Search results for: the binding energy

Authors: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from x-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for x-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across x-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: biomacromolecular structure, coenzyme, electron density discrepancy analysis, x-ray crystallography

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Authors: J. Gochermann

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German energy market is under historical change. Turning-off the nuclear power plants and intensive subsidization of the renewable energies causes a paradigm change from big central energy production and distribution to more local structures, bringing the energy production near to the consumption. The formerly big energy market with only a few big energy plants and grid operating companies is changing into a disperse market with growing numbers of small and medium size companies (SME) generating new value-added products and services. This change in then energy market, in Germany called the “Energiewende”, inverts also the previous innovation system. Big power plants and large grids required also big operating companies. Innovations in the energy market focused mainly on big projects and complex energy technologies. Innovation in the new energy market structure is much more dispersed. Increasing number of SME is now able to develop energy production and storage technologies, smart technologies to control the grids, and numerous new energy related services. Innovation is now regional distributed, which is a remarkable problem for the old big energy companies. The paper will explain the change in the German energy market and the paradigm change as well as the consequences for the innovation structure in the German energy market. It will show examples how SME participate from this change and how innovation systems, as well for the big companies and for SME, can be adapted.

Keywords: changing energy markets, disperse innovation, new value-added products and services, SME

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Authors: Adavbiele Airewe Stephen

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Sustainable energy use is exploiting energy resources within acceptable levels of global resource depletion without destroying the ecological balance of an area. In the context of sustainability, the rush to quell the energy crisis of the fossil fuels of the 1970's by embarking on nuclear energy technology has now been seen as a disaster. In the circumstance, action (policy) suggested in this study to avoid future occurrence is exergy maximization/entropy generation minimization and the use is renewable energy technologies that are hybrid based. Thirty-two (32) selected hybrid renewable energy technologies were assessed with respect to their energetic efficiencies and entropy generation. The results indicated that determining which of the hybrid technologies is the most efficient process and sustainable is a matter of defining efficiency and knowing which of them possesses the minimum entropy generation.

Keywords: entropy, exergy, hybrid renewable energy technologies, sustainability

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Authors: Francisco Duarte, Adelino Ferreira, Paulo Fael

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With the growing need for alternative energy sources, research into energy harvesting technologies has increased considerably in recent years. The particular case of energy harvesting on road pavements is a very recent area of research, with different technologies having been developed in recent years. However, none of them have presented high conversion efficiencies nor technical or economic viability. This paper deals with the development of a mechanical system to implement on a road pavement energy harvesting electromechanical device, to transmit energy from the device surface to an electrical generator. The main goal is to quantify the energy harvesting, transmission and conversion efficiency of the proposed system and compare it with existing systems. Conclusions about the system’s efficiency are presented.

Keywords: road pavement, energy harvesting, energy conversion, system modelling

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Authors: Umar Saeed

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Peptidyl-prolyl cis/trans isomerases Par14 and Par17 in humans play crucial roles in diverse cellular processes, including protein folding, chromatin remodeling, DNA binding, ribosome biogenesis, and cell cycle progression. However, the effects of Par14 and Par17 on viral replication have been explored to a limited extent. We first time discovered their influential roles in promoting Hepatitis B Virus replication. In this study, we observed that in the presence of HBx, either Par14 or Par17 could upregulate HBV replication. However, in the absence of HBx, neither Par14 nor Par17 had any effect on replication. Their mechanism of action involves binding to specific motifs within HBc and HBx proteins. Notably, they target the conserved 133Arg-Pro134 (RP) motif of HBc and the 19RP20-28RP29 motifs of HBx. This interaction is fundamental for the stability of HBx, core particles, and HBc. Par14 and Par17 exhibit versatility by binding both outside and inside core particles, thereby facilitating core particle assembly through their participation in HBc dimer-dimer interactions. NAGE and immunoblotting analyses unveiled the binding of Par14/Par17 to core particles. Co-immunoprecipitation experiments further demonstrated the interaction of Par14/Par17 with core particle assembly-defective and dimer-positive HBc-Y132A. It's essential to emphasize that R133 is the key residue in the HBc RP motif that governs their interaction with Par14/Par17. Chromatin immunoprecipitation conducted on HBV-infected cells elucidated the participation of residues S19 and E46/D74 in Par14 and S44 and E71/D99 in Par17 in the recruitment of 133RP134 motif-containing HBc into cccDNA. Depleting PIN4 in liver cell lines results in a significant reduction in cccDNA levels, pgRNA, sgRNAs, HBc, core particle assembly, and HBV DNA synthesis. Notably, parvulin inhibitors like juglone and PiB have proven to be effective in substantially reducing HBV replication. These inhibitors weaken the interaction between HBV core particles and Par14/Par17, underscoring the dynamic nature of this interaction. It's also worth noting that specific Par14/Par17 inhibitors hold promise as potential therapeutic options for chronic hepatitis B.

