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    Dependency of codon usage on protein sequence patterns: A statistical study

    , Article Theoretical Biology and Medical Modelling ; Vol. 11, issue. 1 , 2014 ; ISSN: 17424682 Foroughmand-Araabi, M. H ; Goliaei, B ; Alishahi, K ; Sadeghi, M ; Sharif University of Technology
    Background: Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods. We used the likelihood ratio test, Pearson's chi-squared test, and mutual information... 

    The Differential Diagnosis of Crohn's Disease and Celiac Disease Using Nuclear Magnetic Resonance Spectroscopy

    , Article Applied Magnetic Resonance ; Volume 45, Issue 5 , May , 2014 , Pages 451-459 Fathi, F ; Kasmaee, L. M ; Sohrabzadeh, K ; Nejad, M. R ; Tafazzoli, M ; Oskouie, A. A ; Sharif University of Technology
    Crohn's disease and celiac disease belong to a group of autoimmune conditions that affect the digestive system, specifically the small intestine. They both attack the digestive tract and share many symptoms. Thus, the discovery of proper methods would be a major step toward differentiating celiac disease from Crohn's disease. The aim of this study was to search for the metabolic biomarkers to differentiate between these two diseases. Proton nuclear magnetic resonance spectroscopy (1H NMR) was employed as the metabolic profiling method to look for serum metabolites that differentiate between celiac disease and Crohn's disease. Classification of celiac disease and Crohn's disease was done... 

    Electrostatically defying cation-cation clusters: Can likes attract in a low-polarity environment?

    , Article Journal of Physical Chemistry A ; Volume 117, Issue 38 , 2013 , Pages 9252-9258 ; 10895639 (ISSN) Shokri, A ; Ramezani, M ; Fattahi, A ; Kass, S. R ; Sharif University of Technology
    Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the... 

    Immobilization of α -chymotrypsin on the surface of magnetic/gold core/shell nanoparticles

    , Article Journal of Nanotechnology ; Volume 2013 , 2013 ; 16879503 (ISSN) Kamal Ahmadi, M ; Vossoughi, M ; Sharif University of Technology
    Hindawi Publishing Corporation  2013
    Over the last decade, nanoparticles used as protein carriers have opened new avenues for a variety of biomedical applications. The main concern for these applications is changes in biological activity of immobilized proteins due to conformational changes on the surface of the carrier. To evaluate this concern, the preparation and biocatalyst activity of α-chymotrypsin-Fe 3O4 @ Au core/shell nanoparticles were investigated. First, Fe3O4 @ Au core/shell nanoparticles were synthesized by coprecipitation method and citrate reduction of HAuCl 4. TEM imaging revealed a core size of 13 ± 3 nm and a shell thickness of 4 ± 1 nm for synthesized nanoparticles. X-ray diffraction (XRD) was used to study... 

    A simple approach to the synthesis of 3-substituted rhodanines and thiazolidine-2,4-diones

    , Article Scientia Iranica ; Volume 20, Issue 6 , 2013 , Pages 1833-1838 ; 10263098 (ISSN) Aryanasab, F ; Shokri, A ; Saidi, M. R ; Sharif University of Technology
    Sharif University of Technology  2013
    A novel synthesis of 3-substituted rhodanine and thiazolidine-2,4-dione derivatives, starting from aliphatic primary amines, carbon disulfide, and methyl 2-bromoacetate, is described. The reaction proceeds successfully both in water and under solvent-free conditions, but 2-thioxothiazolidin-4-one (rhodanine) derivatives were obtained under solvent free-conditions, and thiazolidine-2,4-dions were formed when water was used as the solvent  

    Production of l-asparaginase from Escherichia coli ATCC 11303: Optimization by response surface methodology

    , Article Food and Bioproducts Processing ; Volume 89, Issue 4 , Oct , 2011 , Pages 315-321 ; 09603085 (ISSN) Kenari, S. L. D ; Alemzadeh, I ; Maghsodi, V ; Sharif University of Technology
    This paper discusses the studies carried out for the optimal production of enzyme l-asparaginase (l-asparagine amidohydrolase, EC from Escherichia coli (ATCC 11303). It was found that inoculum age of 18 h and inoculum size of 10% were the most favorable operating conditions for enzyme production. Lactose, yeast extract and KH 2PO 4 were found to be the best carbon, nitrogen and ion sources, respectively. Statistical method was used to survey how various medium conditions affect the enzyme production. By response surface methodology, the values of lactose, tryptone, yeast extract, KH 2PO 4 and l-asparagine concentration were investigated to obtain the maximum enzyme activity. The... 

