Search results for: integral membrane protein folding
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 4168

Search results for: integral membrane protein folding

4138 Optical and Double Folding Analysis for 6Li+16O Elastic Scattering

Authors: Abd Elrahman Elgamala, N. Darwish, I. Bondouk, Sh. Hamada

Abstract:

Available experimental angular distributions for 6Li elastically scattered from 16O nucleus in the energy range 13.0–50.0 MeV are investigated and reanalyzed using optical model of the conventional phenomenological potential and also using double folding optical model of different interaction models: DDM3Y1, CDM3Y1, CDM3Y2, and CDM3Y3. All the involved models of interaction are of M3Y Paris except DDM3Y1 which is of M3Y Reid and the main difference between them lies in the different values for the parameters of the incorporated density distribution function F(ρ). We have extracted the renormalization factor NR for 6Li+16O nuclear system in the energy range 13.0–50.0 MeV using the aforementioned interaction models.

Keywords: elastic scattering, optical model, folding potential, density distribution

Procedia PDF Downloads 142
4137 Kinetic Façade Design Using 3D Scanning to Convert Physical Models into Digital Models

Authors: Do-Jin Jang, Sung-Ah Kim

Abstract:

In designing a kinetic façade, it is hard for the designer to make digital models due to its complex geometry with motion. This paper aims to present a methodology of converting a point cloud of a physical model into a single digital model with a certain topology and motion. The method uses a Microsoft Kinect sensor, and color markers were defined and applied to three paper folding-inspired designs. Although the resulted digital model cannot represent the whole folding range of the physical model, the method supports the designer to conduct a performance-oriented design process with the rough physical model in the reduced folding range.

Keywords: design media, kinetic facades, tangible user interface, 3D scanning

Procedia PDF Downloads 414
4136 Further Investigation of α+12C and α+16O Elastic Scattering

Authors: Sh. Hamada

Abstract:

The current work aims to study the rainbow like-structure observed in the elastic scattering of alpha particles on both 12C and 16O nuclei. We reanalyzed the experimental elastic scattering angular distributions data for α+12C and α+16O nuclear systems at different energies using both optical model and double folding potential of different interaction models such as: CDM3Y1, DDM3Y1, CDM3Y6 and BDM3Y1. Potential created by BDM3Y1 interaction model has the shallowest depth which reflects the necessity to use higher renormalization factor (Nr). Both optical model and double folding potential of different interaction models fairly reproduce the experimental data.

Keywords: density distribution, double folding, elastic scattering, nuclear rainbow, optical model

Procedia PDF Downloads 237
4135 The Phosphatidate Phosphatase Pah1 and Its Regulator Nem1/spo7 Protein Phosphatase Required for Nucleophagy

Authors: Muhammad Arifur Rahman, Talukdar M. Waliullah, Takashi Ushimaru

Abstract:

Nucleophagy selectively degrades nuclear materials, especially nucleolus after nutrient starvation or inactivation of TORC1 kinase in budding yeast. Budding yeast phosphatidate (PA) phosphatase Pah1 that converts PA to diacylglycerol is essential for partitioning of lipid precursors between membrane and storage that is crucial for many aspects of cell growth and development. Pah1 is required for nuclear/ER membrane biogenesis and vacuole function, but whether Pah1 and its activator Nem1/Spo7 protein phosphatase complex are involved in autophagy is largely unknown. Loss of Pah1 causes expansion of the nucleus and fragmentation of the vacuole. Here we show that Pah1 is required for bulk autophagy and nucleophagy after TORC1 inactivation. Loss of Pah1 impaired nucleophagy severely and bulk autophagy to a lesser extent. Loss of the Pah1 activator Nem1-Spo7 protein phosphatase exhibited similar features.

Keywords: autophagy, Nem1/Spo7 phosphatase, Pah1, nucleophagy, TORC1

Procedia PDF Downloads 231
4134 Gas Permeation Behavior of Single and Mixed Gas Components Using an Asymmetric Ceramic Membrane

Authors: Ngozi Claribelle Nwogu, Mohammed Nasir Kajama, Godson Osueke, Edward Gobina

Abstract:

A unique sol–gel dip-coating process to form an asymmetric silica membrane with improved membrane performance and reproducibility has been reported. First, we deposited repeatedly a silica solution on top of a commercial alumina membrane support to improve its structural make up. The coated membrane is further processed under clean room conditions to avoid dust impurity and subsequent drying in an oven for high thermal, chemical and physical stability. The resulting asymmetric membrane exhibits a gradual change in the membrane layer thickness. Compared to a single-layer process using only the membrane support, the dual-layer process improves both flux and selectivity. For the scientifically significant difficulties of natural gas purification, collective CO2, CH4 and H2 gas fluxes and separation factors obtained gave reasonably excellent values. In addition, the membrane selectively separated hydrogen as demonstrated by a high concentration of hydrogen recovery.