Keywords: Par14Par17, HBx, HBc, cccDNA, HBV

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Authors: Rojin Bana Derakhshan, Abbas Toloie

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For the purpose of optimizing and developing energy efficiency in building, it is required to recognize key elements of success in optimization of energy consumption before performing any actions. Surveying Principal Components is one of the most valuable result of Linear Algebra because the simple and non-parametric methods are become confusing. So that energy management system implemented according to energy management system international standard ISO50001:2011 and all energy parameters in building to be measured through performing energy auditing. In this essay by simulating used of data mining, the key impressive elements on energy saving in buildings to be determined. This approach is based on data mining statistical techniques using feature selection method and fuzzy logic and convert data from massive to compressed type and used to increase the selected feature. On the other side, influence portion and amount of each energy consumption elements in energy dissipation in percent are recognized as separated norm while using obtained results from energy auditing and after measurement of all energy consuming parameters and identified variables. Accordingly, energy saving solution divided into 3 categories, low, medium and high expense solutions.

Keywords: energy saving, key elements of success, optimization of energy consumption, data mining

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Authors: Asli Faiza, Khamouli Saida

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With the development of computer tools over the past 20 years. Molecular modeling and, more precisely, molecular docking has very quickly entered field of pharmaceutical research. EGFR enzyme involved in cancer disease.Our work consists of studying the inhibition of EGFR (1M17) with deferent inhibitors derived from quinazoline and quinoline by molecular docking. The values of ligands L148 and L177 are the best ligands for inhibit the activity of 1M17 since it forms a stable complex with this enzyme by better binding to the active site. The results obtained show that the ligands L148 and L177 give weak interactions with the active site residues EGFR (1M17), which stabilize the complexes formed of this ligands, which gives a better binding at the level of the active site, and an RMSD of L148 [1,9563 Å] and of L177 [ 1,2483 Å]. [1, 9563, 1.2483] Å

Keywords: docking, EGFR, quinazoline, quinoliène, MOE

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Authors: Yuichi Miyamoto

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In regards to the energy sector in the modern period, two points were raised. First is a vast and growing energy demand, and second is an environmental impact associated with it. The enormous consumption of fossil fuel to the mobile unit is leading to its rapid depletion. Nuclear power is not the only problem. A modal shift that utilizes personal transporters and independent power, in order to realize a sustainable society, is very effective. The paper proposes that the world will continue to work on this. Energy of the future society, innovation in battery technology and the use of natural energy is a big key. And it is also necessary in order to save on energy consumption.

Keywords: natural energy, modal shift, personal transportation, battery

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Authors: Deepika Bhaskar, Neena Wadehra, Megha Gulati, Aruna Narula, R. Vishnu, Gunjan Katyal

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With drug resistance becoming widespread in Plasmodium falciparum infections, development of the alternative drugs is the desired strategy for prevention and cure of malaria. Three drug targets were selected to screen promising drug molecules from the GSK library of around 14000 molecules. Using an in silico structure-based drug designing approach, the differences in binding energies of the substrate and inhibitor were exploited between target sites of parasite and human to design a drug molecule against Plasmodium. The docking studies have shown several promising molecules from GSK library with more effective binding as compared to the already known inhibitors for the drug targets. Though stronger interaction has been shown by several molecules as compare to reference, few molecules have shown the potential as drug candidates though in vitro studies are required to validate the results.

