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    Finding protein active sites using approximate sub-graph isomorphism

    , Article 2011 1st Middle East Conference on Biomedical Engineering, MECBME 2011, Sharjah, 21 February 2011 through 24 February 2011 ; 2011 , Pages 432-435 ; 9781424470006 (ISBN) Dezfouli, M. E. A ; Arab, S. S ; Fatemizadeh, E ; Hosseynimanesh, N ; Sharif University of Technology
    2011
    Abstract
    Prediction of the amino acids that have a catalytic effect on the enzymes is a major stage in appointing the activity of the enzymes and classification. The biological activity of a protein usually depends on the existence of a small number of amino acids. Recently, many algorithms have been proposed in the literature for finding these amino acids which are complex and time consuming. In this paper, we will introduce a new method for predicting the active sites that will use the spatial coordinates and the type of amino acids that contain the active sites. In order to increase the speed we use an approximate graph isomorphism algorithm. Furthermore, this algorithm allows us to find several... 

    A methionine chemical shift based order parameter characterizing global protein dynamics

    , Article ChemBioChem ; Volume 22, Issue 6 , 2021 , Pages 1001-1004 ; 14394227 (ISSN) Chashmniam, S ; Teixeira, J. M. C ; Paniagua, J. C ; Pons, M ; Sharif University of Technology
    John Wiley and Sons Inc  2021
    Abstract
    Coupling of side chain dynamics over long distances is an important component of allostery. Methionine side chains show the largest intrinsic flexibility among methyl-containing residues but the actual degree of conformational averaging depends on the proximity and mobility of neighboring residues. The 13C NMR chemical shifts of the methyl groups of methionine residues located at long distances in the same protein show a similar scaling with respect to the values predicted from the static X-ray structure by quantum methods. This results in a good linear correlation between calculated and observed chemical shifts. The slope is protein dependent and ranges from zero for the highly flexible... 

    Kinetic studies of glucose electrocatalytic oxidation on GC/Ni electrode

    , Article International Journal of Chemical Kinetics ; Volume 44, Issue 11 , 2012 , Pages 712-721 ; 05388066 (ISSN) Danaee, I ; Jafarian, M ; Forouzandeh, F ; Gobal, F ; Sharif University of Technology
    2012
    Abstract
    Nickel-modified glassy carbon electrode (GC/Ni) prepared by galvanostatic deposition was used for the electrocatalytic oxidation of glucose in alkaline solutions where different electrochemical methods were employed. In cyclic voltammetry studies, in the presence of glucose an increase in the peak current of the oxidation of nickel hydroxide is followed by a decrease in the corresponding cathodic current. This suggests that the oxidation of glucose is being catalyzed through mediated electron transfer across the nickel hydroxide layer comprising nickel ions of various valence states. Under the chronoamperometric regime, the reaction followed a Cottrellian behavior and the diffusion... 

    Electrochemical oxidation of saccharose on copper (hydr)oxide-modified electrode in alkaline media

    , Article Cuihua Xuebao/Chinese Journal of Catalysis ; Volume 31, Issue 11 , 2010 , Pages 1351-1357 ; 02539837 (ISSN) Jafarian, M ; Rashvand Avei, M ; Danaee, I ; Gobal, F ; Mahjani, M. G ; Sharif University of Technology
    2010
    Abstract
    A stable copper (hydr)oxide-modified electrode was prepared in 0.5 mol/L NaOH solution by cyclic voltammetry in the range of -250 to 1000 mV. It can be used for electrochemical studies in the range of -250 to 1000 mV without interfering peaks because there is no oxidation of copper. During an anodic potential sweep, the electro-oxidation of saccharose on Cu occurred by the formation of CuIII and this reaction also occurred in the early stages of the reversed cycle until it is stopped by the negative potentials. A mechanism based on the electro-chemical generation of CuIII active sites and their subsequent consumption by saccharose was proposed, and the rate law and kinetic parameters were... 