    Failure tolerance of motif structure in biological networks

    , Article PLoS ONE ; Volume 6, Issue 5 , May , 2011 ; 19326203 (ISSN) Mirzasoleiman, B ; Jalili, M ; Sharif University of Technology
    Complex networks serve as generic models for many biological systems that have been shown to share a number of common structural properties such as power-law degree distribution and small-worldness. Real-world networks are composed of building blocks called motifs that are indeed specific subgraphs of (usually) small number of nodes. Network motifs are important in the functionality of complex networks, and the role of some motifs such as feed-forward loop in many biological networks has been heavily studied. On the other hand, many biological networks have shown some degrees of robustness in terms of their efficiency and connectedness against failures in their components. In this paper we... 

    Colorimetric detection of glutathione based on transverse overgrowth of high aspect ratio gold nanorods investigated by MCR-ALS

    , Article RSC Advances ; Volume 5, Issue 101 , 2015 , Pages 82906-82915 ; 20462069 (ISSN) Fahimi Kashani, N ; Shadabipour, P ; Hormozi-Nezhad, M. R ; Sharif University of Technology
    Royal Society of Chemistry  2015
    In this paper, we present a simple platform for colorimetric detection of glutathione using gold nanorods (AR ∼ 6.5 ± 0.2) as a plasmonic sensor. The functional mechanism of the sensor is based on shifts of longitudinal plasmon resonance during selective transverse overgrowth induced by preferential binding of glutathione at the nanorod tips. Under the optimum conditions, a calibration curve showed two linear regimes at the range of 50 nM to 20 μM of glutathione with a detection limit as low as 40 nM. The nanosensor maintains relatively high selectivity for determination of glutathione in the presence of several other amino acids. However, cysteine at similar concentration levels strongly... 

    Dual improvement of DNA-directed antibody immobilization utilizing magnetic fishing and a polyamine coated surface

    , Article RSC Advances ; Volume 6, Issue 112 , 2016 , Pages 111210-111216 ; 20462069 (ISSN) Esmaeili, E ; Soleimani, M ; Shamloo, A ; Mahmoudifard, M ; Vossoughi, M ; Sharif University of Technology
    Royal Society of Chemistry  2016
    The present study is aimed at the development of a novel approach based on the magnetic improvement of DNA-directed antibody immobilization to prepare a highly efficient sensing platform. Magnetic nanoparticle substrates with high surface area capture the dual DNA-conjugated antibodies in a solution. This allows overcoming the typical mass transport limitation of the surface-based antibody immobilization. Antibody-magnetic nanoparticle conjugation is based on a robust hybridization between a DNA tether (attached to the antibody) and its complementary sequence (immobilized on the nanoparticle). Conventional antibody immobilization for the detection of proteins is often insignificant for the... 

    A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory

    , Article Journal of Computational Chemistry ; Volume 37, Issue 14 , 2016 , Pages 1296-1305 ; 01928651 (ISSN) Shaghaghi, H ; Ebrahimi, H. P ; Fathi, F ; Bahrami Panah, N ; Jalali Heravi, M ; Tafazzoli, M ; Sharif University of Technology
    John Wiley and Sons Inc  2016
    The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of 13Cα chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of 13Cβ, and 1Hα chemical shifts nor on the variation of absolute deviation of 13Cα chemical shifts relative to ψ dihedral angle. The 13Cα absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of... 

    Experimental investigation and thermodynamic modeling of amino acids partitioning in a water/ionic liquid system

    , Article Journal of Molecular Liquids ; Volume 260 , 15 June , 2018 , Pages 386-390 ; 01677322 (ISSN) Nazem, H ; Ghotbi, C ; Habibi Zare, M ; Shirazian, S ; Sharif University of Technology
    Elsevier B.V  2018
    Amino acids partitioning including phenylalanine, glutamic acid, and tryptophan in aqueous and ionic liquid phases at temperature of 298.15 K and atmospheric pressure were measured. 1-Butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide used in this work can produce two phases with water immediately. The effect of aqueous solution pH on amino acids partitioning was studied and revealed that amino acid partitioning coefficient was decreased with increasing pH. This phenomenon pertains to the electrostatic interaction between cations of amino acid and the anions of ionic liquid which is decreased when pH increases. Considering the effect of pH, liquid-liquid equilibrium data of amino... 

