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    Dft study of bond energies and attachment sites of sample divalent cations (mg2+, ca2+, zn2+) to histidine in the gas phase

    , Article Journal of Theoretical and Computational Chemistry ; Volume 8, Issue 3 , 2009 , Pages 347-371 ; 02196336 (ISSN) Tavasoli, E ; Fattahi, A ; Sharif University of Technology
    In view of better understanding interactions of amino acids and peptides with metallic cations in the isolated state, the model system histidineM 2+ (M2+ = Mg2+, Ca2+, Zn 2+) has been studied theoretically. The computations have been performed with the help of the density functional theory (DFT) and the B3LYP functional. The extended basis set was the standard 6-311++G**. All the molecular complexes obtained by the interaction between several energetically low-lying tautomers/conformers/zwitterions of histidine and the cations on different binding sites were considered. Our study shows that complexes of histidine with Mg2+, Ca2+, Zn2+ are rather similar. In the isolated state, the most... 

    Interaction of Mg2+, Ca2+, Zn2+ and Cu+ with cytosine nucleosides: Influence of metal on sugar puckering and stability of N-Glycosidic bond, a DFT study

    , Article Journal of Molecular Structure: THEOCHEM ; Volume 913, Issue 1-3 , 2009 , Pages 117-125 ; 01661280 (ISSN) AliakbarTehrani, Z ; Fattahi, A ; Pourjavadi, A ; Sharif University of Technology
    The coordination geometries, electronic features, absolute metal ion affinities, geometrical multiplicity and binding strength for the complexes formed by Mg2+, Ca2+, Zn2+ and Cu+ with cytidine and deoxycytidine have been determined theoretically employing the hybrid B3LYP exchange-correlation functional and using 6-311++G(d,p) orbital basis sets. Our study shows that the most stable coordination modes of cytosine nucleosides with these cations are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with three oxygen atoms: one from the carbonyl oxygen of cytosine moiety and two from the sugar unit (i.e., O5′ and O4′).... 

    DFT/B3LYP study of thermochemistry of D-glucosamine, a representative polyfunctional bioorganic compound

    , Article Scientia Iranica ; Volume 15, Issue 4 , 2008 , Pages 422-429 ; 10263098 (ISSN) Fattahi, A ; Ghorat, M ; Pourjavadi, A ; Kurdtabar, M ; Torabi, A. A ; Sharif University of Technology
    Sharif University of Technology  2008
    D-glucosamine, as a representative polyfunctional compound, is a bioactive amino sugar. In this study, the gas phase thermochemical properties of D-glucosamine, including its Metal Ion Affinity (MIA), metal binding sites, Anion Affinity (AA), acidity and proton affinity, have been explored, using the Density Functional Theory (DFT) and a 6-311++G**basis set. The summary of the MIA and AA results (in kcal/mol-1) are: Li+ = 67.6, Na+ = 51.1, K+ = 37.3, Mg2+ = 207.9, Ca2+ = 150.4, Zn2+ = 251.2, Cl- = 27.4, CN- = 28.0. The acidity values calculated at different sites, including four -OH groups and one -NH2 group, range from 344.0 to 373.0 kcal/mol-1. These results, surprisingly, indicate how... 

    A clustering-based algorithm for de novo motif discovery in DNA sequences

    , Article 2017 24th Iranian Conference on Biomedical Engineering and 2017 2nd International Iranian Conference on Biomedical Engineering, ICBME 2017, 30 November 2017 through 1 December 2017 ; 2018 ; 9781538636091 (ISBN) Ebrahim Abadi, M. H ; Fatemizadeh, E ; Sharif University of Technology
    Motif discovery is a challenging problem in molecular biology and has been attracting researcher's attention for years. Different kind of data and computational methods have been used to unravel this problem, but there is still room for improvement. In this study, our goal was to develop a method with the ability to identify all the TFBS signals, including known and unknown, inside the input set of sequences. We developed a clustering method specialized as part of our algorithm which outperforms other existing clustering methods such as DNACLUST and CD-HIT-EST in clustering short sequences. A scoring system was needed to determine how much a cluster is close to being a real motif. Multiple... 

    A Thesis Submitted in Partial Fulfillment of the Requirement for the Degree of Master of Science in Electrical Engineering

    , M.Sc. Thesis Sharif University of Technology Mohammadi, Mahsa (Author) ; Jahed, Mehran (Supervisor) ; Motahhari, Abolfazl (Co-Advisor)
    Dnase I Hypersensitive Sites (DHSs) are known as comprehensive markers of DNA regulatory elements. The main function of regulatory elements is repressing or enhancing transcription of genes. Hence, the recruitment of the data is prevalent in many studies of genome. One of the applications of this data is to utilize it to predict active regulatory regions (Transcription Factor Binding Sites).There are different means to do this, divided in three major groups: first, the methods only use the number of DNase-seq reads that surround a candidate binding site. While robust, these methods do not reflect the shape of the signal. A second strategy uses a variety of approaches to model and identify... 

