Sharif Digital Repository

Bio-sequence comparators are one of the most basic and significant methods for assessing biological data, and so, due to the importance of proteins, protein sequence comparators are particularly crucial. On the other hand, the complexity of the problem, the growing number of extracted protein sequences, and the growth of studies and data analysis applications addressing protein sequences have necessitated the development of a rapid and accurate approach to account for the complexities in this field. As a result, we propose a protein sequence comparison approach, called PCV, which improves comparison accuracy by producing vectors that encode sequence data as well as physicochemical properties... 

The existence of nonrandom patterns in codon assignments is supported by many statistical and biochemical studies. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations. For example, it is known that when an error induces the conversion of an amino acid to another, the biochemical properties of the resulting amino acid are usually very similar to that of the original. Prior studies include many attempts at quantitative estimation of the fraction of randomly generated codes which, based upon load minimization, score higher than the canonical genetic code. In this study, we took into consideration both the relative... 

A new two-parameter model based on the perturbation of a hard-sphere reference has been developed to correlate the activity coefficients of several amino acids and simple peptides in aqueous solutions. The hard-sphere equation of state used as the reference in the model was proposed recently by Ghotbi and Vera. The perturbation terms coupled with the reference hard-sphere equation of state are attributed to the dispersion forces and the dipole-dipole interactions. The Lennard-Jones and Keesom potential functions are used to represent the dispersion and dipole-dipole interactions, respectively. The results of the new model are compared with those obtained by other models. It is shown that the... 

The main aim of this paper was to study the effect of a new tripodal chelating agent on La1-x Sr x Co1-y Fe y O3-δ perovskite prepared by the complexation method. For this purpose, a phenolic derivative of glycine (L) was synthesized applying the Mannich reaction and characterized by NMR and IR spectroscopies as well as by elemental analysis. To evaluate the complexation capability of L, its formation constants with the perovskite cations were measured. Comparison of these results with those reported for the complexaion with glycine, introduced L as a good candidate for the complexation with Fe(III) and La(III) cations. Furthermore, the powder XRD observations confirmed an improvement in the... 

Three ternary copper(II) complexes [Cu(5-bromo-salTyr)(bipy)]·1/ 2CH3OH (1), [Cu(5-bromo-salLue)(bipy)]·CH3OH (2) and [Cu(5-bromo-salTrp)(bipy)]·3CH3OH (3) (where 5-bromo-salTyr, 5-bromo-salLue and 5-bromo-salTrp are tridentate Schiff base ligands derived from the condensation of 5-bromosalicylaldehyde with tyrosine, leucine and tryptophan, respectively, and bipy is 2,2′-bipyridine) have been prepared and characterized by elemental analysis, electronic, IR spectroscopies, magnetic measurement and cyclic voltammetry. The complexes, 1 and 3 have been also structurally characterized by X-ray diffraction technique. Crystal structures of 1 and 3 complexes displayed a distorted square-pyramidal... 

Electrochemical cells with two ion-selective electrodes, a cation ion-selective electrode against an anion ion-selective electrode, were used to measure the activity coefficient of amino acids in aqueous electrolyte solutions. Activity coefficient data were measured for (H2O + NaBr + glycine) and (H2O + NaBr + L-valine) at T = 298.15 K. The maximum concentrations of sodium bromide, glycine, and L-valine were (1.0, 2.4, and 0.4) mol · kg-1, respectively. The results show that the presence of an electrolyte and the nature of both the cation and the anion of the electrolyte have significant effects on the activity coefficients of amino acid in aqueous electrolyte solutions  

The activity coefficient data were reported for (water + potassium chloride + DL-valine) at T = 298.15 K and (water + sodium chloride + L-valine) at T = 308.15 K. The measurements were performed in an electrochemical cell using ion-selective electrodes. The maximum concentrations of the electrolytes and the amino acids studied were 1.0 molality and 0.4 molality, respectively. The results of the activity coefficients of DL-valine are compared with the activity coefficients of DL-valine in (water + sodium chloride + DL-valine) system obtained from the previous study. The results show that the presence of an electrolyte and the nature of its cation have a significant effect on the activity... 

PIM-1 is a serine-threonine kinase mainly expressed in tissues like the Thymus, spleen, bone marrow, and liver. Overexpression of PIM kinases occurs in various types of human tumours, such as lymphomas, prostate cancer, and oral cancer. As a result, the design of drugs to inhibit PIM-1 in cancerous cells has attracted much attention in recent years. This study aimed to design the alternative inhibitors for PIM-1 kinase, which are based on carbohydrates and amino acids and are expected to be non-toxic with the same chemotherapeutic effects as the traditional known anticancer drugs. The combinatorial use of quantum mechanics (QM) and molecular dynamic simulation (MD) has enabled us to... 

The use of super-swelling polymers is steadily increasing and the applications in industry are continuing to grow. With the authorization of the superabsorbents in food packaging by the Food and Drug Administration recently, demand may soon take off in the market. However, the increase in prices of petroleum products in recent years may be a drawback for these acrylic-based materials. Thus, there is now a need to develop natural-based super-swelling hydrogels which are more economical and environment friendly. In addition, the super-swelling gels are promising novel functions in the biomedical and pharmaceutical applications. This review is aimed to highlight research and trends in protein-... 

Statistical and biochemical studies have revealed nonrandom patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational 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, we have taken into consideration both relative frequencies of amino acids and relative gene copy frequencies of tRNAs in genomic sequences in order to introduce a fitness function which models the mistranslational probabilities more accurately in modern organisms. The... 

DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of... 

Tridentate Schiff-base ligands derived from condensation of 3-formyl-4-hydroxybenzyl-triphenylphosphonium chloride with glycine, L-alanine, L-valine, L-leucine and L-phenylalanine in the presence of Zn(OAc)2·2H2O form five new water-soluble Zn(II) complexes, which were characterized by elemental analyses, IR, electronic absorption and 1H, 13C NMR spectroscopies. In the IR spectra of the complexes, the difference between the asymmetric and the symmetric carboxylate stretching frequencies is larger than ∼210 cm-1, which implies that the carboxylate groups are monodentate. UV-Vis electronic absorption studies show that Zn(II) functions as a trap for the Schiff-base intermediate. Schiff-base... 

New water-soluble zinc(II) Schiff-base complexes derived from amino acids (glycine, L-phenylalanine, and L-valine) and salicylaldehyde-5-sulfonates (sodium salicylaldehyde-5-sulfonate and sodium 3-methoxy-salicylaldehyde-5- sulfonate) have been synthesized. The complexes were characterized by elemental analysis, IR, electronic, 1H NMR, and 13C NMR spectra. In the IR spectra of the complexes, the large difference between the asymmetric νas(COO) and symmetric νs(COO) carboxylate stretch, Δν(νas(COO)-νs(COO)) of 199-247 cm-1, indicates monodentate coordination of the carboxylate group. Spectral data showed that in these complexes the ligand is a tridentate ONO moiety, coordinating to the metal... 

Influence of the addition of water molecules (n = 1-6) on the interaction energy between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d, p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation-π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation-π interaction indicates that there is a correlation between the... 

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... 

The folding rates of protein were shown to correlate with the degree of heterogeneity in the formation of native contacts. It was shown that both experimental rates and simulated free energy barriers for 2-state proteins depend on the degree of heterogeneity present in the folding process. Heterogeneity due to variance in the distribution of native loop lengths, and variance in the distribution of φ values, were observed to increase folding rates and reduce folding barriers. The observed effect due to φ variance was found to be the most statistically significant, because φ variance captures both heterogeneity arising from native topology and that arising from energetics