The Effects of Three-Dimensional Ligand Immobilization on Kinetic Measurements in Biosensors

The field of biosensing is in constant evolution, propelled by the need for sensitive, reliable platforms that provide consistent results, especially in the drug development industry, where small molecule characterization is of uttermost relevance. Kinetic characterization of small biochemicals is particularly challenging, and has required sensor developers to find solutions to compensate for the lack of sensitivity of their instruments. In this regard, surface chemistry plays a crucial role. The ligands need to be efficiently immobilized on the sensor surface, and probe distribution, maintenance of their native structure and efficient diffusion of the analyte to the surface need to be optimized. In order to enhance the signal generated by low molecular weight targets, surface plasmon resonance sensors utilize a high density of probes on the surface by employing a thick dextran matrix, resulting in a three-dimensional, multilayer distribution of molecules. Despite increasing the binding signal, this method can generate artifacts, due to the diffusion dependence of surface binding, affecting the accuracy of measured affinity constants. On the other hand, when working with planar surface chemistries, an incredibly high sensitivity is required for low molecular weight analytes, and furthermore the standard method for immobilizing single layers of molecules based on self-assembled monolayers (SAM) of epoxysilane has been demonstrated to promote protein denaturation, thus being far from ideal. Here, we will give a concise overview of the impact of tridimensional immobilization of ligands on label-free biosensors, mostly focusing on the effect of diffusion on binding affinity constants measurements. We will comment on how multilayering of probes is certainly useful in terms of increasing the sensitivity of the sensor, but can cause steric hindrance, mass transport and other diffusion effects. On the other hand, probe monolayers on epoxysilane chemistries do not undergo diffusion effect but rather other artifacts can occur due to probe distortion. Finally, a combination of tridimensional polymeric chemistry and probe monolayer is presented and reviewed, showing advantages and disadvantages over the other two approaches.

Nonneutralizing FVIII-specific antibody signatures in patients with Hemophilia A and in healthy donors

Previous studies identified nonneutralizing FVIII-specific antibodies in the circulation of severe and non-severe hemophilia A patients without FVIII inhibitors and also in some healthy individuals. To gain a better understanding of the nature of these nonneutralizing antibody responses, we analyzed and compared anti-FVIII antibody signatures in three study cohorts - previously treated severe as well as non-severe hemophilia A patients without FVIII inhibitors, and healthy donors. FVIII-binding IgM, IgG1-4 and IgA antibodies were differentiated, FVIII-specificity was assessed and associated apparent affinity constants were determined. Our results indicate that the nonneutralizing FVIII-specific antibody response in all study cohorts is dominated by IgG1 and IgA. Prevalences, titers and affinities of these nonneutralizing antibodies were higher in the hemophilia A cohorts than in healthy donors. Stratification for the anti-HCV antibody status demonstrated the presence of FVIII-specific IgA with elevated titers in severe hemophilia A patients with an active or past HCV infection when compared to HCV antibody positive non-severe patients or HCV antibody negative patients and healthy donors. Increased titers and affinities of FVIII-specific IgG1 antibodies were observed in a considerable number of hemophilia A patients as opposed to healthy subjects independently of the patients' anti-HCV antibody status. Overall, our findings support the hypothesis that the generation of nonneutralizing anti-FVIII antibodies in healthy individuals and in non-inhibitor hemophilia A patients might be based on similar immune mechanisms. However, differences in prevalences, titers and affinities of these antibodies indicate distinct differences in the antibody evolution between healthy individuals and patients.

Eukaryotic catecholamine hormones influence the chemotactic control of Vibrio campbellii by binding to the coupling protein CheW

In addition to their well-known role as stress-associated catecholamine hormones in animals and humans, epinephrine (EPI) and norepinephrine (NE) act as interkingdom signals between eukaryotic hosts and bacteria. However, the molecular basis of their effects on bacteria is not well understood. In initial phenotypic studies utilizing Vibrio campbellii as a model organism, we characterized the bipartite mode of action of catecholamines, which consists of promotion of growth under iron limitation, and enhanced colony expansion on soft agar. In order to identify the molecular targets of the hormones, we designed and synthesized tailored probes for chemical proteomic studies. As the catechol group in EPI and NE acts as iron chelator and is prone to form a reactive quinone moiety, we devised a photoprobe based on the adrenergic agonist phenylephrine (PE), which solely influenced colony expansion. Using this probe, we identified CheW, located at the core of the chemotaxis signaling network, as a major target. In vitro studies confirmed that EPI, NE, PE, as well as labetalol, a clinically applied antagonist, bind to purified CheW with affinity constants in the sub-micromolar range. In line with these findings, exposure of V. campbellii to these adrenergic agonists affects the chemotactic control of the bacterium. This study highlights a previously unknown effect of eukaryotic signaling molecules on bacterial motility.

