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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...
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...
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,...
An in vitro study of bare and poly(ethylene glycol)-co-fumarate-coated superparamagnetic iron oxide nanoparticles: A new toxicity identification procedure
, Article Nanotechnology ; Volume 20, Issue 22 , 2009 ; 09574484 (ISSN) ; Simchi, A ; Imani, M ; Milani, A. S ; Stroeve, P ; Sharif University of Technology
2009
Abstract
As the use of superparamagnetic iron oxide nanoparticles (SPION) in biomedical applications increases (e.g. for targeting drug delivery and imaging), patients are likely to be exposed to products containing SPION. Despite their high biomedical importance, toxicity data for SPION are limited to date. The aim of this study is to investigate the cytotoxicity of SPION and its ability to change cell medium components. Bare and poly(ethylene glycol)-co-fumarate (PEGF)-coated SPION with narrow size distributions were synthesized. The particles were prepared by co-precipitation using ferric and ferrous salts with a molar Fe3+/Fe2+ ratio of 2. Dulbecco's modified Eagle's medium (DMEM) and primary...
Synthesis and properties of novel fluorinated polyamides based on noncoplanar sulfoxide containing aromatic bis(ether amine)
, Article Polymer Journal ; Volume 41, Issue 3 , 2009 , Pages 174-180 ; 00323896 (ISSN) ; Abouzari Lotf, E ; Javadi, A ; Taheri, S ; Sharif University of Technology
2009
Abstract
A novel sulfoxide containing bis(ether amine) monomer, 2,2'-sulfoxide- bis[4-methyl(2-trifluoromethyl)4-aminophenoxy) phenyl ether] (M2), was synthesized from the halogen displacement of 2-chloro-5-nitrobenzotrifluoride with dibenzosulfoxide (DH) in the presence of potassium carbonate, followed by catalytic reduction of bis(ether nitro) intermediate with Zinc/Ammonium chloride. A series of organic-soluble poly(ether amide)s (PA1-7) bearing sulfoxide and electronwithdrawing trifiuoromethyl group were synthesized from bis(ether amine) with various aromatic diacids (1-7) via a direct polycondensation with triphenyl phosphite and pyridine. The resulting polymers had inherent viscosities ranging...
Study and optimization of amino acid extraction by emulsion liquid membrane
, Article Separation Science and Technology ; Volume 43, Issue 11-12 , 2008 , Pages 3075-3096 ; 01496395 (ISSN) ; Alemzadeh, I ; Vossoughi, M ; Sharif University of Technology
2008
Abstract
A batch extraction of an essential amino acid, phenylalanine, from an aqueous solution of different concentrations by an Emulsion Liquid Membrane (ELM) was developed using D2EHPA as a cationic carrier, Span 80 as the surfactant, paraffin, and kerosene as the diluents, and HCl as the internal electrolyte. All effective parameters such as the initial pH of the aqueous external phase, the electrolyte concentration in the aqueous internal phase, carrier, and surfactant concentration in the emulsion, the volume ratio of the organic to aqueous internal phase (Roi), the volume ratio of the W/O emulsion to the aqueous external phase (Rew) and time were examined and optimized using the Taguchi...
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) ; Vossoughi, M ; Almzadeh, I ; Zeinali, M ; Sharif University of Technology
2008
Abstract
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...
Interaction of water-soluble amino acid Schiff base complexes with bovine serum albumin: Fluorescence and circular dichroism studies
, Article Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy ; Volume 71, Issue 4 , 2008 , Pages 1617-1622 ; 13861425 (ISSN) ; Mohammadi Boghaei, D ; Sharif University of Technology
2008
Abstract
Fluorescence spectroscopy in combination with circular dichroism (CD) spectroscopy were used to investigate the interaction of water-soluble amino acid Schiff base complexes, [Zn(L1,2)(phen)] where phen is 1,10-phenanthroline and H2L1,2 is amino acid Schiff base ligands, with bovine serum albumin (BSA) under the physiological conditions in phosphate buffer solution adjusted to pH 7.0. The quenching mechanism of fluorescence was suggested as static quenching according to the Stern-Volmer equation. Quenching constants were determined using the Stern-Volmer equation to provide a measure of the binding affinity between amino acid Schiff base complexes and BSA. The thermodynamic parameters ΔG, ΔH...
A theoretical study of repeating sequence in HRP II: A combination of molecular dynamics simulations and 17O quadrupole coupling tensors
, Article Biophysical Chemistry ; Volume 137, Issue 2-3 , 2008 , Pages 76-80 ; 03014622 (ISSN) ; Esrafili, M. D ; van der spoel, D ; Hadipour, N. L ; Parsafar, G ; Sharif University of Technology
2008
Abstract
Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and 17O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with α-helix initial structure. It was found that peptide loses its initial α-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate 17O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31 + G* basis set. Calculated 17O EFG tensors were used to...