    Synthesis of “L-cysteine–graphene oxide” hybrid by new methods and elucidation of its uptake properties for Hg(II) ion

    , Article Separation Science and Technology (Philadelphia) ; Volume 53, Issue 6 , 2018 , Pages 843-855 ; 01496395 (ISSN) Daneshmand, M ; Outokesh, M ; Akbari, A ; Kosari, M ; Tayyebi, A ; Sharif University of Technology
    Taylor and Francis Inc  2018
    This study introduces two new, simple, and scalable methods for synthesis of “cysteine–graphene oxide” hybrid, namely nucleophilic and covalent methods. Produced adsorbents could uptake 500 and 600 mg Hg2+/g, respectively, which are larger than capacities of most of the commercial adsorbents. By means of different instrumental techniques, chemical structures of the obtained graphene products were disclosed, and two pertinent mechanisms for their formations were suggested. Time for attaining uptake equilibrium for nucleophilic/covalent samples was 30 min/150 min, and kinetics was controlled by liquid film resistance/chemical reaction mechanisms, respectively. High selectivity and good... 

    Numerical investigations of hepatic spheroids metabolic reactions in a perfusion bioreactor

    , Article Frontiers in Bioengineering and Biotechnology ; Volume 7 , 2019 ; 22964185 (ISSN) Sharifi, F ; Firoozabadi, B ; Firoozbakhsh, K ; Sharif University of Technology
    Frontiers Media S.A  2019
    Miniaturized culture systems of hepatic cells are emerging as a strong tool facilitating studies related to liver diseases and drug discovery. However, the experimental optimization of various parameters involved in the operation of these systems is time-consuming and expensive. Hence, developing numerical tools predicting the function of such systems can significantly reduce the associated cost. In this paper, a perfusion-based three dimensional (3D) bioreactor comprising encapsulated human liver hepatocellular carcinoma (HepG2) spheroids are analyzed. The flow and mass transfer equations for oxygen as well as different metabolites such as albumin, glucose, glutamine, ammonia, and urea were... 

    The effect of chitosan and PEG polymers on stabilization of GF-17 structure: A molecular dynamics study

    , Article Carbohydrate Polymers ; Volume 237 , 2020 Asadzadeh, H ; Moosavi, A ; Arghavani Hadi, J ; Sharif University of Technology
    Elsevier Ltd  2020
    We examine the interactions of chitosan and polyethylene glycol (PEG) with antimicrobial peptide GF-17 to identify a suitable carrier to improve the peptide drug delivery systems. To this end, the molecular dynamics simulations are used to determine the interactions of a typical antimicrobial peptide GF-17 with the chitosan and PEG polymers. The findings indicate the great potential of the peptide to maintain its secondary structure in the adjacent to chitosan polymers. During the interaction with chitosan polymers, the structure of the peptide has smaller fluctuations compared to the PEG polymers. Also, in the presence of both the polymers, the PEG polymers are situated closer to the... 

    Site-specific protein conjugation onto fluorescent single-walled carbon nanotubes

    , Article Chemistry of Materials ; Volume 32, Issue 20 , 2020 , Pages 8798-8807 Zubkovs, V ; Wu, S. J ; Rahnamaee, S. Y ; Schuergers, N ; Boghossian, A. A ; Sharif University of Technology
    American Chemical Society  2020
    Semiconducting single-walled carbon nanotubes (SWCNTs) are among the few photostable optical emitters that are ideal for sensing, imaging, drug delivery, and monitoring of protein activity. These applications often require strategies for immobilizing proteins onto the nanotube while preserving the optical properties of the SWCNTs. Site-specific and oriented immobilization strategies, in particular, offer advantages for improving sensor and optical signaling responses. In this study, we demonstrate site-specific protein immobilization of a model of enhanced yellow fluorescent protein with a single engineered cysteine residue, using either single-stranded DNA or a pyrene-containing linker to... 

    Bioconjugation of interferon-alpha molecules to lysine-capped gold nanoparticles for further drug delivery applications

    , Article Journal of Dispersion Science and Technology ; Volume 29, Issue 8 , 2008 , Pages 1062-1065 ; 01932691 (ISSN) Ghorbani Aghdam, A ; Vossoughi, M ; Almzadeh, I ; Zeinali, M ; Sharif University of Technology
    Gold nanoparticles are potentially very attractive components for therapeutic delivery since they can be synthesized with any diameter from 1 to 200 nm to carry a payload of therapeutic molecules into a cell without triggering an immune response. Gold nanoparticles must undergo surface transformations before coupling to therapeutic molecules to become eligible for this purpose. It is now more understood that amine groups can bind to gold nanoparticles strongly, which has enabled surface modification of gold nanoparticles with amino acid lysine through its amine group. These lysine capped gold nanoparticles can further be coupled to therapeutic molecules for delivery purposes. In this study... 

