Subunit interaction is an important phenomenon for protein optimally functions. Their final structures are mostly the result of clustering of several individual peptide chains. A variety of interactions including hydrogen bonds, salt bridges and disulfide bonds hold the various chains into a particular geometry. In fact, these bonds between the amino acids of polypeptide chains have significant influence on the topography of protein quaternary structure. Thus, the nature of these amino acids is considerable in protein engineering. Thereby manipulating them can help the biologists to improve the stability of the final structure.CFinder is web based software that has been designed to facilitate the processes of identifying amino acids which are in contact with a specified polypeptide chain. CFinder as an interactive interface assists users by determining the amino acids which are associated to generate a complex multi-subunit shape.User can enter the input information by either uploading PDB file or entering PDB code and the desired chain name. CFinder calculates the ACCESSIBLE SURFACE AREA of each amino acid in two states: the complete protein and the desired chain alone. The amino acids which show different ACCESSIBLE SURFACE AREA in these two states are the output results. CFinder is freely available at URL: http: //bioinf.modares.ac.ir/software/cfinder.

In the Bacillusamyloliquefaciens α-amylase (BAA)، the loop (residues from 177-185; region І ) is the constructive part of the cage responsible for attachment to calcium. It has two more amino acid residues than the α-amylase from Bacillus licheniformis (BLA). Arg176 in this region makes an ionic interaction with Glu126 from region І І (residues 118-131) but this interaction is lost in BLA due to substitution of R176Q and E126V. It is the common feature of α-amylases that calcium ion is required for their thermal stability. The present work quantitatively estimates the effect of ionic interaction on the overall stability of the enzyme. To clarify the functional and structural significance of corresponding salt bridge، first an automated homology model of the mutant enzyme (∆ E126) was built by the Swiss-Model Protein Modeling Server. Bacillus amyloliquefaciens α-amylase (3BH4. pdb) was used as the template and examined by GETAREA and WHAT IF programs، then Glu126 was deleted (∆ E126) by site-directed mutagenesis and the thermostability was examined for the wild-type and mutant enzymes. Modeling results showed that deletion of salt bridge affected on the hydrophobic and hydrophilic residues orientation of two discussed regions (Ι ، Ι Ι ). The mutant enzyme also exhibited lower thermostability relative to the wild-type enzyme. Thus، it may be suggested that salt bridge could affect on ACCESSIBLE SURFACE AREA of the discussed regions، decrease water diffusion، prevent diffusion of cations and improve the thermostability of the whole protein.

Diminishing protein aggregation by chaperone is very important factor in medicine and industry. In this paper, it is induced the chaperone ability for; b-casein upon modification of its acidic residues by Woodward reagent K (WRK) and examined on lysozyme as a target protein at pH 7.2 and outlined the mechanism for chaperone ability of modified system by UV-Vis and fluorescence spectroscopy and theoretical calculation methods.

Counter-urbanization has been defined with many definitions in research literature as increasing of the small town population in the process of urban expansion and development. This study investigates the counter-urbanization process in Isfahan metropolitan AREA based on an exploratory method using the population and immigration data, diurnal commuting, and the immigration motivators. The results show that, during different periods, population growth has been changed from the greater cities’ metropolitan AREA to the small towns. So that, there is less population growth near the main greater cities during the last decade. Regarding the immigration as well as migration effectiveness over the population, and immigration motivators, it can be said that the most important parameters of small towns’ expansion near the greater cities are better habitation opportunities, and finding better jobs. Furthermore, decreasing the diurnal commuting close to the greater cities shows that small towns, which are farther from the greater city, have more autonomy. In addition, based on polarization reversal model, and population development investigation in metropolitan AREAs, there are population development from the greater cities’ centre to the periphery AREA, which is leaded to decrease the population of the main greater city, and increase the population absorption in small towns. Consequently, the urbanization of Isfahan metropolitan AREA has entered to a counter-urbanization phase.

In comparison to the previous researches, ZrO2 nanoparticles with higher SURFACE AREA (85 m2/g) have been synthesized in this research. The as-prepared ZrO2 nanoparticles by co-precipitation method were characterized with X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM). The SURFACE AREA of the sample was characterized by BET method. The effect of the growth parameters such as temperature, pH, Zr4+/template ratio and kind of template on the growth and morphology of ZrO2 nanoparticles have been investigated in detail. The results revealed that pH, temperature, Zr4+/template and kind of template have an important effect on the morphology and size of the ZrO2 nanoparticles. X Ray Diffraction (XRD) analysis of the superior nanoparticles that was prepared at pH=4, Temperature=70oC, Zr4+/template ratio=2 and by sorbitol as template indicates the formation of nanocrystalline ZrO2 tetragonal phase structure. The average particle size of the product is about 4.45 nm that was calculated from XRD pattern by the Debye-Scherrer formula.

Specific liquid–vapor interfacial AREA (SLVIA) converges to soil specific SURFACE AREA (SSA) in very low soil moisture content. In this study, 20 soil samples were collected from different locations in Fars province, and soil moisture characteristic curve of each soil sample was measured, and the residual soil moisture content (qr ) of each soil sample based on van Genuchten equation was determined. Also, soil texture and SSA of each soil sample were measured. The results indicated that for all soil samples, the moisture equality (qss ) of SLVIA and SSA was occurred at soil moisture content greater than residual soil moisture content (qr ) and less than soil moisture content at soil water pressure of-1500 kPa (q-1500 ). The ratio of qss to q-1500 ranged between 0.466 to 0.923 with an average of 0.639.

Aim and background: Pathological studies have suggested that formation of fibrous plaques and accumulated masses of amyloid beta peptides in central nervous system is one of the causes to Alzheimer’s disease. Since these diseases depend on conformational structure of protein, we investigate initial conformational changes of Ab (1-42) and Ab (1-40 by molecular dynamic simulations in this paper.Materials and methods: The solution NMR structures of Ab (1-42) and Ab (1-40) (protein data bank: 1IYT 1& BA4) was chosen as a template for comparative modeling. All simulations and data analysis were performed by GROMACS program with the united-atom protein force field. The final sampling simulations were 20-ns MD simulations, 310K and constant pressure (1 bar).Results: The results of RMSD, radius of gyration and solvent ACCESSIBLE SURFACE AREA showed that structural changes, flexibility and the propensity to aggregation of Ab (1-42) is more than Ab (1-40).Conclusions: The solvent ACCESSIBLE SURFACE AREA show the hydrophobicity interaction have important role in aggregation and creation of deformed structures. Our data showed that Ab (1-42) have critical role in the development of Alzheimer’s disease.