Mass spectrometry and non-covalent protein-ligand complexes: confirmation of binding sites and changes in tertiary structure

An experimental approach is described for determining protein-small molecule non-covalent ligand binding sites and protein conformational changes induced by ligand binding. The methodology utilizes time resolved limited proteolysis and the high throughput analysis capability of MALDI TOF MS to determine the binding site in a tetanus toxin C-fragment (51 kDa)-doxorubicin (543 Da) non-covalent complex. Comparing relative ion abundances of peptides released from the time resolved limited proteolysis of tetanus toxin C-fragment (TetC) and the TetC-doxorubicin complex every 10 min from 10 to 120 min of digestion revealed that the binding of doxorubicin induced a significant change in surface topology of TetC. Four of the twenty-nine peptides observed by MALDI MS, including amino acids 351-360, 299-304, 305-311 and 312-316, had a lower abundance in the TetC-doxorubicin complex relative to TetC from 10 to 100 min of digestion. A decrease in ion abundance suggests doxorubicin obstructs the access of the protease to one or both termini of these peptides, identifying doxorubicin binding site(s). Conversely, five peptide ions, including amino acids 335-350, 364-375, 364-376, 281-298, and 316-328, all had a greater abundance in the digest of the complex, indicating an increase in accessibility to these sites. These five peptides flank regions of decreased ion abundance, suggesting that doxorubicin not only binds to the surface, but also induces a conformational change in TetC.     

Effects of alkyltrimethylammonium bromide surfactants on the kinetics of the oxidation of tris(1,10-phenanthroline)iron(II) by azido-pentacyanocobaltate(III) complex

The redox reaction between tris(1,10-phenanthroline)iron(II), [Fe(phen)₃]²⁺, and azido-pentacyanocobaltate(III), [Co(CN)₅N₃]^3? was investigated in three cationic surfactants: dodecyltrimethylammonium bromide (DTAB), tetradecyltrimethylammonium bromide (TTAB) and cetyltrimethylammonium bromide (CTAB) in the presence of 0.1?M NaCl at 35°C. Second-order rate constant in the absence and presence of surfactant, k_w and k_ψ, respectively, were obtained in the concentration ranges DTAB?=?0???4.667?×?10^?4?mol?dm^?3, TTAB?=?0–9.364?×?10^?5?mol?dm^?3, CTAB?=?0???6.220?×?10^?5?mol?dm^?3. Electron transfer rate was inhibited by the surfactants with premicelllar activity. Inhibition factors, k_w/k_ψ followed the trend CTAB?>?TTAB?>?DTAB with respect to the surfactant concentrations used. The magnitudes of the binding constants obtained suggest significant electrostatic and hydrophobic interactions. Activation parameters ΔH^≠, ΔS^≠, and E_a have larger positive values in the presence of surfactants than in surfactant-free medium. The electron transfer is proposed to proceed via outer-sphere mechanism in the presence of the surfactants.     

A first‐principles study of diatomic NiAl: Ground state,structure, and spectroscopic constants

A computational study of diatomic NiAl is reported. Molecular properties evaluated include the equilibrium bond length (r_e), equilibrium stretching frequency (ω_e), doublet‐quartet energy splitting, and nickel‐aluminum bond strength. Several interesting conclusions have resulted from this research. First, convergence in calculated properties is smoother with recently reported correlation consistent basis sets than earlier basis sets for Ni and Al. Second, with the exception of bond strength, basis set limit properties extrapolated using correlation basis sets are in agreement with reported data. Third, this research suggests that caution may be needed with regard to the use of DFT for developing interatomic potentials for larger scale simulations. For example, B97‐1 showed better agreement with reported r_e for ²NiAl than B3LYP. However, the situation was reversed for the calculation of ω_e. With respect to bond strength, the situation is unclear due to the scatter among experiment and calculations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

“Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination”

Protein secondary structural analysis is important for understanding the relationship between protein structure and function, or more importantly how changes in structure relate to loss of function. The structurally sensitive protein vibrational modes (amide I, II, III and S) in deep-ultraviolet resonance Raman (DUVRR) spectra resulting from the backbone C–O and N–H vibrations make DUVRR a potentially powerful tool for studying secondary structure changes. Experimental studies reveal that the position and intensity of the four amide modes in DUVRR spectra of proteins are largely correlated with the varying fractions of α-helix, β-sheet and disordered structural content of proteins. Employing multivariate calibration methods and DUVRR spectra of globular proteins with varying structural compositions, the secondary structure of a protein with unknown structure can be predicted. A disadvantage of multivariate calibration methods is the requirement of known concentration or spectral profiles. Second-order curve resolution methods, such as parallel factor analysis (PARAFAC), do not have such a requirement due to the “second-order advantage.” An exceptional feature of DUVRR spectroscopy is that DUVRR spectra are linearly dependent on both excitation wavelength and secondary structure composition. Thus, higher order data can be created by combining protein DUVRR spectra of several proteins collected at multiple excitation wavelengths to give multi-excitation ultraviolet resonance Raman data (ME-UVRR). PARAFAC has been used to analyze ME-UVRR data of nine proteins to resolve the pure spectral, excitation and compositional profiles. A three factor model with non-negativity constraints produced three unique factors that were correlated with the relative abundance of helical, β-sheet and poly-proline II dihedral angles. This is the first empirical evidence that the typically resolved “disordered” spectrum represents the better defined poly-proline II type structure.     