Understanding the effects of different residual lignin fractions in acid-pretreated bamboo residues on its enzymatic digestibility

Background During the dilute acid pretreatment process, the resulting pseudo-lignin and lignin droplets deposited on the surface of lignocellulose and inhibit the enzymatic digestibility of cellulose in lignocellulose. However, how these lignins interact with cellulase enzymes and then affect enzymatic hydrolysis is still unknown. In this work, different fractions of surface lignin (SL) obtained from dilute acid-pretreated bamboo residues (DAP-BR) were extracted by various organic reagents and the residual lignin in extracted DAP-BR was obtained by the milled wood lignin (MWL) method. All of the lignin fractions obtained from DAP-BR were used to investigate the mechanism for interaction between lignin and cellulase using surface plasmon resonance (SPR) technology to understand how they affect enzymatic hydrolysis Results The results showed that removing surface lignin significantly decreased the yield for enzymatic hydrolysis DAP-BR from 36.5% to 18.6%. The addition of MWL samples to Avicel inhibited its enzymatic hydrolysis, while different SL samples showed slight increases in enzymatic digestibility. Due to the higher molecular weight and hydrophobicity of MWL samples versus SL samples, a stronger affinity for MWL (KD = 6.8–24.7 nM) was found versus that of SL (KD = 39.4–52.6 nM) by SPR analysis. The affinity constants of all tested lignins exhibited good correlations (r > 0.6) with the effects on enzymatic digestibility of extracted DAP-BR and Avicel. Conclusions This work revealed that the surface lignin on DAP-BR is necessary for maintaining enzyme digestibility levels, and its removal has a negative impact on substrate digestibility.

Functional Roles of PARP2 in Assembling Protein–Protein Complexes Involved in Base Excision DNA Repair

Poly(ADP-ribose) polymerase 2 (PARP2) participates in base excision repair (BER) alongside PARP1, but its functions are still under study. Here, we characterize binding affinities of PARP2 for other BER proteins (PARP1, APE1, Polβ, and XRCC1) and oligomerization states of the homo- and hetero-associated complexes using fluorescence-based and light scattering techniques. To compare PARP2 and PARP1 in the efficiency of PAR synthesis, in the absence and presence of protein partners, the size of PARP2 PARylated in various reaction conditions was measured. Unlike PARP1, PARP2 forms more dynamic complexes with common protein partners, and their stability is effectively modulated by DNA intermediates. Apparent binding affinity constants determined for homo- and hetero-oligomerized PARP1 and PARP2 provide evidence that the major form of PARP2 at excessive PARP1 level is their heterocomplex. Autoregulation of PAR elongation at high PARP and NAD+ concentrations is stronger for PARP2 than for PARP1, and the activity of PARP2 is more effectively inhibited by XRCC1. Moreover, the activity of both PARP1 and PARP2 is suppressed upon their heteroPARylation. Taken together, our findings suggest that PARP2 can function differently in BER, promoting XRCC1-dependent repair (similarly to PARP1) or an alternative XRCC1-independent mechanism via hetero-oligomerization with PARP1.

Towards redox-switchable organocatalysts based on bidentate halogen bond donors

Novel redox-switchable halogen bond donors were synthesized. Thermodynamic affinity constants towards anions have been determined by electrochemical and spectroscopic techniques. The compounds were successfully employed as effective organocatalysts.

Native mass spectrometry of human carbonic anhydrase I and its inhibitor complexes

Native mass spectrometry is a potent technique to study and characterize biomacromolecules in their native state. Here, we have applied this method to explore the solution chemistry of human carbonic anhydrase I (hCA I) and its interactions with four different inhibitors, namely three sulfonamide inhibitors (AAZ, MZA, SLC-0111) and the dithiocarbamate derivative of morpholine (DTC). Through high-resolution ESI-Q-TOF measurements, the native state of hCA I and the binding of the above inhibitors were characterized in the molecular detail. Native mass spectrometry was also exploited to assess the direct competition in solution among the various inhibitors in relation to their affinity constants. Additional studies were conducted on the interaction of hCA I with the metallodrug auranofin, under various solution and instrumental conditions. Auranofin is a selective reagent for solvent-accessible free cysteine residues, and its reactivity was analyzed also in the presence of CA inhibitors. Overall, our investigation reveals that native mass spectrometry represents an excellent tool to characterize the solution behavior of carbonic anhydrase. Graphic abstract