Structural rearrangement of Neisseria meningitidis transferrin binding protein A (TbpA) prior to human transferrin protein (hTf) binding

Gram-negative bacterium Neisseria meningitidis, responsible for human infectious disease meningitis, acquires the iron (Fe³⁺) ion needed for its survival from human transferrin protein (hTf). For this transport, transferrin binding proteins TbpA and TbpB are facilitated by the bacterium. The transfer cannot occur without TbpA, while the absence of TbpB only slows down the transfer. Thus, understanding the TbpA-hTf binding at the atomic level is crucial for the fight against bacterial meningitis infections. In this study, atomistic level of mechanism for TbpA-hTf binding is elucidated through 100 ns long all-atom classical MD simulations on free (uncomplexed) TbpA. TbpA protein underwent conformational change from ‘open’ state to ‘closed’ state, where two loop domains, loops 5 and 8, were very close to each other. This state clearly cannot accommodate hTf in the cleft between these two loops. Moreover, the helix finger domain, which might play a critical role in Fe³⁺ ion uptake, also shifted downwards leading to unfavorable Tbp-hTf binding. Results of this study indicated that TbpA must switch between ‘closed’ state to ‘open’ state, where loops 5 and 8 are far from each other creating a cleft for hTf binding. The atomistic level of understanding to conformational switch is crucial for TbpA-hTf complex inhibition strategies. Drug candidates can be designed to prevent this conformational switch, keeping TbpA locked in ‘closed’ state.     

Real-time prostate-specific antigen detection with prostate-specific antigen imprinted capacitive biosensors

Prostate specific antigen (PSA) is a valuable biomarker for early detection of prostate cancer, the third most common cancer in men. Ultrasensitive detection of PSA is crucial to screen the prostate cancer in an early stage and to detect the recurrence of the disease after treatment. In this report, microcontact-PSA imprinted (PSA-MIP) capacitive biosensor chip was developed for real-time, highly sensitive and selective detection of PSA. PSA-MIP electrodes were prepared in the presence of methacrylic acid (MAA) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the cross-linker via UV polymerization. Immobilized Anti-PSA antibodies on electrodes (Anti-PSA) for capacitance measurements were also prepared to compare the detection performances of both methods. The electrodes were characterized by atomic force microscopy (AFM), scanning electron microscopy (SEM) and cyclic voltammetry (CV) and real-time PSA detection was performed with standard PSA solutions in the concentration range of 10 fg mL⁻¹–100 ng mL⁻¹. The detection limits were found as 8.0 × 10⁻⁵ ng mL⁻¹ (16 × 10⁻¹⁷ M) and 6.0 × 10⁻⁴ ng mL⁻¹ (12 × 10⁻¹⁶ M) for PSA-MIP and Anti-PSA electrodes, respectively. Selectivity studies were performed against HSA and IgG and selectivity coefficients were calculated. PSA detection was also carried out from diluted human serum samples and finally, reproducibility of the electrodes was tested. The results are promising and show that when the sensitivity of the capacitive system is combined with the selectivity and reproducibility of the microcontact-imprinting procedure, the resulting system might be used successfully for real-time detection of various analytes even in very low concentrations.     

The preparation of new palladium (II) complexes with Schiff base type ligands and its impregnated Al2O3 materials: As the catalysts for degradation/reduction of organic dyes

The removal of organic dyes used in many sectors such as textile, paper, leather, and packaging from water sources is very important in terms of preventing the spread of industrial pollutants to the environment. Transition metal complexes supported to an inorganic solid material are frequently used for the degradation/reduction of organic dyes causing this pollution. In this study, new Pd (II) complexes with Schiff base ligands were synthesized and structurally characterized by nuclear magnetic resonance (NMR), Fourier-transform infrared spectroscopy (FT-IR), mass spectrometry (MS), and single-crystal X-ray diffraction (sc-XRD) spectroscopic methods. Then, the Al₂O₃-impregnated materials of these Pd (II) complexes were prepared and characterized by scanning electron microscopy with energy dispersive X-ray analysis (SEM-EDX), FT-IR, and thermogravimetry (TG) techniques. The catalytic activities of the synthesized Pd (II) complexes and their Al₂O₃-impregnated materials were comparatively analyzed to investigate the degradation/reduction of organic dyes (2-nitroaniline, 4-nitroaniline, 4-nitrophenol, eosin yellow, and methylene blue). The catalytic results indicate that Al₂O₃-impregnated materials are very active catalysts for the degradation/reduction of organic dyes under those circumstances. Conversions of up to 98% for all substrates were obtained after 5 min at ambient temperature.     

On the Adjacency-Jacobsthal numbers

In this article, we define the adjacency-Jacobsthal sequence and then we obtain the combinatorial representations and the sums of adjacency-Jacobsthal numbers by the aid of generating function and generating matrix of the adjacency-Jacobsthal sequence. Also, we derive the determinantal and the permanental representations of adjacency-Jacobsthal numbers by using certain matrices which are obtained from generating matrix of adjacency-Jacobsthal numbers. Furthermore, using the roots of characteristic polynomial of the adjacency-Jacobsthal sequence, we produce the Binet formula for adjacency-Jacobsthal numbers. Finally, we give the relationships between adjacency-Jacobsthal numbers and Fibonacci, Pell, and Jacobsthal numbers.     

Nucleophilic substitution reactions of monofunctional nucleophilic reagents with cyclotriphosphazenes containing 2,2-dioxybiphenyl units

The nucleophilic substitution reactions of mono- and bis-spiro-2,2′ -dioxybiphenyl cyclotriphosphazenes (3 and 4) with cyclopropanemethylamine (5) and aniline (6) were performed in the presence of trimethylamine in THF. Five novel cyclopropanemethylamino- and anilino-substituted spiro-2,2′ -dioxybiphenyl cyclotriphosphazene derivatives (7–11) were obtained from these reactions. The molecular structures of the new cyclotriphosphazene derivatives (7–11) were characterized by elemental analysis, MALDI-TOF MS, FT-IR, and NMR ( ³¹ P and ¹ H) spectroscopies. The structure of the spiro-(2,2′ -dioxybiphenyl)-bis-(anilino)-cyclotriphosphazene (11) was also determined by single-crystal X-ray crystallography.     

Expected escape times from attractor basins due to low intensity noise

In this paper, a numerical approach is described to estimate escape times from attractor basins when a dynamical system is subjected to noise or stochastic perturbations. Noise can affect nonlinear system response by driving solution trajectories to different attractors. The changes in physical behavior can be observed as amplitude and phase change of periodic oscillations, initiation or annihilation of chaotic motion, phase synchronization, and so on. Estimating probability of transitions from one attractor to another, and predicting escape times are essential for quantifying the effects of noise on the system response. In this paper, a numerical approach is outlined where probability transition maps are generated between grids. Then, these maps are iterated to find the probability distribution after long durations, wherein, a constant escape rate can be observed between basins. The constant escape rate is then used to estimate the average escape times. The approach is applicable to systems subjected to low-intensity stochastic disturbances and with long escape times, where Monte Carlo simulations are impractical. Escape times up to \(10^{13}\) periods are estimated without relying on computationally expensive computations.