The concentrations of fat soluble vitamins (A and E) and various metal ions (Ca, Cd, Cr, Co, Cu, Fe, Mg, Mn, Pb, Zn) have been determined in Polygonum cognatum Meissn plant samples collected from Sivas, Turkey. Analysis of vitamins were carried out by HPLC after Soxhlet extraction and metal ions were determined by FAAS after microwave digestion, respectively. The reliability of results were confirmed by recovery experiments in spiked samples. Recovery values were calculated in the range of 96 % and 105% while relative standard deviations (RSD) were in the range of 1.7 % and 8.5 %. The contents of vitamin E in plant samples were determined as 63.008±4.548 mg kg-1 and 59.178±5.142 mg kg-1. The amount of essential metals such as Mn, Zn, Fe were higher than most of common edible plants and the concentrations of toxic metals were lower than critical limits.

Synthesized compound 5, (C13H15N2S2)[PF6], was fully characterized with X-ray diffraction method. In this compound, the asymmetric unit contains a 1,3-(2-thiophenylmethyl)-4,5-dihydroimidazolidinium cation and a hexafluorophosphate anion. Due to an 180° rotation about the thiophene-CH2 bonds, the thiophene rings in the cation are disordered [site-occupancy factors = 0.903(4)/0.097(4) and 0.837(5)/0.163(5), respectively]. The short C—N bond lengths [1.303(4) and 1.287(4) Å] in the imidazolidine ring display partial electron delocalization within the N—C—N fragment. Anion and cations are connected through intermolecular C—H...F hydrogen bonds and three p-p stacking interactions [centroid-centroid distances = 3.890(3), 3.852(5) and 3.816(7) Å] between the thiophene rings of the adjacent cations, forming layers parallel to (011). Furthermore, we studied theoretical studies of this compound, too. Geometry optimization was carried out in gas phase by Density Functional Theory (DFT) method with B3LYP applying 6-311++G** basis set. The obtained results from experimental and theoretical structural properties of compound 5 had been compared to each other.

This research entails the modelling of the toxicity of anticancer compounds on K562 cell line, where 112 compounds that make up the data set were divided into training and test set to be used for developing and validating the model respectively. The internal and external validation parameter R2 for the training and test set given as 0.845 and 0.5316 respectively justifies the robustness and the ability of the model to predict toxicity of the compounds. WPSA-3 and minHBint7 molecular descriptor is responsible for about 50% of the overall effect on the model.

In this study, the adsorption capacity of caffeic acid (CFA) functionalized Fe3O4 magnetic recyclable nanocomposite (Fe3O4@CFA MNCs) for removal of industrial dye Acid Red 114 (AR 114) was investigated. The max. adsorption (qm) of the Fe3O4@CFA MNCs for AR114 was 333 mg/g without pH correction of the solution. Compared with other studies these adsorbent possess very adsorption capacity for AR114 dye. The adsorption isotherm data and the process of adsorption kinetics were fitted using the Langmuir equation and a pseudo-second-order kinetic model that showed chemisorption may be the rate controlling step in the adsorption processes. It was proved which the magnetic NMs technology was contributed by this study which can be a new and covetable alternative for organic contaminant adsorption. Furthermore, the reusability of the Fe3O4@CFA MNCs was investigated and significant removal of AR114 obtained even after five cycles

The systematic background of mass spectrometry (MS) was established by using the Valency Interaction Formula theory in an efficient manner. A new graph theoretical method was developed as a pure quantum mechanical survey and applied on a variety of molecules and assemblies to elucidate the quantum mechanical systematics behind mass spectrometry. The topological indexes and graph theoretical methods in chemistry and physics as the striking features of this new method was applied onto the mass spectra of several molecules and assemblies due to the insufficiencies of the obselete fragmentation procedures. These fundamental topological indexes were determined to make quick deductions pictorially on the mass spectra of molecules. The major fragmentation pathways for several molecules, as the striking features of Mass Spectometry, were examined in a pure theoretical way and a priori decomposition products were predicted. The systematic theory was provided in the light of our examination and a great deal of qualitative information was obtained just by knowing which interactions are soft among the others. The results are of general validity in comparison with the experimental data.