Keywords: plasmodium, malaria, drug targets, in silico studies

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Authors: Alireza Jalalvand, Maryam Saleh, Somayeh Behjat Khatouni, Zahra Bahri Najafi, Foroozan Fatahinia, Narges Ismailzadeh, Behrokh Farahmand

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Object: In the last two decades, the recent outbreak of Coronavirus (SARS-CoV-2) imposed a global pandemic in the world. Despite the increasing prevalence of the disease, there are no effective drugs to treat it. A suitable and rapid way to afford an effective drug and treat the global pandemic is a computational drug study. This study used molecular docking methods to examine the potential inhibition of over 50 antiviral drugs against three fundamental proteins of SARS-CoV-2. METHODS: Through a literature review, three important proteins (a key protease, RNA-dependent RNA polymerase (RdRp), and spike) were selected as drug targets. Three-dimensional (3D) structures of protease, spike, and RdRP proteins were obtained from the Protein Data Bank. Protein had minimal energy. Over 50 antiviral drugs were considered candidates for protein inhibition and their 3D structures were obtained from drug banks. The Autodock 4.2 software was used to define the molecular docking settings and run the algorithm. RESULTS: Five drugs, including indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, exhibited the highest inhibitory potency against all three proteins based on the binding energies and drug binding positions deduced from docking and hydrogen-bonding analysis. Conclusions: According to the results, among the drugs mentioned, saquinavir and lopinavir showed the highest inhibitory potency against all three proteins compared to other drugs. It may enter laboratory phase studies as a dual-drug treatment to inhibit SARS-CoV-2.

Keywords: covid-19, drug repositioning, molecular docking, lopinavir, saquinavir

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Authors: Florence Chinyere Nwangwu, Rosemary Ene

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An experimental study was carried out to develop an adhesive from Prosopis africana seed endosperm. The Prosopis seeds for this work were obtained from Enugu State in the South East part of Nigeria. The Prosopis seeds were prepared by separating the Prosopis endosperm from the seed coat and cotyledon. The dry adhesive gotten from the endosperm was later dissolved to get the adhesive solution. Confirmatory tests like viscosity, density, pH, and binding strength were carried out. The effect of time, temperature, concentration on the yield and properties of the adhesive were investigated. The results obtained showed that increase in concentration, time, temperature decreases the viscosity of the Prosopis adhesive and yield of Prosopis endosperm. It was also deduced that increase in viscosity increases the binding strength of the Prosopis adhesive. The percentage of the adhesive yield from Prosopis endosperm showed that the commercialization of the seed in Nigeria will be possible and profitable.

Keywords: adhesive, Prosopis, viscosity, endosperm

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Authors: Habib Ur Rahman Habib

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Renewable energy resources are being realized as suitable options in hybrid energy planning for on-grid and micro grid. In this paper, operation, planning and optimal design of on-grid distributed energy resources based hybrid system are investigated. The aim is to minimize the cost of the overall energy system keeping in view the environmental emission and minimum penetration of conventional energy resources. Seven grid connected different case studies including diesel only, diesel-renewable based, and renewable based only are designed to perform economic analysis, operational planning and emission. Sensitivity analysis is implemented to investigate the impact of different parameters on the performance of energy resources.

Keywords: data management, renewable energy, distributed energy, smart grid, micro-grid, modeling, energy planning, design optimization

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Authors: Sara Mota Carmo

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Nowadays, there is an increasing demand for buildings to be energetically autonomous through energy generation systems from renewable sources, according to the concept of a net zero energy building (NZEB). In this sense, the present study aims to study the integration of wind energy through piezoelectricity applied to the building skin. As a methodology, a reduced-scale prototype of a building was developed and tested in a wind tunnel, with the four façades monitored by recording the energy produced by each. The applied wind intensities varied between 2m/s and 8m/s and the four façades were compared with each other regarding the energy produced according to the intensity of wind and position in the wind. The results obtained concluded that it was not a sufficient system to generate sources to cover family residential buildings' energy needs. However, piezoelectricity is expanding and can be a promising path for a wind energy system in architecture as a complement to other renewable energy sources.

