Here the advantages of employing a biorefinery approach in conjunction with optimization techniques were utilized to attain high overall process efficiency. Initially, an alkaline pH-shift process assisted by ultrasonic and its subsequent optimization were employed to maximize the extraction yield and whiteness index of muscle proteins isolated from lanternfish (B. pterotum). The optimal strategy was determined as follows: 6 mL g-1, pH1 (solubilization) 11.5, 310 W, and pH2 (precipitation) 5.8 with desirability of 0.84. Collagen hydrolysate was obtained from the connective tissue-containing sediment residue emerging during pH-shift process. The optimal isolated protein (OIP) was utilized to produce heat-set gels in combination with collagen hydrolysate. Breaking force and deformation of the OIP gel were measured at 123 (g) and 10.12 (mm) respectively. Collagen hydrolysate made breaking force (up to 2% w/w) and deformation (up to 10% w/w) improved and had positive effects on color characteristics (especially whiteness index) as well as water holding capacity. Hence, it can be concluded that the integration of a novel extraction technique such as ultrasonic with pH-shift process followed by optimization, as well as concurrent utilization of muscle and connective tissue proteins through a biorefinery approach; provides a significant advancement towards scaling up the extraction process.

Dragline silk with extraordinary mechanical properties, is an interesting substance for commercial purposes and medical researches but unfortunately its three-dimensional structure has not been resolved yet. This protein consists of two large proteins: Major ampullate Spidroin 1 (MaSp1) and MaSp2. Recently, the whole sequences of these two proteins were resolved for Black Widow spider (Latrodectus hesperus) with 3129 and 3779 amino acids, respectively. These proteins are very similar, they are big proteins made of alternating polyalanine and' glycine-rich blocks between nonrepetitive N- and C-terminal domains. Here because of limitation of computational tools to work on such long sequences, we modeled one of the most common repetitive patterns with 117 amino acids for MaSp1 protein. The entrance structural file, was made using MAGMA program. Then molecular dynamics simulations were performed for this structure using GROMACS (version 3.3.1). The system was energy minimized, followed by equilibration for 100 picoseconds (ps). The simulation was carried out for 100 ps in vacuo and then for 300 nanoseconds (ns) in water.' Final structure was analyzed using GROMACS analysis tools. Our results showed significant initiation of secondary structure conformations in the first quarter of 117 amino acid consensus sequence. Beta strands are present in Gly-X regions as was shown in earlier studies.

Nanobiotechnology has provided promising novel diagnostic and therapeutic strategies which capable to create a broad spectrum of nano-based imaging agents and medicines for human administrations. Several studies have demonstrated that the surface of nanomaterials is immediately coated with suspended proteins after contact with plasma or other biological fluids to form protein corona-nanoparticle complexes. Cells react after exposure with these complexes. since, the biological fate and functions of nanomaterials are determined by physiological responses to protein-nanoparticle complexes in this article, we aimed to review some studies about the effects of the protein profiles and physicochemical characteristics of nanoparticles in the biological environment on the formation of protein corona and subsequent the biological responses upon exposure to nanoparticles. Also, some used methods for of protein corona analysis has been reviewed. It has been shown that the biological impacts of protein corona may be both constructive and/or destructive in the biomedical applications of nanomaterials. The protein corona–, cell interactions can facilitate targeted delivery and cellular absorption of therapeutic nanomaterials and also, they mitigate the unfavorable cytotoxic effects of nanoparticles. On the other hand, these interactions may cause rapid clearance of nanoparticles from the body as well as the activation of undesirable inflammatory responses. Hence, the study of the formation mechanism and biological effects of protein corona plays an important role in the design of nanoparticles with specific physicochemical properties proportional with their intended biological activity.

A biological network represents the interaction between a set of macromolecules to drive a particular biological process. In a biological environment, abnormalities happen not only in one molecule but also through a biological network. One of the most effective methods to detect anomaly is the comparison between healthy and diseased networks. In this regard, biological network alignment is one of the most efficient ways to find the difference between healthy and diseased cells. This problem, protein-protein interaction network alignment, has been raised in two main types: Local network alignment and Global network alignment. According to the NP-completeness of this problem, different non-deterministic approaches have been proposed to tackle the Global network alignment problem. Recently, NetAl has been introduced as a common algorithm to align two networks. Although this algorithm can align two networks at the appropriate time, it does not consider biological features. In this study, we present a new framework called PRAF to improve the results of network alignment algorithms such as NetAl by considering some biological features like gene ontology (GO).