    Supercritical synthesis of a magnetite-reduced graphene oxide hybrid with enhanced adsorption properties toward cobalt & strontium ions

    , Article RSC Advances ; Volume 6, Issue 17 , 2016 , Pages 13898-13913 ; 20462069 (ISSN) Tayyebi, A ; Outokesh, M ; Sharif University of Technology
    Royal Society of Chemistry  2016
    Abstract
    The current study presents a supercritical synthesis of magnetite-reduced graphene oxide (M-RGO) in methanol media, in which Fe3O4 nanoparticles are simultaneously formed, surface modified and decorated on the surface of the reduced graphene oxide. Simulations using density functional theory, which were performed using the M06-2x/cc-pVDZ level of theory, indicate that upon adsorption of a Fe3O4 cluster on the graphene, the overall charge on the graphene surface becomes about -0.0236e, indicating charge transfer from the Fe3O4 cluster to the graphene surface. Instrumental and chemical analyses exhibited the formation of strong bonds between Fe3O4 and graphene, through C-O-Fe and C-Fe bridges.... 

    Cis-trans proline isomers in the catalytic domain of calcineurin

    , Article FEBS Journal ; Volume 286, Issue 6 , 2019 , Pages 1230-1239 ; 1742464X (ISSN) Teixeira, J. M. C ; Guasch, A ; Biçer, A ; Aranguren Ibáñez, Á ; Chashmniam, S ; Paniagua, J. C ; Pérez Riba, M ; Fita, I ; Pons, M ; Sharif University of Technology
    Blackwell Publishing Ltd  2019
    Abstract
    Calcineurin is an essential calcium-activated serine/threonine phosphatase. The six NMR-observable methionine methyl groups in the catalytic domain of human calcineurin Aα (CNA) were assigned and used as reporters of the presence of potential cis-trans isomers in solution. Proline 84 is found in the cis conformation in most calcineurin X-ray structures, and proline 309, which is part of a highly conserved motif in phosphoprotein phosphatases, was modeled with a cis peptide bond in one of the two molecules present in the asymmetric unit of CNA. We mutated each of the two prolines to alanine to force the trans conformation. Solution NMR shows that the P84A CNA mutant exists in two forms,... 

    Sustainable starfish like cobalt electrocatalyst grown on optimized CNT-graphene hybrid host for efficient water oxidation

    , Article Applied Surface Science ; Volume 524 , 15 September , 2020 Naseri, N ; Ghasemi, S ; Pourreza, M ; Moshfegh, A. Z ; Sharif University of Technology
    Elsevier B.V  2020
    Abstract
    Solar energy generation is one of the most efficient approach to solve emerging environment and energy challenges. In this context, solar assisted dissociation of water into oxygen and hydrogen utilizing scalable and high performance electrocatalysts plays key role since the produced hydrogen is a clean energy carrier. Here, cobalt based nanoflakes with metallic core and oxidized surface were grown on the designed carbonaceous layer for anodic oxygen evolution reaction (OER) using an electrochemical approach. Carbonaceous layers containing proper amount of carbon nanotubes (CNT) and reduced graphene oxide (rGO) species were used to optimize the system. Although higher weight percent of rGO... 

    Photocatalytic decolorization of red dye in aqueous ZnO-TiO2 suspensions

    , Article International Conference on Smart Materials-Smart! Intelligent Materials and Nano Technology, (SmartMat-'08) and also the 2nd International Workshop on Functional Materials and Nanomaterials (IWOFM-2) ; Volume 55-57 , 2008 , Pages 577-580 ; 10226680 (ISSN); 9780878493562 (ISBN) Khameneh Asl, S ; Sadrnezhaad, K ; Kianpoor Rad, M ; Sharif University of Technology
    2008
    Abstract
    The photocatalytic decolorization of aqueous solutions of Direct Red 27 in the presence of various amounts of semiconductor powder suspensions has been investigated in a batch reactor with the use of artificial light sources. ZnO and TiO2 have been found the most active photocatalysts; the effect of catalyst loading and type on the reaction rate was optimized for maximum degradation. The results imply that 1:1 ratio is proper for the photocatalytic removal of Direct Red 27. In addition, the effects of particle size and surface area were examined in this photocatalytic process. The results showed that the decolorization efficiency increases with increase in surface area, and decrease in... 

