Search for: protein-secondary-structure
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    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) Shaghaghi, H ; Ebrahimi, H. P ; Fathi, F ; Bahrami Panah, N ; Jalali Heravi, M ; Tafazzoli, M ; Sharif University of Technology
    John Wiley and Sons Inc  2016
    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... 

    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
    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.... 

    Design and physicochemical characterization of lysozyme loaded niosomal formulations as a new controlled delivery system

    , Article Pharmaceutical Chemistry Journal ; Volume 53, Issue 10 , 2020 , Pages 921-930 Sadeghi, S ; Ehsani, P ; Cohan, R. A ; Sardari, S ; Akbarzadeh, I ; Bakhshandeh, H ; Norouzian, D ; Sharif University of Technology
    Springer  2020
    Lysozyme loaded niosomes containing various molar ratios of two kinds of surfactants were prepared and the properties of these niosomal formulations were studied. The results revealed that the size of niosomes varied between 240.06 ± 32.41 and 895.2 ± 20.84 nm. Formulations with the lowest size and no precipitation had entrapment efficiencies ranging from 60.644 ± 3.310 to 66.333 ± 1.98%. Their controlled release profiles after 48 h were 15.67, 20.67 and 31.50%. After 2 months, the most stable formulation in terms of size, PDI, zeta potential, and entrapment efficiency was used to study the secondary structures of lysozyme in niosomal and free forms. Lysozyme loaded niosome and lysozyme... 

    Nanomechanics of actin filament: a molecular dynamics simulation

    , Article Cytoskeleton ; Volume 75, Issue 3 , March , 2018 , Pages 118-130 ; 19493584 (ISSN) Shamloo, A ; Mehrafrooz, B ; Sharif University of Technology
    John Wiley and Sons Inc  2018
    Actin is known as the most abundant essentially protein in eukaryotic cells. Actin plays a crucial role in many cellular processes involving mechanical forces such as cell motility, adhesion, muscle contraction, and intracellular transport. However, little is known about the mechanical properties of this protein when subjected to mechanical forces in cellular processes. In this article, a series of large-scale molecular dynamics simulations are carried out to elucidate nanomechanical behavior such as elastic and viscoelastic properties of a single actin filament. Here, we used two individual methods namely, all-atoms and coarse-grained molecular dynamics, to evaluate elastic properties of a... 

    Identification of a novel multifunctional ligand for simultaneous inhibition of amyloid-beta (aβ42) and chelation of zinc metal ion

    , Article ACS Chemical Neuroscience ; Volume 10, Issue 11 , 2019 , Pages 4619-4632 ; 19487193 (ISSN) Asadbegi, M ; Shamloo, A ; Sharif University of Technology
    American Chemical Society  2019
    Zinc binding to β-amyloid structure could promote amyloid-β aggregation, as well as reactive oxygen species (ROS) production, as suggested in many experimental and theoretical studies. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. The present study has evaluated the efficacy of a new bifunctional peptide drug using molecular docking and molecular dynamics (MD) simulations. This drug comprises two different domains, an inhibitor domain, obtained from the C-terminal hydrophobic region of Aβ, and a Zn2+ chelating domain, derived from rapeseed meal, merge with a... 

    Design of peptide-based inhibitor agent against amyloid-β aggregation: Molecular docking, synthesis and in vitro evaluation

    , Article Bioorganic Chemistry ; Volume 102 , September , 2020 Jokar, S ; Erfani, M ; Bavi, O ; Khazaei, S ; Sharifzadeh, M ; Hajiramezanali, M ; Beiki, D ; Shamloo, A ; Sharif University of Technology
    Academic Press Inc  2020
    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... 

    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 Khodabakhsh, F ; 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
    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... 

    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) Gharagozlou, M ; Mohammadi Boghaei, D ; Sharif University of Technology
    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... 

    Structural stability and sustained release of protein from a multilayer nanofiber/nanoparticle composite

    , Article International Journal of Biological Macromolecules ; Volume 75 , April , 2015 , Pages 248-257 ; 01418130 (ISSN) Vakilian, S ; Mashayekhan, S ; Shabani, I ; Khorashadizadeh, M ; Fallah, A ; Soleimani, M ; Sharif University of Technology
    Elsevier  2015
    The cellular microenvironment can be engineered through the utilization of various nano-patterns and matrix-loaded bioactive molecules. In this study, a multilayer system of electrospun scaffold containing chitosan nanoparticles was introduced to overcome the common problems of instability and burst release of proteins from nanofibrous scaffolds. Bovine serum albumin (BSA)-loaded chitosan nanoparticles was fabricated based on ionic gelation interaction between chitosan and sodium tripolyphosphate. Suspension electrospinning was employed to fabricate poly-e{open}-caprolacton (PCL) containing protein-loaded chitosan nanoparticles with a core-shell structure. To obtain the desired scaffold... 

    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?... 

    Interaction of copper(II) complex of compartmental Schiff base ligand N,N′-bis(3-hydroxysalicylidene)ethylenediamine with bovine serum albumin

    , Article Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy ; Volume 66, Issue 3 , 2007 , Pages 650-655 ; 13861425 (ISSN) Boghaei, D. M ; Farvid, S. S ; Gharagozlou, M ; Sharif University of Technology
    Circular dichroism (CD) spectroscopy, cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were used to investigate the interaction between copper(II) complex of compartmental Schiff base ligand (L), N,N′-bis(3-hydroxysalicylidene)ethylenediamine, and bovine serum albumin (BSA) in 0.1 mol dm-3 phosphate buffer solution adjusted to physiological pH 7.0 containing 20% (w/w) dimethylsulfoxide at room temperature. CD spectra show that the interaction of the copper(II) complex with BSA leads to changes in the α-helical content of BSA and therefore changes in secondary structure of the protein with the slight red shift (2 nm) in CD spectra. From the voltammetric data, i.e. changes in... 

    Discovery of a tetracyclic indole alkaloid that postpones fibrillation of hen egg white lysozyme protein

    , Article International Journal of Biological Macromolecules ; Volume 183 , 2021 , Pages 1939-1947 ; 01418130 (ISSN) Ashrafian, H ; Zadeh, E.H ; Tajbakhsh, M ; Majid, N ; Srivastava, G.N ; Khan, R.H ; Sharif University of Technology
    Elsevier B.V  2021
    Protein aggregation, such as amyloid fibril formation, is molecular hallmark of many neurodegenerative disorders including Alzheimer's, Parkinson's, and Prion disease. Indole alkaloids are well-known as the compounds having the ability to inhibit protein fibrillation. In this study, we experimentally and computationally have investigated the anti-amyloid property of a derivative of a synthesized tetracyclic indole alkaloid (TCIA), possessing capable functional groups. The fibrillation reaction of Hen White Egg Lysozyme (HEWL) was performed in absence and presence of the indole alkaloid. For quantitative analysis, we used Thioflovin T binding assay which showed ~50% reduction in fibril... 

    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) Khodabakhsh, F ; Norouzian, D ; Vaziri, B ; Ahangari Cohan, R ; Sardari, S ; Mahboudi, F ; Behdani, M ; Mansouri, K ; Mehdizadeh, A ; Sharif University of Technology
    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...