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Increase in the β-sheet character of an amyloidogenic peptide upon adsorption onto gold and silver surfaces
, Article ChemPhysChem ; Volume 18, Issue 5 , 2017 , Pages 526-536 ; 14394235 (ISSN) ; Gholami, M. R ; Sharif University of Technology
Wiley-VCH Verlag
2017
Abstract
Fibrillation of amyloid beta (Aβ) peptide is the hallmark of Alzheimer's disease. Given that interactions at the bio–nano interface affect the fibrillation tendency of this peptide, an understanding of the interactions at Aβ peptide–inorganic surfaces on the microscopic level can help to determine the possible neurotoxicity of nanoparticles. Here, the interactions between a fibril-forming peptide, Aβ25–35, and (111) and (100) facets of gold and silver surfaces have been studied by conducting atomistic molecular dynamics simulations. The obtained results indicate that the adsorption onto gold and silver surfaces force the peptide into the β-sheet-rich conformations, which is prone to...
The non-significant benefit of BCG vaccination for the treatment of iranian patients with type 1 diabetes up to 48 weeks: a controversial result
, Article Medical Journal of the Islamic Republic of Iran ; Volume 35, Issue 1 , 2021 , Pages 1-5 ; 10161430 (ISSN) ; Zarei, P ; Shakerian, B ; Babaei, M ; Mostafavi, A ; Modaressi, M ; Sharif University of Technology
Iran University of Medical Sciences
2021
Abstract
Background: There has been considerable interest in target immunotherapy in patients with diabetes. This study was designed to identify the effect of BCG vaccination in the treatment of Iranian patients with longstanding diabetes mellitus type 1. Methods: After approval of the cross-sectional study protocol by the ethics committee under number IRCT2017042919940N2, a total of 19 Iranian volunteers with diabetes mellitus type 1 completed this 48-month study. These patients received three 0.1 ml intradermal injections of BCG vaccination in weeks 0, 4 and 24. The serum level of glucose, HgbA1C and c-peptide was measured before and serially after the interventions. Insulin requirements were...
Immobilization of modular peptides on graphene cocktail for differentiation of human mesenchymal stem cells to hepatic-like cells
, Article Frontiers in Chemistry ; Volume 10 , 2022 ; 22962646 (ISSN) ; Hashemi, E ; Akhavan, O ; Khezri, J ; Rezaei, A ; Zamani Amir Zakria, J ; Siadat, S. D ; Sahebghadam Lotfi, A ; Farmany, A ; Sharif University of Technology
Frontiers Media S.A
2022
Abstract
In this study, two novel biomimetic modular peptide motifs based on the alpha-2 subunit of type IV collagen (CO4A2) were designed and immobilized on a graphene platform to imitate integrin and heparan sulfate- (HS-) binding proteins. The in silico study was used to design 9-mer K[KGDRGD]AG and 10-mer KK[SGDRGD]AG for testing designed Integrin-Binding Peptide (dIBP) and HS-Binding Peptide (dHBP). The virtual docking technique was used to optimize the peptide motifs and their relevant receptors. Molecular dynamic (MD) simulation was used to evaluate the stability of peptide-receptor complexes. The effect of the platform on the differentiation of human mesenchymal stem cells (hMSCs) to...
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...
Expression and Purification of Amyloid Beta Recombinant Peptide and the Effecs of Ultrasmall Peptides Enriched in Branch Chain Amino Acids as Inhibitors in Amyloid Formation
, M.Sc. Thesis Sharif University of Technology ; Kalhor, Hamid Reza (Supervisor)
Abstract
Nowdays, it has been shown that protein misfolding is involved in more than forty diseases including Alzheimer’s and Parkinson’s. Alzheimer’s disease is one of the most common neurodegenerative diseases that disrupts brain function. The main cause of this illness is due to formation of extracellular amyloid plaque from a 42-amino acid-peptide called amyloid beta. Amyloidosis is caused by missfolding of peptides and proteins mainly because of physical and chemical changes in biomolecule or their environment.
