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Purification and characterization of a novel biosurfactant produced by Bacillus licheniformis MS3
, Article World Journal of Microbiology and Biotechnology ; Volume 26, Issue 5 , 2010 , Pages 871-878 ; 09593993 (ISSN) ; Maghsoudi, E ; Roostaazad, R ; Dadafarin, H ; Sahebghadam Lotfi, A ; Amoozegar, M. A ; Sharif University of Technology
2010
Abstract
The physical properties and chemical structure of a new biosurfactant (licheniformin) produced by Bacillus licheniformis MS3 were investigated. The purified biosurfactant was identified as a lipopeptide with amino acid sequence of Gly, Ala, Val, Asp, Ser, Gly, Tyr and a lactone linkage between the carboxyl group of Aspargine and hydroxyl group of Tyrosine residue. The fatty acid moiety was attached to N-terminal amino acid residue through an amide bond. The purified licheniformin could lower the surface tension of water from 72 to 38 mN/m at concentrations higher than 15 μg/mL and its relative emulsion volume (EV%) was equal to 36%. It also showed stable surface activity over a wide range of...
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) ; Soleimani, M ; Shamloo, A ; Mahmoudifard, M ; Vossoughi, M ; Sharif University of Technology
Royal Society of Chemistry
2016
Abstract
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...
NMR- and GC/MS-based metabolomics of sulfur mustard exposed individuals: a pilot study
, Article Biomarkers ; Volume 21, Issue 6 , 2016 , Pages 479-489 ; 1354750X (ISSN) ; Aliannejad, R ; Rezaei Tavirani, M ; Arefi Oskouie, A ; Naseri, M. T ; Parastar, H ; Aliakbarzadeh, G ; Fathi, F ; Taheri, S ; Sharif University of Technology
Taylor and Francis Ltd
Abstract
Sulfur Mustard (SM) is a potent alkylating agent and its effects on cells and tissues are varied and complex. Due to limitations in the diagnostics of sulfur mustard exposed individuals (SMEIs) by noninvasive approaches, there is a great necessity to develop novel techniques and biomarkers for this condition. We present here the first nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC/MS) metabolic profiling of serum from and healthy controls to identify novel biomarkers in blood serum for better diagnostics. Of note, SMEIs were exposed to SM 30 years ago and that differences between two groups could still be found. Pathways in which differences between SMEIs and...
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) ; Ebrahimi, H. P ; Fathi, F ; Bahrami Panah, N ; Jalali Heravi, M ; Tafazzoli, M ; Sharif University of Technology
John Wiley and Sons Inc
2016
Abstract
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...
Effective surface modification of MnFe2O4@SiO2@PMIDA magnetic nanoparticles for rapid and high-density antibody immobilization
, Article Applied Surface Science ; Volume 426 , 2017 , Pages 1023-1029 ; 01694332 (ISSN) ; Soleimani, M ; Ghahremanzadeh, R ; Vossoughi, M ; Esmaeili, E ; Sharif University of Technology
Abstract
The present study is aimed at the synthesis of MnFe2O4@SiO2@PMIDA in terms of highly efficient sensing platform for anti-prostate specific membrane antigen (PSMA) immobilization. Superparamagnetic manganese ferrite nanoparticles were synthesized following co-precipitation method and then SiO2 shell was coated on the magnetic core with tetraethyl orthosilicate (TEOS) through a silanization reaction to prevent oxidation, agglomeration and, increase the density of OH groups on the surface of MnFe2O4. Subsequently, MnFe2O4@SiO2@PMIDA obtained as a result of the reaction between N-(phosphonomethyl)iminodiacetic acid (PMIDA) and MnFe2O4@SiO2. The reactive carboxyl groups on the surface of magnetic...
Development of a novel nano-sized anti-VEGFA nanobody with enhanced physicochemical and pharmacokinetic properties
, Article Artificial Cells, Nanomedicine and Biotechnology ; 2017 , Pages 1-13 ; 21691401 (ISSN) ; Norouzian, D ; Vaziri, B ; Ahangari Cohan, R ; Sardari, S ; Mahboudi, F ; Behdani, M ; Mansouri, K ; Mehdizadeh, A ; Sharif University of Technology
Abstract
Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD...
NMR spectroscopy-based metabolomic study of serum in sulfur mustard exposed patients with lung disease
, Article Biomarkers ; Volume 22, Issue 5 , 2017 , Pages 413-419 ; 1354750X (ISSN) ; Arefi Oskouie, A ; Rezaei Tavirani, M ; Aliannejad, R ; Taheri, S ; Fathi, F ; Naseri, M. T ; Sharif University of Technology
Taylor and Francis Ltd
2017
Abstract
Sulfur mustard (SM) is a vesication chemical warfare agent for which there is currently no antidote. Despite years of research, there is no common consensus about the pathophysiological basis of chronic pulmonary disease caused by this chemical warfare agent. In this study, we combined chemometric techniques with nuclear magnetic resonance (NMR) spectroscopy to explore the metabolic profile of sera from SM-exposed patients. A total of 29 serum samples obtained from 17 SM-injured patients, and 12 healthy controls were analyzed by Random Forest. Increased concentrations of seven amino acids, glycerol, dimethylamine, ketone bodies, lactate, acetate, citrulline and creatine together with the...