Keywords: gas permeation, silica membrane, separation factor, membrane layer thickness

Procedia PDF Downloads 360
4133 Analytical Modeling of Globular Protein-Ferritin in α-Helical Conformation: A White Noise Functional Approach

Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

Abstract:

This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: globular protein, modulating function, white noise, winding probability

Procedia PDF Downloads 478
4132 Bioinformatics Approach to Identify Physicochemical and Structural Properties Associated with Successful Cell-free Protein Synthesis

Authors: Alexander A. Tokmakov

Abstract:

Cell-free protein synthesis is widely used to synthesize recombinant proteins. It allows genome-scale expression of various polypeptides under strictly controlled uniform conditions. However, only a minor fraction of all proteins can be successfully expressed in the systems of protein synthesis that are currently used. The factors determining expression success are poorly understood. At present, the vast volume of data is accumulated in cell-free expression databases. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with successful cell-free expression. Here, we describe an approach aimed at identification of multiple physicochemical and structural properties of amino acid sequences associated with protein solubility and aggregation and highlight major correlations obtained using this approach. The developed method includes: categorical assessment of the protein expression data, calculation and prediction of multiple properties of expressed amino acid sequences, correlation of the individual properties with the expression scores, and evaluation of statistical significance of the observed correlations. Using this approach, we revealed a number of statistically significant correlations between calculated and predicted features of protein sequences and their amenability to cell-free expression. It was found that some of the features, such as protein pI, hydrophobicity, presence of signal sequences, etc., are mostly related to protein solubility, whereas the others, such as protein length, number of disulfide bonds, content of secondary structure, etc., affect mainly the expression propensity. We also demonstrated that amenability of polypeptide sequences to cell-free expression correlates with the presence of multiple sites of post-translational modifications. The correlations revealed in this study provide a plethora of important insights into protein folding and rationalization of protein production. The developed bioinformatics approach can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

Keywords: bioinformatics analysis, cell-free protein synthesis, expression success, optimization, recombinant proteins

Procedia PDF Downloads 419
4131 Effect of Fluidized Granular Activated Carbon for the Mitigation of Membrane Fouling in Wastewater Treatment

Authors: Jingwei Wang, Anthony G. Fane, Jia Wei Chew

Abstract:

The use of fluidized Granular Activated Carbon (GAC) as a means of mitigation membrane fouling in membrane bioreactors (MBRs) has received much attention in recent years, especially in anaerobic fluidized bed membrane bioreactors (AFMBRs). It has been affirmed that the unsteady-state tangential shear conferred by GAC fluidization on membrane surface suppressed the extent of membrane fouling with energy consumption much lower than that of bubbling (i.e., air sparging). In a previous work, the hydrodynamics of the fluidized GAC particles were correlated with membrane fouling mitigation effectiveness. Results verified that the momentum transfer from particle to membrane held a key in fouling mitigation. The goal of the current work is to understand the effect of fluidized GAC on membrane critical flux. Membrane critical flux values were measured by a vertical Direct Observation Through the Membrane (DOTM) setup. The polystyrene particles (known as latex particles) with the particle size of 5 µm were used as model foulant thus to give the number of the foulant on the membrane surface. Our results shed light on the positive effect of fluidized GAC enhancing the critical membrane flux by an order-of-magnitude as compared to that of liquid shear alone. Membrane fouling mitigation was benefitted by the increasing of power input.

Keywords: membrane fouling mitigation, liquid-solid fluidization, critical flux, energy input

Procedia PDF Downloads 408
4130 Micro-Filtration with an Inorganic Membrane

Authors: Benyamina, Ouldabess, Bensalah

Abstract:

The aim of this study is to use membrane technique for filtration of a coloring solution. the preparation of the micro-filtration membranes is based on a natural clay powder with a low cost, deposited on macro-porous ceramic supports. The micro-filtration membrane provided a very large permeation flow. Indeed, the filtration effectiveness of membrane was proved by the total discoloration of bromothymol blue solution with initial concentration of 10-3 mg/L after the first minutes.

Keywords: the inorganic membrane, micro-filtration, coloring solution, natural clay powder

Procedia PDF Downloads 513
4129 Three-Dimensional Numerical Analysis of the Harmfulness of Defects in Oil Pipes

Authors: B. Medjadji, L. Aminallah, B. Serier, M. Benlebna

Abstract:

In this study, the finite element method in 3-D is used to calculate the integral J in the semi-elliptical crack in a pipe subjected to internal pressure. The stress-strain curve of the pipe has been determined experimentally. The J-integral was calculated in two fronts crack (Ф = 0 and Ф = π/2). The effect of the configuration of the crack on the J integral is analysed. The results show that an external longitudinal crack in a pipe is the most dangerous. It also shows that the increase in the applied pressure causes a remarkable increase of the integral J. The effect of the depth of the crack becomes important when the ratio between the depth of the crack and the thickness of the pipe (a / t) tends to 1.