Therefore, in this dissertation, using synthetic and recombinant abeta peptide, kinetic of amyloidosis was examined. Ultrasmall peptides (three-amino acid), containing branched chain...
Therefore, in this dissertation, using synthetic and recombinant abeta peptide, kinetic of amyloidosis was examined. Ultrasmall peptides (three-amino acid), containing branched chain...
Evaluation of Plasmid Transmission in Bacillus Subtilis by Cell Wall Modification
, M.Sc. Thesis Sharif University of Technology ; Roosta Azad, Reza (Supervisor) ; Aghamollaei, Hossein (Supervisor)
Abstract
Today, almost all the country's needs in the field of industrial enzymes are met through imports. In this regard, much attention has been paid to the industrial production of various enzymes in the country. The production of recombinant proteins through strain engineering is one of the most important ways to meet this demand due to its many benefits. One of the most important microorganisms that is widely used in the enzyme industry is Bacillus subtilis. Due to its thick peptidoglycan wall, this gram-positive bacterium hardly accepts engineered carriers for genetic modification as hosts. The aim of this study was to evaluate the permeability of the wall and cell membrane of Bacillus subtilis...
Linear and Non-Linear Modeling of Electrophoretic Mobility of Peptides
,
M.Sc. Thesis
Sharif University of Technology
;
Jalali Heravi, Mehdi
(Supervisor)
Abstract
Regarding the importance of biological systems in daily life and the complexity of these systems, this project is concerned with this problem and especially with applications of chemometrics in proteomics. In this respect, specific importance of peptides has been taken into account in the process of construction of especial and necessary proteins for human body. Due to the risks involved in some experimental investigations, it is quite preferable to utilize modeling approaches using different sets of data. Achieving a number of specific descriptors, a powerful can be established. This model could be quiet comprehensive for the prediction of the electrophoretic mobility of peptides. This...
Evaluating the multifunctionality of a new modulator of zinc-induced Aβ aggregation using a novel computational approach
, Article Journal of Chemical Information and Modeling ; Volume 61, Issue 3 , 2021 , Pages 1383-1401 ; 15499596 (ISSN) ; Shamloo, A ; Sharif University of Technology
American Chemical Society
2021
Abstract
The high concentration of zinc metal ions in Aβ aggregations is one of the most cited hallmarks of Alzheimer's disease (AD), and several substantial pieces of evidence emphasize the key role of zinc metal ions in the pathogenesis of AD. In this study, while designing a multifunctional peptide for simultaneous targeting Aβ aggregation and chelating the zinc metal ion, a novel and comprehensive approach is introduced for evaluating the multifunctionality of a multifunctional drugs based on computational methods. The multifunctional peptide consists of inhibitor and chelator domains, which are included in the C-terminal hydrophobic region of Aβ, and the first four amino acids of human albumin....
Three-body interactions improve the prediction of rate and mechanism in protein folding models
, Article Proceedings of the National Academy of Sciences of the United States of America ; Volume 101, Issue 42 , 2004 , Pages 15088-15093 ; 00278424 (ISSN) ; Avall, S. P ; Plotkin, S. S ; Sharif University of Technology
2004
Abstract
Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained Cα-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Gō-like Hamiltonian with native pairwise interactions only, we have found (i) a significantly increased correlation with experimental φ values and folding rates, (ii) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ≈20%, and (iii) a considerably larger amount of three-body energy present in chymotripsin...