Development of a novel nano-sized anti-VEGFA nanobody with enhanced physicochemical and pharmacokinetic properties
, Article Artificial Cells, Nanomedicine and Biotechnology ; Volume 46, Issue 7 , 2018 , Pages 1402-1414 ; 21691401 (ISSN) ; Norouzian, D ; Vaziri, B ; Ahangari Cohan, R ; Sardari, S ; Mahboudi, F ; Behdani, M ; Mansouri, K ; Mehdizadeh, A ; Sharif University of Technology
Abstract
Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD...
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) ; Ghotbi, C ; Habibi Zare, M ; Shirazian, S ; Sharif University of Technology
Elsevier B.V
2018
Abstract
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...
Multifunctional core-shell nanoplatforms (gold@graphene oxide) with mediated NIR thermal therapy to promote miRNA delivery
, Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 14, Issue 6 , 2018 , Pages 1891-1903 ; 15499634 (ISSN) ; Akhavan, O ; Adeli, M ; Razzazan, S ; Dinarvand, R ; Zanganeh, S ; Soleimani, M ; Dinarvand, M ; Atyabi, F ; Sharif University of Technology
Elsevier Inc
2018
Abstract
Recent insights into the nanomedicine have revealed that nanoplatforms enhance the efficacy of carrier in therapeutic applications. Here, multifunctional nanoplatforms were utilized in miRNA-101 delivery and NIR thermal therapy to induce apoptosis in breast cancer cells. Au nanorods (NRs) or nanospheres (NSs) covered with graphene oxide (GO) were prepared and functionalized with polyethylene glycol as a stabilizer and poly-L-arginine (P-L-Arg) as a targeting agent. In nanoplatforms, coupling Au@GO prepared stable structures with higher NIR reactivity. P-L-Arg substantially enhanced the cellular uptake and gene retardation of stuffs coated by them. However, rod-shape nanoplatforms indicated...
Effect of Cysteine Substitutions on the Structural and Magnetic Properties of Fe3O4–Cysteine/RGO and Fe3O4/RGO–Cysteine Nanocomposites
, Article Journal of Superconductivity and Novel Magnetism ; 2018 ; 15571939 (ISSN) ; Mehrani, K ; Madaah Hosseini, H. R ; Zare, K ; Sharif University of Technology
Springer New York LLC
2018
Abstract
We synthesized by electrostatic self-assembly route in basic solution Fe3O4–cysteine/RGO and Fe3O4/RGO–cysteine nanocomposites. In this method, electrostatic interaction was created via negatively charged surface of the reduced graphene oxide and reduced graphene oxide–cysteine sheets and positively charged surface of the Fe3O4 and Fe3O4–Cys nanoparticles in aqueous solution. The structural and magnetic properties of the prepared samples were analyzed by x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, transmission electron microscopy (TEM), and vibrating sample magnetometer (VSM), respectively. The dependences of magnetization as a function of...
Oxido-peroxido W(VI)-histidine–MgAl-layered double hydroxide composite as an efficient catalyst in sulfide oxidation
, Article Applied Organometallic Chemistry ; Volume 32, Issue 6 , 2018 ; 02682605 (ISSN) ; Amini, M ; Morteza, S ; Farnia, F ; Bayrami, A ; Bagherzadeh, M ; Gautam, S ; Chae, K. H ; Sharif University of Technology
John Wiley and Sons Ltd
2018
Abstract
Oxido-peroxido W(VI)-histidine–MgAl-layered double hydroxide composite was prepared by using MgAl-layered double hydroxide as a host and oxido-peroxido W(VI)-histidine complex as a guest. The composite was characterized by XRD, IR, EDX,SEM and TEM techniques. This composite is tested for catalytic selective sulfoxidation reactions using hydrogen peroxide as oxidant showing good to moderate conversion along with high selectivity. Copyright © 2018 John Wiley & Sons, Ltd
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) ; Outokesh, M ; Akbari, A ; Kosari, M ; Tayyebi, A ; Sharif University of Technology
Taylor and Francis Inc
2018
Abstract
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...
Molecular simulation of protein dynamics in nanopores. II. Diffusion
, Article Journal of Chemical Physics ; Volume 130, Issue 8 , 2009 ; 00219606 (ISSN) ; Tabar, M.R.R ; Sahimi, M ; Sharif University of Technology
2009
Abstract
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the α-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the...