Keywords: J integral, pipeline, crack, MEF

Procedia PDF Downloads 410
4128 Evaluation of Differential Interaction between Flavanols and Saliva Proteins by Diffusion and Precipitation Assays on Cellulose Membranes

Authors: E. Obreque-Slier, V. Contreras-Cortez, R. López-Solís

Abstract:

Astringency is a drying, roughing, and sometimes puckering sensation that is experienced on the various oral surfaces during or immediately after tasting foods. This sensation has been closely related to the interaction and precipitation between salivary proteins and polyphenols, specifically flavanols or proanthocyanidins. In addition, the type and concentration of proanthocyanidin influences significantly the intensity of the astringency and consequently the protein/proanthocyanidin interaction. However, most of the studies are based on the interaction between saliva and highly complex polyphenols, without considering the effect of monomeric proanthoancyanidins present in different foods. The aim of this study was to evaluate the effect of different monomeric proanthocyanidins on the diffusion and precipitation of salivary proteins. Thus, solutions of catechin, epicatechin, epigallocatechin and gallocatechin (0, 2.0, 4.0, 6.0, 8.0 and 10 mg/mL) were mixed with human saliva (1: 1 v/v). After incubation for 5 min at room temperature, 15 µL aliquots of each mix were dotted on a cellulose membrane and allowed to dry spontaneously at room temperature. The membrane was fixed, rinsed and stained for proteins with Coomassie blue. After exhaustive washing in 7% acetic acid, the membrane was rinsed once in distilled water and dried under a heat lamp. Both diffusion area and stain intensity of the protein spots were semiqualitative estimates for protein-tannin interaction (diffusion test). The rest of the whole saliva-phenol solution mixtures of the diffusion assay were centrifuged, and 15-μL aliquots from each of the supernatants were dotted on a cellulose membrane. The membrane was processed for protein staining as indicated above. The blue-stained area of protein distribution corresponding to each of the extract dilution-saliva mixtures was quantified by Image J 1.45 software. Each of the assays was performed at least three times. Initially, salivary proteins display a biphasic distribution on cellulose membranes, that is, when aliquots of saliva are placed on absorbing cellulose membranes, and free diffusion of saliva is allowed to occur, a non-diffusible protein fraction becomes surrounded by highly diffusible salivary proteins. In effect, once diffusion has ended, a protein-binding dye shows an intense blue-stained roughly circular area close to the spotting site (non-diffusible fraction) (NDF) which becomes surrounded by a weaker blue-stained outer band (diffusible fraction) (DF). Likewise, the diffusion test showed that epicatechin caused the complete disappearance of DF from saliva with 2 mg/mL. Also, epigallocatechin and gallocatechin caused a similar effect with 4 mg/mL, while catechin generated the same effect at 8 mg/mL. In the precipitation test, the use of epicatechin and gallocatechin generated evident precipitates at the bottom of the Eppendorf tubes. In summary, the flavanol type differentially affects the diffusion and precipitation of saliva, which would affect the sensation of astringency perceived by consumers.

Keywords: astringency, polyphenols, tannins, tannin-protein interaction

Procedia PDF Downloads 201
4127 Experimental Analysis on the Thermal Performance of Vacuum Membrane Distillation Module Using Polyvinylidene Fluoride Hollow Fiber Membrane

Authors: Hong-Jin Joo, Hee-Yoel Kwak

Abstract:

Vacuum Membrane Distillation (VMD) uses pressure lower than the atmospheric pressure. The feed seawater is capable of producing more vapor at the same temperature than Direct Contact Membrane Distillation (DCMD), Air Gap Membrane Distillation (AGMD) or Sweep Gas Membrane Distillation (SGMD). It is advantageous because it is operable at a lower temperature than other membrane distillations. However, no commercial product is available that uses the VMD method, as it is still in the study stage. In this study, therefore, thermal performance test according to the feed water conditions was performed prior to both construction of the demonstration plant, which uses VMD module of the capacity of 400m³/d in South Korea, and commercialization of VMD module with hollow fiber membrane. Such study was performed by designing and constructing the VMD module of the capacity of 2 m³/day which utilizes the polyvinylidene fluoride (PVDF) hollow fiber membrane. The results obtained from the VMD module manufactured by ECONITY Co., Ltd in South Korea, showed that the maximum performance ratio (PR) value of 0.904, feed water temperature of 75 ℃, and the flow rate of 8 m3/h. As the temperature of and flow rate of the feed water increased, the PR value of the VMD module also increased.

Keywords: membrane distillation, vacuum membrane distillation, hollow fiber membrane, desalination

Procedia PDF Downloads 211
4126 A Comparative Study on a Tilt-Integral-Derivative Controller with Proportional-Integral-Derivative Controller for a Pacemaker

Authors: Aysan Esgandanian, Sabalan Daneshvar

Abstract:

The study is done to determine the comparison between proportional-integral-derivative controller (PID controller) and tilt-integral-derivative (TID controller) for cardiac pacemaker systems, which can automatically control the heart rate to accurately track a desired preset profile. The controller offers good adaption of heart to the physiological needs of the patient. The parameters of the both controllers are tuned by particle swarm optimization (PSO) algorithm which uses the integral of time square error as a fitness function to be minimized. Simulation results are performed on the developed cardiovascular system of humans and results demonstrate that the TID controller produces superior control performance than PID controllers. In this paper, all simulations were performed in Matlab.