Dynamics of antimicrobial peptide encapsulation in carbon nanotubes: the role of hydroxylation
, Article International Journal of Nanomedicine ; Volume 17 , 2022 , Pages 125-136 ; 11769114 (ISSN) ; Yousefi, F ; Seidi, F ; Sajadi, S. M ; Rabiee, N ; Habibzadeh, S ; Esmaeili, A ; Mashhadzadeh, A. H ; Spitas, C ; Mostafavi, E ; Saeb, M. R ; Sharif University of Technology
Dove Medical Press Ltd
2022
Abstract
Introduction: Carbon nanotubes (CNTs) have been widely employed as biomolecule carriers, but there is a need for further functionalization to broaden their therapeutic application in aqueous environments. A few reports have unraveled biomolecule–CNT interactions as a measure of response of the nanocarrier to drug-encapsulation dynamics. Methods: Herein, the dynamics of encapsulation of the antimicrobial peptide HA-FD-13 (accession code 2L24) into CNTs and hydroxylated CNTs (HCNTs) is discussed. Results: The van der Waals (vdW) interaction energy of CNT–peptide and HCNT–peptide complexes decreased, reaching −110.6 and −176.8 kcal.Mol−1, respectively, once encapsulation of the peptide inside...
Mechanism Investigation of Metallic Nanoparticles Interaction with Biological Molecules using Molecular Dynamic Simulation
, M.Sc. Thesis Sharif University of Technology ; Gholami, Mohammad Reza (Supervisor)
Abstract
Amyloid β (Aβ) peptide is believed to be associated with the progression of Alzheimer's disease. One of the main obstacles in developments of therapeutic agents to combat progression of Alzheimer's disease, is the presence of the blood–brain barrier (BBB), which prevents the penetration of the majority of drugs. However, nanoscale objects are able to cross the BBB at low concentrations. Therefore, it is worthwhile to study the interactions of these peptides at the interface of nanomaterials. In this work we have employed molecular dynamics, and weighted histogram analysis methods in order to study the dynamic behavior and affinity of Aβ25-35 peptide on metallic surfaces of different...
High antimicrobial activity and low human cell cytotoxicity of core-shell magnetic nanoparticles functionalized with an Antimicrobial Peptide
, Article ACS Applied Materials and Interfaces ; Volume 8, Issue 18 , 2016 , Pages 11366-11378 ; 19448244 (ISSN) ; Rai, A ; Pinto, S ; Evangelista, M ; Cardoso, R. M. S ; Paulo, C ; Carvalheiro, T ; Paiva, A ; Imani, M ; Simchi, A ; Durães, L ; Portugal, A ; Ferreira, L ; Sharif University of Technology
American Chemical Society
2016
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) functionalized with antimicrobial agents are promising infection-targeted therapeutic platforms when coupled with external magnetic stimuli. These antimicrobial nanoparticles (NPs) may offer advantages in fighting intracellular pathogens as well as biomaterial-associated infections. This requires the development of NPs with high antimicrobial activity without interfering with the biology of mammalian cells. Here, we report the preparation of biocompatible antimicrobial SPION@gold core-shell NPs based on covalent immobilization of the antimicrobial peptide (AMP) cecropin melittin (CM) (the conjugate is named AMP-NP). The minimal inhibitory...
Investigation of the interactions between Melittin and the PLGA and PLA polymers: Molecular dynamic simulation and binding free energy calculation
, Article Materials Research Express ; Volume 6, Issue 5 , 2019 ; 20531591 (ISSN) ; Moosavi, A ; Sharif University of Technology
Institute of Physics Publishing
2019
Abstract
Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could...
Investigation of the interactions between Melittin and the PLGA and PLA polymers: Molecular dynamic simulation and binding free energy calculation
, Article Materials Research Express ; Volume 6, Issue 5 , 2019 ; 20531591 (ISSN) ; Moosavi, A ; Sharif University of Technology
Institute of Physics Publishing
2019
Abstract
Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could...
Mechanical characteristics of SPG-178 hydrogels: Optimizing viscoelastic properties through microrheology and response surface methodology
, Article Iranian Biomedical Journal ; Volume 24, Issue 2 , 2020 , Pages 110-118 ; Mirzadeh, H ; Mohammadi, A ; Bagheri Khoulenjani, S ; Sharif University of Technology
Pasteur Institute of Iran
2020
Abstract
Background: SApeptides have growing applications in tissue engineering and regenerative medicine. The application of SApeptide-based hydrogels depends strongly on their viscoelastic properties. Optimizing the properties is of importance in tuning the characteristics of the hydrogels for a variety of applications. Methods: In this study, we employed statistical modeling, conducted with the RSM and particle tracking microrheology, to investigate the effects of self-assembling SPG-178 peptide and added NaCl salt concentrations and milieu type (DI water or blood serum) on the viscoelastic properties of SPG-178 hydrogels. A central composite RSM model was employed for finding the optimum value of...
