Sharif Digital Repository

Asparagainase is a therapeutic enzyme which has been a subject of research for decades. The enzyme catalyzes the hydrolysis of the amide group in asparagine and similar amides. Altering the substrate specificity and stabilization of this enzyme can increase its therapeutic properties. Moreover, asparaginases may be evolved to catalyze the hydrolysis of other similar compounds. These can be achieved through directed evolution and computational methods.In this study, the gene encoding L-asparaginase II enzyme from E. coli was amplified by polymerase chain reaction (PCR) and was cloned into an expression vector. The recombinant protein was expressed by an appropriate host secreting the... 

Proteins carry out most important roles in the organisms and they have a number of functions including structural, catalytically, regulatory and transportal, However for protein to have functional role they must be able to possess tridimensional structure. Several proteins due to various genetic and physico-chemical conditions have shown to alter their tridimensional structure leading to insoluble fibrilar structure. One of the properties of these insoluble fibrils is conformational change, converting to β-sheet rich structures; the entire process of converting soluble to proteins insoluble fibrils known as amyloid formation. The proteins amyloidosis have been seen as causative role in a... 

Separation of biomolecules such as enzymes is the most important part of biotechnology process which 10-90 % of costs is for separation and purification. There are several methods for purification of bio materials and one of them is chromatography which use in enzyme purification but this method have several problem such as cost ,time consuming and scale up Because of this a suitable alternative demands for industrial separation. An alternative is aqueous two-phase systems (ATPS). In this project was studied about partial purification of alkaline protease produced by Bacillus licheniformis ATCC 21424 in aqueous two-phase system and comparison with chromatography method. an aqueous two-phase... 

Conjugation of proteins to nanoparticles has numerous applications in sensing, imaging, delivery, catalysis, therapy and control of protein structure and activity. Therefore, characterizing the nanoparticle–protein interface is of great importance. A variety of covalent and non-covalent linking chemistries have been reported for nanoparticle attachment. Typically, a specific protein residue is linked directly to the nanoparticle core or to the ligand. As conjugation often affects the protein structure and function, techniques to probe structure and activity are assessed Characterization studies of nanoparticle–protein complexes show that the structure and function are influenced by the... 

This study aims to investigate the influence of important operational parameters on membrane fouling with the approach of fouling layers and to model these influences in the membrane bioreactor (MBR) for municipal wastewater treatment. At the first phase, 11 operational scenarios were executed using a pilot setup for identifying the system behavior and the optimal scenario. Protein and carbohydrate as the fouling components (SMP) and the transmembrane pressure (TMP) as the fouling criteria were measured in the tests. By studying the influence of operational parameters (sludge retention time (SRT), aeration rate and filtration mode), some useful results obtained for the next phase, including... 

Colorectal cancer (CRC) is one of the most common cause of cancer death worldwide. Identification of pivot genes in colorectal cancer can play an important role as biomarkers in predicting and early diagnosis and reducing the number of deaths caused by this disease. In this study, the aim of which is to discover pivot genes in colorectal cancer, six microarray datasets selected from the GEO database including 277 tumor tissue samples and 325 normal colon tissue samples. After data processing, differentially expressed genes and CRC-related genes were screened and 285 shared genes between them were identified for subsequent analysis. Based on 285 shared genes, the protein-protein interaction... 

In the present thesis, intracellular fluid flows have investigated for study cell motions. It is due to firmly relation between the cell motion and these flows. Generally, the cell firstly adheres to a surface, then, moves forward with the effects of the internal fluid flows. In this study, the cell structure is invided to two general parts; the front part of the cell and the cell body. The front part of the cell plays a essential roles in the cell motion, however, the cell body is considered as a extra cargo that is carried by the front of the cell. Therefor, in the present modellings, the front part is only considered. Here, using four different models for the front part of the cell, many... 

F-BAR protein is one of the Bin/Amphiphysin/Rvs (BAR) superfamily proteins which contributes in curvature generation and stabilization of lipid membranes. These proteins usualy form lattices on the membrane and can sculpt the membrane. In this project the interaction of F-BAR protein with a lipid membrane is modeled using coarse grained molecular dynamics approach. In order to describe the curvature generation and stabilization we would need an appropriate coarse grained model for the lipid membrane. In this project the proposed model for the membrane describes a membrane in liquid phase with a lateral diffusion in the lipid bilayer. Depth and width of the lipids potential is determined in... 

The aim of this study is to devise innovative compounds that impede the function of CK2α enzyme by incorporating amino acids and sugars into their molecular structure. CK2α, a catalytic subunit of CK2 enzyme, operates autonomously and is the only continuously active kinase that does not require an upstream regulator. Emerging evidence highlights CK2α's crucial role in various cancers and infectious diseases, including Covid-19, indicating that suppressing its function could provide a promising approach to improve patient outcomes. To accomplish this objective, the drug design process must take into account both pharmacokinetic and pharmacodynamic properties. Pharmacokinetics, encompassing... 

In the present investigation, experimental design, synthesis and evaluation of Verapamil, Albumin, Immonuglubline G and Trypsin imprinted polymers and finally Albumin imprinted poly(dopamine) nano-layer were presented. A bimodal polymerization approach as a combination of precipitation and dispersion polymerization was taken towards producing 500 nm particles for verapamil imprinting purpose. In this case the imprinting factor was 2.17. In a challenge for producing spherical particles with predefined size and pore properties the hierarchical polymerization in packed beds, using porous silica particles (particle size ca. 40 µm) was developed, as well. The method resolving the problems... 