Benzimidazole derivatives are interesting heterocycles and are found in many naturally occurring products and various drugs. They exhibit several pharmacological activities such as antitumor, diuretic, fungicidal, bactericidal, antihelmintic, antiallergic, antihistaminic, vasodilator, hypotensive, spasmolytic activities and local analgesic. Owing to the importance of these heterocyclic compounds, the aim of this review is to present the main aspects of the microwave synthesis methods of the benzimidazole derivatives unill 2013.

Xanthine biosensor based on glassy carbon electrode (GC) modified with graphene (GR), Co3O4 nanoparticles and chitosan (CH) composite was fabricated. Xanthine oxidase (XAO) solution was dropped on the surface of Co3O4/CH/GR/GC and electrode was placed in saturated glutaraldehyde vapor for the crosslinking of the enzymes. The modified electrode was characterized by scanning electron microscopy, cyclic voltammetry and electrochemical impedance spectroscopy. Under the optimized experimental conditions, xanthine was detected in the concentration range from 5.0×10-7 to 8.0×10-5 M with a detection limit of 2.0×10-7 M. The low Michaelis–Menten constant (0.17 mM) suggested enhanced enzyme affinity for the immobilized enzyme as compared to previously reported xanthine biosensors. Moreover, the biosensor exhibited some advantages, such as short response time (10 s), high sensitivity (6.58 µA/mM or 74.8 µA/mMcm2) and good reproducibility (RSD = 1.2%). The suitability of the device was verified by xanthine assay in a fish meat. The biosensor provide to be a reliable, easy, fast and economical method for the evaluation of fish freshness.

Titanium and zirconium 2-((p-tolylamino/p-tolylimino)methyl)phenolate (TAMP and TIMP) were prepared by reaction of Ti- and Zr-alcoholates with 2-((p-tolylamino)methyl)phenol (TAMPH) and 2-((p-tolylimino)methyl)phenol (TIMPH) in alcohol. To characterize these compounds, 1H, 13C NMR, FTIR, mass spectroscopies, and elemental analysis were used. The TAMP and TIMP metal compounds can be formulated as (TAMP)3M2(OR)O2 and (TIMP)4M2O2, respectively. The catalytic activity of these compounds was checked in polymerization reactions with propylene oxide (PO) and e-caprolactone (e-CL) and Ti-TAMP was effective. Poly-propylene oxide (PPO) and poly-caprolactone (PCL) were identified by 1H, 13C NMR and gel permeation chromatography (GPC).

In this research Taguchi method was applied to determine optimum parameters of doping process of cerium vanadate with Be, Mg, Ca, Sr and Ba ions. Percentage and type of doping ions are used as parameters in optimization process applied as orthogonal array to decrease the number of experiments. The calculated unit cell volume by Rietveld Refinement analysis via X-ray diffraction data (XRD) were used to confirm the formation of doped cerium vanadates. ANOVA method was applied to determine the effectiveness of the parameters.

Four novel antimony(III) compounds (SbX3; X = Cl or Br) of thiourea derivatives; N-methylthiourea (NMTU) and N-ethylthiourea (NETU) of formulae [SbCl3(NMTU)3] (1), [SbBr3(NMTU)3] (2), [SbCl3(NETU)3] (3) and [SbBr3(NETU)3] (4) were synthesized. These new antimony(III) halide compounds were characterized by melting point, elemental analysis, molar conductivity, FT-Infrared spectroscopy, FT-Raman spectroscopy, UV-Vis spectroscopy, NMR (1H and 13C) spectroscopy and TG-DTA analysis. The reactions of N-methylthiourea (NMTU) and N-ethylthiourea (NETU) with SbX3 (X = Cl or Br) in a 2:1 ligand/metal rate but unexpectedly products were formed in a 3:1 ligand/metal rate. The compounds are non-electrolytes in solution and spectroscopic data of the compounds are appropriate with six coordinate octahedral geometry by three halide ions and three sulfur atoms from thiourea ligands. N-methythiourea and N-ethylthiourea ligands behave as monodentate in compounds 1-4 with the binding through sulfur. The influence of these compounds 1–4, N-methythiourea and N-ethylthiourea upon the catalytic peroxidation of linoleic acid to hyperoxolinoleic acid by lipoxygenase was kinetically studied.

