Extreme thermal stability of the antiGFP nanobody - GFP complex

OBJECTIVE

The green fluorescent protein (GFP) and its derivatives are widely used in biomedical research. The manipulation of GFP-tagged proteins by GFP-specific binders, e.g. single-domain antibodies (nanobodies), is of increasing significance. It is therefore important to better understand the properties of antiGFP-GFP interaction in order to establish methodological applications. In this work the interaction of superfolder GFP (sfGFP) and its enhancer nanobody (aGFP_enh) was characterized further.

RESULTS

Previous calorimetric experiments demonstrated that the aGFP_enh nanobody binds strongly to sfGFP with a nanomolar affinity. Here we show that this interaction results in a substantial structural stabilization of aGFP_enh reflected in a significant increase of its melting temperature by almost 30 °C. The thermal stability of the sfGFP-aGFP_enh complex is close to 85 °C in the pH range 7.0-8.5. For therapeutic applications thermoresistance is often an essential factor. Our results suggest that methodologies based on GFP-aGFP interaction can be applied under a wide range of physicochemical conditions. The aGFP_enh nanobody seems to be suitable for manipulating sfGFP-labeled targets even in extreme thermophilic organisms.

Microbead-based extracorporeal immuno-affinity virus capture: a feasibility study to address the SARS-CoV-2 pandemic

In this paper, we report on the utilization of micro-technology based tools to fight viral infections. Inspired by various hemoperfusion and immune-affinity capture systems, a blood virus depletion device has been developed that offers highly efficient capture and removal of the targeted virus from the circulation, thus decreasing virus load. Single-domain antibodies against the Wuhan (VHH-72) virus strain produced by recombinant DNA technology were immobilized on the surface of glass micro-beads, which were then utilized as stationary phase. For feasibility testing, the virus suspension was flown through the prototype immune-affinity device that captured the viruses and the filtered media left the column. The feasibility test of the proposed technology was performed in a Biosafety Level 4 classified laboratory using the Wuhan SARS-CoV-2 strain. The laboratory scale device actually captured 120,000 virus particles from the culture media circulation proving the feasibility of the suggested technology. This performance has an estimated capture ability of 15 million virus particles by using the therapeutic size column design, representing three times over-engineering with the assumption of 5 million genomic virus copies in an average viremic patient. Our results suggested that this new therapeutic virus capture device could significantly lower virus load thus preventing the development of more severe COVID-19 cases and consequently reducing mortality rate.

Dean-Flow Affected Lateral Focusing and Separation of Particles and Cells in Periodically Inhomogeneous Microfluidic Channels

The purpose of the recent work is to give a better explanation of how Dean vortices affect lateral focusing, and to understand how cell morphology can alter the focusing position compared to spherical particles. The position and extent of the focused region were investigated using polystyrene fluorescent beads with different bead diameters (Ø = 0.5, 1.1, 1.97, 2.9, 4.8, 5.4, 6.08, 10.2, 15.8, 16.5 µm) at different flow rates (0.5, 1, 2 µL/s). Size-dependent focusing generated a precise map of the equilibrium positions of the spherical beads at the end of the periodically altering channels, which gave a good benchmark for focusing multi-dimensional particles and cells. The biological samples used for experiments were rod-shaped Escherichia coli (E. coli), discoid biconcave-shaped red blood cells (RBC), round or ovoid-shaped yeast, Saccharomyces cerevisiae, and soft-irregular-shaped HeLa cancer-cell-line cells to understand how the shape of the cells affects the focusing position at the end of the channel.

Enhanced Recombinant Protein Production of Soluble, Highly Active and Immobilizable PNGase F

High resolution analysis of N-glycans can be performed after their endoglycosidase mediated removal from proteins. N-glycosidase F peptide (PNGase F) is one the most frequently used enzyme for this purpose. Because of the significant demand for PNGase F both in basic and applied research, rapid and inexpensive methods are of great demand for its large-scale production, preferably in immobilizable form to solid supports or surfaces. In this paper, we report on the high-yield production of N-terminal 6His-PNGase F enzyme in a bacterial Escherichia coli SHuffle expression system. The activity profile of the generated enzyme was compared to commercially available PNGase F enzymes, featuring higher activity for the former. The method described here is thus suitable for the cost-effective production of PNGase F in an active, immobilizable form.