Keywords: adaptative building skin, kinetic façade, wind energy in architecture, NZEB

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Authors: Kate Smith, Shuming Liu, Yi Liu, Dragan Savic, Gustaf Olsson, Tian Chang, Xue Wu

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In a water supply system, a great deal of care goes into sourcing, treating and delivering water to consumers, but less thought is given to the energy consumed during these processes. This study uses 2011 data to quantify energy use for urban water supply in China and investigates population density as a possible influencing factor. The objective is to provide information that can be used to develop energy-conscious water infrastructure policy, calculate the energy co-benefits of water conservation and compare energy use between China and other countries. The average electrical energy intensity and per capita electrical energy consumption for urban water supply in China in 2011 were 0.29 kWh/m3 and 33.2 kWh/cap•yr, respectively. Comparison between provinces revealed a direct correlation between energy intensity of urban water supply and population served per unit length of pipe. This could imply energy intensity is lower when more densely populated areas are supplied by relatively dense networks of pipes. This study also found that whereas the percentage of energy used for urban water supply tends to increase with the percentage of population served this increase is slower where water supply is more energy efficient and where a larger percentage of population is already supplied.

Keywords: china, electrical energy use, water-energy nexus, water supply

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Authors: Amir Sattari

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For newly produced houses and energy renovations, an energy calculation needs to be conducted. This is done to verify whether the energy consumption criteria of the house -to reach the energy targets by 2020 and 2050- are in-line with the norms. The main purpose of this study is to confirm whether easy to use energy calculation software or hand calculations used by small companies or individuals give logical results compared to advanced energy simulation program used by researchers or bigger companies. There are different methods for calculating energy consumption. In this paper, two energy calculation programs are used and the relation of energy consumption with solar radiation is compared. A hand calculation is also done to validate whether the hand calculations are still reasonable. The two computer programs which have been used are TMF Energi (the easy energy calculation variant used by small companies or individuals) and IDA ICE - Indoor Climate and Energy (the advanced energy simulation program used by researchers or larger companies). The calculations are done for a standard house from the Swedish house supplier Fiskarhedenvillan. The method is based on having the same conditions and inputs in the different calculation forms so that the results can be compared and verified. The house has been faced differently to see how the orientation affects energy consumption in different methods. The results for the simulations are close to each other and the hand calculation differs from the computer programs by only 5%. Even if solar factors differ due to the orientation of the house, energy calculation results from different computer programs and even hand calculation methods are in line with each other.

Keywords: energy calculation, energy consumption, energy simulation, IDA ICE, TMF energi

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Authors: Anjani Kumar Tiwari, Neelam Kumari, Anil Mishra

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The 18-kDa translocator protein (TSPO) previously called as peripheral benzodiazepine receptor, is proven biomarker for variety of neuroinflammation. TSPO is tryptophane rich five transmembranal protein found on outer mitochondrial membrane of steroid synthesising and immunomodulatory cells. In case of neuronal damage or inflammation the expression level of TSPO get upregulated as an immunomodulatory response. By utilizing Benzoxazolone as a basic scaffold, series of TSPO ligands have been designed followed by their screening through in silico studies. Synthesis has been planned by employing convergent methodology in six high yielding steps. For the synthesized ligands the ‘in vitro’ assay was performed to determine the binding affinity in term of Ki. On ischemic rat brain, autoradiography studies were also carried to check the specificity and affinity of the designed radiolabelled ligand for TSPO.Screening was performed on the basis of GScore of CADD based schrodinger software. All the modified and better prospective compound were successfully carried out and characterized by spectroscopic techniques (FTIR, NMR and HRMS). In vitro binding assay showed best binding affinity Ki = 6.1+ 0.3 for TSPO over central benzodiazepine receptor (CBR) Ki > 200. ARG studies indicated higher uptake of two analogues on the lesion side compared with that on the non-lesion side of ischemic rat brains. Displacement experiments with unlabelled ligand had minimized the difference in uptake between the two sides which indicates the specificity of the ligand towards TSPO receptor.

Keywords: TSPO, PET, imaging, Acetamidobenzoxazolone

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Authors: Abdelhak Bouchakour, Mustafa Brahami, Layachi Zaghba

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The use of photovoltaic energy offers an inexhaustible supply of energy but also a clean and non-polluting energy, which is a definite advantage. The geographical location of Algeria promotes the development of the use of this energy. Indeed, given the importance of the intensity of the radiation received and the duration of sunshine. For this reason, the objective of our work is to develop a data-processing tool (software) of calculation and optimization of dimensioning of the photovoltaic installations. Our approach of optimization is basing on mathematical models, which amongst other things describe the operation of each part of the installation, the energy production, the storage and the consumption of energy.