    Inhibition mechanisms of a pyridazine-based amyloid inhibitor: as a β-sheet destabilizer and a helix bridge maker

    , Article Journal of Physical Chemistry B ; Volume 121, Issue 32 , 2017 , Pages 7633-7645 ; 15206106 (ISSN) Kalhor, H. R ; Jabbari, M. P ; Sharif University of Technology
    Conformational diseases have been investigated extensively in recent years; as a result, a number of drug candidates have been introduced as amyloid inhibitors; however, no effective therapies have been put forward. RS-0406 with pyridazine as its core chemical structure has so far shown promising results in inhibiting amyloid formation. In the present work, using molecular dynamics, we undertook the investigation of RS-0406 interactions with U-shaped Aβ1−42 and Aβ1−40 pentamers, Aβ1−42 monomers, and double-horseshoe-like Aβ1−42. To set better parameters for the small molecule, experimental and computational log P values were obtained. In addition, an analogue of RS-0406 was also simulated... 

    GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation

    , Article Glycobiology ; Volume 29, Issue 11 , 2019 , Pages 803-812 ; 14602423 (ISSN) Azimzadeh Irani, M ; Ejtehadi, M. R ; Sharif University of Technology
    NLM (Medline)  2019
    IL-1RI is the signaling receptor for the IL-1 family of cytokines that are involved in establishment of the innate and acquired immune systems. Glycosylated extracellular (EC) domain of the IL-1RI binds to agonist such as IL-1β or antagonist ligands and the accessory protein to form the functional signaling complex. Dynamics and ligand binding of the IL-1RI is influenced by presence of the glycosaminoglycans (GAGs) of the EC matrix. Here a combination of molecular dockings and molecular dynamics simulations of the unglycosylated, partially N-glycosylated and fully N-glycosylated IL-1RI EC domain in the apo, GAG-bound and IL-1β-bound states were carried out to explain the co-occurring... 

    S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study

    , Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) Rahnama, S ; Azimzadeh Irani, M ; Amininasab, M ; Ejtehadi, M. R ; Sharif University of Technology
    Nature Research  2021
    SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans... 

    Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions

    , Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 72, Issue 6 , 2005 ; 15393755 (ISSN) Radja, N.H ; Farzami, R. R ; Ejtehadi, M. R ; Sharif University of Technology
    We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically nondegenerate vectors (structures) as proteinlike structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of... 

    Elastic properties of actin assemblies in different states of nucleotide binding

    , Article Cellular and Molecular Bioengineering ; Volume 5, Issue 1 , 2012 , Pages 1-13 ; 18655025 (ISSN) Ghodsi, H ; Kazemi, M. T ; Sharif University of Technology
    In this paper, the elastic properties of monomeric actin (G-actin) and the trimer nucleus (G-actin trimer) in different states of nucleotide binding are estimated using steered molecular dynamic (SMD) simulations. Three nucleotide binding states are considered: ADP- and ATP-bound actin and nucleotide-free actin assemblies. Our results show that nucleotide binding and the corresponding changes in structure have significant effects on the mechanical behaviors of actin assemblies. Simulations reveal that the deformation behavior of G-actin monomers is generally elastic up to engineering strains of 16 and 40% in the tension and shear tests, respectively. In addition, the G-actin trimers react... 

    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... 

    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) Ebrahim Habibi, M. B ; Ghobeh, M ; Aghakhani Mahyari, F ; Rafii Tabar, H ; Sasanpour, P ; Sharif University of Technology
    Elsevier Inc  2019
    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... 

    A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

    , Article BMC Bioinformatics ; Volume 9 , 2008 ; 14712105 (ISSN) Sheari, A ; Kargar, M ; Katanforoush, A ; Arab, S ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Marashi, S. A ; Sharif University of Technology
    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?... 

    Rigid-body molecular dynamics of DNA inside a nucleosome

    , Article European Physical Journal E ; Volume 36, Issue 3 , March , 2013 ; 12928941 (ISSN) Fathizadeh, A ; Berdy Besya, A ; Ejtehadi, M. R ; Schiessel, H ; Sharif University of Technology
    The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use... 

    High-capacity hierarchically imprinted polymer beads for protein recognition and capture

    , Article Angewandte Chemie - International Edition ; Volume 50, Issue 2 , December , 2011 , Pages 495-498 ; 14337851 (ISSN) Nematollahzadeh, A ; Sun, W ; Aureliano, C. S. A ; Lütkemeyer, D ; Stute, J ; Abdekhodaie, M. J ; Shojaei, A ; Sellergren, B ; Sharif University of Technology
    Leaving an imprint: Hierarchical protein imprinting starting from wide-pore silica modified with a submonolayer of adsorbed protein (IgG or HSA) leads to an inverse polymeric replica of the silica template that features highly accessible protein-complementary binding sites (see picture). The resulting poly(acrylamide) beads (PIgG or PHSA) feature high binding capacities and can be used to selectively capture the proteins HSA and IgG from blood serum  

