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protein-structure
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Study of Enzyme (Chymotrypsin) -Core/Shell (Fe3O4 @ Au) Nanoparticle Bioconjugate
, M.Sc. Thesis Sharif University of Technology ; 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...
Failure tolerance of motif structure in biological networks
, Article PLoS ONE ; Volume 6, Issue 5 , May , 2011 ; 19326203 (ISSN) ; Jalili, M ; Sharif University of Technology
2011
Abstract
Complex networks serve as generic models for many biological systems that have been shown to share a number of common structural properties such as power-law degree distribution and small-worldness. Real-world networks are composed of building blocks called motifs that are indeed specific subgraphs of (usually) small number of nodes. Network motifs are important in the functionality of complex networks, and the role of some motifs such as feed-forward loop in many biological networks has been heavily studied. On the other hand, many biological networks have shown some degrees of robustness in terms of their efficiency and connectedness against failures in their components. In this paper we...
Protein Function Prediction Using Protein Structure and Computational Methods
, M.Sc. Thesis Sharif University of Technology ; Fatemizadeh, Emad (Supervisor) ; Arab, Shahriar ($item.subfieldsMap.e)
Abstract
Predicting the Amino Acids that have a catalytic effect in the enzymes, is a big step in appointing the activity of the enzymes and classifying them. This is a very challenging job, because an Amino Acid can appear in a variety of active sites.The biological activity of a protein usually depends on the existence of a small number of Amino Acids. Detecting these Amino Acids from the sequence of Amino Acids has many applications. Usually, the Amino Acids that are preserved are known as the Amino Acids that build up the active site, but the algorithms for finding the preserved Amino Acids are much more complex. There are a lot of algorithms for predicting the active sites of Amino Acids, but...
Theoretical Prediction of Free-Energy for Complex Macromolecules Self-Assembly
, M.Sc. Thesis Sharif University of Technology ; Tafazzoli, Mohsen (Supervisor) ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
These days, self-assembly is one of the most significant phenomena in chemistry and biology. Although There are some Experiments and Simulations which help us to understand self-assembly much more than before, their mechanism is poorly understood. As a result, Calculating Free-energy landscape could be a great development in this area.We use the Flat-histogram monte Carlo algorithm to calculate the density of states of a complex system. In this way, there is a comparison between the exact density of states of Ising Model and the same quantities that are obtained from Flat histogram Method. After that, there would be a combination of statistical thermodynamics and Graph theory toward drawing...
Evolution of 'ligand-deffusion chreodes' on protein-surface models: A genetic-algorithm study
, Article Chemistry and Biodiversity ; Volume 4, Issue 12 , 2007 , Pages 2766-2771 ; 16121872 (ISSN) ; Kargar, M ; Katanforoush, A ; Abolhassani, H ; Sadeghi, M ; Sharif University of Technology
2007
Abstract
Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed. © 2007 Verlag Helvetica Chimica Acta AG, Zürich
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...
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) ; Mashayekhan, S ; Shabani, I ; Khorashadizadeh, M ; Fallah, A ; Soleimani, M ; Sharif University of Technology
Elsevier
2015
Abstract
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...
The Effect of Hydrophobic Mismatch and Rigidity of Protein on the Cluster Formation of Transmembrane Proteins in Biomembranes
, M.Sc. Thesis Sharif University of Technology ; Ahmadiyan, Mohammad Taghi (Supervisor) ; Jalali, Mir Abbas (Co-Advisor) ; Khoshnood, Atefeh (Co-Advisor)
Abstract
Membrane proteins aggregation is a very important biological phenomenon in a variety of cell functions. It has been suggested that aggregation behavior of membrane proteins is influenced by the shape of the hydrophobic domain of the proteins, proteins hydrophobic mismatch and bilayer curvature. However, in this study by means of coarse grained membrane simulations it has been found that in thermal equilibrium, protein-protein interactions also depend on protein rigidity and structural strength. Based on simulation results, we have observed stable large clusters even in the absence of hydrophobic mismatch between lipids and proteins. Interestingly, our results also indicate that proteins with...
Electrostatically defying cation-cation clusters: Can likes attract in a low-polarity environment?
, Article Journal of Physical Chemistry A ; Volume 117, Issue 38 , 2013 , Pages 9252-9258 ; 10895639 (ISSN) ; Ramezani, M ; Fattahi, A ; Kass, S. R ; Sharif University of Technology
2013
Abstract
Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the...
FBAR Syndapin 1 recognizes and stabilizes highly curved tubular membranes in a concentration dependent manner
, Article Scientific Reports ; Volume 3 , 2013 ; 20452322 (ISSN) ; Baroji, Y. F ; S. Reihani, S. Nader ; Stamou, D ; Oddershede, L. B ; Bendix, P. M ; Sharif University of Technology
2013
Abstract
Syndapin 1 FBAR, a member of the Bin-amphiphysin-Rvs (BAR) domain protein family, is known to induce membrane curvature and is an essential component in biological processes like endocytosis and formation and growth of neurites. We quantify the curvature sensing of FBAR on reconstituted porcine brain lipid vesicles and show that it senses membrane curvature at low density whereas it induces and reinforces tube stiffness at higher density. FBAR strongly up-concentrates on the high curvature tubes pulled out of Giant Unilamellar lipid Vesicles (GUVs), this sorting behavior is strongly amplified at low protein densities. Interestingly, FBAR from syndapin 1 has a large affinity for tubular...