Integrated workflow for urinary prostate specific antigen N-glycosylation analysis using sdAb partitioning and downstream capillary electrophoresis separation

Prostate cancer represents the second highest malignancy rate in men in all cancer diagnoses worldwide. The development and progression of prostate cancer is not completely understood yet at molecular level, but it has been reported that changes in the N-glycosylation of prostate-specific antigen (PSA) occur during tumor genesis. In this paper we report on the development and implementation of a high-throughput capillary electrophoresis based glycan analysis workflow for urinary PSA analysis. The technology utilizes selective, high yield single domain antibody based PSA capture, followed by preconcentration and capillary electrophoresis coupled with laser-induced fluorescence detection, resulting in high resolution N-glycan profiles. Urinary PSA glycan profiles were compared to a commercially available PSA standard revealing differences in their α2,3- and α2,6-sialylated isomers, proving the excellent selectivity of the suggested workflow. This is important as sialylation classification plays an important role in the differentiation between indolent, significant and aggressive forms of prostate cancer.

N-glycomic Analysis of Z(IgA1) Partitioned Serum and Salivary Immunoglobulin A by Capillary Electrophoresis

AIMS

Application of capillary electrophoresis with laser induced fluorescence detection (CE-LIF) to identify the N-glycosylation structures of serum and saliva IgA from healthy controls and patients with malignant hematological diseases having cytostatic treatment induced mild oral mucosal lesions.

BACKGROUND

Altered N-glycosylation of body fluid glycoproteins can be an effective indicator of most inflammatory processes. Immunoglobulin A (IgA) is the second highest abundant immunoglobulin and has a major role in the immune-defense against potential pathogen attacks. While IgA is abundant in serum, secretory immunoglobulin A (sIgA) is one of the most prevalent proteins in mucosal surfaces, such as in saliva.

OBJECTIVE

Our aim was to investigate the changes of IgA glycosylation in serum and saliva as a response to an administered cytostatic treatment in patients with malignant hematological disorders.

METHODS

Capillary electrophoresis with laser induced fluorescent detection (CE-LIF) was used to analyze the N-glycosylation profiles of Z(IgA1) partitioned immunoglobulin A in pooled serum and saliva of 10 control subjects and 8 patients with malignant hematological diseases having cytostatic treatment induced mild oral mucosal lesions.

RESULTS

Eight of 31 and four of 38 N-glycans in serum and saliva, respectively, showed significant (p<0.05) differences upon comparison to the control group. Thirteen glycans were present in the saliva but not in the serum, on the other hand, six structures were found in the serum samples not present in the saliva.

CONCLUSION

The developed Z(IgA1) partitioning and the high resolution CE-LIF based glyocoanalytical methods provided an efficient and sensitive workflow to detect and monitor IgA glycosylation alterations in serum and saliva with the scope for widespread molecular medicinal use.

Grating-coupled interferometry reveals binding kinetics and affinities of Ni ions to genetically engineered protein layers

Reliable measurement of the binding kinetics of low molecular weight analytes to their targets is still a challenging task. Often, the introduction of labels is simply impossible in such measurements, and the application of label-free methods is the only reliable choice. By measuring the binding kinetics of Ni(II) ions to genetically modified flagellin layers, we demonstrate that: (1) Grating-Coupled Interferometry (GCI) is well suited to resolve the binding of ions, even at very low protein immobilization levels; (2) it supplies high quality kinetic data from which the number and strength of available binding sites can be determined, and (3) the rate constants of the binding events can also be obtained with high accuracy. Experiments were performed using a flagellin variant incorporating the C-terminal domain of the nickel-responsive transcription factor NikR. GCI results were compared to affinity data from titration calorimetry. We found that besides the low-affinity binding sites characterized by a micromolar dissociation constant (Kd), tetrameric FliC-NikRC molecules possess high-affinity binding sites with Kd values in the nanomolar range. GCI enabled us to obtain real-time kinetic data for the specific binding of an analyte with molar mass as low as 59 Da, even at signals lower than 1 pg/mm2.

Sensing Layer for Ni Detection in Water Created by Immobilization of Bioengineered Flagellar Nanotubes on Gold Surfaces

The environmental monitoring of Ni is targeted at a threshold limit value of 0.34 μM, as set by the World Health Organization. This sensitivity target can usually only be met by time-consuming and expensive laboratory measurements. There is a need for inexpensive, field-applicable methods, even if they are only used for signaling the necessity of a more accurate laboratory investigation. In this work, bioengineered, protein-based sensing layers were developed for Ni detection in water. Two bacterial Ni-binding flagellin variants were fabricated using genetic engineering, and their applicability as Ni-sensitive biochip coatings was tested. Nanotubes of mutant flagellins were built by in vitro polymerization. A large surface density of the nanotubes on the sensor surface was achieved by covalent immobilization chemistry based on a dithiobis(succimidyl propionate) cross-linking method. The formation and density of the sensing layer was monitored and verified by spectroscopic ellipsometry and atomic force microscopy. Cyclic voltammetry (CV) measurements revealed a Ni sensitivity below 1 μM. It was also shown that, even after two months of storage, the used sensors can be regenerated and reused by rinsing in a 10 mM solution of ethylenediaminetetraacetic acid at room temperature.

