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    Overcoming drug resistance by co-targeting

    , Article Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, 18 December 2010 through 21 December 2010 ; December , 2010 , Pages 198-202 ; 9781424483075 (ISBN) Ayati, M ; Taheri, G ; Arab, S ; Wong, L ; Eslahchi, C ; Sharif University of Technology
    2010
    Abstract
    Removal or suppression of key proteins in an essential pathway of a pathogen is expected to disrupt the pathway and prohibit the pathogen from performing a vital function. Thus disconnecting multiple essential pathways should disrupt the survival of a pathogen even when it has multiple pathways to drug resistance. We consider a scenario where the drug-resistance pathways are unknown. To disrupt these pathways, we consider a cut set S of G, where G is a connected simple graph representing the protein interaction network of the pathogen, so that G-S splits to two partitions such that the endpoints of each pathway are in different partitions. If the difference between the sizes of the two... 

    Nanomechanical properties of MscL α helices: A steered molecular dynamics study

    , Article Channels ; Volume 11, Issue 3 , 2017 , Pages 209-223 ; 19336950 (ISSN) Bavi, N ; Bavi, O ; Vossoughi, M ; Naghdabadi, R ; Hill, A. P ; Martinac, B ; Jamali, Y ; Sharif University of Technology
    Taylor and Francis Inc  2017
    Abstract
    Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during... 

    The ITO-capped WO3 nanowires biosensor based on field-effect transistor in label-free protein sensing

    , Article Applied Physics A: Materials Science and Processing ; Volume 123, Issue 5 , 2017 ; 09478396 (ISSN) Shariati, M ; Sharif University of Technology
    Springer Verlag  2017
    Abstract
    The fabrication of ITO-capped WO3 nanowires associated with their bio-sensing properties in field-effect transistor diagnostics basis as a biosensor has been reported. The bio-sensing property for manipulated nanowires elucidated that the grown nanostructures were very sensitive to protein. The ITO-capped WO3 nanowires biosensor showed an intensive bio-sensing activity against reliable protein. Polylysine strongly charged bio-molecule was applied as model system to demonstrate the implementation of materialized biosensor. The employed sensing mechanism was ‘label-free’ and depended on bio-molecule’s intrinsic charge. For nanowires synthesis, the vapor–liquid–solid mechanism was used.... 

    Disease-related metabolites affect protein-nanoparticle interactions

    , Article Nanoscale ; Volume 10, Issue 15 , 2018 , Pages 7108-7115 ; 20403364 (ISSN) Tavakol, M ; Montazeri, A ; Naghdabadi, R ; Hajipour, M. J ; Zanganeh, S ; Caracciolo, G ; Mahmoudi, M ; Sharif University of Technology
    Royal Society of Chemistry  2018
    Abstract
    Once in biological fluids, the surface of nanoparticles (NPs) is rapidly covered with a layer of biomolecules (i.e., the "protein corona") whose composition strongly determines their biological identity, regulates interactions with biological entities including cells and the immune system, and consequently directs the biological fate and pharmacokinetics of nanoparticles. We recently introduced the concept of a "personalized protein corona" which refers to the formation of different biological identities of the exact same type of NP after being exposed to extract plasmas from individuals who have various types of diseases. As different diseases have distinct metabolomic profiles and... 

    Graphene-based nanoparticles as potential treatment options for parkinson’s disease: A molecular dynamics study

    , Article International Journal of Nanomedicine ; Volume 15 , 2020 , Pages 6887-6903 Alimohammadi, E ; Khedri, M ; Jahromi, A. M ; Maleki, R ; Rezaian, M ; Sharif University of Technology
    Dove Medical Press Ltd  2020
    Abstract
    Introduction: The study of abnormal aggregation of proteins in different tissues of the body has recently earned great attention from researchers in various fields of science. Concerning neurological diseases, for instance, the accumulation of amyloid fibrils can contribute to Parkinson’s disease, a progressively severe neurodegenerative disorder. The most prominent features of this disease are the degeneration of neurons in the substantia nigra and accumulation of α-synuclein aggregates, especially in the brainstem, spinal cord, and cortical areas. Dopamine replacement therapies and other medications have reduced motor impairment and had positive consequences on patients’ quality of life.... 