Exergy analysis of vapor compression refrigeration system using R450A as a replacement of R134a

This paper experimentally investigated exergetic performance analysis of vapor compression refrigeration system using R450a as a replacement for R134a at different evaporator and condenser temperatures within controlled environmental conditions. The exergetic performance analysis of the vapor compression refrigeration system with test parameters including efficiency defects in the components, total irreversibility, and exergy efficiency of the refrigeration system was performed. Findings showed that the total irreversibility and exergy efficiency of the vapor compression refrigeration system using R450A refrigerant were lower and higher than R134a by about 15.25–27.32% and 10.07–130.93%, respectively. However, the efficiency defect in the condenser, compressor, and evaporator of the R450A refrigeration system was lower than R134a by about 16.99–26.08%, 5.03–20.11%, and 1.85–15.85%, respectively. Conversely, efficiency defect in the capillary tube of the R450A refrigeration system was higher than R134a by about 14.66–78.97% under similar operating conditions. Overall, it was found that the most efficient component was the evaporator, and the least efficient component was the compressor for both refrigerants.

     

Thermal decomposition of rice husk: a comprehensive artificial intelligence predictive model

Journal of Thermal Analysis and Calorimetry - This study explored the predictive modelling of the pyrolysis of rice husk to determine the thermal degradation mechanism of rice husk. The study can...     

Microwave-assisted synthesis and antibacterial activity of some pyrazol-1-ylquinoxalin- 2(1H)-one derivatives

3-Hydrazinoquinoxalin-2(1H)-one was prepared from quinoxaline-2,3-dione and subsequently used for the synthesis of some potentially biologically active 3-(pyrazol-1-yl)quinoxalin-2(1H)-one derivatives. While 3-(3,5-dimethylpyrazol-1-yl)quinoxalin-2(1H)-one showed a comparative effect with streptomycin, 3-(5-oxo-3-phenyl-4,5-di- hydropyrazol-1-yl)quinoxalin-2(1H)-one was found to be the most active with an MIC value of 7.8 μg/ml.     

Pre-processing of ultraviolet resonance Raman spectra

The application of UV excitation sources coupled with resonance Raman have the potential to offer information unavailable with the current inventory of commonly used structural techniques including X-ray, NMR and IR analysis. However, for ultraviolet resonance Raman (UVRR) spectroscopy to become a mainstream method for the determination of protein secondary structure content and monitoring protein dynamics, the application of multivariate data analysis methodologies must be made routine. Typically, the application of higher order data analysis methods requires robust pre-processing methods in order to standardize the data arrays. The application of such methods can be problematic in UVRR datasets due to spectral shifts arising from day-to-day fluctuations in the instrument response. Additionally, the non-linear increases in spectral resolution in wavenumbers (increasing spectral data points for the same spectral region) that results from increasing excitation wavelengths can make the alignment of multi-excitation datasets problematic. Last, a uniform and standardized methodology for the subtraction of the water band has also been a systematic issue for multivariate data analysis as the water band overlaps the amide I mode. Here we present a two-pronged preprocessing approach using correlation optimized warping (COW) to alleviate spectra-to-spectra and day-to-day alignment errors coupled with a method whereby the relative intensity of the water band is determined through a least-squares determination of the signal intensity between 1750 and 1900 cm(-1) to make complex multi-excitation datasets more homogeneous and usable with multivariate analysis methods.     

Bi-exponential diffusion signal decay in normal appearing white matter of multiple sclerosis

Purpose

Our aim was to characterize bi-exponential diffusion signal changes in normal appearing white matter of multiple sclerosis (MS) patients.

Methods

Diffusion parameters were measured using mono-exponential (0–1000 s/mm²) and bi-exponential (0–5000 s/mm²) approaches from 14 relapsing-remitting subtype of MS patients and 14 age- and sex-matched controls after acquiring diffusion-weighted images on a 3T MRI system. The results were analyzed using parametric or nonparametric tests and multiple linear regression models.

Results

Mono-exponential apparent diffusion coefficient (ADC) slightly increased in controls (P=.09), but decreased significantly in MS as a function of age, nonetheless an elevated ADC was observed with increasing lesion number in patients. Bi-exponential analyses showed that the increased ADC is the result of decreased relative volume fraction of slow diffusing component (f_s). However, the fast and slow diffusion components (ADC_f, ADC_s) did not change as a function of either age in controls or lesion number and age in MS patients.

Conclusions

These data demonstrated that the myelin content of the white matter affects diffusion in relapsing-remitting subtype of multiple sclerosis that is possibly a consequence of the shift between different water fractions.     

Component-wise exergy analysis using adaptive neuro-fuzzy inference system in vapor compression refrigeration system

Journal of Thermal Analysis and Calorimetry - In this work, the adaptive neuro-fuzzy inference (ANFIS) system as an artificial intelligence method was used to predict the destruction of exergy in...