Carica papaya leaves samples (Green) were freshly harvested from Islamic village in Ilorin, Ilorin west local Government, Kwara State Nigeria. The leaves were extracted with methanol; the resulting extracts were screened for the phytochemical constituents using standard procedure. Phytochemical screening revealed the presence of bioactive compounds such as tannins, saponins, terpenoids, glycosides and alkaloids. The in-vitro anti-diabetic potential of the plant was also determined so as to justify the traditional usage of the plant in treating diabetes. The result of the present study confirmed that the methanolic extract of C.papaya leaves possess significant anti-diabetic activity in-vitro, this shows that the leaves has the potential for the development of drugs in combating diabetes.

The proximate, amino acid and fatty acid compositions of the fillet and oil from Clarias gariepinus (Catfish) and Oreochromis niloticus (Tilapia) were determined. The moisture content ranged from 76.27 % for catfish to 79.97 % for tilapia while the oil content ranged from 7.80 % for tilapia and 11.00 % for catfish. Ash content was in the range 8.03 – 9.16 % and the protein content was 15.83 - 18.48 %. Cooking – boiling, roasting or frying – resulted in a variation in the nutrient composition but with no significant effect on the amino acid composition except for the samples fried with palm oil which resulted in significantly reduced essential amino acids contents. All the fish samples – both fresh and processed – have amino acid scores less than 100, with lysine, threonine and the sulphur-containing amino acids being among the limiting amino acids. Both fish samples contain more unsaturated than saturated fatty acids.

The separation and purification methods for the isolation of an important biomolecule calmoduline protein is extremely important. Among these methods, the adsorption technique is extremely popular, and the cryogels as adsorbents with the macro porous structure and interconnected flow channels cryogel they have are preferred in this field. In this study, the adsorption of calmoduline via Ca(II) immobilized poly (2-hydroxyethyl methacrylate-glycidyl methacrylate), poly (HEMA-GMA), cryogels through changing interaction time, calmoduline initial concentration and temperature conditions. For the characterization of cryogels, the swelling test, Fourier Transform Infrared (FT-IR) Spectroscopy, Scanning Electron Microscopy (SEM), surface area (BET), elemental analysis and ICP-OES methods were performed. Nicotinamide molecule was used as Ca (II) chelating agent and the adsorption capacity of the cryogels was estimated as 1.812 mg calmoduline / g cryogel. The adsorption models of the adsorption reaction were examined by the Langmuir and Freundlich isotherm models and was determined to be more appropriate for Langmuir isotherm model.

Flowers (1000g) of Ocimum canum harvested at different time (7am, 10am, 1pm, 4pm and 7pm) in a day were separately hydrodistilled and yielded 0.19 - 0.27% (w/w) of essential oils. GC, GC-MS analyses revealed that the oils were predominated by oxygenated monoterpenoids (51.2-74.4%). Hydrocarbon monoterpenoids constituted 6.2-10.2% of the oils. Percentage composition of hydrocarbon and oxygenated sesquiterpenoids in the oils were in the range of 1.3-22.0%. The most abundant constituent of the oils was linalool (40.5-58.7%). Other principal constituents were; limonene (0.6 –7.5%), terpinen-4-ol (1.4–5.6%), eugenol (4.4–8.9%), geranyl acetate (0.2–4.9%), a-trans-bergamotene (3.2–9.4%) and E-isoeugenol (4.1–5.5%). The predominance of linalool in the oils showed that the oils were of linalool chemotype. Antibacterial activity of the oils was evaluated against Staphylococcus aureus and Escherichia coli using agar diffusion method. Irrespective of the time of collection of the flower, the oils were found to be active against the tested organisms. However, they are more active on Escherichia coli than Staphylococcus aureus. The activity of the oils on the organisms was concentration dependent.

