curves, which had been obtained by measurements of the protein concentration in the supernatant and an excellent agreement of the curves was detected. The procedure was performed for two different proteins (lysozyme and human IgG) on two different media for protein adsorption (SP Sepharose Fast Flow and SP Sepharose XL; Pharmacia Biotech) and in all cases it could be shown, that the results from the direct measurements by confocal microscopy correspond very well to the data obtained from the indirect measurements in the fluid phase.

Morphological observations on liposomes bearing covalently bound protein: studies with freeze-fracture and cryo electron microscopy and small angle X-ray scattering techniques

The appearance of protein bound to the surface of intact and microfluidized liposomes and its possible influence on their morphology was examined by freeze-fracture electron microscopy, cryo electron microscopy and small angle X-ray scattering (SAXS) techniques. Results obtained by the two microscopy techniques were in agreement with one another in terms of vesicle size and localization of protein (tetanus toxoid or immunoglobulin G) on the surface of vesicles. Surface-bound protein was observed as particles (10-12 nm diameter) by freeze-fracture electron microscopy and was confirmed by immunogold cryo microscopy. SAXS was shown to be a suitable means to further characterize liposomes with, or without bound protein.

Folding of the Fab fragment within the intact antibody

At present it is not clear to which extent the Fab fragment and the Fc part of an antibody interact in the intact immunoglobulin structure. To determine such potential interactions the unfolding and refolding of an isolated Fab fragment and the respective antibody MAK 33 (kappa/IgG1) are compared. It could be shown that the proline independent renaturation kinetics of both an unfolding intermediate and the fully denatured form of both proteins are identical. Upon denaturation, the loss of antigen binding activity occurs with the same rate for both the Fab fragment and the intact antibody. However, the complete structural unfolding of the Fab part of the antibody is significantly slower than that of the isolated Fab fragment. These kinetic data suggest that the structure of the Fab fragment within the intact antibody is stabilized by interactions, presumably with the Fc part, missing in the isolated Fab.

Probing single biomolecules with atomic force microscopy

During the last years, atomic force microscopy (AFM) has developed from a microscopy tool for solid-state surface science toward a method employed in many scientific disciplines, such as biology, for investigating individual molecules on a nanometer scale. This article describes the current status of the imaging possibilities of AFM on RNA, IgG, and gold-labeled cell adhesion proteoglycans, as well as of measurements of intermolecular binding forces between biomolecules in order to investigate their molecular structure, function, and elasticity.

Biological cryo atomic force microscopy: a brief review

Despite many successes, atomic force microscopy (AFM) of biological specimens at room temperature is still severely limited by at least two factors: the softness and the thermal motion of flexible multi-domain/subunit molecules. Both problems can be overcome by imaging biological structures at cryogenic temperatures. Even though the instrumentation is considerably more complex and earlier attempts were largely unsuccessful, cryo-AFM has recently been demonstrated on a number of biological specimens, using an AFM operated in liquid nitrogen vapor under ambient pressure. In this brief review, both the method of instrumentation and the latest biological applications are discussed. Not only has the cryo-AFM attained high resolution on those specimens that could not be well imaged at room temperature, but it has also produced potentially important information on several specimens. These results firmly establish the cryo-AFM as a useful and versatile structural probe in biology with its own unique capabilities.

Striving for atomic resolution in biomolecular topography: the scanning force microscope (SFM)

The invention in 1986 of scanning force microscopy (SFM) provided a new and powerful tool for the investigation of biological structures. SFM yields a three-dimensional view at nanometer resolution of the surface topography associated with biological objects. The potential for imaging either macromolecules or biomolecules and cells under native (physiological) conditions is currently being exploited to obtain functional information at the molecular level. In addition, the forces involved in individual bimolecular interactions are being assessed under static and dynamic conditions. In this report we focus on the imaging capability of the SFM. The rather broad spectrum of applications represented is intended to orient the prospective user of biological SFM.