Keywords: solar panel, solar radiation, inverter, optimization

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Authors: Francesca Scalisi, Cesare Sposito

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The building construction industry consumes a large amount of resources and energy, both during construction (embodied energy) and during the operational phase (operating energy). This paper presents a review of the literature on low carbon and low embodied energy materials in buildings. The embodied energy comprises the energy consumed during the extraction, processing, transportation, construction, and demolition of building materials. While designing a nearly zero energy building, it is necessary to choose and use materials, components, and technologies that allow to reduce the consumption of energy and also to reduce the emissions in the atmosphere during all the Life Cycle Assessment phases. The appropriate choice of building materials can contribute decisively to reduce the energy consumption of the building sector. The increasing worries for the environmental impact of construction materials are witnessed by a lot of studies. The mentioned worries have brought again the attention towards natural materials. The use of more sustainable construction materials and construction techniques represent a major contribution to the eco-efficiency of the construction industry and thus to a more sustainable development.

Keywords: embodied energy, embodied carbon, life cycle assessment, architecture, sustainability, material construction

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Authors: Noel Chellan

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Energy is the life-blood of development. All human societies have been and still are dependent on energy – some societies more than others. With regard to energy in South Africa, previous policies of the apartheid regime neglected the energy needs of poor black communities in general – and rural communities in particular. Since South Africa’s first democratic elections in 1994 – whilst millions of South African households have received electricity from the national electricity grid, there are still many rural communities that are still experiencing challenges in relation to both electricity deprivation as well as provision. This paper looks at the energy-mix of the Mnweni rural community in South Africa and argues that understanding energy is key to understanding the nature and forms of development of any community or country, for that matter. The paper engages with the energy trends in the rural community of Mnweni from the days of apartheid until 2021. It also looks at agricultural practises from an energy perspective. Such an energy perspective will enable one to assess the pace and scale of development in rural Mnweni.

Keywords: rural, energy, development, apartheid

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Authors: Juan Sepúlveda

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Energy is a fundamental component in sustainability, the access and use of this resource is related with economic growth, social improvements, and environmental impacts. In this sense, energy efficiency has been studied as a factor that enhances the positive impacts of energy in communities; however, the implementation of efficiency requires strong policy and strategies that usually rely on individual measures focused in independent dimensions. In this paper, the problem of energy efficiency as a multi-objective problem is studied, using scientometric analysis to discover trends and patterns that allow to identify the main variables and study approximations related with a further development of models to integrate energy efficiency and MCA into policy making for small communities.

Keywords: energy efficiency, MCA, scientometric, trends

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Authors: Esther Ushike Akashie

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No matter who you are, where you are from and irrespective of age and gender, there is a universal need for power and energy. Every year, this need grows even more urgent the more scientific and technological inventions advance. Due to this fact, we find that majority of the research related to energy and power has been focused on finding new and innovative ways to produce power. Furthermore, we observe that because of the environmental state of our world today and the impact of climate change, one of the most explored routes of study has been the use of renewable energies. In this paper, we will be looking at one of the oldest forms of renewable energy, hydroelectric energy. First off, an overview of its history, sources, technical aspects, and applications will be evaluated. After which, we will then proceed to understand the main benefits and drawbacks of this form of renewable energy and offer insights on how it can be better utilized in our world today.

Keywords: hydropower, hydroelectric energy, advantages, disadvantages

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Authors: Onur Elma, Giray E. Kıral, Ugur S. Selamoğuları, Mehmet Uzunoğlu, Bulent Vural

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Electrical energy has become indispensable for people's lives and with rapidly developing technology and continuously changing living standards the need for the electrical energy has been on the rise. Therefore, both energy generation and efficient use of energy are very important topics. Smart grid concept has been introduced to provide monitoring, energy efficiency, reliability and energy quality. Under smart grid concept, smart homes, which can be considered as key component in smart grid operation, have appeared as another research area. In this study, first, smart grid research in the world will be reviewed. Then, overview of smart grid applications in Turkey will be given.