Keywords: integral of time square error, pacemaker systems, proportional-integral-derivative controller, PSO algorithm, tilt-integral-derivative controller

Procedia PDF Downloads 463
4125 Super-Hydrophilic TFC Membrane with High Stability in Oil

Authors: M. Obaid, Nasser A. M. Barakat, Fadali O.A

Abstract:

Low stability in oil media and the hydrophobicity problems of the ploysulfone electrospun membranes could be overcome in the present study. Synthesis of super-hydrophilic and highly stable in oil polysulfone electrospun nanofiber membrane was achieved by electrospinning of polysulfone solution containing NaOH salt followed by activation of the dried electrospun membrane by deposition of polyamide layer on the surface using m-phenylenediamine and 1,3,5-benzenetricarbonyl chloride. The introduced membrane has super-hydrophilicity characteristic (contact angle=3o), excellent stability in oil media and distinct performance in oil-water separation process.

Keywords: electrospinning, oil-degradability, membrane, nanofibers

Procedia PDF Downloads 483
4124 In-Situ Fabrication of ZnO PES Membranes for Treatment of Pharmaceuticals

Authors: Oranso T. Mahlangi, Bhekie B. Mamba

Abstract:

The occurrence of trace organic compounds (TOrCs) in water has raised health concerns for living organisms. The majority of TorCs, including pharmaceuticals and volatile organic compounds, are poorly monitored, partly due to the high cost of analysis and less strict water quality guidelines in South Africa. Therefore, the removal of TorCs is important to guarantee safe potable water. In this study, ZnO nanoparticles were fabricated in situ in polyethersulfone (PES) polymer solutions. This was followed by membrane synthesis using the phase inversion technique. Techniques such as FTIR, Raman, SEM, AFM, EDS, and contact angle measurements were used to characterize the membranes for several physicochemical properties. The membranes were then evaluated for their efficiency in treating pharmaceutical wastewater and resistance to organic (sodium alginate) and protein (bovine serum albumin) fouling. EDS micrographs revealed uniform distribution of ZnO nanoparticles within the polymer matrix, while SEM images showed uniform fingerlike structures. The addition of ZnO increased membrane roughness as well as hydrophilicity (which in turn improved water fluxes). The membranes poorly rejected monovalent and divalent salts (< 10%), making them resistant to flux decline due to concentration polarization effects. However, the membranes effectively removed carbamazepine, caffeine, sulfamethoxazole, ibuprofen, and naproxen by over 50%. ZnO PES membranes were resistant to organic and protein fouling compared to the neat membrane. ZnO PES ultrafiltration membranes may provide a solution in the reclamation of wastewater.

Keywords: trace organic compounds, pharmaceuticals, membrane fouling, wastewater reclamation

Procedia PDF Downloads 141
4123 The Development of an Automated Computational Workflow to Prioritize Potential Resistance Variants in HIV Integrase Subtype C

Authors: Keaghan Brown

Abstract:

The prioritization of drug resistance mutations impacting protein folding or protein-drug and protein-DNA interactions within macromolecular systems is critical to the success of treatment regimens. With a continual increase in computational tools to assess these impacts, the need for scalability and reproducibility became an essential component of computational analysis and experimental research. Here it introduce a bioinformatics pipeline that combines several structural analysis tools in a simplified workflow, by optimizing the present computational hardware and software to automatically ease the flow of data transformations. Utilizing preestablished software tools, it was possible to develop a pipeline with a set of pre-defined functions that will automate mutation introduction into the HIV-1 Integrase protein structure, calculate the gain and loss of polar interactions and calculate the change in energy of protein fold. Additionally, an automated molecular dynamics analysis was implemented which reduces the constant need for user input and output management. The resulting pipeline, Automated Mutation Introduction and Analysis (AMIA) is an open source set of scripts designed to introduce and analyse the effects of mutations on the static protein structure as well as the results of the multi-conformational states from molecular dynamic simulations. The workflow allows the user to visualize all outputs in a user friendly manner thereby successfully enabling the prioritization of variant systems for experimental validation.

Keywords: automated workflow, variant prioritization, drug resistance, HIV Integrase

Procedia PDF Downloads 78
4122 Integral Image-Based Differential Filters

Authors: Kohei Inoue, Kenji Hara, Kiichi Urahama

Abstract:

We describe a relationship between integral images and differential images. First, we derive a simple difference filter from conventional integral image. In the derivation, we show that an integral image and the corresponding differential image are related to each other by simultaneous linear equations, where the numbers of unknowns and equations are the same, and therefore, we can execute the integration and differentiation by solving the simultaneous equations. We applied the relationship to an image fusion problem, and experimentally verified the effectiveness of the proposed method.