    Amine-functionalized magnetic nanocomposite particles for efficient immobilization of lipase: effects of functional molecule size on properties of the immobilized lipase

    , Article RSC Advances ; Volume 5, Issue 42 , Apr , 2015 , Pages 33313-33327 ; 20462069 (ISSN) Esmaeilnejad Ahranjani, P ; Kazemeini, M ; Singh, G ; Arpanaei, A ; Sharif University of Technology
    Royal Society of Chemistry  2015
    A cost-effective design of reusable enzyme-functionalized particles with better catalytic activity is of great scientific interest due to their applications in a wide range of catalytic reactions in several industrial processes. In this work, a systematic approach for preparing amine-functionalized magnetic nanocomposite particles through the surface modification of core/shell type Fe3O4 cluster@SiO2 particles by the small molecules of 3-(2-aminoethyl)aminopropyltrimethoxysilane (AAS) or the large molecules of polyethyleneimine (PEI) with two different molecular weights, as the support materials for enzyme immobilization, has been demonstrated. The functional... 

    Theoretical aspects of the enhancement of metal binding affinity by intramolecular hydrogen bonding and modulating p: K a values

    , Article New Journal of Chemistry ; Volume 41, Issue 24 , 2017 , Pages 15110-15119 ; 11440546 (ISSN) Motahari, A ; Fattahi, A ; Sharif University of Technology
    Royal Society of Chemistry  2017
    Polyols were used as model ligands for Mg2+, Ca2+, and Zn2+ complexes to study the role of the hydrogen bond network on the metal binding affinity and modulation of successive pKa values using density functional theory. The results confirm that the acidity of polyols dramatically increases upon metal complexation in the order Zn2+ > Mg2+ > Ca2+. For example, the three H-site positions in the hydroxyl groups of the heptaol, bound to Zn2+, are 11.2, 29.9, and 30.9 pKa units (in methanol) more acidic than those of pure heptaol. This acidity enhancement leads to making polyols as good ligands toward complexation. For instance, the formation constants of the heptaol in the presence of Zn2+, Mg2+,... 

    Single-centered hydrogen-bonded enhanced acidity (SHEA) acids: a new class of Bronsted acids

    , Article Journal of the American Chemical Society ; Volume 131, Issue 46 , 2009 , Pages 16984-16988 ; 00027863 (ISSN) Tian, Z ; Fattahi, A ; Lis, L ; Kass, S. R ; Sharif University of Technology
    Hydrogen bonds are the dominant motif for organizing the three-dimensional structures of biomolecules such as carbohydrates, nucleic acids, and proteins, and serve as templates for proton transfer reactions. Computations, gas-phase acidity measurements, and pKa determinations in dimethyl sulfoxide on a series of polyols indicate that multiple hydrogen bonds to a single charged center lead to greatly enhanced acidities. A new class of Brønsted acids, consequently, is proposed. © 2009 American Chemical Society  

    Comparison between two different hemichromes of hemoglobins (HbA and HbS) induced by n-dodecyl trimethylammonium bromide: Chemometric study

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 63, Issue 2 , 2008 , Pages 183-191 ; 09277765 (ISSN) Mojtahedi, M ; Parastar, H ; Jalali Heravi, M ; Chamani, J ; Chilaka, F. C ; Moosavi Movahedi, A. A ; Sharif University of Technology
    The interaction of n-dodecyl trimethylammonium bromide (DTAB) with oxyhemoglobin A and oxyhemoglobin S is investigated using UV-visible absorption spectra and chemometric resolution techniques. Oxyhemoglobins (A and S) induced to partial oxidized form (ferrihemoglobin) by DTAB and finally transform to fully oxidized hemichrome. Hemichrome mole fractions of HbS are more than HbA because of more hydrophobic interaction of DTAB-HbS in second set of binding site relative to DTAB-HbA. The visible spectra between 500 and 650 nm are used for identifying the present components in solution because each species of hemoglobin has a specific spectrum in this region. The number of components and mole... 

    H 2 adsorption mechanism in Mg modified multi-walled carbon nanotubes for hydrogen storage

    , Article International Journal of Hydrogen Energy ; Volume 37, Issue 2 , January , 2012 , Pages 1919-1926 ; 03603199 (ISSN) Reyhani, A ; Mortazavi, S. Z ; Mirershadi, S ; Golikand, A. N ; Moshfegh, A. Z ; Sharif University of Technology
    Multi-walled carbon nanotubes (MWCNTs) with diameter of about 50 nm were synthesized using thermal chemical vapor deposition. We have investigated the influence of Mg doping to the MWCNTs on its hydrogen storage property. TEM micrographs showed that Mg was attached to the MWCNTs and discontinuous arrangement of the carbon walls was recognized in the MWCNTs. According to XPS and BET analyses, the surface functional groups and pore size of the Mg-MWCNTs are increased by interactions between the Mg and the MWCNT's outer walls. The electrochemical discharging curves of the MWCNTs and Mg-doped MWCNTs revealed that the hydrogen storage capacity was 363 and 450 mAhg -1, respectively. Volumetric...