Keywords: energy efficiency, smart grids, smart home, applications

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Authors: Elham Delzendeh, Song Wu, Mustafa Al-Adhami, Rima Alaaeddine

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Over the last 15 years, prediction of energy consumption has become a common practice and necessity at different stages of the building’s lifecycle, particularly, at the design and post-occupancy stages for planning and maintenance purposes. This is due to the ever-growing response of governments to address sustainability and reduction of CO₂ emission in the building sector. However, there is a level of uncertainty in the estimation of energy consumption in buildings. The accuracy of energy consumption predictions is directly related to the precision of the initial inputs used in the energy assessment process. In this study, multiple cases of large non-residential buildings at design, construction, and post-occupancy stages are investigated. The energy consumption process and inputs, and the actual and predicted energy consumption of the cases are analysed. The findings of this study have pointed out and evidenced various parameters that cause uncertainty in the prediction of energy consumption in buildings such as modelling, location data, and occupant behaviour. In addition, unavailability and insufficiency of energy-consumption-related inputs at different stages of the building’s lifecycle are classified and categorized. Understanding the roots of uncertainty in building energy analysis will help energy modellers and energy simulation software developers reach more accurate energy consumption predictions in buildings.

Keywords: building lifecycle, efficiency, energy analysis, energy performance, uncertainty

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Authors: Nneka Osuchukwu, Leonid Shpanin

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The concept of converting the kinetic energy of quadcopter propellers into electrical energy is considered in this contribution following the feasibility study of the propeller vibrations, theoretical energy conversion, and simulation techniques. Analysis of the propeller vibration performance is presented via graphical representation of calculated and simulated parameters, in order to demonstrate the possibility of recovering the harvested energy from the propeller vibrations of the quadcopter while the quadcopter is in operation. Consideration of using piezoelectric materials in such concept, converting the mechanical energy of the propeller into the electrical energy, is given. Photographic evidence of the propeller in operation is presented and discussed together with experimental results to validate the theoretical concept.

Keywords: energy harvesting, piezoelectric material, propeller vibration, unmanned aerial vehicle

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Authors: Santosh Ghosh, Vinod Kumar Yadav, Vivekananda Mukherjee, Ishta Garg

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India, akin to the rest of the world today, is grappling with balancing act between ever increasing demand for energy and alarmingly high level of green house gas emission, which is inevitable corollary of energy production in the conventional way. Researchers and energy policy makers around the world are now focusing on renewable energy (RE) technologies to find solution to this crisis. In India various agencies at both national and state level has been set up and bestowed with responsibility of development of renewable energy technologies, viz. Ministry of New Renewable Energy (MNRE), National Vidyut Vyapar Nigam Ltd. (NVVNL), Indian Renewable Energy Development Agency Limited (IREDA) and RE Development Agencies in respective states. In the present work, the preparedness of India in terms of forming institutional and policy frame work briefly discussed. Status of implementation of RE technologies state wise and of India as a whole, critically reviewed.

Keywords: energy policy, energy sustainability, renewable energy, IREDA

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Authors: Joanna Gerszon, Aleksandra Rodacka

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In the pathogenesis of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease, protein and peptide aggregation processes play a vital role in contributing to the formation of intracellular and extracellular protein deposits. One of the major components of these deposits is the oxidatively modified glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Therefore, the purpose of this research was to answer the question whether piceatannol, a stilbene derivative, counteracts and/or slows down oxidative stress-induced GAPDH aggregation. The study also aimed to determine if this natural occurring compound prevents unfavorable nuclear translocation of GAPDH in hippocampal cells. The isothermal titration calorimetry (ITC) analysis indicated that one molecule of GAPDH can bind up to 8 molecules of piceatannol (7.3 ± 0.9). As a consequence of piceatannol binding to the enzyme, the loss of activity was observed. Parallel with GAPDH inactivation the changes in zeta potential, and loss of free thiol groups were noted. Nevertheless, the ligand-protein binding does not influence the secondary structure of the GAPDH. Precise molecular docking analysis of the interactions inside the active center allowed to presume that these effects are due to piceatannol ability to assemble a covalent binding with nucleophilic cysteine residue (Cys149) which is directly involved in the catalytic reaction. Molecular docking also showed that simultaneously 11 molecules of ligand can be bound to dehydrogenase. Taking into consideration obtained data, the influence of piceatannol on level of GAPDH aggregation induced by excessive oxidative stress was examined. The applied methods (thioflavin-T binding-dependent fluorescence as well as microscopy methods - transmission electron microscopy, Congo Red staining) revealed that piceatannol significantly diminishes level of GAPDH aggregation. Finally, studies involving cellular model (Western blot analyses of nuclear and cytosolic fractions and confocal microscopy) indicated that piceatannol-GAPDH binding prevents GAPDH from nuclear translocation induced by excessive oxidative stress in hippocampal cells. In consequence, it counteracts cell apoptosis. These studies demonstrate that by binding with GAPDH, piceatannol blocks cysteine residue and counteracts its oxidative modifications, that induce oligomerization and GAPDH aggregation as well as it prevents hippocampal cells from apoptosis by retaining GAPDH in the cytoplasm. All these findings provide a new insight into the role of piceatannol interaction with GAPDH and present a potential therapeutic strategy for some neurological disorders related to GAPDH aggregation. This work was supported by the by National Science Centre, Poland (grant number 2017/25/N/NZ1/02849).