Synthesis and characterization of water-soluble zinc(II) Schiff-base complexes derived from amino acids and 3-formyl-4-hydroxybenzyl- triphenylphosphonium chloride
, Article Journal of Coordination Chemistry ; Volume 61, Issue 12 , 2008 , Pages 1917-1926 ; 00958972 (ISSN) ; Askarizadeh, E ; Sharif University of Technology
2008
Abstract
Tridentate Schiff-base ligands derived from condensation of 3-formyl-4-hydroxybenzyl-triphenylphosphonium chloride with glycine, L-alanine, L-valine, L-leucine and L-phenylalanine in the presence of Zn(OAc)2·2H2O form five new water-soluble Zn(II) complexes, which were characterized by elemental analyses, IR, electronic absorption and 1H, 13C NMR spectroscopies. In the IR spectra of the complexes, the difference between the asymmetric and the symmetric carboxylate stretching frequencies is larger than ∼210 cm-1, which implies that the carboxylate groups are monodentate. UV-Vis electronic absorption studies show that Zn(II) functions as a trap for the Schiff-base intermediate. Schiff-base...
A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins
, Article BMC Bioinformatics ; Volume 9 , 2008 ; 14712105 (ISSN) ; Kargar, M ; Katanforoush, A ; Arab, S ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Marashi, S. A ; Sharif University of Technology
2008
Abstract
Background: It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete. Results: In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments?...
LiClO4-accelerated three-component Mannich-type reaction of diethyl malonate with imines: An efficient synthesis of β-amino esters under solvent-free conditions
, Article Synthetic Communications ; Volume 38, Issue 22 , 2008 , Pages 4036-4044 ; 00397911 (ISSN) ; Saidi, M. R ; Sharif University of Technology
2008
Abstract
LiClO4 is used as catalyst for direct Mannich-type reaction of aryl aldehydes, aryl amines, and diethyl malonic ester under solvent-free conditions. This three-component reaction afforded the corresponding β-amino esters in good yields with simple and environmentally benign procedure. Copyright © Taylor & Francis Group, LLC
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) ; Aghaie, H ; Gholami, M. R ; Sharif University of Technology
World Scientific Publishing Co. Pte Ltd
2008
Abstract
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...
Correlation and prediction the activity coefficients and solubility of amino acids and simple peptide in aqueous solution using the modified local composition model
, Article Fluid Phase Equilibria ; Volume 255, Issue 2 , 2007 , Pages 160-166 ; 03783812 (ISSN) ; Taghikhani, V ; Vossoughi, M ; Sharif University of Technology
2007
Abstract
In this work, the modified Wilson model was used to obtain the activity coefficients of amino acids and simple peptides in non-electrolyte aqueous solutions. The Wilson model was modified using the new local mole fraction proposed by Zhao et al. and non-random case for the reference state. The binary interaction parameters (BIP) of the modified Wilson model for amino acid-water pairs were obtained using the experimental data of the activity coefficients for amino acids available in the literature. The modified Wilson model was also used to correlate the solubility of amino acids in water and the values of Δh/R, Δs/R, and Δg/R of the solutions studied were reported. The results obtained...
Spectral characterization of novel ternary zinc(II) complexes containing 1,10-phenanthroline and schiff bases derived from amino acids and salicylaldehyde-5-sulfonates
, Article Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy ; Volume 67, Issue 3-4 , 2007 , Pages 944-949 ; 13861425 (ISSN) ; Gharagozlou, M ; Sharif University of Technology
2007
Abstract
A series of new ternary zinc(II) complexes [Zn(L1-10)(phen)], where phen is 1,10-phenanthroline and H2L1-10 = tridentate Schiff base ligands derived from the condensation of amino acids (glycine, l-phenylalanine, l-valine, l-alanine, and l-leucine) and salicylaldehyde-5-sulfonates (sodium salicylaldehyde-5-sulfonate and sodium 3-methoxy-salicylaldehyde-5-sulfonate), have been synthesized. The complexes were characterized by elemental analysis, IR, UV-vis, 1H NMR, and 13C NMR spectra. The IR spectra of the complexes showed large differences between νas(COO) and νs(COO), Δν (νas(COO) - νs(COO)) of 191-225 cm-1, indicating a monodentate coordination of the carboxylate group. Spectral data...
Synthesis and characterization of novel water-soluble zinc(II) Schiff-base complexes derived from amino acids and salicylaldehyde-5-sulfonates
, Article Journal of Coordination Chemistry ; Volume 60, Issue 3 , 2007 , Pages 339-346 ; 00958972 (ISSN) ; Gharagozlou, M ; Sharif University of Technology
2007
Abstract
New water-soluble zinc(II) Schiff-base complexes derived from amino acids (glycine, L-phenylalanine, and L-valine) and salicylaldehyde-5-sulfonates (sodium salicylaldehyde-5-sulfonate and sodium 3-methoxy-salicylaldehyde-5- sulfonate) have been synthesized. The complexes were characterized by elemental analysis, IR, electronic, 1H NMR, and 13C NMR spectra. In the IR spectra of the complexes, the large difference between the asymmetric νas(COO) and symmetric νs(COO) carboxylate stretch, Δν(νas(COO)-νs(COO)) of 199-247 cm-1, indicates monodentate coordination of the carboxylate group. Spectral data showed that in these complexes the ligand is a tridentate ONO moiety, coordinating to the metal...