Loading...
Search for:
amino-acids
0.007 seconds
Total 140 records
Investigating the effects of amino acid-based surface modification of carbon nanoparticles on the kinetics of insulin amyloid formation
, Article Colloids and Surfaces B: Biointerfaces ; Volume 176 , 2019 , Pages 471-479 ; 09277765 (ISSN) ; Yahyazadeh, A ; Sharif University of Technology
Elsevier B.V
2019
Abstract
Surface functionality of nanoparticles has been pivotal in defining interactions of nanoparticles and biomolecules. To explore various functionalities on the surface of nanoparticle through a facile procedure, various carbon-based nanoparticles, modified with a specific natural amino acid, were synthesized; the amino acids were chosen in order that almost all classes of amino acids were included. After characterizations of the nanoparticles using several spectroscopic methods, the effects of surface modification of nanoparticles were examined against amyloid formation, exploiting insulin as a model amyloidogenic polypeptide. Although most amino acids afforded carbon nanoparticles, only...
AntAngioCOOL: computational detection of anti-angiogenic peptides
, Article Journal of Translational Medicine ; Volume 17, Issue 1 , 2019 ; 14795876 (ISSN) ; Khorsand, B ; Yousefi, A. A ; Kargar, M. J ; Shirali Hossein Zade, R ; Mahdevar, G ; Sharif University of Technology
BioMed Central Ltd
2019
Abstract
Background: Angiogenesis inhibition research is a cutting edge area in angiogenesis-dependent disease therapy, especially in cancer therapy. Recently, studies on anti-angiogenic peptides have provided promising results in the field of cancer treatment. Methods: A non-redundant dataset of 135 anti-angiogenic peptides (positive instances) and 135 non anti-angiogenic peptides (negative instances) was used in this study. Also, 20% of each class were selected to construct an independent test dataset (see Additional files 1, 2). We proposed an effective machine learning based R package (AntAngioCOOL) to predict anti-angiogenic peptides. We have examined more than 200 different classifiers to build...
The metabolomics signature associated with responsiveness to steroid therapy in focal segmental glomerulosclerosis: A pilot study
, Article Revista de Investigacion Clinica ; Volume 71, Issue 2 , 2019 , Pages 106-115 ; 00348376 (ISSN) ; Kalantari, S ; Nafar, M ; Boroumandnia, N ; Sharif University of Technology
Instituto Nacional de la Nutricion Salvador Zubiran
2019
Abstract
Background: Focal segmental glomerulosclerosis (FSGS) is considered one of the most severe glomerular diseases and around 80% of cases are resistant to steroid treatment. Since a large proportion of steroid-resistant (SR) FSGS patients progress to end-stage renal disease, other therapeutic strategies may benefit this population. However, identification of non-invasive biomarkers to predict this high-risk population is needed. Objective: We aimed to identify the biomarker candidates to distinguish SR from steroid-sensitive (SS) patients using metabolomics approach and to identify the possible molecular mechanism of resistance. Methods: Urine was collected from biopsy-proven FSGS patients...
Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study
, Article Journal of Molecular Graphics and Modelling ; Volume 87 , 2019 , Pages 257-267 ; 10933263 (ISSN) ; Ghobeh, M ; Aghakhani Mahyari, F ; Rafii Tabar, H ; Sasanpour, P ; Sharif University of Technology
Elsevier Inc
2019
Abstract
Background: Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. Methods: Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. Results: Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the...
Cis-trans proline isomers in the catalytic domain of calcineurin
, Article FEBS Journal ; Volume 286, Issue 6 , 2019 , Pages 1230-1239 ; 1742464X (ISSN) ; 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,...
The effect of chitosan and PEG polymers on stabilization of GF-17 structure: A molecular dynamics study
, Article Carbohydrate Polymers ; Volume 237 , 2020 ; Moosavi, A ; Arghavani Hadi, J ; Sharif University of Technology
Elsevier Ltd
2020
Abstract
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...
