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کاربرد نوع شرط:
- جایگاه : پژوهشی
- مجله: Physical Chemistry Research
- نوع مقاله: Journal Article
- کلمات کلیدی: UV-Vis Spectroscopy,Detergent,Triton™ X-100,Membrane proteins,Periplasmic proteins,α-Synuclein,Beer-Lambert law
- چکیده:
- چکیده انگلیسی: As a known non-ionic, -denaturing detergent and emulsifier, Triton™ X-100 is often used in various biochemical studies including in the isolation of membrane-protein complexes for solubilizing membrane proteins, in the process of periplasmic protein extraction as a component of the lysis buffer, in both indirect immunofluorescence staining and flow cytometry as a permeabilization reagent, etc. It has been shown that the diluted solution of Triton™ X-100 with the optimal pH range of 6.0-8.0 has a significant absorption of UV light. In the present project, we show that the absorption spectrum of Triton™ X-100, when dissolved in 1X phosphate-buffered saline, is similar to that of α-synuclein, as a representative of those proteins lack tryptophan but contain tyrosine as their main UV absorber. These results show that whenever the use of Triton™ X-100 for extracting membrane and periplasmic proteins is inevitable, scavenging it before the characterization of the proteins by UV-Vis spectroscopy, especially the determination of their concentration using Beer-Lambert Law, would be necessary.
- انتشار مقاله: 04-05-1399
- نویسندگان: Hadi Nedaei,Ali Akbar Saboury
- مشاهده
- جایگاه : پژوهشی
- مجله: Physical Chemistry Research
- نوع مقاله: Journal Article
- کلمات کلیدی: Salicylic acid,Human Serum Albumin,Molecular dynamics simulations,Binding free energy,Molecular mechanics-generalized born surface area
- چکیده:
- چکیده انگلیسی: Human serum albumin (HSA) is the most abundant protein in the blood plasma. Molecular dynamics simulations of subdomain IIA of HSA and its complex with salicylic acid (SAL) were performed to investigate structural changes induced by the ligand binding. To estimate the binding affinity of SAL molecule to subdomains IB and IIA in HSA protein, binding free energies were calculated using the Molecular Mechanics-Generalized Born Surface Area (MM-GBSA). It is found that the presence of SAL molecule resulted in the stability of HSA. Also, ligand binding decreases the α-helix content of HSA. Binding free energy calculations demonstrate that the binding affinity of the SAL molecule to subdomain IIA of HSA is more than that of subdomain IB of HSA and the contributions of van der Waals interactions are more than that of electrostatics interactions. The per-residue decomposition of binding free energy suggested that the favorable residues with the most contribution in the binding free energy are hydrophobic, contributing to van der Waals interactions. Our important finding is that the subdomain IIA of HSA is the main HSA-SAL binding site. The results obtained are in good agreement with the corresponding experimental data.
- انتشار مقاله: 29-07-1395
- نویسندگان: Leila Karami,Elham Tazikeh-Lemeski,Ali Akbar Saboury
- مشاهده
- جایگاه : پژوهشی
- مجله: Physical Chemistry Research
- نوع مقاله: Journal Article
- کلمات کلیدی: Drug design,Ligand binding,Enthalpy of binding,Isothermal titration calorimetry,Enzyme kinetics
- چکیده:
- چکیده انگلیسی: Most of the biological phenomena are influenced by intermolecular recognition and interaction. Thus, understanding the thermodynamics of biomacromolecule ligand interaction is a very interesting area in biochemistry and biotechnology. One of the most powerful techniques to obtain precise information about the energetics of (bio) molecules binding to other biological macromolecules is isothermal titration calorimetry (ITC). In a typical ITC experiment, a macromolecule solution is titrated by a solution containing a reactant at a constant temperature, and exchanged heat of the reaction is measured, allowing determination of thermodynamic parameters (enthalpy change, entropy change, change in Gibbs free energy, binding affinity and stoichiometry) of molecular interactions. In this review article, we describe the ITC approach briefly and review some applications of ITC for studying protein-ligand interactions, protein-protein interactions, self-association, and drug design processes. Furthermore, the application of ITC for determination of kinetic parameters of enzyme catalyzed reactions as well as thermodynamic parameters will be discussed.