Correlation and prediction the activity coefficients and solubility of amino acids and simple peptide in aqueous solution using the modified local composition model
, Article Fluid Phase Equilibria ; Volume 255, Issue 2 , 2007 , Pages 160-166 ; 03783812 (ISSN) ; Taghikhani, V ; Vossoughi, M ; Sharif University of Technology
2007
Abstract
In this work, the modified Wilson model was used to obtain the activity coefficients of amino acids and simple peptides in non-electrolyte aqueous solutions. The Wilson model was modified using the new local mole fraction proposed by Zhao et al. and non-random case for the reference state. The binary interaction parameters (BIP) of the modified Wilson model for amino acid-water pairs were obtained using the experimental data of the activity coefficients for amino acids available in the literature. The modified Wilson model was also used to correlate the solubility of amino acids in water and the values of Δh/R, Δs/R, and Δg/R of the solutions studied were reported. The results obtained...
Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides
, Article Journal of Colloid and Interface Science ; Volume 606 , 2022 , Pages 2038-2050 ; 00219797 (ISSN) ; Hosseini, A ; Loloee, R ; Perry, G ; Lee, K. B ; Lund, M ; Ejtehadi, M. R ; Mahmoudi, M ; Sharif University of Technology
Academic Press Inc
2022
Abstract
We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (C6H12O2S) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (AuTS) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of AuTS/linker/tau//Ga2O3/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide. Quantum mechanical simulation...
Label-free detection of β-amyloid peptides (Aβ40 and Aβ42): a colorimetric sensor array for plasma monitoring of alzheimer's disease
, Article Nanoscale ; Volume 10, Issue 14 , 2018 , Pages 6361-6368 ; 20403364 (ISSN) ; Hormozi Nezhad, M. R ; Mahmoudi, M ; Sharif University of Technology
Royal Society of Chemistry
2018
Abstract
Monitoring the ratio of 40- and 42-residue amyloid β peptides (i.e., Aβ40 and Aβ42) in human plasma is considered one of the hallmarks of detection of the early stage of Alzheimer's disease (AD). Therefore, development of a specific, yet non-antibody-based method for simultaneous detection of Aβ40 and Aβ42 may have considerable clinical applications. Here, we developed a 'nanoparticle-based colorimetric sensor array' utilizing label-free gold and silver nanoparticles for visual detection of Aβ42 and Aβ40. Different aggregation behaviors of nanoparticles through their conjugation with Aβ42 and Aβ40 followed by the coordination of Aβ42 and Aβ40 with Cu(ii) led to diverse spectral and color...
Artificial neural network modeling of peptide mobility and peptide mapping in capillary zone electrophoresis
, Article Journal of Chromatography A ; Volume 1096, Issue 1-2 , 2005 , Pages 58-68 ; 00219673 (ISSN) ; Shen, Y ; Hassanisadi, M ; Khaledi, M. G ; Sharif University of Technology
2005
Abstract
Recently, we have developed an artificial neural network model, which was able to predict accurately the electrophoretic mobilities of relatively small peptides. To examine the robustness of this methodology, a 3-3-1 back-propagation artificial neural network (BP-ANN) model was developed using the same inputs as the previous model, which were the Offord's charge over mass term (Q/M2/3), corrected steric substituent constant (E s,c) and molar refractivity (MR). The data set consisted of 102 peptides with a larger range of size than that of our earlier report - up to 42 amino acid residues as compared to 13 amino acids in the initial study - that also included highly charged and hydrophobic...
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...