N-Glycosylation Alteration of Serum and Salivary Immunoglobulin a Is a Possible Biomarker in Oral Mucositis

Background: Oral and enteral mucositis due to high-dose cytostatic treatment administered during autologous and allogeneic stem-cell transplantation increases mortality. Salivary secretory immunoglobulin A (sIgA) is a basic pillar of local immunity in the first line of defense. Altered salivary sialoglycoprotein carbohydrates are important in the pathologies in the oral cavity including inflammation, infection and neoplasia. Therefore, we assessed whether changes in the salivary and serum IgA glycosylation correlated with development and severity of oral mucositis. Methods: Using capillary electrophoresis, comparative analysis of serum and salivary IgA total N-glycans was conducted in 8 patients with autologous peripheral stem-cell transplantation (APSCT) at four different stages of transplantation (day −3/−7, 0, +7, +14) and in 10 healthy controls. Results: Fourteen out of the 31 structures identified in serum and 6 out of 38 in saliva showed significant changes upon transplantation compared with the control group. Only serum core fucosylated, sialylated bisecting biantennary glycan (FA2BG2S2) showed significant differences between any two stages of transplantation (day −3/−7 and day +14; p = 0.0279). Conclusion: Our results suggest that changes in the serum IgA total N-glycan profile could serve as a disease-specific biomarker in patients undergoing APSCT, while analysis of salivary IgA N-glycan reflects the effect of APSCT on local immunity.

Deletion analysis of the flagellum-specific secretion signal in Salmonella flagellin

The export signal recognized by the flagellum-specific export machinery is harbored within the highly conserved 26-47 segment of the disordered N-terminal part of Salmonella flagellin. In this work, we aimed to further localize the essential part of the export signal by deletion analysis and investigated how the length of the spacer segment preceding the signal affects export efficiency. Export signal variants were attached to a reporter protein, the CCP2 domain of human C1r protein, and export efficiency of the fusion constructs was studied. Our results suggest that almost any continuous oligopeptide of 8-10 residues within the 26-47 segment can efficiently direct flagellar export if preceded by a spacer segment of at least 15 amino acids without any specific sequential requirement.

Nanobody-Displaying Flagellar Nanotubes

In this work we addressed the problem how to fabricate self-assembling tubular nanostructures displaying target recognition functionalities. Bacterial flagellar filaments, composed of thousands of flagellin subunits, were used as scaffolds to display single-domain antibodies (nanobodies) on their surface. As a representative example, an anti-GFP nanobody was successfully inserted into the middle part of flagellin replacing the hypervariable surface-exposed D3 domain. A novel procedure was developed to select appropriate linkers required for functional internal insertion. Linkers of various lengths and conformational properties were chosen from a linker database and they were randomly attached to both ends of an anti-GFP nanobody to facilitate insertion. Functional fusion constructs capable of forming filaments on the surface of flagellin-deficient host cells were selected by magnetic microparticles covered by target GFP molecules and appropriate linkers were identified. TEM studies revealed that short filaments of 2–900 nm were formed on the cell surface. ITC and fluorescent measurements demonstrated that the fusion protein exhibited high binding affinity towards GFP. Our approach allows the development of functionalized flagellar nanotubes against a variety of important target molecules offering potential applications in biosensorics and bio-nanotechnology.

Structural plasticity of the Salmonella FliS flagellar export chaperone

The Salmonella FliS flagellar export chaperone is a highly α-helical protein. Proteolytic experiments suggest that FliS has a compact core. However, the calorimetric melting profile of FliS does not show any melting transition in the 25-110 °C temperature range. Circular dichroism measurements reveal that FliS is losing its helical structure over a broad temperature range upon heating. These observations indicate that FliS unfolds in a noncooperative way and its native state shows features reminiscent of the molten globule state of proteins possessing substantial structural plasticity. As FliS has several binding partners within the cell, conformational adaptability seems to be an essential requirement to fulfill its multiple roles.

A polymerizable GFP variant

Flagellin has the ability to polymerize into long filaments under appropriate conditions. Our work aims at the construction of flagellin-based fusion proteins which possess polymerization ability and preserve the functional properties of the fusion partner as well. The hypervariable D3 domain of Salmonella flagellin, containing residues 190-283, is a good target for genetic engineering studies since it can be extensively modified or removed without disturbing the self-assembling ability. In this work a fusion construct of flagellin and the superfolder mutant of the green fluorescent protein were created by replacing D3 with superfolder green fluorescent protein (GFP). The obtained GFP variant was capable of forming stable, highly fluorescent filamentous assemblies. Our results imply that other proteins (enzymes, binding proteins, etc.) can also be furnished by polymerization ability in a similar way. This approach paves the way for the construction of multifunctional tubular nanostructures.