- انتشار مقاله: 03-12-1393
- نویسندگان: Maliheh Sadat Atri,Ali Akbar Saboury,Faizan Ahmad
- مشاهده
- جایگاه : پژوهشی
- مجله: Iranian Journal of Pharmaceutical Sciences
- نوع مقاله: Journal Article
- کلمات کلیدی: Methylene blue,Nanoparticles,Nafion,Riboflavin,Functional membrane
- چکیده:
- چکیده انگلیسی: Nafion is a perfluorinated anionic polyelectrolyte. The increasing popularity of nafion for the fabrication of redox polymer modified electrodes in recent years arises from easy fabrication, good electrical conductivity and high partition coefficients of many redox compounds in nafion. To investigate the production of nano-compositions by mixing electron transfer material and nafion polymer for the modification of electrodes, a functional membrane composed of nano-particles of methylene blue, and nafion was constructed. The materials were characterized by the methods of scanning electron microscopy (SEM), transmission electron microscopy (TEM), ultraviolet (UV)-visible and FT-IR. The average diameter of new nano-particles was estimated to be about 60 nm. A novel nafion-riboflavin membrane was also constructed and characterized by the methods of SEM, TEM and UV-visible spectroscopy. The estimated average diameter of new nanoparticles was about 60 nm. Our data has proven that nafion can be very interesting and helpful material in constructing nanoparticles of different electro-active materials and it can immobilize this material with a very good stability.
- انتشار مقاله: 19-09-1386
- نویسندگان: Ali Akbar Saboury,Saeed Rezaei-Zarchi,Aisha Javed
- مشاهده
- جایگاه : پژوهشی
- مجله: Iranian Journal of Chemistry and Chemical Engineering
- نوع مقاله: Journal Article
- کلمات کلیدی: Inhibition,thermodynamic changes,dithiocarbamate sodium salts,mushroom tyrosinase
- چکیده:
- چکیده انگلیسی: A mono- and a bi-functional dithiocarbamates as sodium salts were obtained by treating p-peridine or p-perazine in aceton-water mixture with CS2 in the presence of NaOH. These anionic water soluble compounds have been characterized by elemental analysis, IR and 1H NMR spectroscopic studies. Both compounds (p-peridine (I) and p-perazine-bis dithiocarbamate (II) sodium salts) were examined for inhibition of mushroom tyrosinase (MT) activity. The results showed that they inhibit MT competitively. KI values of two compounds at 27°C are 2 and 4 mM. Therefore, the compound (I) is more potent than (II). They chelate active site of tyrosinase via electrostatic interactions. These conclusions are proved by obtained thermodynamic parameters and fluorescence studies. Extrinsic fluorescence studies disprove any tertiary structure changes of MT. Major enthalpy changes in binding of compound (II) in comparison to (I) show that including two carbamate tails in such compounds disturb balancing of hydrophobic interactions with vicinity of active site of enzyme.
- انتشار مقاله: 13-09-1396
- نویسندگان: Ehsan Amin,Ali Akbar Saboury,Hassan Mansouri-Torshizi,Samaneh Zolghadri
- مشاهده
- جایگاه : پژوهشی
- مجله: Iranian Journal of Chemistry and Chemical Engineering
- نوع مقاله: Journal Article
- کلمات کلیدی: Human growth hormone,Nickel ion,Metal binding,Titration calorimetry
- چکیده:
- چکیده انگلیسی: A binding study of nickel ions by a new recombinant human Growth Hormone (hGH), produced as an injected drug, has been done at 27˚C in NaCl solution (50 mM) using an isothermal titration calorimetry. There is a set of three identical and non-interacting binding sites for nickel ions. The intrinsic dissociation equilibrium constant and the molar enthalpy of binding are 40 μM and -16.5 kJ/mol, respectively. Thermodynamic parameters of nickel ion binding are compared to the other metal ions. The molar entropy of binding is 29.3 J K-1 mol-1 for Ni2+, less than Cu2+ and more than other metal ions, means that the disorder of the protein structure due to the binding of nickel ions is more than to the other ion metals, except Cu2+. It is expected that nickel ions can prevent from the aggregation of the protein.
- انتشار مقاله: 08-02-1389
- نویسندگان: Ali Akbar Saboury,Safoura Amiri
- مشاهده