Pyrolysis of Isochrysis microalgae was carried out in a fixed-bed reactor without and with metal oxide catalysts (CeO2, TiO2, Al2O3) at the temperatures of 450, 500 and 550 oC with a constant heating rate of 40 oC/min. The pyrolysis conditions including catalyst and temperature were studied in terms of their effects on the yields of pyrolysis products and quality. The amount of bio-char, bio-oil and gas products was calculated. The composition of the produced bio-oils was determined by Elemental analysis (EA), Fourier transform infrared spectroscopy (FT-IR), proton nuclear magnetic resonance (1H NMR) and Gas chromatography/mass spectrometry (GC–MS) techniques. As a result of the pyrolysis experiments, it is shown that there have been significant effects of both catalyst and temperature on the conversion of Isochrysis microalgae into solid, liquid (bio-oil) and gas products. The highest bio-oil yield (24.30 %) including aqueous phase was obtained in the presence of TiO2 (50%) as catalyst at 500 °C. 98 different compounds were identified by GC-MS in bio-oils obtained at 500 oC. According to 1H NMR analysis, bio-oils contained ~60-64 % aliphatic and ~17-19 % aromatic structural units. EA showed that the bio-oils contained ~66-69 % C and having 31-34 MJ/kg higher heating values.

In order to determine the nutrition load in the Sea of Marmara, sampling was realized on appointed 25 stations, at standard vertical sections from the surface to the deepest point of the station, bi-annually between 2010 and 2013. NO2–N, NO3–N, NH4–N, and PO4–P were analysed from unfiltered water samples; in addition, some physicochemical parameters that play important roles, such as salinity, temperature, dissolved oxygen, and pH, were measured for each station. This study reports on nutrients load in the Sea of Marmara for a preliminary assessment of the status of these nutrients and a brief discussion about the unique oceanographical status of the Sea of Marmara.

Parabens have been regarded as a substitute group to increase DNA interactions as well as cytotoxic and antimicrobial activities of ferrocenylphosphazenes. For this reason, new ferrocenylphosphazenes compounds bearing paraben (ethyl-4-hydroxybenzoate) have been synthesized for the first time (6-10) and their structures have been determined using elemental analysis, FTIR (Fourier transform), 1H (one-dimensional-1D), 31P NMR techniques and X-ray crystallography (for 9 and 10).

Poly-ß-alanine (PBA) and poly(3-hidroxypropionate) (PHP) were synthesized via base-catalyzed hydrogen transfer polymerization (HTP) of acrylamide and acrylic acid, respectively. Blends of PBA/PHP with different composition (PHP content, 5% to 75%) were studied using FTIR, DSC, TGA, XRD and polarized optical microscope to reveal both miscibility and thermal degradation kinetics of PBA/PHP blends. Optical images of blends were transparent and entirely uniform. Characteristic IR bands of both components shifted in higher frequencies with increasing fraction of other component. Melting temperature (Tm), thermal decomposition temperatures (Td) and enthalpy of fusion (?Hf) of PHP decreased with increasing PBA fraction in blends. Thermal degradation kinetics of both components were studied by Freeman-Carroll method. Activation energies of thermal degradations of blend components were determined with a good regression coefficients (at least 0.994). Activation energies of decomposition decreased from 224.14 to 86.125 kJmol-1 with increasing PHP content. XRD spectra of blends exhibited lower peak intensities than those of neat polymers. The spectroscopic, thermal and optic methods revealed that PBA and PHP were miscible with a good compatibility in amorphous phase.