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) ; Ebrahimi, H. P ; Fathi, F ; Bahrami Panah, N ; Jalali Heravi, M ; Tafazzoli, M ; Sharif University of Technology
John Wiley and Sons Inc
2016
Abstract
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...
Nano reengineering of horseradish peroxidase with dendritic macromolecules for stability enhancement
, Article Enzyme and Microbial Technology ; Volume 50, Issue 1 , 2012 , Pages 10-16 ; 01410229 (ISSN) ; Vossoughi, M ; Shahrokhian, S ; Alemzadeh, I ; Sharif University of Technology
Abstract
A simple bio-conjugation procedure to surround a single horseradish peroxidase (HRP) enzyme molecule with dendritic polyester macromolecules (polyester-32-hydroxyl-1-carboxyl bis-MPA dendron, generation 5) was proposed. The characterization of resultant nanoparticles entitled HRP dendrozyme, was performed by transmission electron microscopy, dynamic light scattering, gel permeation chromatography and Fourier transform infrared spectroscopy. The results showed that HRP nanoparticles were spherical in shape and have an average size of 14 ± 2. nm in diameter. Furthermore, bio-conformational characterization of HRP dendrozyme was performed by means of circular dichroism and fluorescence...
Gating and conduction of nano-channel forming proteins: A computational approach
, Article Journal of Biomolecular Structure and Dynamics ; Volume 31, Issue 8 , 2013 , Pages 818-828 ; 07391102 (ISSN) ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
2013
Abstract
Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used...
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) ; Shamloo, A ; Sharif University of Technology
American Chemical Society
2019
Abstract
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...
Artificial neural network aided estimation of the electrochemical signals of monosaccharides on gold electrode
, Article Carbohydrate Research ; Volume 343, Issue 8 , 2008 , Pages 1359-1365 ; 00086215 (ISSN) ; Sadeghpour Dilmaghani, A ; Sharif University of Technology
2008
Abstract
Artificial neural networks were used to predict the oxidation peaks potentials of 7 monosaccharides under linear sweep voltammetry regime. Two sets of descriptors, one based on molecular properties calculated through DFT and another based on simple geometric distributions of hydroxyl groups and asymmetric carbon atoms along molecular chains, were employed to introduce the molecules to networks. Relatively, simple networks of (3,3,1) and (3,3,3,1) structures with the number of epochs not exceeding 15 through training process were capable of correctly predicting the peaks positions with R values in the range of 0.97-0.99. © 2008 Elsevier Ltd. All rights reserved
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) ; Farzami, R. R ; Ejtehadi, M. R ; Sharif University of Technology
2005
Abstract
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...
Plant protein-based hydrophobic fine and ultrafine carrier particles in drug delivery systems
, Article Critical Reviews in Biotechnology ; Volume 38, Issue 1 , 2018 , Pages 47-67 ; 07388551 (ISSN) ; Mirshekari, H ; Sahandi Zangabad, P ; Moosavi Basri, S. M ; Baniasadi, F ; Sharifi Aghdam, M ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
Taylor and Francis Ltd
2018
Abstract
For thousands of years, plants and their products have been used as the mainstay of medicinal therapy. In recent years, besides attempts to isolate the active ingredients of medicinal plants, other new applications of plant products, such as their use to prepare drug delivery vehicles, have been discovered. Nanobiotechnology is a branch of pharmacology that can provide new approaches for drug delivery by the preparation of biocompatible carrier nanoparticles (NPs). In this article, we review recent studies with four important plant proteins that have been used as carriers for targeted delivery of drugs and genes. Zein is a water-insoluble protein from maize; Gliadin is a 70% alcohol-soluble...
Targeting AMPK signaling pathway by natural products for treatment of diabetes mellitus and its complications
, Article Journal of Cellular Physiology ; Volume 234, Issue 10 , 2019 , Pages 17212-17231 ; 00219541 (ISSN) ; Singh, A. K ; Haratipour, P ; Sah, A. N ; Pandey, A. K ; Naseri, R ; Juyal, V ; Farzaei, M. H ; Sharif University of Technology
Wiley-Liss Inc
2019
Abstract
Diabetes affects a large population of the world. Lifestyle, obesity, dietary habits, and genetic factors contribute to this metabolic disease. A target pathway to control diabetes is the 5′-adenosine monophosphate-activated protein kinase (AMPK) signaling pathway. AMPK is a heterotrimeric protein with α, β, and γ subunits. In several studies, AMPK activation enhanced glucose uptake into cells and inhibited intracellular glucose production. Impairment of AMPK activity is present in diabetes, according to some studies. Drugs used in the treatment of diabetes, such as metformin, are also known to act through regulation of AMPK. Thus, drugs that activate and regulate AMPK are potential...
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...
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...