Imaging biological structures with the cryo atomic force microscope

It has long been recognized that one of the major limitations in biological atomic force microscopy (AFM) is the softness of most biological samples, which are easily deformed or damaged by the AFM tip, because of the high pressure in the contact area, especially from the very sharp tips required for high resolution. Another is the molecular motion present at room temperature due to thermal fluctuation. Using an AFM operated in liquid nitrogen vapor (cryo-AFM), we demonstrate that cryo-AFM can be applied to a large variety of biological samples, from immunoglobulins to DNA to cell surfaces. The resolution achieved with cryo-AFM is much improved when compared with AFM at room temperature with similar specimens, and is comparable to that of cryo-electron microscopy on randomly oriented macromolecules. We will also discuss the technical problems that remain to be solved for achieving even higher resolution with cryo-AFM and other possible applications of this novel technique.

Two-dimensional paracrystalline glycoprotein S-layers as a novel matrix for the immobilization of human IgG and their use as microparticles in immunoassays

In the present study, cup-shaped 1-3 microns large cell wall fragments from Thermoanaerobacter thermohydrosulfuricus L111-69 covered with a hexagonal S-layer lattice composed of glycoprotein subunits were shown to act as a matrix for the immobilization of human IgG. After cross-linking the S-layer glycoprotein lattice with glutaraldehyde (S-layer microparticles), IgG was either bound to carbodiimide activated carboxyl groups from acidic amino acids from the protein moiety or to the carbohydrate chains activated with cyanogen bromide or oxidized with periodate. After determining the binding capacity of the S-layer lattice for human IgG, the orientation of the immobilized antibody molecules was investigated using anti-human IgG peroxidase conjugates with different specificity. Attachment of S-layer microparticles with covalently bound human IgG to microplates precoated with anti-human IgG of different specificity led to clear correlations between the amount of applied human IgG and the absorption values in the immunoassays. The steepest absorption curves were obtained when human IgG was bound to the carbohydrate chains exposed on the surface of the S-layer lattice. This confirmed that the location and the accessibility of the immobilized antibodies on S-layer microparticles is of major importance for the response in immunoassays. In addition to the high reproducibility of the amount of IgG which could be bound to the S-layer lattice and the high reproducibility of the absorption curves in the immunoassays, one major advantage of using cup-shaped S-layer microparticles can be seen in the considerable increase of the actual surface available for binding processes and immunological reactions.

Specific antigen/antibody interactions measured by force microscopy

Molecular recognition between biotinylated bovine serum albumin and polyclonal, biotin-directed IG antibodies has been measured directly under various buffer conditions using an atomic force microscope (AFM). It was found that even highly structured molecules such as IgG antibodies preserve their specific affinity to their antigens when probed with an AFM in the force mode. We could measure the rupture force between individual antibody-antigen complexes. The potential and limitations of this new approach for the measurement of individual antigen/antibody interactions and some possible applications are discussed.

Protein tracking and detection of protein motion using atomic force microscopy

Height fluctuations over three different proteins, immunoglobulin G, urease, and microtubules, have been measured using an atomic force microscope (AFM) operating in fluid tapping mode. This was achieved by using a protein-tracking system, where the AFM tip was periodically repositioned above a single protein molecule (or structure) as thermal drifting occurred. Height (z-piezo signal) data were taken in 1 - or 2-s time slices with the tip over the molecule and compared to data taken on the support. The measured fluctuations were consistently higher when the tip was positioned over the protein, as opposed to the support the protein was adsorbed on. Similar measurements over patches of an amphiphile, where the noise was identical to that on the support, suggest that the noise increase is due to some intrinsic property of proteins and is not a result of different tip-sample interactions over soft samples. The orientation of the adsorbed proteins in these preliminary studies was not known; thus it was not possible to make correlations between the observed motion and specific protein structure or protein function beyond noting that the observed height fluctuations were greater for an antibody (anti-bovine IgG) and an enzyme (urease) than for microtubules.

The discrimination of IgM and IgG type antibodies and Fab' and F(ab)2 antibody fragments on an industrial substrate using scanning force microscopy

We have previously employed scanning force microscopy (SFM) to study antibody-antigen molecular interactions on microtiter wells used for enzyme linked immunosorbant assays (ELISA). Here we demonstrate the ability of SFM to image and discriminate different types of antibody and antibody fragments bound to an ELISA well surface. The samples studied include a type IgG antibody with a proportion of bound IgM and two-dimensional films of whole IgG antibody, and Fab' and F(ab)2 antibody fragments. Molecular resolution is achieved in each case despite the size of substrate features exceeding most of the molecular dimensions observed. Analysis of the data shows that the SFM overestimates molecular dimensions by an approximately constant amount, which is proposed to principally result from the effects of a finite probe size and not from deformation of the molecular species due to the imaging forces employed.