Sorption regularities of Zn2+ and Pb2+ ions from water solutions by ion exchangers of Diaion CR 11, Amberlite IRC 748 with iminodiacetic acid functional group and Dowex M 4195 with bis-picolilamine functional group are investigated, sorption isotherms are plotted, isotherms are analyzed on the basis of known models, thermodynamic parameters are calculated on the basis of kinetic data, thermodynamic factor controlling processes is determined.

Ammonia is one of the syngas contaminants that must be removed before using the syngas downstream applications. The most promising hot-gas clean-up techniques of ammonia are selective catalytic oxidation (SCO) and catalytic decomposition. In this study, the catalytic activities over Zeolite Hß supported iron catalyst (Fe/HZß) were compared both for the two catalytic routes. For SCO experiments; temperature (300-550 °C), O2 (2000-6000 ppmv) and (0-10%) H2 concentrations were investigated with the presence of 800 ppm NH3 in each of the final gas mixture. In the second route, catalytic ammonia decomposition experiments were carried out with H2 in balance N2 (0-30%) containing 800 ppm NH3 at 700°C and 800°C. In the SCO, NH3 conversions were increased with increasing reaction temperatures with the absence of H2 in the reaction mixture. With 10% H2, it was shown that NH3 conversions increased with decreasing the reaction temperature. This was interpreted as the competing H2 and NH3 oxidations over the catalyst. On the other hand, in the catalytic decomposition, thermodynamic equilibrium conversion of almost 100% was attained at both 700 and 800 °C. Upon H2 addition, all conversions decreased. The decrease in conversion seemed to be linear with inlet hydrogen concentration. Hydrogen was seen to inhibit ammonia decomposition reaction. It was shown that Fe/HZß catalyst is better to use for catalytic decomposition of NH3 in syngas rather than SCO of NH3 in spite of higher reaction temperatures needed in the decomposition reaction.

This research work targets the effectiveness of the prepared activated carbon from Jatropha curcas and Terminalia catappa seed coats for the sorption of methylene blue (MB) from aqueous solution. The prepared Jatropha activated carbon (JAC) and Terminalia activated carbon (TAC) were characterised using Fourier transform infrared spectroscopy (FTIR), Scanning electron microscopy (SEM) and Branauer- Emmett-Teller (BET) surface area analysis. Effect of initial concentration, pH, contact time, adsorbent dose and temperature on the sorption experiments were studied and the adsorption capacity of these adsorbents were found to be 37.84 mg/g and 17.44 mg/g for methylene blue uptake by JAC and TAC respectively. The experimental data were analysed using Langmuir, Fruendlich, and Dubinin-Radushkevich isotherms. The data fitted best into Langmuir isotherm for Methylene blue-JAC and Methylene blue-TAC systems. The kinetic studies fitted into pseudo second order kinetics model. The process chemistry was exothermic.

Nowadays, AIDS still remains as a worldwide pandemic and continues to cause many death which arise from HIV-1 virus. For nearly 35 years, drugs that target various steps of virus life cycle have been developed. HIV-1 integrase is the one of these steps which is essential for virus life cycle. Computer aided drug design is being used in many drug design studies as also used in development of the first HIV-1 integrase inhibitor Raltegravir. In this study 3 ligands which are used as HIV-1 integrase inhibitors and 4 newly designed ligands were docked to catalytic core domain of HIV-1 integrase. Each of ligands docked to three different conformations of protein. Prepared complexes (21 item) were carried out by 50 ns MD simulations and results were analyzed. Finally, the binding free energies of ligands were calculated. Hereunder, it was determined that designed ligands L01 and L03 gave favorable results. The questions about the ligands which have low docking scores in a conformation of protein could give better scores in another conformation of protein and if the MD simulations carry the different oriented and different localized ligands in same position at the end of simulation were answered.