After proteins, one of the important biological macromolecules, are synthesized by ribosomes,they automatically reach their own special 3-D structure. This native structur or better known as folded state is what determines the function of a protein. In some situations, the proteins become misfolded leading to its lack of biological function through aggregation or fibril formation known as "amyloid". The amyloid fibrils have been shown to be a causative factor in nerve decay such as Alzheimer's. Therefore, inhibition of amyloid formation using different approaches such as synthetic organic and natural compounds has, recently, been under spotlight. A pyridazine basedcompound (RS-0406) has... 

A drug can be defined as a substance made to prevent disease, cure a specific symptom, relieve pain, and reduce anomalies in the body. The process of drug designing is so laborious, complex, costly, and time-consuming that chance of failure during the lab experiment stages is high. These challenges have persuaded researchers to find new usage for existing drugs, referred to as drug repurposing, with the main advantage of reducing cost, risk, and time. To this aim, computational methods have been applied to discover hidden pharmaceutical capabilities of drugs in terms of predicting whether a particular drug can interact with a particular protein.Graph Neural Networks (GNNs) have recently... 

The purpose of this study is to assess the inhibitory effects of an appropriate nanoparticles loaded with gallic acid on the fibrillation of alpha-synuclein. Alpha-synuclein is a major component of protein plaques in synucleinopathies, particularly Parkinson’s disease. Gallic acid (GA, 3,4,5-trihydroxy benzoic acid) is a well–known small molecule which can inhibit the formation of α-synuclein fibrils. For the process of fibrillation, purified protein was incubated at 37◦C and pH 7.2. Fibrillation was analyzed by the standard fibril methods.after that investigated fabricating of gallic acid trapped in the chitosan nanoparticles and gallic acid loaded in chitosan –coated mesoporous silica... 

In examining protein-protein interaction networks, we often encounter similar and repetitive schemes. Examination of these designs, which often appear in the form of motifs and similar patterns, reveals important information such as the type of protein linkage and many of the internal similarities between these networks. The ability to recognize these similarities plays an important role in identifying the function of genes, recognizing the relationships between diseases, and making drugs. We know that exact algorithms for examining subgraph isomorphism are np-hard and time-consuming and infeasible in large networks; Therefore, in practice, approximate and heuristic algorithms are used and... 

Milk is One of the most important source s of protein in the world. during the process of cheese the most of these protein remain in whey. There are different methods to separate these protein from whey. The one of advanced method is ultrafiltartion, this method is based on a permeable membranes, with different pore size. There are many research works in this field. In this project we have tried to study the effect ofpressure, temperature, concentration and resistance time on membrane porosity. In order to design the experiment and analyze the results tagochi L 16 methods is used. The PVC membranes were prepaid by gas anti solvent method, experiment showed that changes of temperature and... 

The most important factor in protein's function and its 3D structure is folding. Misfolding or native folding perturbation in some peptides and proteins force them get into amyloid fibril aggregation. It has been observed that these aggregations are the cause of some debilitative diseases especially ones that are related to aging like Alzheimer disease, Hantington's disease, typeII diabets etc. Recently it has been shown that specific regions in human catalase protein interact with some amyloid fibrils, such as Aß, IAPP, PrP etc. Inteins are self-splicing protein enzymes, which excise themselves from the mature protein and join the two flanking adjacent sequences by a new peptide bond in a... 

Datasets extracted from gene expression microarrays contain information about the phenotypic behavior of organisms. Turning this information into knowledge, i.e. finding associative genes with a given phenotype, is a daunting task. This is due to the high dimensionality of the data as the number of features on a gene expression microarray is usually very large. Moreover, a phenotype may change the expression pattern of a set of genes rather than changing each gene’s expression independently. To tackle the second problem, integrating other sources of information such as Protein-Protein Interaction (PPI) networks is required. In this thesis, the PPI network extracted from the String database... 

Axon is an important part of the neuronal cells and axonal microtubules are bundles in axons.In axons, microtubules are coated with microtubule-associated protein tau, a natively unfolded filamentous protein in the central nervous system. These proteins are responsible for cross-linking axonal microtubule bundles. Through complimentary dimerization with other tau proteins, bridges are formed between nearby microtubules creating bundles. Formation of bundles of microtubules causes their transverse reinforcement and has been shown to enhance their ability to bear compressive loads. Though microtubules are conventionally regarded as bearing compressive loads, in certain circumstances such as in... 

Transglutaminase 2 enzyme is expressed in various parts of the human body and is present in almost all tissue cells. The function of this enzyme is multiple and it catalyzes different reactions depending on where it is located in the cell. The most important activities of this enzyme are: isopeptide bond formation between the side chains of two proteins (transamidation reaction), diamidation reaction (hydrolysis of amide bond), esterification, kinase activity. The hen egg white lysozyme protein is another natural antimicrobial protein that has been extensively studied. The muramidase activity of egg white lysozyme against highly gram-positive bacteria is well known, and this property has... 

Enzymes are proteins that carry out chemical reactions in the form of chemo, stereo, and regioselective under mild conditions. One of the characteristics of enzymes is that they perform a specific chemical reaction on a selective substrate and under specific environmental conditions. However, in recent years, a number of enzymes have been identified to display promiscous behavior. This promiscousity includes catalytic activity, variety of substrates, and environmental conditions. Promiscous activities of enzymes can be a good starting point for creating new and more favorable engineered pathways for the production of chemical and medicinal drugs. One of the aims of this project is to exploit...