Imaging of single antigens, antibodies, and specific immunocomplex formation by scanning force microscopy

The most sensitive analytical techniques available today for detecting immuno assay complexes are radio or enzyme immuno analytical techniques, by which quantities of 10(7)-10(8) analyte molecules can be detected. With the introduction of scanning force microscopy, a new method for detecting biological processes became available. Here, we examine the feasibility of using scanning force microscopy as a biosensitive tool. We demonstrate that single or multiple rabbit anti-human serum albumin molecules form complexes with preadsorbed single human serum albumin molecules on mica. However, no interaction is observed between human immunoglobulin G molecules and preadsorbed single albumin molecules; only separate antigens and antibodies are observed at random positions on the mica. This shows the ability of scanning force microscopy to act as a biosensor for detection of immunocomplexes, and to act as a very powerful tool to study molecule-surface interactions in general.

A scanning tunnelling microscopic study of site-specifically immobilized immunoglobulin G on gold

A convenient and efficient method for the site-specific incorporation of foreign cysteine residues at the C-termini of immunoglobulin G (IgG) using carboxypeptidase-Y-catalyzed transpeptidation is explored as a means of ensuring oriented immobilization of IgG on gold. A scanning tunnelling microscopic study of the immobilization of the modified IgG molecules on gold surfaces is reported. The results show not only that some globular features are observed to form striking surface patterns with a geometric size close to that of the fragments of IgG but also that the conformation of the bound IgG molecules appears more stable when adsorbed on gold. The effect of the immobilization method on these topographic features is discussed.

Influence of surface and protein modification on immunoglobulin G adsorption observed by scanning force microscopy

Scanning force microscopy has been used successfully to produce images of individual protein molecules. However, one of the problems with this approach has been the high mobility of the proteins caused by the interaction between the sample and the scanning tip. To stabilize the proteins we have modified the adsorption properties of immunoglobulin G on graphite and mica surfaces. We have used two approaches: first, we applied glow discharge treatment to the surface to increase the hydrophilicity, favoring adhesion of hydrophilic protein molecules; second, we used the arginine modifying reagent phenylglyoxal to increase the protein hydrophobicity and thus enhance its adherence to hydrophobic surfaces. We used scanning force microscopy to show that the glow discharge treatment favors a more homogeneous distribution and stronger adherence of the protein molecules to the graphite surface. Chemical modification of the immunoglobulin caused increased aggregation of the proteins on the surface but did not improve the adherence to graphite. On mica, clusters of modified immunoglobulins were also observed and their adsorption was reduced. These results underline the importance of the surface hydrophobicity and charge in controlling the distribution of proteins on the surface.

Characterization of biosynthetic IgG oligomers resulting from light chain variable domain duplication

We have characterized a human IgG1 monoclonal antibody composed of altered light chains. Each light chain consists of two identical variable domains and a kappa constant domain, in association with a normal gamma chain. This antibody assembled biosynthetically into a mixture of stable oligomers and monomers. Employing gel filtration, PAGE, and electron microscopy, we examined the antibody and the nature of the associations involved in oligomer formation. By engineering a protease factor Xa site between the duplicated light chain variable domains and examining the fragments produced following factor Xa cleavage, we demonstrated the association of the IgG monomers occurred through their duplicated VL domains. Electron microscopy showed the oligomeric antibody to be predominantly dimers and trimers in which the monomeric units were associated through the tips of the Fab portion of the antibody, presumably through the protruding N-terminal VL domains. Similar examination of monomers demonstrated several molecular forms, including individual molecules with self-crosslinked Fab arms and others displaying the open Y and T shapes typically observed for IgG antibodies. The monomers also displayed distally protruding domain-like structures. The oligomers produced by this cell line therefore occurred through the noncovalent interaction between the extra light chain variable domains.

Molecular resolution atomic force microscopy of soluble proteins in solution

We introduce a simple specimen preparatory method for atomic force microscopy of soluble proteins in aqueous solutions. It is demonstrated that the mica surface is suitable for direct adsorption of macromolecules that are sufficiently stable to withstand the disturbance of the probe for reproducible imaging at high resolution. It is also shown that the main problem impeding successful imaging is the excessive adsorption of macromolecules, as loosely bound macromolecules readily stick to the tip and produce various imaging artifacts.