The metabolome profiling of obese and non-obese individuals: Metabolically healthy obese and unhealthy non-obese paradox
, Article Iranian Journal of Basic Medical Sciences ; Volume 23, Issue 2 , 2020 , Pages 186-194 ; Madani, N. H ; Ghoochani, B. F. N. M ; Safari Alighiarloo, N ; Khamseh, M. E ; Sharif University of Technology
Mashhad University of Medical Sciences
2020
Abstract
Objective(s): The molecular basis of “metabolically healthy obese” and “metabolically unhealthy non-obese” phenotypes is not fully understood. Our objective was to identify metabolite patterns differing in obese (metabolically healthy vs unhealthy (MHO vs MUHO)) and non-obese (metabolically healthy vs unhealthy (MHNO vs MUHNO)) individuals. Materials and Methods: This case-control study was performed on 86 subjects stratified into four groups using anthropometric and clinical measurements: MHO (21), MUHO (21), MHNO (22), and MUHNO (22). Serum metabolites were profiled using nuclear magnetic resonance (NMR). Multivariate analysis was applied to uncover discriminant metabolites, and enrichment...
Development of a quartz crystal microbalance biodetector based on cellulose nanofibrils (CNFs) for glycine
, Article Journal of Materials Science: Materials in Electronics ; Volume 31, Issue 20 , 2020 , Pages 17451-17460 ; Iraji zad, A ; Vossoughi, M ; Kalantarian, A ; Sharif University of Technology
Springer
2020
Abstract
The performance of a quartz crystal microbalance (QCM) used as a sensor/detector relies on the performance and quality of the film coated onto the quartz crystal sensor. This study focuses on the sensor coating preparation for the detection of glycine. Cellulose nanofibrils (CNFs), natural polymers, were coated on a quartz crystal (QC) surface by a spin-coating method. The prepared CNF-coated QC was characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), cyclic voltammetry (CV), Fourier transform infrared spectrophotometry-attenuated total reflectance (FTIR-ATR), Raman spectroscopy, and water contact angle (WCA). The stable and fully covered QCs without further...
Design of peptide-based inhibitor agent against amyloid-β aggregation: Molecular docking, synthesis and in vitro evaluation
, Article Bioorganic Chemistry ; Volume 102 , September , 2020 ; Erfani, M ; Bavi, O ; Khazaei, S ; Sharifzadeh, M ; Hajiramezanali, M ; Beiki, D ; Shamloo, A ; Sharif University of Technology
Academic Press Inc
2020
Abstract
Formation of the amyloid beta (Aβ) peptide aggregations represents an indispensable role in appearing and progression of Alzheimer disease. β-sheet breaker peptides can be designed and modified with different amino acids in order to improve biological properties and binding affinity to the amyloid beta peptide. In the present study, three peptide sequences were designed based on the hopeful results of LIAIMA peptide and molecular docking studies were carried out onto the monomer and fibril structure of amyloid beta peptide using AutoDock Vina software. According to the obtained interactions and binding energy from docking, the best-designed peptide (D-GABA-FPLIAIMA) was chosen and...
Development of a nano biosensor for anti-gliadin detection for Celiac disease based on suspension microarrays
, Article Biomedical Physics and Engineering Express ; Volume 6, Issue 5 , August , 2020 ; Rabiee, M ; Rostami Nejad, M ; Aghamohammadi, E ; Asadzadeh Aghdaei, H ; Zali, M. R ; Rabiee, N ; Fatahi, Y ; Bagherzadeh, M ; Webster, T. J ; Sharif University of Technology
IOP Publishing Ltd
2020
Abstract
Celiac disease is an autoimmune disorder represented by the ingestion of the gluten protein usually found in wheat, barley and rye. To date, ELISA has been the most accurate method for determining the presence of anti-gliadin, which is cumbersome, expensive (compared to a suspension microarray technique), and requires extensive sample preparation. In this study, in order to establish a more accurate assay to identify gliadin at lower concentrations, optical nano biosensors using an indirect immunoassay method for gliadin detection was designed and fabricated. For this, polycaprolactone (PCL) nano- to micro-beads were fabricated as a platform for the gliadin antigen which were optimized and...