Characterization of diorganotin(IV) complexes with captopril. The first crystallographically authenticated metal complex of this anti-hypertensive agent

Diorganotin(IV) complexes R(2)Sn(cap) (capH(2)=N-[(S)-3-mercapto-2-methylpropionyl]-L-proline; R=Me, Et, n-Bu and t-Bu) were prepared and characterised. The FTIR and Raman spectra demonstrated that the organotin(IV) moieties interact with the [S] atom of the ligand, while the other coordination sites are the carboxylate and the amide -CO groups. Mössbauer Delta data showed that the diorganotin(IV) compounds adopt slightly distorted trigonal-bipyramidal (tbp) geometry. A single-crystal X-ray study was performed on the compound Me(2)Sn(cap): the Sn atom is five-coordinated in a distorted tbp environment, with two [O] atoms in the axial positions and the [S] and two [C] atoms in the equatorial (eq) plane. Each cap ligand coordinates to two different Sn atoms, and infinite zigzag chains are formed, directed parallel to each other and to the b axis of the unit cell. NMR (CDCl(3)) of the Me(2)Sn(IV) and n-Bu(2)Sn(IV) complexes indicated the presence of different oligomeric species.

Coordination properties of adenosine-5'-monophosphate and related ligands towards Me2Sn(IV)2+ in aqueous solution

The coordination of Me2Sn(IV)2+ to adenosine-5'-monophosphate (AMP) and the related compounds D-ribose-5-phosphate (R5P), D-glucose-1-phosphate (G1P) and D-glucose-6-phosphate (G6P) in aqueous solution was investigated by means of potentiometric titration, and 1H-, 31P-NMR and Mössbauer spectroscopic methods in the pH range 2-11 (I=0.1 M NaClO4, 298 K). The complex of AMP and Me2Sn(IV)2+ precipitated at low pH was characterised by elemental analysis, FT-IR and Mössbauer spectroscopic methods. From a comparison of the pK values obtained in the presence and absence of metal ion and the stability constants for the different systems, the coordination of [N] is excluded, while bidentate coordination of the phosphate group is presumed. Mössbauer spectroscopic measurements recorded in the glassy state confirmed bidentate coordination of the phosphate and the formation of mixed hydroxo complexes in the weakly acidic, neutral and strongly basic pH range. With increasing pH, the phosphate groups were replaced by the deprotonated alcoholic [O] atoms of the sugar moiety. The solid complex proved to be tbp structure with bidentate phosphate coordination.

Synthesis and structural and spectroscopic characterization of a complex between Co(II) and imino-bis(methylphosphonic acid): gaining insight into biologically relevant metal-ion phosphonate interactions or looking at a new Co(II)-organophosphonate material?

Cobalt is an essential metal ion involved in key biomolecules, regulating processes in human physiology. As a metal ion, Co(II) assumes forms, which are dictated by the nature of organic binders in biological fluids, and the conditions under which metal ion ligand interactions arise. Among the various low molecular mass metal ion binders in biological fluids are amino acids, organic acids, as well as their variably phosphorylated forms. As a representative metal ion binder, the organophosphonate ligand H(2)O(3)P-CH(2)-NH(2)(+)-CH(2)-PO(3)H(-) was employed in aqueous reactions with Co(II), ultimately leading to the isolation of complex [Co(C(2)H(8)O(6)NP(2))(2)(H(2)O)(2)] (1) at pH 2. The complex was characterized analytically, spectroscopically (FTIR, UV-vis, EPR), and magnetically. Compound 1 crystallizes in the monoclinic space group P2(1)/n, with a = 7.361(3) A, b = 8.133(3) A, c = 14.078(5) A, beta = 104.40(1) degrees, V = 816.3(5) A(3), and Z = 2. X-ray crystallography reveals that 1 is a compound with a molecular type of lattice. In it, there exist mononuclear octahedral sites of Co(II) surrounded by oxygens, belonging to terminal phosphonates and bound water molecules. Both ends of the ligand zwitterionic form are involved in binding to adjacent Co(II) ions, thus creating tetranuclear 32-membered rings, with cavities extending in two dimensions and holes in the third dimension throughout the lattice of 1. Similar structural features were observed in other metal organophosphonate lattices of potential catalytic and chemical reactivity. The magnetic and EPR data on 1 support the presence of a high-spin octahedral Co(II) in an oxygen environment, having a ground state with an effective spin S = (1)/(2). The solution UV-vis and EPR data suggest retention of the high-spin octahedral Co(II) ion, consistent with the magnetization measurements on 1. Collectively, the data reflect the existence of a soluble Co(II)-iminodiphosphonate species not unlike those expected in biological fluids containing the specific ligand or ligands similar to that. Both biologically relevant perspectives and a synthetic outlook into Co(II)-organophosphonate materials are discussed.