A COOH-terminal peptide confers regiospecific orientation and facilitates atomic force microscopy of an IgG1

An antibody (IgG1) was designed for oriented adherence to a metal-containing surface. This was achieved by adding a metal-chelating peptide, (CP = His-Trp-His-His-His-Pro), to the COOH-terminus of the heavy chain through genetic engineering. Electroporation of the engineered heavy chain gene into cells expressing the complimentary light chain yielded colonies secreting an intact antibody containing the metal-chelating peptide (IgG1-CP) which had high affinity for a nickel-loaded iminodiacetate column. Purified IgG1-CP was bound to nickel-treated mica and imaged by atomic force microscopy (AFM). Antibody lacking the COOH-terminal metal binding peptide failed to produce discernible AFM images. The AFM images of individual IgG1-CP molecules and their calculated dimensions demonstrated that regiospecific binding and uniform orientation of the antibody was imparted by the peptide. The ability to stably orient macromolecules in their native state to a surface may be used advantageously to visualize them.

Structure of human rhinovirus complexed with Fab fragments from a neutralizing antibody

We have determined the structure of a human rhinovirus (HRV)-Fab complex by using cryoelectron microscopy and image reconstruction techniques. This is the first view of an intact human virus complexed with a monoclonal Fab (Fab17-IA) for which both atomic structures are known. The surface area on HRV type 14 (HRV14) in contact with Fab17-IA was approximately 500 A2 (5 nm2), which is much larger than the area that constitutes the NIm-IA epitope (on viral protein VP1) defined by natural escape mutants. From modeling studies and electrostatic potential calculations, charged residues outside the neutralizing immunogenic site IA (NIm-IA) were also predicted to be involved in antibody recognition. These predictions were confirmed by site-specific mutations and analysis of the Fab17-IA-HRV14 complex, along with knowledge of the crystallographic structures of HRV14 and Fab17-IA. The bound Fab17-IA reaches across a surface depression (the canyon) and meets a related Fab at the nearest icosahedral twofold axis. By adjusting the elbow angles of the bound Fab fragments from 162 degrees to 198 degrees, an intact antibody molecule can be easily modeled. This, along with aggregation and binding stoichiometry results, supports the earlier proposal that this antibody binds bivalently to the surface of HRV14 across icosahedral twofold axes. One prediction of this model, that the intact canyon-spanning immunoglobulin G molecule would block attachment of the virus to HeLa cells, was confirmed experimentally.

Imaging of proteins by scanning tunnelling microscopy

Scanning tunnelling microscopy has been used to examine the structure of proteins deposited on a graphite surface. Three molecules have been studied; immunoglobulin G (IgG), Complement component 1q (C1q) and ATP-citrate lyase (ACL). The images show IgG as a tri-lobed molecule, consistent with the known 3D structure as determined by X-ray crystallography. The C1q images differ from the well known "tulip bunch" model derived by electron microscopy, but are consistent with the model if it is assumed that the six globular heads have aggregated. Molecules of ACL are visible as discrete units, with some hints of substructure. These results highlight the potential of STM in studying protein structures, but also illustrate the difficulties of interpreting micrographs of proteins whose structure is currently unknown.

Structural evidence for induced fit as a mechanism for antibody-antigen recognition

The three-dimensional structure of a specific antibody (Fab 17/9) to a peptide immunogen from influenza virus hemagglutinin [HA1(75-110)] and two independent crystal complexes of this antibody with bound peptide (TyrP100-LeuP108) have been determined by x-ray crystallographic techniques at 2.0 A, 2.9 A, and 3.1 A resolution, respectively. The nonapeptide antigen assumes a type I beta turn in the antibody combining site and interacts primarily with the Fab hypervariable loops L3, H2, and H3. Comparison of the bound and unbound Fab structures shows that a major rearrangement in the H3 loop accompanies antigen binding. This conformational change results in the creation of a binding pocket for the beta turn of the peptide, allowing TyrP105 to be accommodated. The conformation of the peptide bound to the antibody shows similarity to its cognate sequence in the HA1, suggesting a possible mechanism for the cross-reactivity of this Fab with monomeric hemagglutinin. The structures of the free and antigen bound antibodies demonstrate the flexibility of the antibody combining site and provide an example of induced fit as a mechanism for antibody-antigen recognition.