    Facile synthesis and self-assembling of transition metal phosphide nanosheets to microspheres as a high-performance electrocatalyst for full water splitting

    , Article Journal of Alloys and Compounds ; Volume 875 , 2021 ; 09258388 (ISSN) Nourmohammadi Khiarak, B ; Golmohammad, M ; Shahraki, M. M ; Simchi, A ; Sharif University of Technology
    Elsevier Ltd  2021
    Abstract
    The development of noble-metal-free electrocatalysts with enhanced active sites is of great significance for the production of renewable energy on large scale. Ultrathin transition metal compounds (e.g., phosphides and sulfides) have unique structural features but their stability and electroactivity must still be improved for practical applications. We propose a new strategy to synthesis ultrathin sheets of Ni-Cu-Co transition metals on porous nickel and self-assemble them into yarn-shaped microspheres. Enhance catalytic activity and stability are then attained by thermochemical phosphorization without morphological modifications. We employed various analytical techniques including XRD, SEM,... 

    Low loaded MoS2/Carbon cloth as a highly efficient electrocatalyst for hydrogen evolution reaction

    , Article International Journal of Hydrogen Energy ; 2021 ; 03603199 (ISSN) Shaker, T ; Mehdipour, H ; Moshfegh, A. Z ; Sharif University of Technology
    Elsevier Ltd  2021
    Abstract
    Active edge sites of MoS2 nanosheets exhibit promising futures for hydrogen evolution reaction (HER), comparable with remarkable performances of highly cost platinum. However, 3D structures of MoS2 suffer from a lack of high mobility and unexposed active sites which lower the electrocatalytic activity. In this study, we show that there is a balance between increasing the active sites on the one hand and managing the charge transfer to facilitate the reaction on the other hand, and achieving this balance increases the efficiency of the electrocatalyst tremendously. For this purpose, we directly attached exfoliated MoS2 nanosheets onto carbon cloth (CC) substrate as a 3D network of conductive... 

    Investigating the nodulation mechanism of copper cathode based on microscopic approach: As a punch failure factor

    , Article Engineering Failure Analysis ; Volume 133 , 2022 ; 13506307 (ISSN) Reza Shojaei, M ; Reza Khayati, G ; Mohammad Javad Korasani, S ; Kafi Harnashki, R ; Sharif University of Technology
    Elsevier Ltd  2022
    Abstract
    The presence of nodules on the surface of cathode copper plates was the most important reason for the failure of the punch of mechanical clinching of copper cathode sheets. This study demonstrated a comprehensive investigation into the nodulation growth of copper cathodes in the electrorefining plant based on metallographic analysis. More than 15 random samples were selected from the top, middle, and bottom of the cathodes produced in the Khatoon Abad copper refinery, Iran. Studies were carried out based on the determination of growth modes including field oriented isolated crystal (FT), basis-oriented reproduction (BR), field-oriented texture (FT), and unoriented dispersion (UD). A scanning... 

    Low loaded MoS2/Carbon cloth as a highly efficient electrocatalyst for hydrogen evolution reaction

    , Article International Journal of Hydrogen Energy ; Volume 47, Issue 3 , 2022 , Pages 1579-1588 ; 03603199 (ISSN) Shaker, T ; Mehdipour, H ; Moshfegh, A. Z ; Sharif University of Technology
    Elsevier Ltd  2022
    Abstract
    Active edge sites of MoS2 nanosheets exhibit promising futures for hydrogen evolution reaction (HER), comparable with remarkable performances of highly cost platinum. However, 3D structures of MoS2 suffer from a lack of high mobility and unexposed active sites which lower the electrocatalytic activity. In this study, we show that there is a balance between increasing the active sites on the one hand and managing the charge transfer to facilitate the reaction on the other hand, and achieving this balance increases the efficiency of the electrocatalyst tremendously. For this purpose, we directly attached exfoliated MoS2 nanosheets onto carbon cloth (CC) substrate as a 3D network of conductive... 