Keywords: integral images, differential images, differential filters, image fusion

Procedia PDF Downloads 508
4121 Single Layer Carbon Nanotubes Array as an Efficient Membrane for Desalination: A Molecular Dynamics Study

Authors: Elisa Y. M. Ang, Teng Yong Ng, Jingjie Yeo, Rongming Lin, Zishun Liu, K. R. Geethalakshmi

Abstract:

By stacking carbon nanotubes (CNT) one on top of another, single layer CNT arrays can perform water-salt separation with ultra-high permeability and selectivity. Such outer-wall CNT slit membrane is named as the transverse flow CNT membrane. By adjusting the slit size between neighboring CNTs, the membrane can be configured to sieve out different solutes, right down to the separation of monovalent salt ions from water. Molecular dynamics (MD) simulation results show that the permeability of transverse flow CNT membrane is more than two times that of conventional axial-flow CNT membranes, and orders of magnitude higher than current reverse osmosis membrane. In addition, by carrying out MD simulations with different CNT size, it was observed that the variance in desalination performance with CNT size is small. This insensitivity of the transverse flow CNT membrane’s performance to CNT size is a distinct advantage over axial flow CNT membrane designs. Not only does the membrane operate well under constant pressure desalination operation, but MD simulations further indicate that oscillatory operation can further enhance the membrane’s desalination performance, making it suitable for operation such as electrodialysis reversal. While there are still challenges that need to be overcome, particularly on the physical fabrication of such membrane, it is hope that this versatile membrane design can bring the idea of using low dimensional structures for desalination closer to reality.

Keywords: carbon nanotubes, membrane desalination, transverse flow carbon nanotube membrane, molecular dynamics

Procedia PDF Downloads 196
4120 Identification and Characterization of Nuclear Envelope Protein Interactions

Authors: Mohammed Hakim Jafferali, Balaje Vijayaraghavan, Ricardo A. Figueroa, Ellinor Crafoord, Veronica J. Larsson, Einar Hallberg, Santhosh Gudise

Abstract:

The nuclear envelope which surrounds the chromatin of eukaryotic cells contains more than a hundred transmembrane proteins. Mutations in some genes encoding nuclear envelope proteins give rise to human diseases including neurological disorders. The function of many nuclear envelope proteins is not well established. This is partly because nuclear envelope proteins and their interactions are difficult to study due to the inherent resistance to extraction of nuclear envelope proteins. We have developed a novel method called MCLIP, to identify interacting partners of nuclear envelope proteins in live cells. Using MCLIP, we found three new binding partners of the inner nuclear membrane protein Samp1: the intermediate filament protein Lamin B1, the LINC complex protein Sun1 and the G-protein Ran. Furthermore, using in vitro studies, we show that Samp1 binds both Emerin and Ran directly. We have also studied the interaction between Samp1 and Ran in detail. The results show that the Samp1 binds stronger to RanGTP than RanGDP. Samp1 is the first transmembrane protein known to bind Ran and it is tempting to speculate that Samp1 may provide local binding sites for RanGTP at membranes.

Keywords: MCLIP, nuclear envelope, ran, Samp1

Procedia PDF Downloads 353
4119 Computational Approach for Grp78–Nf-ΚB Binding Interactions in the Context of Neuroprotective Pathway in Brain Injuries

Authors: Janneth Gonzalez, Marco Avila, George Barreto

Abstract:

GRP78 participates in multiple functions in the cell during normal and pathological conditions, controlling calcium homeostasis, protein folding and unfolded protein response. GRP78 is located in the endoplasmic reticulum, but it can change its location under stress, hypoxic and apoptotic conditions. NF-κB represents the keystone of the inflammatory process and regulates the transcription of several genes related with apoptosis, differentiation, and cell growth. The possible relationship between GRP78-NF-κB could support and explain several mechanisms that may regulate a variety of cell functions, especially following brain injuries. Although several reports show interactions between NF-κB and heat shock proteins family members, there is a lack of information on how GRP78 may be interacting with NF-κB, and possibly regulating its downstream activation. Therefore, we assessed the computational predictions of the GRP78 (Chain A) and NF-κB complex (IkB alpha and p65) protein-protein interactions. The interaction interface of the docking model showed that the amino acids ASN 47, GLU 215, GLY 403 of GRP78 and THR 54, ASN 182 and HIS 184 of NF-κB are key residues involved in the docking. The electrostatic field between GRP78-NF-κB interfaces and molecular dynamic simulations support the possible interaction between the proteins. In conclusion, this work shed some light in the possible GRP78-NF-κB complex indicating key residues in this crosstalk, which may be used as an input for better drug design strategy targeting NF-κB downstream signaling as a new therapeutic approach following brain injuries.

Keywords: computational biology, protein interactions, Grp78, bioinformatics, molecular dynamics

Procedia PDF Downloads 343
4118 Cannabidiol (CBD) Resistant Salmonella Strains Are Susceptible to Epsilon 34 Phage Tailspike Protein

Authors: Ibrahim Iddrisu, Joseph Ayariga, Junhuan Xu, Ayomide Adebanjo, Boakai K. Robertson, Michelle Samuel-Foo, Olufemi Ajayi

Abstract:

The rise of antimicrobial resistance is a global public health crisis that threatens the effective control and prevention of infections. Due to the emergence of pan drug-resistant bacteria, most antibiotics have lost their efficacy. Bacteriophages or their components are known to target bacterial cell walls, cell membranes, and lipopolysaccharides (LPS) and hydrolyze them. Bacteriophages, being the natural predators of pathogenic bacteria, are inevitably categorized as ‘human friends’, thus fulfilling the adage that ‘the enemy of my enemy is my friend’. Leveraging on their lethal capabilities against pathogenic bacteria, researchers are searching for more ways to overcome the current antibiotic resistance challenge. In this study, we expressed and purified epsilon 34 phage tail spike protein (E34 TSP) from the E34 TSP gene, then assessed the ability of this bacteriophage protein in the killing of two CBD-resistant strains of Salmonella spp. We also assessed the ability of the tail spike protein to cause bacteria membrane disruption and dehydrogenase depletion. We observed that the combined treatment of CBD-resistant strains of Salmonella with CBD and E34 TSP showed poor killing ability, whereas the mono treatment with E34 TSP showed considerably higher killing efficiency. This study demonstrates that the inhibition of the bacteria by E34 TSP was due in part to membrane disruption and dehydrogenase inactivation by the protein. The results of this work provide an interesting background to highlight the crucial role phage proteins such as E34 TSP could play in pathogenic bacterial control.

Keywords: cannabidiol, resistance, Salmonella, antimicrobials, phages

Procedia PDF Downloads 71
4117 Development of Peptide Inhibitors against Dengue Virus Infection by in Silico Design

Authors: Aussara Panya, Nunghathai Sawasdee, Mutita Junking, Chatchawan Srisawat, Kiattawee Choowongkomon, Pa-Thai Yenchitsomanus

Abstract:

Dengue virus (DENV) infection is a global public health problem with approximately 100 million infected cases a year. Presently, there is no approved vaccine or effective drug available; therefore, the development of anti-DENV drug is urgently needed. The clinical reports revealing the positive association between the disease severity and viral titer has been reported previously suggesting that the anti-DENV drug therapy can possibly ameliorate the disease severity. Although several anti-DENV agents showed inhibitory activities against DENV infection, to date none of them accomplishes clinical use in the patients. The surface envelope (E) protein of DENV is critical for the viral entry step, which includes attachment and membrane fusion; thus, the blocking of envelope protein is an attractive strategy for anti-DENV drug development. To search the safe anti-DENV agent, this study aimed to search for novel peptide inhibitors to counter DENV infection through the targeting of E protein using a structure-based in silico design. Two selected strategies has been used including to identify the peptide inhibitor which interfere the membrane fusion process whereby the hydrophobic pocket on the E protein was the target, the destabilization of virion structure organization through the disruption of the interaction between the envelope and membrane proteins, respectively. The molecular docking technique has been used in the first strategy to search for the peptide inhibitors that specifically bind to the hydrophobic pocket. The second strategy, the peptide inhibitor has been designed to mimic the ectodomain portion of membrane protein to disrupt the protein-protein interaction. The designed peptides were tested for the effects on cell viability to measure the toxic to peptide to the cells and their inhibitory assay to inhibit the DENV infection in Vero cells. Furthermore, their antiviral effects on viral replication, intracellular protein level and viral production have been observed by using the qPCR, cell-based flavivirus immunodetection and immunofluorescence assay. None of tested peptides showed the significant effect on cell viability. The small peptide inhibitors achieved from molecular docking, Glu-Phe (EF), effectively inhibited DENV infection in cell culture system. Its most potential effect was observed for DENV2 with a half maximal inhibition concentration (IC50) of 96 μM, but it partially inhibited other serotypes. Treatment of EF at 200 µM on infected cells also significantly reduced the viral genome and protein to 83.47% and 84.15%, respectively, corresponding to the reduction of infected cell numbers. An additional approach was carried out by using peptide mimicking membrane (M) protein, namely MLH40. Treatment of MLH40 caused the reduction of foci formation in four individual DENV serotype (DENV1-4) with IC50 of 24-31 μM. Further characterization suggested that the MLH40 specifically blocked viral attachment to host membrane, and treatment with 100 μM could diminish 80% of viral attachment. In summary, targeting the hydrophobic pocket and M-binding site on the E protein by using the peptide inhibitors could inhibit DENV infection. The results provide proof of-concept for the development of antiviral therapeutic peptide inhibitors to counter DENV infection through the use of a structure-based design targeting conserved viral protein.

Keywords: dengue virus, dengue virus infection, drug design, peptide inhibitor

Procedia PDF Downloads 358
4116 Effect of Inclination Angle on Productivity of a Direct Contact Membrane Distillation (Dcmd) Process

Authors: Adnan Alhathal Alanezi, Alanood A. Alsarayreh

Abstract:

A direct contact membrane distillation (DCMD) system was modeled using various angles for the membrane unit and a Reynolds number range of 500 to 2000 in this numerical analysis. The Navier-Stokes, energy, and species transport equations were used to create a two-dimensional model. The finite volume method was used to solve the governing equations (FVM). The results showed that as the Reynolds number grows up to 1500, the heat transfer coefficient increases for all membrane angles except the 60ᵒ inclination angle. Additionally, increasing the membrane angle to 90ᵒreduces the exit influence while increasing heat transfer. According to these data, a membrane with a 90o inclination angle (also known as a vertical membrane) and a Reynolds number of 2000 might have the smallest temperature differential. Similarly, decreasing the inclination angle of the membrane keeps the temperature difference constant between Reynolds numbers 1000 and 2000; however, between Reynolds numbers 500 and 1000, the temperature difference decreases dramatically.

Keywords: direct contact membrane distillation, membrane inclination angle, heat and mass transfer, reynolds number

Procedia PDF Downloads 121
4115 Enhanced Functional Production of a Crucial Biomolecule Human Serum Albumin in Escherichia coli

Authors: Ashima Sharma

Abstract:

Human Serum Albumin (HSA)- one of the most demanded therapeutic proteins with immense biotechnological applications- is a large multidomain protein containing 17 disulfide bonds. The current source of HSA is human blood plasma which is a limited and unsafe source. Thus, there exists an indispensable need to promote non-animal derived recombinant HSA (rHSA) production. Escherichia coli is one of the most convenient hosts which had contributed to the production of more than 30% of the FDA approved recombinant pharmaceuticals. It grows rapidly and reaches high cell density using inexpensive and simple substrates. E. coli derived recombinant products have more economic potential as fermentation processes are cheaper compared to the other expression hosts. The major bottleneck in exploiting E. coli as a host for a disulfide-rich multidomain protein is the formation of aggregates of overexpressed protein. The majority of the expressed HSA forms inclusion bodies (more than 90% of the total expressed rHSA) in the E. coli cytosol. Recovery of functional rHSA from inclusion bodies is not preferred because it is difficult to obtain a large multidomain disulfide bond rich protein like rHSA in its functional native form. Purification is tedious, time-consuming, laborious and expensive. Because of such limitations, the E. coli host system was neglected for rHSA production for the past few decades despite its numerous advantages. In the present work, we have exploited the capabilities of E. coli as a host for the enhanced functional production of rHSA (~60% of the total expressed rHSA in the soluble fraction). Parameters like intracellular environment, temperature, induction type, duration of induction, cell lysis conditions etc. which play an important role in enhancing the level of production of the desired protein in its native form in vivo have been optimized. We have studied the effect of assistance of different types of exogenously employed chaperone systems on the functional expression of rHSA in the E. coli host system. Different aspects of cell growth parameters during the production of rHSA in presence and absence of molecular chaperones in E. coli have also been studied. Upon overcoming the difficulties to produce functional rHSA in E. coli, it has been possible to produce significant levels of functional protein through engineering the biological system of protein folding in the cell, the E. coli-derived rHSA has been purified to homogeneity. Its detailed physicochemical characterization has been performed by monitoring its conformational properties, secondary and tertiary structure elements, surface properties, ligand binding properties, stability issues etc. These parameters of the recombinant protein have been compared with the naturally occurring protein from the human source. The outcome of the comparison reveals that the recombinant protein resembles exactly the same as the natural one. Hence, we propose that the E. coli-derived rHSA is an ideal biosimilar for human blood plasma-derived serum albumin. Therefore, in the present study, we have introduced and promoted the E. coli- derived rHSA as an alternative to the preparation from a human source, pHSA.

Keywords: recombinant human serum albumin, Escherichia coli, biosimilar, chaperone assisted protein folding

Procedia PDF Downloads 210
4114 Lentil Protein Fortification in Cranberry Squash

Authors: Sandhya Devi A

Abstract:

The protein content of the cranberry squash (protein: 0g) may be increased by extracting protein from the lentils (9 g), which is particularly linked to a lower risk of developing heart disease. Using the technique of alkaline extraction from the lentils flour, protein may be extracted. Alkaline extraction of protein from lentil flour was optimized utilizing response surface approach in order to maximize both protein content and yield. Cranberry squash may be taken if a protein fortification syrup is prepared and processed into the squash.

Keywords: alkaline extraction, cranberry squash, protein fortification, response surface methodology

Procedia PDF Downloads 112
4113 Characterization of the GntR Family Transcriptional Regulator Rv0792c: A Potential Drug Target for Mycobacterium tuberculosis

Authors: Thanusha D. Abeywickrama, Inoka C. Perera, Genji Kurisu

Abstract:

Tuberculosis, considered being as the ninth leading cause of death worldwide, cause from a single infectious agent M. tuberculosis and the drug resistance nature of this bacterium is a continuing threat to the world. Therefore TB preventing treatment is expanding, where this study designed to analyze the regulatory mechanism of GntR transcriptional regulator gene Rv0792c, which lie between several genes codes for some hypothetical proteins, a monooxygenase and an oxidoreductase. The gene encoding Rv0792c was cloned into pET28a and expressed protein was purified to near homogeneity by Nickel affinity chromatography. It was previously reported that the protein binds within the intergenic region (BS region) between Rv0792c gene and monooxygenase (Rv0793). This resulted in binding of three protein molecules with the BS region suggesting tight control of monooxygenase as well as its own gene. Since monooxygenase plays a key role in metabolism, this gene may have a global regulatory role. The natural ligand for this regulator is still under investigation. In relation to the Rv0792 protein structure, a Circular Dichroism (CD) spectrum was carried out to determine its secondary structure elements. Percentage-wise, 17.4% Helix, 21.8% Antiparallel, 5.1% Parallel, 12.3% turn and 43.5% other were revealed from CD spectrum data under room temperature. Differential Scanning Calorimetry (DSC) was conducted to assess the thermal stability of Rv0792, which the melting temperature of protein is 57.2 ± 0.6 °C. The graph of heat capacity (Cp) versus temperature for the best fit was obtained for non-two-state model, which concludes the folding of Rv0792 protein occurs through stable intermediates. Peak area (∆HCal ) and Peak shape (∆HVant ) was calculated from the graph and ∆HCal / ∆HVant was close to 0.5, suggesting dimeric nature of the protein.