The description of a simple method for simultaneous determination of chloride, nitrate, sulfate, iodide, phosphate, thiocyanate, perchlorate, and orotic acid in milk samples was outlined. The method involves the use of dialysis cassettes for matrix elimination, followed by ion chromatography on a high capacity anion exchange column with suppressed conductivity detection. The novelty of dialysis process was that it did not need any chemical and organic solvent for elimination of macromolecules such as fat, carbohydrates and proteins from milk samples. External standard calibration curves for these analytes were linear with great correlation coefficients. The relative standard deviations of analyte concentrations were acceptable both inter-day and intra-day evaluations. Under optimized conditions, the limit of detection (Signal-to-Noise ratio = 3) for chloride, phosphate, thiocyanate, perchlorate, iodide, nitrate, sulfate, and orotate was found to be 0.012, 0.112, 0.140, 0.280, 0.312, 0.516, 0.520, and 0.840 mg L-1, respectively. Significant results were obtained for various spiked milk samples with % recovery in the range of 93.88 - 109.75 %. The proposed method was successfully applied to milk samples collected from Istanbul markets. The advantages of the method described herein are reagent-free, simple, and reliable

Lavander (Lavandula sp.) is a precious essential oil plant from the Lamiaceae family. There are 39 lavender species (Lavandula sp.) most of which have Mediterranean origin and among them three have high commercial value. While the essential oil quality of the lavender species (British lavender) is high the lavandin species (hybrid lavender) have high essential oil yield [2, 52]. In this study, the content of the extracts obtained from Lavandula angustifolia, which were grown in Burdur Örtülü locality, was determined via HPLC and GC analysis and the anti-microbial effect of the essential oil L. angustifolia was investigated. The study was made with the dried flowers of L. angustifolia. Some of the dried flowers were extracted and the essential oil was distilled from the remaining part. Various phenolic compounds in the extract were quantitatively determined by HPLC. Quantitatively cafeic, rosemeric and the 4-hydroxybenzoic acids were the most abundant phenolic acids in the content in decreasing order. In the GC analysis 31 different compounds were determined: Linalool and Linalil Acetate having the highest concentration. Anti-microbial effect was determined against the most frequently encountered microorganisms in the cosmetics: Candida albicans, Staphylococcus aureus, Pseudomonas aeruginosa, Aspergillus brasiliensis. According to the results it is concluded that the essential oil, L. angustifolia, can be used either directly or incorporated into the cosmetics without the necessity for any other extra preservative against the said microrganisms. According to the literature these microorganisms, which are frequently found in creams, cause various diseases. It was observed that the essential oil L. Angustifolia could completely remove the contamination caused by the said micro-organisms as of the 14. day.

In this study, a persistent system is aimed to be established which contributes to slow basal digoxin release in the treatment of cardiac failure. Poly(2-hydroxyethyl-metacrylate-methylmetacrylate) (p(HEMA-MMA) copolymer that can swell by taking on water is prepared in cylindirical form by UV photopolymerization method for the controlled-release of digoxin and effective hydrogel implant formulation. A batch of p(HEMA-MMA) composition is prepared in different monomer ratios. Biocompatibility is improved by adding PEO, PEG and serum albumine to the structures of p(HEMA-MMA), respectively. Scanning electron microscope (SEM) studies are carried out for the surface structure of the prepared carrier implant material and differential scanning calorimetry (DSC) studies for the thermal stability analysis. Swelling behaviors are investigated by transferring solvent molecules to the hydrogels. Digoxin release kinetics are evaluated by applying three different accumulative digoxin doses (100, 250 and 500 U/mL) in the persistent flow release system containing physiological phosphate. Power law, level-zero, and Higuchi model equations are utilized so as to evaluate the release mechanism of digoxin. The most suitable results are acquired from the composition whose HEMA:MMA monomer ratio is 1:0.5 (v/v) in drug accumulation and release studies. It is observed from the SEM image that the carrier implant in the structure of the acquired hydrogel has a smooth surface. According to DSC results, it is seen that thermal stability decreases in the event that MMA comonomer is added to the structure of the pHEMA hydrogel. Balance water amount within the physiological phosphate buffer of the p(HEMA-MMA) copolymer is observed to be less than the pHEMA. Digoxin release loaded to carrier implants by different ratios takes a long-term period as expected. It is decided that the formulation established in the study can be successfully applied for the basal digoxin level over four weeks in the treatment of chronic cardiac failure.