    The use of a cis-dioxomolybdenum(VI) dinuclear complex with quadradentate 1,4-benzenediylbis(benzyldithiocarbamate)(2-) as model compound for the active site of oxo transfer molybdoenzymes: Reactivity, kinetics, and catalysis

    , Article Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy ; Volume 88 , 2012 , Pages 210-215 ; 13861425 (ISSN) Moradi Shoeili, Z ; Boghaei, D. M ; Sharif University of Technology
    2012
    Abstract
    Dinuclear cis-dioxomolybdenum(VI) complex [{MoO 2(Bz 2Benzenediyldtc)} 2] coordinated by a quadradentate dithiocarbamate (Bz 2Benzenediyldtc 2- = 1,4-benzenediylbis(benzyldithiocarbamate)(2-)) has been prepared and characterized by elemental analysis, 13C NMR, IR and UV-vis spectroscopy. The kinetics of the oxygen atom transfer between [{MoO 2(Bz 2Benzenediyldtc)} 2] and PPh 3 was studied spectrophotometrically in CH 2Cl 2 medium at 520 nm and four different temperatures, 288, 293, 298 and 303 K, respectively. The reaction follows second order kinetics with the rate constant k = 0.163(2) M -1 S -1 and its increasingly strong absorption at 520 nm clearly indicate the formation of a μ-oxo... 

    Electrooxidation of methanol on NiMn alloy modified graphite electrode

    , Article Electrochimica Acta ; Volume 55, Issue 6 , 2010 , Pages 2093-2100 ; 00134686 (ISSN) Danaee, I ; Jafarian, M ; Mirzapoor, A ; Gobal, F ; Mahjani, M. G ; Sharif University of Technology
    Abstract
    Nickel and nickel-manganese alloy modified graphite electrodes (G/Ni and G/NiMn) prepared by galvanostatic deposition were examined for their redox process and electrocatalytic activities towards the oxidation of methanol in alkaline solutions. The methods of cyclic voltammetery (CV), chronoamperometry (CA) and impedance spectroscopy (EIS) were employed. In CV studies, in the presence of methanol NiMn alloy modified electrode shows a significantly higher response for methanol oxidation. The peak current of the oxidation of nickel hydroxide increase is followed by a decrease in the corresponding cathodic current in presence of methanol. The anodic peak currents show linear dependency upon the... 

    Ruthenium/Ruthenium oxide hybrid nanoparticles anchored on hollow spherical Copper-Cobalt Nitride/Nitrogen doped carbon nanostructures to promote alkaline water splitting: Boosting catalytic performance via synergy between morphology engineering, electron transfer tuning and electronic behavior modulation

    , Article Journal of Colloid and Interface Science ; Volume 626 , 2022 , Pages 1070-1084 ; 00219797 (ISSN) Rezaee, S ; Shahrokhian, S ; Sharif University of Technology
    Academic Press Inc  2022
    Abstract
    Exploring bi-functional electrocatalysts with excellent activity, good durability, and cost-effectiveness for electrochemical hydrogen and oxygen evolution reactions (HER and OER) in the same electrolyte is a critical step towards a sustainable hydrogen economy. Three main features such as high density of active sites, improved charge transfer, and optimized electronic configuration have positive effects on the electrocatalyst activity. In this context, understanding structure–composition–property relationships and catalyst activity is very important and highly desirable. Herein, for the first time, we present the design and fabrication of novel MOF-derived ultra-small Ru/RuO2 nanoparticles... 

    Development of nanocrystalline TiO2-Er2O3 and TiO2-Ta2O5 thin film gas sensors: Controlling the physical and sensing properties

    , Article Sensors and Actuators, B: Chemical ; Volume 141, Issue 1 , 2009 , Pages 76-84 ; 09254005 (ISSN) Mohammadi, M. R ; Fray, D. J ; Sharif University of Technology
    2009
    Abstract
    A systematic comparison of single and binary metal oxide TiO2, TiO2-Er2O3 and TiO2-Ta2O5 thin film gas sensors with nanocrystalline and mesoporous microstructure, prepared by sol-gel route, was conducted. The gas sensitivity was increased by secondary phase introduction into TiO2 film via two mechanisms, firstly due to the inhibition of anatase-to-rutile transformation, since the anatase phase accommodates larger amounts of adsorbed oxygen, and secondly due to the retardation of grain growth, since the higher surface area provides more active sites for gas molecule adsorption. The binary metal oxide gas sensors exhibited a remarkable response towards low concentrations of CO and NO2 gases at...