Sharif Digital Repository

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... 

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... 

Dilational and shear viscoelasticities are important properties of interfacial layers. These quantities are particularly relevant in all systems which contain a huge internal interfacial area such as foams and emulsions. Therefore, also the 3D rheological behavior of foams or emulsions studied by respective methods is superimposed by the 2D interfacial rheology.We report on recent developments in dilational and shear rheology from an experimental point of view as well as discuss the state of the art of the underlying theories. Examples of most relevant experiments are also presented and discussed. Although not yet extensively investigated, the links between bulk rheology of foams and... 

Bridgehead C-H bond dissociation enthalpies of 105.7 ± 2.0, 102.9 ± 1.7, and 102.4 ± 1.9 kcal mol -1 for bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, and adamantane, respectively, were determined in the gas phase by making use of a thermodynamic cycle (i.e., BDE(R-H) = ΔH° acid(H-X) - IE(H •) + EA(X •)). These results are in good accord with high-level G3 theory calculations, and the experimental values along with G3 predictions for bicyclo[1.1.1]pentane, bicyclo[2.1.1]hexane, bicyclo[3.1.1]heptane, and bicyclo[4.2.1]nonane were found to correlate with the flexibility of the ring system. Rare examples of alkyl anions in the gas phase are also provided  

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... 

Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with... 

Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of upmost importance in the living cell. Thymol derivatives exhibit various antioxidant activities and potential health benefits. Exploration of structure-radical scavenging activity (SAR) was approached with a wide range of thymol derivatives. To accomplish this task, the DPPH experimental assay along with quantum-chemical calculations were also employed for these compounds. By comparing the structural properties of the derivatives of interest, their antioxidant activity was explained by the formation of an intramolecular hydrogen bond and the presence of unsaturated double bond (–CHdouble bond; length... 

Surface functionality of nanoparticles has been pivotal in defining interactions of nanoparticles and biomolecules. To explore various functionalities on the surface of nanoparticle through a facile procedure, various carbon-based nanoparticles, modified with a specific natural amino acid, were synthesized; the amino acids were chosen in order that almost all classes of amino acids were included. After characterizations of the nanoparticles using several spectroscopic methods, the effects of surface modification of nanoparticles were examined against amyloid formation, exploiting insulin as a model amyloidogenic polypeptide. Although most amino acids afforded carbon nanoparticles, only... 

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... 

Chondroitinase ABC I (cABC I) has received notable attention in treatment of spinal cord injuries and its application as therapeutics has been limited due to low thermal stability at physiological temperature. In this study, cABC I enzyme was immobilized on the dextran-coated Fe3O4 nanoparticles through physical adsorption to improve the thermal stability. The nanoparticles were characterized using XRD, SEM, VSM, and FTIR analyses. Response surface methodology and central composite design were employed to assess factors affecting the activity of immobilized cABC I. Experimental results showed that pH 6.3, temperature 24 °C, enzyme/support mass ratio 1.27, and incubation time 5.7 h were the...