    Produse of whey Membrane with Super Critical Methods

    , M.Sc. Thesis Sharif University of Technology Milani Hosseini, Mohammad Sadegh (Author) ; Goodarznia, Iraj (Supervisor)
    Abstract
    Milk is One of the most important source s of protein in the world. during the process of cheese the most of these protein remain in whey. There are different methods to separate these protein from whey. The one of advanced method is ultrafiltartion, this method is based on a permeable membranes, with different pore size. There are many research works in this field. In this project we have tried to study the effect ofpressure, temperature, concentration and resistance time on membrane porosity. In order to design the experiment and analyze the results tagochi L 16 methods is used. The PVC membranes were prepaid by gas anti solvent method, experiment showed that changes of temperature and... 

    Study of Enzyme (Chymotrypsin) -Core/Shell (Fe3O4 @ Au) Nanoparticle Bioconjugate

    , M.Sc. Thesis Sharif University of Technology Kamal Ahmadi, Mahmoud (Author) ; Vosoughi, Manoochehr (Supervisor) ; Seyf Kordi, Ali Akbar (Supervisor)
    Abstract
    Conjugation of proteins to nanoparticles has numerous applications in sensing, imaging, delivery, catalysis, therapy and control of protein structure and activity. Therefore, characterizing the nanoparticle–protein interface is of great importance. A variety of covalent and non-covalent linking chemistries have been reported for nanoparticle attachment. Typically, a specific protein residue is linked directly to the nanoparticle core or to the ligand. As conjugation often affects the protein structure and function, techniques to probe structure and activity are assessed Characterization studies of nanoparticle–protein complexes show that the structure and function are influenced by the... 

    Protein-Nanoparticle Interactions

    , M.Sc. Thesis Sharif University of Technology Moharamkhani, Halime (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Abstract
    In this thesis, proteinnanoparticle interactions have been studied using Molecular Dynamics simulation. sT fN, is the studied protein in this work. It is one of the most important proteins in the blood fluid. In this work, nanoparticle has been modeled as a surface; because the radius of gyration of sT fN is less than 3nm, so when it is near an enough big nanoparticle (100200 nm), nanoparticle seems as a surface from the view of protein. The surface of nanoparticle consists of sodium ions. Surface of nanoparticle, has been modeled using two types of surface:flat surface and nonflat surface. Protein interaction with surface, has been studied in two different initial orientations with respect... 

    Identification and Characterization Natural Products from Borage Leaves Extract Acting as Anti-amyloid Inhibitors

    , M.Sc. Thesis Sharif University of Technology Ashrafian, Hossein (Author) ; Kalhor, Hamid Reza (Supervisor) ; Sajadi, Ali Akbar (Co-Advisor)
    Abstract
    Natural products obtained from plant extract are well known as a valuable source for research and assessments which eventuates to the discovery of some compounds possessing biological and pharmacological properties. Our aims have been to investigate and identify some natural products having the ability to effect on protein misfolding. In neurodegenerative disorders, like Alzheimer’s and Parkinson’s, a protein or a peptide undergoes conformational changes, and consequently the protein transform to fibrils coined amyloid. To determine the effective anti-amyloid compounds in natural products, Borage leaves was chosen. The plant extract was extracted using soxhlet and applied to hen white egg... 

    A triple fouling layers perspective on evaluation of membrane fouling under different scenarios of membrane bioreactor operation

    , Article Journal of Environmental Health Science and Engineering ; Volume 12, Issue 1 , June 2014 Pourabdollah, M ; Torkian, A ; Hashemian, S. J ; Bakhshi, B ; Sharif University of Technology
    Abstract
    One of the main factors affecting membrane fouling in MBRs is operational conditions. In this study the influence of aeration rate, filtration mode, and SRT on hollow fiber membrane fouling was investigated using a triple fouling layers perspective. The sludge microbial population distribution was also determined by PCR method. Through various applied operational scenarios the optimal conditions were: aeration rate of 15 LPM; relaxation mode with 40s duration and 8 min. interval; and SRT of 30 days. The similarity between SMP variations in triple fouling layers with its corresponding hydraulic resistance confirmed the effect of SMP on membrane fouling. Among three fouling fractions, the... 

    Protein degradation and RNA efflux of viruses photocatalyzed by graphene-tungsten oxide composite under visible light irradiation

    , Article Journal of Physical Chemistry C ; Volume 116, Issue 17 , 2012 , Pages 9653-9659 ; 19327447 (ISSN) Akhavan, O ; Choobtashani, M ; Ghaderi, E ; Sharif University of Technology
    2012
    Abstract
    Graphene-tungsten oxide composite thin films with sheetlike surface morphology were fabricated and applied in photoinactivation of viruses under visible light irradiation. Using X-ray photoelectron spectroscopy, it was found that the chemically exfoliated graphene oxide sheets incorporated in the tungsten oxide film reduced through a visible light photocatalytic reduction. In addition, annealing the films at 450 °C in air resulted in formation of W-C and W-O-C bonds to obtain graphene-tungsten oxide composite films. The composite films fabricated by this method showed an excellent visible light photocatalytic performance in photoinactivation of bacteriophage MS2 viruses, as compared to... 