Three Arabian eye kohl brands were analyzed for the presence of lead and cadmium using atomic absorption spectroscopy (AAS) and X-ray diffraction techniques. In this work, the chemical analysis of the samples were studied according to concentration of heavy metals, solubility in different medium, reaction with KI, moisture and organic contents. XRD pattern proposed the presence of some crystalline material in an amorphous background for all investigated brands. Atomic absorption spectroscopy (AAS) showed that the average percentage of Pb was in the range 0.2411 to 6.173 %; and from zero to 0.0019 % for Cd. The maximum concentration of Pb and Cd was found in Natural Arab Kohl (NAK) sample and is equal to 30.865 mg/g and 9.50 µg/g respectively. The minimum concentration of heavy metal was found in Natural Black Al-Athmod Kohl (NBAK) sample. Moisture was present in a very low percent (~ 1%) while organics was being in a reasonable amount (maximum = 69 %). All eye kohl brands are soluble in acidic medium with different proportions and forms yellow precipitate of PbI2 when react with KI which is considered as a chemical evidence for the presence of lead.

Synthesis of coordination compounds of Zinc(II), Copper(II), Nickel(II), Cobalt(II) and Iron(II) with mixed piperaquine-acetaminophen and piperaquine-acetylsalicylic acid has been studied. The complexes were characterized via: solubility test, melting point determination, conductivity measurement, Atomic Absorption Spectroscopy, UV-Visible Spectroscopy, FTIR Spectroscopy and magnetic susceptibility. The complexes were proposed to have a stoichiometry ratio of 1:1:1 between each metal salt and the ligands with tetrahedral and octahedral geometry following the reaction pattern of MX.yH2O + L1L2/3 to give ML1L2/3X.yH2O. Biological activities of the synthesized complexes have been evaluated against Escherichia coli and Staphylococcus aureus.

Elongation factor Tu (EF-Tu) is a member of G protein family, and as part of a ternary complex with GTP, plays a critical function in translation by delivering aminoacyl-tRNA to the ribosome. Like other G proteins, the function of EF-Tu depends on whether GTP or GDP is bound. When EFTu is complexed with GTP, it can bind the aminoacyl-tRNA. Upon cognate codon-anticodon pairing, GTP is hydrolyzed and EF-Tu is separated from the ribosome leaving the aminoacyl-tRNA at the A-site. Hence, GTP hydrolysis is the critical step for the activity of the protein [1, 2]. To identify the residues involved in GTP hydrolysis mechanism of EF-Tu, we have used QM/MM methods. In particular, we have focused on the roles of Histidine 85 (His85) and Arginine 57 (Arg57) (T. aquaticus numbering). These residues can be situated inside or outside of the active site depending on the conditions. Therefore we have studied three different models: one with His85 in the active, one with Arg57 in the active site and one where both His85 and Arg57 are outside of the active site. Our results indicate that the presence of Arg57 or His85 in the active site decreases the activation energy, indicating that these residues have catalytic roles. Another important issue is to determine whether the hydrolysis reaction proceeds via an associative or dissociative path [3]. To this end, different model structures representing the associative or dissociative path of GTP hydrolysis have been optimised and the energy values have been compared in order to identify the mechanism. All optimised transition structures have associative character. Stationary points involved in a dissociative mechanism could not be located, suggesting that such a mechanism is unlikely, at least for the models studied. We observe that the energy increases at the points where the dissociative path is supposed to occur.

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