Sharif Digital Repository

Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed. © 2007 Verlag Helvetica Chimica Acta AG, Zürich  

Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as efficient as methods developed and processed for protein sequencing. While more than 70 million protein sequences are available today, only the functionality of around one percent of them are known. These facts have encouraged researchers to develop computational methods to infer protein functionalities from their sequences. Gene Ontology is the most well-known database for protein functions which has a hierarchical structure, where deeper terms are... 

Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for... 

Hepcidin is a peptide hormone that plays an important role in iron metabolism. We have produced a recombinant mouse hepcidin-1 by using baculovirus expression system. Its expression yield was 25 μg/ml when cell culture media were supplemented with a protease inhibitor cocktail. The recombinant mouse hepcidin-1 and synthetic human hepcidin-25 had similar effects on reducing ferroportin expression in J774A cell line and in peritoneal macrophages. However, synthetic human hepcidin-25 was more efficient than recombinant mouse hepcidin-1 in reducing iron concentration in blood circulation (p < 0.01)  

The main goal of this research is to use the biomass productivity, carbohydrate content, and carbohydrate productivity as useful responses for optimization of macronutrients concentrations (K2HPO4, NaHCO3, and NaNO3) in cultivation of Spirulina microalgae as a feedstock for bioethanol production. In this study, individual and synergistic effects of medium components on the mentioned responses were investigated. The culture medium was optimized using central composite design for achieving the maximize biomass productivity (165 mg L−1 day−1 at K2HPO4: 438 mg L−1, NaHCO3: 15.92 g L−1, and NaNO3: 0.5 g L−1), carbohydrate content (42.0% of dry mass at K2HPO4: 192 mg L−1, NaHCO3: 5.71 g L−1, and... 

S. lanata has been traditionally used as a medicinal plant due to its various biological activities such as antioxidant activity. Therefore, identification and quality control studies of this plant are of great importance. To this end, gas chromatography (GC) combined with chemometrics was proposed for fingerprint analysis of S. lanata samples. This study sought to classify GC fingerprints of twenty-eight S. lanata samples from eight different regions of Iran and more importantly, to correlate fingerprints to the antioxidant activity to select S. lanata volatile antioxidant markers. S. lanata samples were classified into five and three classes using partial least squares-discriminant... 

Cell survival during the early stages of transplantation and before new blood vessels formation is a major challenge in translational applications of 3D bioprinted tissues. Supplementing oxygen (O2) to transplanted cells via an O2 generating source such as calcium peroxide (CPO) is an attractive approach to ensure cell viability. Calcium peroxide also produces calcium hydroxide that reduces the viscosity of bioinks, which is a limiting factor for bioprinting. Therefore, adapting this solution into 3D bioprinting is of significant importance. In this study, a gelatin methacryloyl (GelMA) bioink that is optimized in terms of pH and viscosity is developed. The improved rheological properties... 

Parkinson's disease (PD) is a neurodegenerative disease, which is not easily diagnosed using clinical tests and the discovery of proper methods would be a major step towards a successful diagnosis. In the present study, we employed metabolic profiling using proton nuclear magnetic resonance spectroscopy to find metabolites in serum, which are helpful for the diagnosis of PD. Classification of PD and healthy subject was done using random forest. Serum levels of selenium measured by atomic absorption spectrometry in PD group were lower than the serum selenium levels in the control group. The metabolites causing selenium changes in PD patients were identified using random forest, and a model... 

Syndapin 1 FBAR, a member of the Bin-amphiphysin-Rvs (BAR) domain protein family, is known to induce membrane curvature and is an essential component in biological processes like endocytosis and formation and growth of neurites. We quantify the curvature sensing of FBAR on reconstituted porcine brain lipid vesicles and show that it senses membrane curvature at low density whereas it induces and reinforces tube stiffness at higher density. FBAR strongly up-concentrates on the high curvature tubes pulled out of Giant Unilamellar lipid Vesicles (GUVs), this sorting behavior is strongly amplified at low protein densities. Interestingly, FBAR from syndapin 1 has a large affinity for tubular... 

To determine the outward permeability of retina-choroid-sclera (RCS) layer for different ophthalmic drugs and to develop correlations between drug physicochemical properties and RCS permeability. A finite volume model was developed to simulate pharmacokinetics in the eye following drug administration by intravitreal injection. The RCS permeability was determined for 32 compounds by best fitting the drug concentration-time profile obtained by simulation with previously reported experimental data. Multiple linear regression was then used to develop correlations between best fit RCS permeability and drugs physicochemical properties. The RCS drug permeabilities had values that ranged over 3 ×... 

Since amyloid beta fibrillation (AβF) plays an important role in the development of neurodegenerative diseases, we investigated the effect of graphene oxide (GO) and their protein-coated surfaces on the kinetics of Aβ fibrillation in the aqueous solution. We showed that GO and their protein-covered surfaces delay the AβF process via adsorption of amyloid monomers. Also, the large available surface of GO sheets can delay the AβF process by adsorption of amyloid monomers. The inhibitory effect of the GO sheet was increased when we increase the concentration from 10% (in vitro; stimulated media) to 100% (in vivo; stimulated media). Conclusion: our results revealed that GO and their surface... 

Interactions of chemically exfoliated graphene oxide (GO) nanosheets and Escherichia coli bacteria living in mixed-acid fermentation with an anaerobic condition were investigated for different exposure times. X-ray photoelectron spectroscopy showed that as the exposure time increased (from 0 to 48 h), the oxygen-containing functional groups of the GO decreased by ∼60%, indicating a relative chemical reduction of the sheets by interaction with the bacteria. Raman spectroscopy and current-voltage measurement confirmed the reduction of the GO exposed to the bacteria. The reduction was believed to be due to the metabolic activity of the surviving bacteria through their glycolysis process. It was... 

The effect of Solid State Fermentation (SSF) on Chitosan production by A. niger was investigated. A. niger BBRC 20004 from Biochemical and Bioenvironmental Research Centre of Sharif University of Technology (Tehran, Iran), was grown on corn residue. Chitosan was extracted from the fungal mycelia using hot alkaline and acid treatment. A. niger was incubated for 12 days on corn residue with moisture content of 35 % and 1.12 % of nitrogen. The Chitosan was obtained and 10.9 g/kg of Urea dry residue was added in various amounts to the medium in order to evaluate the effect of the nitrogen concentration in the production of Chitosan. The highest amount of Chitosan obtained by 6.5 g of urea after... 

Background: The aim of this study was to assess the performance of an original powered foot clearance creator (PFCC) mechanism worn in conjunction with an isocentric reciprocal gait orthosis (IRGO) and evaluate its effect on trunk compensatory movements and spatiotemporal parameters in nine healthy subjects. Method: A PFCC motorized mechanism was designed that incorporated twin sole plates, the movements of which enabled increased toe to floor clearance during swing phase. A prototype was constructed in combination with an IRGO, and hence was re-named as an IRGO-PFCC orthosis. The effects of IRGO-PFCC usage on the spatiotemporal parameters and trunk compensatory movements during walking were... 

In the past few years, a significant body of research has been devoted to designing magnetic micron scale robotic systems for minimally invasive medicine. The motion of different microorganisms is the nature's solution for efficient propulsion of these swimmers. So far, there has been a considerable effort in designing micro swimmers based on the propulsion of bacteria while the motion of numerous other microorganisms has not been a source of inspiration for designing micro swimmers yet. Inspired by propulsion of Paramecium which is a ciliate microorganism, a novel micro swimmer is proposed in this article which is capable of cargo transport. This novel swimmer is composed of multiple...