Hordeum vulgare is a one-year-old herb of the Poaceae family. It is an important cereal used by humans which has been applied in many cases instead of wheat. The limitation of experimental methods is one of the important problems for identifying protein-protein interactions. So, in recent years, computational methods have played an important role in predicting and identifying protein-protein interactions. In this study, for constructing protein-protein interaction (PPI) network, the experimental PPI information of six model organisms includes Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Oryza sativa, and Arabidopsis thalian were extracted from the Intact database. Inparanoid was used for identifying barley orthologous proteins with model organisms. The Interolog method which was used in this study can predict protein-protein interactions by mapping protein interactions of the model organisms on orthologous proteins. After removing repetitive interactions, the final predicted barley PPI network contained 235966 interactions between 7350 proteins. This study is the first report presented on protein-protein interaction prediction in barley.

Homeobox genes encode transcription factors which play important roles in the developmental processes of many multicellular organisms. TGIFLX/Y (TGIFLX and TGIFLY) are members of the homeobox superfamily of genes. Their expressions are specifically detected in the human adult testis but their functions are remained to be investigated. In this investigation we cloned full length of TGIFLY cDNA and produced recombinant GST-TGIFLY protein in bacterial system. Here we present production of GST-TGIFLY fusion protein as a soluble protein. The recombinant protein was confirmed by western blot analysis using anti-GST antibody. Through a single purification procedure using MagneGST Beads, approximately 20 mg of the recombinant protein was obtained per liter of bacterial culture. We suggest that GST-TGIFLY fusion protein could be utilized as a valuable molecular tool on investigation of TGIFLY target genes and identification of co-factors or partner proteins involved in TGIFLY function in normal and abnormal development.

Introduction: The aim of this research work is to optimize the extraction conditions of Scenedesmus Obliquus algae protein by enzymatic and alkaline methods using response surface technique and to investigate the extracted protein’ s functional properties. Materials and Methods: Optimization of enzymatic protein extraction using Minitab software with central composite response surface methodolog was designed for enzyme to substrate ratio factors and enzyme’ s effective time (cellulose enzymes and multi-enzymes under optimum pH conditions) followed by optimization of the best treatment for the maximum extraction efficiency in the shortest time and finally the extracted proteins were identified by electrophoresis. Results: The results showed that, the higher the enzyme concentration, the higher the extraction rate and the protein extraction efficiency, therefore with an increase in the concentration from 4 to 6 μ l/ml, the efficiency of the extraction is increased from 15. 28 to 27. 87 percent using multienzyme, and it increased from 16. 88 to 21. 42 percent using cellulase. The optimum conditions calculated at the highest concentration and lowest response time were 4 μ g / ml for 2. 34 hours. The results obtained from the chemical extraction of samples indicated that, the extraction efficiency was calculated as 19. 13 percent. The results of electrophoresis analysis showed that the proteins extracted from this microalga contained 8 protein bands with molecular weight ranging from 20 to 110 kDa. Conclusion: Enzymatic extraction of proteins indicated a better yield as compared to chemical extraction and also considering the economical aspects this method of extraction is suggested.

in this research gel structure formation process, whey proteins and isolated rice bran proteins mixture textural properties and gel structure was subjected to intensive research. Gel formation ability, ab andazi, pH and also textural properties including rigidity, stickiness, Springiness and adherence for Mentioned protein mixture prepared in various proportions of 1: 2, 1: 5, 1: 10 and different concentrations of 1: 5 and 1: 10 was investigated in 3 identical experiments. Obtained data were analyzed by ANOVA (analysis of variance, a statistical method in which the variation in a set of observations is divided into distinct components) in 5% probability level. Results indicated that adding whey proteins to rice bran proteins has Synergistic effect on gel structure and has strengthened active complex structure. Best influential interaction between these two proteins was observed at 1: 5 and 1: 10 proportions of whey to rice bran proteins, which 1: 10 ratio could be considered as optimized proportion.In fact, the results indicate that a proper of 1: 10 ratio can be used as gel formation in the formulation of food offered.