    Theoretical study of the electron transport through the cysteine amino acid nanomolecular wire

    , Article International Journal of Nanoscience ; Volume 7, Issue 2-3 , 2008 , Pages 95-102 ; 0219581X (ISSN) Ganji, M. D ; Aghaie, H ; Gholami, M. R ; Sharif University of Technology
    World Scientific Publishing Co. Pte Ltd  2008
    In this paper, we study the electrical transport and Negative Differential Resistance (NDR) in a single molecular conductor consisting of a cysteine sandwiched between two Au(111) electrodes via the Density Functional Theory-based Nonequilibrium Green's Function (DFT-NEGF) method. We show that (surprisingly, despite their apparent simplicity, these Au/cysteine/Au nanowires are shown to be a convenient NDR device) the smallest two-terminal molecular wire can exhibit NDR behavior to date. Experiments with a conventional or novel self-assembled monolayer (SAM) are proposed to test these predictions. The projected density of states (PDOSs) and transmission coefficients T(E) under various... 

    Visual recognition of tryptophan enantiomers using chiral self assemblies of quantum dots

    , Article ACS Applied Nano Materials ; 2021 ; 25740970 (ISSN) Fahimi Kashani, N ; Jafar Nezhad Ivrigh, Z ; Bigdeli, A ; Hormozi Nezhad, M.R ; Sharif University of Technology
    American Chemical Society  2021
    Discrimination of chiral targets is generally achieved with chiral nanomaterials. However, the limited number of intrinsic chiral nanostructures as well as their complex synthesis procedure has led to the production of chirality-induced nanomaterials as alternatives. Chirality can be induced in nanomaterials by either chirality transfer or the formation of chiral assemblies. Using the latter approach, in this work, we have provided chiral supramolecular assemblies of CdTe quantum dots (QDs) from achiral starting materials. CTAB-QD assemblies showed chiroptical activities, and their orange emission in combination with the blue emission of carbon dots was utilized as a ratiometric chiral... 

    Nanocomposite of functionalized halloysite and Ag(0) decorated magnetic carbon dots as a reusable catalyst for reduction of dyes in water

    , Article Journal of Physics and Chemistry of Solids ; Volume 152 , 2021 ; 00223697 (ISSN) Latifi Pour, M ; Kazemeini, M ; Sadjadi, S ; Sharif University of Technology
    Elsevier Ltd  2021
    A new magnetic, catalytic nanocomposite of Hal-MT-Cys-Ag/MNCD was fabricated and utilized for catalyzing reductive de-colorization of methyl orange and rhodamin B in aqueous media at room temperature. To prepare this material, Cl-functionalized halloysite nanoclay was successively reacted with melamine and 2,4,6-trichloro-1,3,5-triazine to furnish multi-nitrogen containing ligand on halloysite surface. Then, magnetic carbon dots were crafted through a facile method and decorated with Ag nanoparticles and cysteine to furnish Cys-Ag/MNCD species. The final nanocomposite was obtained via incorporation of this latter species onto functionalized halloysite. This new composite was characterized... 

    Ionic liquid based on α-amino acid anion and N7,N9-dimethylguaninium cation ([dMG][AA]): Theoretical study on the structure and electronic properties

    , Article Journal of Physical Chemistry A ; Volume 116, Issue 22 , April , 2012 , Pages 5436-5444 ; 10895639 (ISSN) Shakourian Fard, M ; Fattahi, A ; Bayat, A ; Sharif University of Technology
    The interactions between five amino acid based anions ([AA] - (AA = Gly, Phe, His, Try, and Tyr)) and N7,N9-dimethylguaninium cation ([dMG] +) have been investigated by the hybrid density functional theory method B3LYP together with the basis set 6-311++G(d,p). The calculated interaction energy was found to decrease in magnitude with increasing side-chain length in the amino acid anion. The interaction between the [dMG] + cation and [AA] - anion in the most stable configurations of ion pairs is a hydrogen bonding interaction. These hydrogen bonds (H bonds) were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations...