Sharif Digital Repository

Prediction of the amino acids that have a catalytic effect on the enzymes is a major stage in appointing the activity of the enzymes and classification. The biological activity of a protein usually depends on the existence of a small number of amino acids. Recently, many algorithms have been proposed in the literature for finding these amino acids which are complex and time consuming. In this paper, we will introduce a new method for predicting the active sites that will use the spatial coordinates and the type of amino acids that contain the active sites. In order to increase the speed we use an approximate graph isomorphism algorithm. Furthermore, this algorithm allows us to find several... 

Oxido-peroxido W(VI)-histidine–MgAl-layered double hydroxide composite was prepared by using MgAl-layered double hydroxide as a host and oxido-peroxido W(VI)-histidine complex as a guest. The composite was characterized by XRD, IR, EDX,SEM and TEM techniques. This composite is tested for catalytic selective sulfoxidation reactions using hydrogen peroxide as oxidant showing good to moderate conversion along with high selectivity. Copyright © 2018 John Wiley & Sons, Ltd  

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?... 

LiClO4 is used as catalyst for direct Mannich-type reaction of aryl aldehydes, aryl amines, and diethyl malonic ester under solvent-free conditions. This three-component reaction afforded the corresponding β-amino esters in good yields with simple and environmentally benign procedure. Copyright © Taylor & Francis Group, LLC  

Stabilised titania sols were prepared using an additive free particulate sol-gel route, via electrostatic stabilisation mechanism, with various processing parameters. Peptisation temperature, 50°C and 70°C, and TiO2 concentration, 0.1, 0.2 and 0.4 molar, were chosen as processing parameters during sol preparation. Results from TiO2 particle size and zeta potential of sols revealed that the smallest titania hydrodynamic diameter (13 nm) and the highest zeta potential (47.7 mV) were obtained for the sol produced at the lower peptisation temperature of 50°C and lower TiO 2 concentration of 0.1 M. On the other hand, between the sols prepared at 70°C, smaller titania particles (20 nm) and higher... 

A batch extraction of an essential amino acid, Phenylalanine, from an aqueous solution of different concentrations by an Emulsion Liquid Membrane (ELM) was developed using D2EHPA as a cationic carrier, Span 80 as the surfactant, paraffin and kerosene as the diluents, and HCl as the internal electrolyte. All effective parameters such as pH of initial aqueous external phase, electrolyte concentration in aqueous internal phase, carrier and surfactant concentration in emulsion, volume ratio of the organic to aqueous internal phase (Roi), volume ratio of the W/O emulsion to aqueous external phase (Rew) and time were examined and optimized using Taguchi method which was the first time of... 

A comparative investigation has been developed for the stability constants of several amino acid complexes with divalent metal ions, which have been determined by potentiometric pH titration. Depending on the metal ion-binding properties, vital differences in the building complexes were observed. The present study indicates that in some M(L) complexes, metal ions are arranged in carboxyl groups, but in other M(L)complexes, some metal ions are able to build chelate over amine groups. The results mentioned-above demonstrate that for some M(L) complexes, the stability constants are also largely determined by the affinity of metal ions for amine group. This leads to a kind of selectivity of... 

Metabonomics and other "omic" fields are essential science in analytical chemistry. Modern analytical instruments such as proton nuclear magnetic resonance (1H-NMR) can provide the great quantity of analytical information. In order to assign unknown samples, chemometric methods recognition build classification model based on experimental data. Firstly, some current strategies regarding disease diagnosis are exhibited in metabonomic studies. Some diseases such as crohn's disease can be difficult to diagnose since its signs and symptoms may be similar to other medical problems or often mimic other symptoms. Applications of NMR and supervised pattern recognition in the field of metabonomics are... 

Cell culture feeds optimization is a critical step in process development of pharmaceutical recombinant protein production. Amino acids are the basic supplements of mammalian cell culture feeds with known effect on their growth promotion and productivity. In this study, we reported the implementation of the Plackett-Burman (PB) multifactorial design to screen the effects of amino acids on the growth promotion and productivity of a Chinese hamster ovary DG-44 (CHO-DG44) cell line producing bevacizumab. After this screening, the amino acid combinations were optimized by the response surface methodology (RSM) to determine the most effective concentration in feeds. Through this strategy, the... 

A batch extraction of an essential amino acid, phenylalanine, from an aqueous solution of different concentrations by an Emulsion Liquid Membrane (ELM) was developed using D2EHPA as a cationic carrier, Span 80 as the surfactant, paraffin, and kerosene as the diluents, and HCl as the internal electrolyte. All effective parameters such as the initial pH of the aqueous external phase, the electrolyte concentration in the aqueous internal phase, carrier, and surfactant concentration in the emulsion, the volume ratio of the organic to aqueous internal phase (Roi), the volume ratio of the W/O emulsion to the aqueous external phase (Rew) and time were examined and optimized using the Taguchi... 

Introduction: Nanotube-based drug delivery systems have received considerable attention because of their large internal volume to encapsulate the drug and the ability to penetrate tissues, cells, and bacteria. In this regard, understanding the interaction between the drug and the nanotube to evaluate the encapsulation behavior of the drug in the nanotube is of crucial importance. Methods: In this work, the encapsulation process of the cationic antimicrobial peptide named cRW3 in the biocompatible boron nitride nanotube (BNNT) was investigated under the Canonical ensemble (NVT) by molecular dynamics (MD) simulation. Results: The peptide was absorbed into the BNNT by van der Waals (vdW)... 

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... 

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... 

Statistical and biochemical studies have revealed non-random patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations, since it is known that when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, using altered forms of the fitness functions used in the prior studies, we have optimized the parameters involved in the calculation of the error minimizing property of the genetic code so that the genetic code outscores the random codes as much as possible. This work also... 

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...