Measuring dissociation rate constants of protein complexes through subunit exchange: experimental design and theoretical modeling

Subunit shuffling dynamics in KaiC's central hub reveal the synchronization mechanism of the cyanobacterial circadian clock

Protein complexes are critical for cellular functions, and subunit exchange within these complexes is increasingly recognized as a key regulatory mechanism. In the cyanobacterial circadian clock, subunits shuffling of the core clock protein KaiC is thought to synchronize the clock, though the underlying mechanism remains unclear. We developed a chromatography-based method to monitor the shuffling dynamics of hexamerization domain of KaiC (KaiC-CI) and found that ATPase activity is essential for this process. By analyzing experiment data with quantitative models, we found that KaiC-CI hexamer stochastically disassembles into two oligomers for shuffling after hydrolysis. Further, by assuming a hidden conformation for post-hydrolysis hexamers, we established an ATPase activity-dependent model that quantitatively describes the shuffling dynamics of KaiC-CI hexamers, linking the shuffling rate to ATP hydrolysis and nucleotide exchange rates. Using this model, we estimated the shuffling dynamics of full-length KaiC with indirect experimental data. Our findings suggest that KaiC's phosphorylation states regulate nucleotide exchange rates in the CI domain, thereby modulating ATPase activity and influencing subunit shuffling. This study provides a mechanistic framework for understanding the role of ATPase activity in subunit exchange and its implications for circadian clock regulation.

Immunoinformatics design of a novel multiepitope vaccine candidate against non-typhoidal salmonellosis caused by Salmonella Kentucky using outer membrane proteins A, C, and F

The global public health risk posed by Salmonella Kentucky (S. Kentucky) is rising, particularly due to the dissemination of antimicrobial resistance genes in human and animal populations. This serovar, widespread in Africa, has emerged as a notable cause of non-typhoidal gastroenteritis in humans. In this study, we used a bioinformatics approach to develop a peptide-based vaccine targeting epitopes from the outer membrane proteins A, C, and F of S. Kentucky. Additionally, we employed flagellin protein (fliC) from Salmonella Typhimurium (S. Typhimurium) as an adjuvant to enhance the vaccine's effectiveness. Through this approach, we identified 14 CD8+ and 7 CD4+ T-cell epitopes, which are predicted to be restricted by various MHC class I and MHC class II alleles. The predicted epitopes are expected to achieve a population coverage of 94.91% when used in vaccine formulations. Furthermore, we identified seven highly immunogenic linear B-cell epitopes and three conformational B-cell epitopes. These T-cell and B-cell epitopes were then linked using appropriate linkers to create a multi-epitope vaccine (MEV). To boost the immunogenicity of the peptide construct, fliC from S. Typhimurium was included at the N-terminal. The resulting MEV construct demonstrated high structural quality and favorable physicochemical properties. Molecular docking studies with Toll-like receptors 1, 2, 4, and 5, followed by molecular dynamic simulations, suggested that the vaccine-receptor complexes are energetically feasible, stable, and robust. Immune simulation results showed that the MEV elicited significant responses, including IgG, IgM, CD8+ T-cells, CD4+ T-cells, and various cytokines (IFN-γ, TGF-β, IL-2, IL-10, and IL-12), along with a noticeable reduction in antigen levels. Despite these promising in-silico findings, further validation through preclinical and clinical trials is required to confirm the vaccine's efficacy and safety.

Surfactant-like Peptide Self-Assembled into Hybrid Nanostructures for Electronic Nose Applications

An electronic nose (e-nose) utilizes a multisensor array, which relies on the vector contrast of combinatorial responses, to effectively discriminate between volatile organic compounds (VOCs). In recent years, hierarchical structures made of nonbiological materials have been used to achieve the required sensor diversity. With the advent of self-assembling peptides, the ability to tune nanostructuration, surprisingly, has not been exploited for sensor array diversification. In this work, a designer surfactant-like peptide sequence, CG₇-NH₂, is used to fabricate morphologically and physicochemically heterogeneous "biohybrid" surfaces on Au-covered chips. These multistructural sensing surfaces, containing immobilized hierarchical nanostructures surrounded by self-assembled monolayers, are used for the detection and discrimination of VOCs. Through a simple and judicious design process, involving changes in pH and water content of peptide solutions, a five-element biohybrid sensor array coupled with a gas-phase surface plasmon resonance imaging system is shown to achieve sufficient discriminatory capabilities for four VOCs. Moreover, the limit of detection of the multiarray system is bench-marked at <1 and 6 ppbv for hexanoic acid and phenol (esophago-gastric biomarkers), respectively. Finally, the humidity effects are characterized, identifying the dissociation rate constant as a robust descriptor for classification, further exemplifying their efficacy as biomaterials in the field of artificial olfaction.