    Binding assessment of two arachidonic-based synthetic derivatives of adrenalin with β-lactoglobulin: Molecular modeling and chemometrics approach

    , Article Biophysical Chemistry ; Volume 207 , 2015 , Pages 97-106 ; 03014622 (ISSN) Gholami, S ; Bordbar, A. K ; Akvan, N ; Parastar, H ; Fani, N ; Gretskaya, N. M ; Bezuglov, V. V ; Haertlé, T ; Sharif University of Technology
    Elsevier  2015
    Abstract
    A computational approach to predict the main binding modes of two adrenalin derivatives, arachidonoyl adrenalin (AA-AD) and arachidonoyl noradrenalin (AA-NOR) with the β-lactoglubuline (BLG) as a nano-milk protein carrier is presented and assessed by comparison to the UV-Vis absorption spectroscopic data using chemometric analysis. Analysis of the spectral data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS) algorithm led to the pure concentration calculation and spectral profiles resolution of the chemical constituents and the apparent equilibrium constants computation. The negative values of entropy and enthalpy changes for both compound indicated... 

    Two-phase acto-cytosolic fluid flow in a moving keratocyte: a 2d continuum model

    , Article Bulletin of Mathematical Biology ; Volume 77, Issue 9 , September , 2015 , Pages 1813-1832 ; 00928240 (ISSN) Nikmaneshi, M. R ; Firoozabadi, B ; Saidi, M. S ; Sharif University of Technology
    Springer New York LLC  2015
    Abstract
    The F-actin network and cytosol in the lamellipodia of crawling cells flow in a centripetal pattern and spout-like form, respectively. We have numerically studied this two-phase flow in the realistic geometry of a moving keratocyte. Cytosol has been treated as a low viscosity Newtonian fluid flowing through the high viscosity porous medium of F-actin network. Other involved phenomena including myosin activity, adhesion friction, and interphase interaction are also discussed to provide an overall view of this problem. Adopting a two-phase coupled model by myosin concentration, we have found new accurate perspectives of acto-cytosolic flow and pressure fields, myosin distribution, as well as... 

    Dead-end microfiltration of rough nonalcoholic beer by different polymeric membranes

    , Article Journal of the American Society of Brewing Chemists ; Volume 68, Issue 2 , 2010 , Pages 83-88 ; 03610470 (ISSN) Yazdanshenas, M ; Tabatabaei Nejad, S. A. R ; Soltanieh, M ; Tavakkoli, A ; Babaluo, A. A ; Fillaudeau, L ; Sharif University of Technology
    2010
    Abstract
    Clarification of rough nonalcoholic beer using microfiltration as an alternative to conventional filtration with filter aids presents scientific and technical challenges for the brewing industry. An experimental pilot plant was used to evaluate the permeability and selectivity of polymeric membranes in the clarification process. Cellulose acetate (CA) with pore sizes of 0.2, 0.45, 0.8, and 1.2 μm, together with cellulose nitrate (CN), nylon (NY), and polytetrafluoroethylene (PTFE) with a pore size of 0.45 μm, were used at transmembrane pressures (TMP) of 1.0 and 2.0 bar. The data corroborated that the flux values of the CA, CN, and NY membranes were almost the same and reduced drastically,... 

    Potential of light-harvesting of bacteriorhodopsin co-sensitized with green fluorescence protein: A new insight into bioenergy application

    , Article Biomass and Bioenergy ; Volume 87 , 2016 , Pages 35-38 ; 09619534 (ISSN) Mohammadpour, R ; Janfaza, S ; Zeinoddini, M ; Sharif University of Technology
    Elsevier Ltd  2016
    Abstract
    Herein we report for the first time on efficient and environmentally friendly bioenergy production from bacteriorhodopsin (bR) and green florescent protein (GFP) as co-sensitizers. bR as a transmembrane protein, acts like a light-driven proton pump in Halobacterium salinarum, converting light energy into a proton gradient. Employing GFP beside bR can enhance the photo-bioenergy production efficiency in two aspects: GFP can increase short circuit current by improvement in light absorption either by extending the sensitizingspectrumor making fluorescence in absorption region of bR. It can also enhance open circuit voltage more than 150 mV by improvement in photoelectrode converging and... 