Self-assembly of tryptophan-capped gold nanoparticles onto DNA network template
, Article Journal of Dispersion Science and Technology ; Volume 30, Issue 2 , 2009 , Pages 254-258 ; 01932691 (ISSN) ; Vosoughi, M ; Alemsadeh, I ; Sharif University of Technology
2009
Abstract
In this study, a simple route to the formation of DNA-gold complex has been reported, using immobilized DNA as a template. The nanoporous gold films have been prepared by the electrostatic self assembly of gold nanoparticles capped with tryptophan. Tryptophan would improve surface properties of gold nanoparticles for strongly attaching to DNA. Fourier transform infrared spectroscopy confirmed that gold nanoparticles have been capped by tryptophan. Also measured zeta potential shows that there are positive charges on the surface of gold nanoparticles. Investigations by atomic force microscopy substantially confirm that tryptophan-capped gold nanoparticles can be bonded to DNA template...
Protein- and homo poly(amino acid)-based hydrogels with super-swelling properties
, Article Polymers for Advanced Technologies ; Volume 20, Issue 8 , 2009 , Pages 655-671 ; 10427147 (ISSN) ; Pourjavadi, A ; Salimi, H ; Kurdtabar, M ; Sharif University of Technology
2009
Abstract
The use of super-swelling polymers is steadily increasing and the applications in industry are continuing to grow. With the authorization of the superabsorbents in food packaging by the Food and Drug Administration recently, demand may soon take off in the market. However, the increase in prices of petroleum products in recent years may be a drawback for these acrylic-based materials. Thus, there is now a need to develop natural-based super-swelling hydrogels which are more economical and environment friendly. In addition, the super-swelling gels are promising novel functions in the biomedical and pharmaceutical applications. This review is aimed to highlight research and trends in protein-...
Modeling of aqueous biomolecules using a new free-volume group contribution model
, Article Industrial and Engineering Chemistry Research ; Volume 48, Issue 8 , 2009 , Pages 4109-4118 ; 08885885 (ISSN) ; Taghikhani, V ; Vossoughi, M ; Sharif University of Technology
2009
Abstract
In this article, a new group contribution model is suggested for obtaining the thermodynamic properties of biomolecules in aqueous solutions. Accordingly, a Freed-FV model has been applied for the combinatorial free-volume term. The activity coefficients, solubilities, densities, and vapor pressures of amino acids and simple peptides in aqueous solutions were correlated, using the proposed group contribution model. Group interaction parameters of the proposed model were obtained by use of experimental data from amino acids available in the literature. The results demonstrate that the group contribution model can accurately correlate activity coefficient, solubility, density, and vapor...
Expremental Studying and Thermodynamic Modeling of Separation of Amino Acids by Ionic Liquids
, M.Sc. Thesis Sharif University of Technology ; Ghotbi, Cyrus (Supervisor) ; Taghikhani, Vahid (Supervisor) ; Vosoghi, Manochehr (Supervisor)
Abstract
In this work, partitioning of amino acids such as glutamic acid, phenyl anine and tryptophan in aqueous and ionic liquid phases at 298.15 K and atmospheric pressure was measured. [C4mim][Tf2N] is used due can produce two phase with water rapidly. Studying the effect of liquid solution pH on amino acids partitioning shows that increasing of pH results in decreasing of amino acid partitioning coefficient. This phenomenon pertains to electrostatic interactions between cation of amino acid and anion of ionic liquid which reduces when pH increases. Considering the effect of pH, liquid-liquid equilibrium data of amino acids was obtained in a pH that owning maximum partioning coefficient. Chemical...
Fabrication of metal nanowires based on self assembly of tryptophan-capped gold nanoparticle onto DNA network template
, Article International Journal of Nanotechnology ; Volume 6, Issue 10-11 , 2009 , Pages 1041-1049 ; 14757435 (ISSN) ; Vossoughi, M ; Alemzadeh, I ; Sharif University of Technology
2009
Abstract
In this study, synthesis of conductive metal nanowires by using aligned and immobilised DNA strand on solid substrate is reported. The nanoporous gold film was prepared by electrostatic self assembly of gold nanoparticles capped with tryptophan. Tryptophan would improve surface properties of gold nanoparticles for strongly attaching to DNA. Fourier transform infrared (FTIR) spectroscopy confirmed that gold nanoparticles have been capped by tryptophan. Also measured zeta potential shows that there are positive charges on the surface of gold nanoparticles. Investigations by AFM observati on substantially confirm that tryptophan-capped gold nanoparticles can be bonded to DNA template...
Highly efficient one-pot three-component mannich reaction under solvent-free conditions
, Article Scientia Iranica ; Volume 16, Issue 2 C , 2009 , Pages 94-98 ; 10263098 (ISSN) ; Ebrahimi, F ; Saidi, M. R ; Sharif University of Technology
2009
Abstract
A mild and practically-convenient one-pot procedure for the direct Mannich reaction has been developed using a condensation of amines, aldehydes and unmodified ketones under solvent free conditions in the presence of Znl 2 with good to excellent yields. The present methodology offers several advantages, such as excellent yields, simple procedures, short reaction times and milder conditions with very small amounts of catalyst. Furthermore, it is the first time that the catalytic activity of several catalysts under solvent free conditions has been studied. It was found that both the diastereoselectivity and the rate of reaction were improved with various Lewis acids and metal oxides. However,...