Thermokinetic Analysis of Protein Subunit Exchange by Variable-Temperature Native Mass Spectrometry

Many protein complexes are assembled from a varying number of subunits, which are continuously exchanging with diverse time scales. This structural dynamics is considered to be important for many regulatory and sensory adaptation processes that occur in vivo. We have developed an accurate method for monitoring protein subunit exchange by using native electrospray ionization mass spectrometry (ESI-MS), exemplified here for an extremely stable Rad50 zinc hook (Hk) dimer assembly, Zn(Hk)₂. The method has two steps: appropriate protein/peptide mutation and native ESI-MS analysis using a variable-temperature sample inlet. In this work, two Hk mutants were produced, mixed with wild-type Hk, and measured at three different temperatures. A thermokinetic analysis of heterodimer formation allowed us to determine the enthalpy, entropy, and Gibbs free energy of activation for subunit exchange, showing that the reaction is slow and associated with a high enthalpic barrier, consistent with the exceptionally high stability of the Zn(Hk)₂ assembly.

A Model for the Binding of Fluorescently Labeled Anti-Human CD4 Monoclonal Antibodies to CD4 Receptors on Human Lymphocytes

The CD4 glycoprotein is a component of the T cell receptor complex which plays an important role in the human immune response. This manuscript describes the measurement and modeling of the binding of fluorescently labeled anti-human CD4 monoclonal antibodies (mAb; SK3 clone) to CD4 receptors on the surface of human peripheral blood mononuclear cells (PBMC). CD4 mAb fluorescein isothiocyanate (FITC) and CD4 mAb allophycoerythrin (APC) conjugates were obtained from commercial sources. Four binding conditions were performed, each with the same PBMC sample and different CD4 mAb conjugate. Each binding condition consisted of the PBMC sample incubated for 30 min in labeling solutions containing progressively larger concentrations of the CD4 mAb-label conjugate. After the incubation period, the cells were re-suspended in PBS-based buffer and analyzed using a flow cytometer to measure the mean fluorescence intensity (MFI) of the labeled cell populations. A model was developed to estimate the equilibrium concentration of bound CD4 mAb-label conjugates to CD4 receptors on PBMC. A set of parameters was obtained from the best fit of the model to the measured MFI data and the known number of CD4 receptors on PBMC surface. Divalent and monovalent binding had to be invoked for the APC and FITC CD4 mAb conjugates, respectively. This suggests that the mAb binding depends on the size of the label, which has significant implications for quantitative flow cytometry. The study supports the National Institute of Standards and Technology program to develop quantitative flow cytometry measurements.

A Point-of-Care Immunosensor for Human Chorionic Gonadotropin in Clinical Urine Samples Using a Cuneated Polysilicon Nanogap Lab-on-Chip

Human chorionic gonadotropin (hCG), a glycoprotein hormone secreted from the placenta, is a key molecule that indicates pregnancy. Here, we have designed a cost-effective, label-free, in situ point-of-care (POC) immunosensor to estimate hCG using a cuneated 25 nm polysilicon nanogap electrode. A tiny chip with the dimensions of 20.5 × 12.5 mm was fabricated using conventional lithography and size expansion techniques. Furthermore, the sensing surface was functionalized by (3-aminopropyl)triethoxysilane and quantitatively measured the variations in hCG levels from clinically obtained human urine samples. The dielectric properties of the present sensor are shown with a capacitance above 40 nF for samples from pregnant women; it was lower with samples from non-pregnant women. Furthermore, it has been proven that our sensor has a wide linear range of detection, as a sensitivity of 835.88 μA mIU^-1 ml^-2 cm^-2 was attained, and the detection limit was 0.28 mIU/ml (27.78 pg/ml). The dissociation constant K_d of the specific antigen binding to the anti-hCG was calculated as 2.23 ± 0.66 mIU, and the maximum number of binding sites per antigen was B_max = 22.54 ± 1.46 mIU. The sensing system shown here, with a narrow nanogap, is suitable for high-throughput POC diagnosis, and a single injection can obtain triplicate data or parallel analyses of different targets.

A fluorimetric readout reporting the kinetics of nucleotide-induced human ribonucleotide reductase oligomerization

Human ribonucleotide reductase (hRNR) is a target of nucleotide chemotherapeutics in clinical use. The nucleotide-induced oligomeric regulation of hRNR subunit α is increasingly being recognized as an innate and drug-relevant mechanism for enzyme activity modulation. In the presence of negative feedback inhibitor dATP and leukemia drug clofarabine nucleotides, hRNR-α assembles into catalytically inert hexameric complexes, whereas nucleotide effectors that govern substrate specificity typically trigger α-dimerization. Currently, both knowledge of and tools to interrogate the oligomeric assembly pathway of RNR in any species in real time are lacking. We therefore developed a fluorimetric assay that reliably reports on oligomeric state changes of α with high sensitivity. The oligomerization-directed fluorescence quenching of hRNR-α, covalently labeled with two fluorophores, allows for direct readout of hRNR dimeric and hexameric states. We applied the newly developed platform to reveal the timescales of α self-assembly, driven by the feedback regulator dATP. This information is currently unavailable, despite the pharmaceutical relevance of hRNR oligomeric regulation.