Keywords: CD spectrum, DSC analysis, GntR transcriptional regulator, protein structure

Procedia PDF Downloads 223
4112 Preferred Left-Handed Conformation of Glycyls at Pathogenic Sites

Authors: Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu

Abstract:

The role of glycyl residues in the protein structure has lingered within the research community for the last several decades. Glycyl residue is the only amino acid that is achiral due to the lack of a side chain and can, therefore, exhibit Ramachandran conformations that are disallowed for L-amino acids. The structural and functional significance of glycyl residues with L-disallowed conformation, however, remains obscure. Through statistical analysis of various datasets, we found that the glycyls with L-disallowed conformations are over-represented at disease-associated sites and tend to be evolutionarily conserved. The mutations of L-disallowed glycyls tend to destabilize the native conformation, reduce protein solubility, and promote inter-molecular aggregations. We uncovered a structural motif referred to as “β-crescent” formed around the L-disallowed glycyl, which prevents β-sheet aggregation by disrupting the alternating pattern of β-pleats. The L-disallowed conformation of glycyls also holds predictive power to infer the pathogenic missense variants. Altogether, our observations highlight that the L-disallowed conformation of glycyls is selected to facilitate native folding and prevent inter-molecular aggregations. The findings may also have implications for designing more stable proteins and prioritizing the genetic lesions implicated in diseases.

Keywords: Ramachandran plot, β-sheet, protein stability, protein aggregation

Procedia PDF Downloads 72
4111 Hydration of Protein-RNA Recognition Sites

Authors: Amita Barik, Ranjit Prasad Bahadur

Abstract:

We investigate the role of water molecules in 89 protein-RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein-RNA interfaces are hydrated less than protein-DNA interfaces, but more than protein-protein interfaces. Majority of the waters at protein-RNA interfaces makes multiple H-bonds; however, a fraction does not make any. Those making Hbonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein-DNA interfaces, mainly due to the presence of the 2’OH, the ribose in protein-RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein-RNA interfaces is hydrated more than the major groove, while in protein-DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein-RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein-RNA recognition and should be carefully treated while engineering protein-RNA interfaces.

Keywords: h-bonds, minor-major grooves, preserved water, protein-RNA interfaces

Procedia PDF Downloads 302
4110 Effect of Silver Nanoparticles in Temperature Polarization of Distillation Membranes for Desalination Technologies

Authors: Lopez J., Mehrvar M., Quinones E., Suarez A., Romero C.

Abstract:

Membrane Distillation is an emerging technology that uses thermal and membrane steps for the desalination process to get drinking water. In this study, silver nanoparticles (AgNP) were deposited by dip-coating process over Polyvinylidene Fluoride, Fiberglass hydrophilic, and Polytetrafluoroethylene hydrophobic commercial membranes as substrate. Membranes were characterized and used in a Vacuum Membrane Distillation cell under Ultraviolet light with sea salt feed solution. The presence of AgNP increases the absorption of energy on the membrane, which improves the transmembrane flux.

Keywords: silver nanoparticles, membrane distillation, desalination technologies, heat deliver

Procedia PDF Downloads 167
4109 Effects of SRT and HRT on Treatment Performance of MBR and Membrane Fouling

Authors: M. I. Aida Isma, Azni Idris, Rozita Omar, A. R. Putri Razreena

Abstract:

40L of hollow fiber membrane bioreactor with solids retention times (SRT) of 30, 15 and 4 days were setup for treating synthetic wastewater at hydraulic retention times (HRT) of 12, 8 and 4 hours. The objectives of the study were to investigate the effects of SRT and HRT on membrane fouling. A comparative analysis was carried out for physiochemical quality parameters (turbidity, suspended solids, COD, NH3-N and PO43-). Scanning electron microscopy (SEM), energy diffusive X-ray (EDX) analyzer and particle size distribution (PSD) were used to characterize the membrane fouling properties. The influence of SRT on the quality of effluent, activated sludge quality, and membrane fouling were also correlated. Lower membrane fouling and slower rise in trans-membrane pressure (TMP) were noticed at the longest SRT and HRT of 30d and 12h, respectively. Increasing SRT results in noticeable reduction of dissolved organic matters. The best removal efficiencies of COD, TSS, NH3-N and PO43- were 93%, 98%, 80% and 30% respectively. The high HRT with shorter SRT induced faster fouling rate. The main fouling resistance was cake layer. The most severe membrane fouling was observed at SRT and HRT of 4 and 12, respectively with thickness cake layer of 17 μm as reflected by higher TMP, lower effluent removal and thick sludge cake layer.

Keywords: membrane bioreactor, SRT, HRT, fouling

Procedia PDF Downloads 527