    Expression of functional recombinant human tissue transglutaminase (TG2) using the bac-to-bac baculovirus expression system

    , Article Advanced Pharmaceutical Bulletin ; Volume 6, Issue 1 , 2016 , Pages 49-56 ; 22285881 (ISSN) Yazdani, Y ; Azari, S ; Kalhor, H. R ; Sharif University of Technology
    Tabriz University of Medical Sciences 
    Abstract
    Tissue transglutaminase (TG2) is a unique multifunctional enzyme. The enzyme possesses enzymatic activities such as transamidation/crosslinking and non-enzymatic functions such as cell migration and signal transduction. TG2 has been shown to be involved in molecular mechanisms of cancers and several neurodegenerative diseases such as Alzheimer's disease. The present study aimed at cloning and expression of full length human TG2 in Bac-to-Bac baculovirus expression system and evaluation of its activity. Methods: pFastBac HTA donor vector containing coding sequence of human TG2 was constructed. The construct was transformed to DH10Bac for generating recombinant bacmid. The verified bacmid was... 

    Sensing of alzheimer's disease and multiple sclerosis using nano-bio interfaces

    , Article Journal of Alzheimer's Disease ; Volume 59, Issue 4 , 2017 , Pages 1187-1202 ; 13872877 (ISSN) Hajipour, M. J ; Ghasemi, F ; Aghaverdi, H ; Raoufi, M ; Linnef, U ; Atyabi, F ; Nabipour, I ; Azhdarzadeh, M ; Derakhshankhah, H ; Lotfabadi, A ; Bargahi, A ; Alekhamis, Z ; Aghaie, A ; Hashemi, E ; Tafakhori, A ; Aghamollaii, V ; Mashhadi, M. M ; Sheibani, S ; Vali, H ; Mahmoudi, M ; Sharif University of Technology
    Abstract
    It is well understood that patients with different diseases may have a variety of specific proteins (e.g., type, amount, and configuration) in their plasmas. When nanoparticles (NPs) are exposed to these plasmas, the resulting coronas may incorporate some of the disease-specific proteins. Using gold (Au) NPs with different surface properties and corona composition, we have developed a technology for the discrimination and detection of two neurodegenerative diseases, Alzheimer's disease (AD) and multiple sclerosis (MS). Applying a variety of techniques, including UV-visible spectra, colorimetric response analyses and liquid chromatography-tandem mass spectrometry, we found the corona-NP... 

    Conversion of 3,6-O-dimethylfluorescein to fluorescein-based xanthylium derivative: characterization and covalent attachment to bovine serum albumin

    , Article ChemistrySelect ; Volume 4, Issue 36 , 2019 , Pages 10681-10687 ; 23656549 (ISSN) Kalhor, H. R ; Rezaei, M ; Sharif University of Technology
    Wiley-Blackwell  2019
    Abstract
    Xanthene dyes, such as fluorescein and rhodamine, have played crucial rules in biological sciences especially covalent attachment of these organic compounds to biomolecules. 3-O-methylfluorescein and 3,6-O-dimethylfluorescein were synthesized and purified using a facile procedure. 3,6-O-dimethylfluorescein, which lacks fluorescence, was treated with sodium hydroxide and sulfuric acid solutions, giving rise to yellow and green fluorescent compounds, respectively. In both basic and acidic conditions, donor-acceptor structures were formed. The reaction of 3,6-O-dimethylfluorescein with acids, in a reversible manner, emitted green fluorescence, whereas its reaction with hydroxide ion,... 

    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,... 

    Comparing the effects of endurance and resistance trainings on gene expression involved in protein synthesis and degradation signaling pathways of Wistar rat soleus muscle

    , Article Tehran University Medical Journal ; Volume 77, Issue 11 , 2020 , Pages 668-677 Gholipour, M ; Seifabad, M ; Asad, M. R ; Sharif University of Technology
    Tehran University of Medical Sciences  2020
    Abstract
    Background: Skeletal muscle mass, which is regulated by a balance between muscle protein synthesis and degradation, is an important factor for movement to meet everyday needs, especially in pathological conditions and aging. The purpose of the present investigation was to compare the alterations of the gene expression involved in muscle protein synthesis and degradation signaling pathways induced by two exercise training protocols. Methods: Eight weeks old Wistar rats have been assigned to the present experimental study, which was conducted from August 2018 to October 2018 at the animal laboratory of Tehran University. They were randomly divided into two resistance and endurance training...