Fast chromium removal by Shewanella sp.: an enzymatic mechanism depending on serine protease
, Article International Journal of Environmental Science and Technology ; Volume 17, Issue 1 , April , 2020 , Pages 143-152 ; Mahmoodi, R ; Mollania, N ; Kheirabadi, M ; Sharif University of Technology
Springer
2020
Abstract
Environmental pollutions with heavy metals pose serious health and ecological risks. Sabzevar in the northeast of Iran has natural chromic mines and then chromium-polluted soils and groundwater. In the present work, the metal-tolerant bacterial strain KR2 was identified as Shewanella sp. following 16S rDNA gene sequence analysis. Bioremediation ability of isolated bacterial from agricultural soils that irrigated by groundwater, Shewanella sp., was evaluated for uptaking of chromium with varying Cr(VI) concentrations from 50 to 500 ppm in aerobic conditions (pH 7.0, 37 °C). The Shewanella sp. strain KR2 showed an obvious heavy metal tolerant in the wide range of heavy metals including: Cr6+,...
New proline, alanine, serine repeat sequence for pharmacokinetic enhancement of anti-vegf single-domain antibody
, Article Journal of Pharmacology and Experimental Therapeutics ; Volume 375, Issue 1 , July , 2020 , Pages 69-75 ; Salimian, M ; Mehdizadeh, A ; Khosravy, M. S ; Vafabakhsh, A ; Karami, E ; Cohan, R. A ; Sharif University of Technology
American Society for Pharmacology and Experimental Therapy
2020
Abstract
Therapeutic fragmented antibodies show a poor pharmacokinetic profile that leads to frequent high-dose administration. In the current study, for the first time, a novel proline, alanine, serine (PAS) repeat sequence called PAS#208 was designed to extend the plasma half-life of a nanosized anti-vascular endothelial growth factor-A single-domain antibody. Polyacrylamide gel electrophoresis, circular dichroism, dynamic light scattering, and electrophoretic light scattering were used to assess the physicochemical properties of the newly designed PAS sequence. The effect of PAS#208 on the biologic activity of a single-domain antibody was studied using an in vitro proliferation assay. The...
PASylation enhances the stability, potency, and plasma half-life of interferon α-2a: A molecular dynamics simulation
, Article Biotechnology Journal ; Volume 15, Issue 8 , 2020 ; Rostami, P ; Mahmoudi, A ; Sharif University of Technology
Wiley-VCH Verlag
2020
Abstract
In this study, the effectiveness of PASylation in enhancing the potency and plasma half-life of pharmaceutical proteins has been accredited as an alternative technique to the conventional methods such as PEGylation. Proline, alanine, and serine (PAS) chain has shown some advantages including biodegradability improvement and plasma half-life enhancement while lacking immunogenicity or toxicity. Although some experimental studies have been performed to find the mechanism behind PASylation, the detailed mechanism of PAS effects on the pharmaceutical proteins has remained obscure, especially at the molecular level. In this study, the interaction of interferon α-2a (IFN) and PAS chain is...
Site-specific protein conjugation onto fluorescent single-walled carbon nanotubes
, Article Chemistry of Materials ; Volume 32, Issue 20 , 2020 , Pages 8798-8807 ; Wu, S. J ; Rahnamaee, S. Y ; Schuergers, N ; Boghossian, A. A ; Sharif University of Technology
American Chemical Society
2020
Abstract
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...
Biomimetic proteoglycan nanoparticles for growth factor immobilization and delivery
, Article Biomaterials Science ; Volume 8, Issue 4 , 2020 , Pages 1127-1136 ; Mostafavi, E ; Shokrgozar, M. A ; Tamjid, E ; Webster, T. J ; Annabi, N ; Simchi, A ; Sharif University of Technology
Royal Society of Chemistry
2020
Abstract
The delivery of growth factors is often challenging due to their short half-life, low stability, and rapid deactivation. In native tissues, the sulfated residual of glycosaminoglycan (GAG) polymer chains of proteoglycans immobilizes growth factors through the proteoglycans'/proteins' complexation with nanoscale organization. These biological assemblies can influence growth factor-cell surface receptor interactions, cell differentiation, cell-cell signaling, and mechanical properties of the tissues. Here, we introduce a facile procedure to prepare novel biomimetic proteoglycan nanocarriers, based on naturally derived polymers, for the immobilization and controlled release of growth factors....
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...