Keywords: glyceraldehyde-3-phosphate dehydrogenase, neurodegenerative disease, neuroprotection, piceatannol, protein aggregation

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Authors: Sujata Sharma, Avinash Singh, Lovely Gautam, Pradeep Sharma, Mau Sinha, Asha Bhushan, Punit Kaur, Tej P. Singh

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Peptidyl-tRNA hydrolase (Pth) Pth is an essential bacterial enzyme that catalyzes the release of free tRNA and peptide moeities from peptidyl tRNAs during stalling of protein synthesis. In order to design inhibitors of Pth from Pseudomonas aeruginosa (PaPth), we have determined the structures of PaPth in its native state and in the bound states with two compounds, amino acylate-tRNA analogue (AAtA) and 5-azacytidine (AZAC). The peptidyl-tRNA hydrolase gene from Pseudomonas aeruginosa was amplified by Phusion High-Fidelity DNA Polymerase using forward and reverse primers, respectively. The E. coliBL21 (λDE3) strain was used for expression of the recombinant peptidyl-tRNA hydrolase from Pseudomonas aeruginosa. The protein was purified using a Ni-NTA superflow column. The crystallization experiments were carried out using hanging drop vapour diffusion method. The crystals diffracted to 1.50 Å resolution. The data were processed using HKL-2000. The polypeptide chain of PaPth consists of 194 amino acid residues from Met1 to Ala194. The centrally located β-structure is surrounded by α-helices from all sides except the side that has entrance to the substrate binding site. The structures of the complexes of PaPth with AAtA and AZAC showed the ligands bound to PaPth in the substrate binding cleft and interacted with protein atoms extensively. The residues that formed intermolecular hydrogen bonds with the atoms of AAtA included Asn12, His22, Asn70, Gly113, Asn116, Ser148, and Glu161 of the symmetry related molecule. The amino acids that were involved in hydrogen bonded interactions in case of AZAC included, His22, Gly113, Asn116, and Ser148. As indicated by fittings of two ligands and the number of interactions made by them with protein atoms, AAtA appears to be a more compatible with the structure of the substrate binding cleft. However, there is a further scope to achieve a better stacking than that of O-tyrosyl moiety because it is not still ideally stacked. These observations about the interactions between the protein and ligands have provided the information about the mode of binding of ligands, nature and number of interactions. This information may be useful for the design of tight inhibitors of Pth enzymes.

Keywords: peptidyl tRNA hydrolase, Acinetobacter baumannii, Pth enzymes, O-tyrosyl

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Authors: Boukli Hacene Faiza, Soufi Wassila, Ghalem Said

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The oral antidiabetics drugs such as alpha glucosidase inhibitors present undesirable effects like acarbose. Flavonoids are class of molecules widely distributed in plants, for this reason we are interested in our work to study the inhibition in silico of alpha glucosidase by natural ligands ( flavonoids analogues) using molecular modeling methods using MOE (Molecular Operating Environment) software to predict their interaction with this enzyme with score energy, ADME /T tests and druglikeness properties experiments. Two flavonoids Beicalein and Apigenin have high binding affinity with alpha glucosidase with lower IC50 supposed potent inhibitors.

Keywords: alpha glucosidase, flavonoides analogues, drug research, molecular modeling

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Authors: S. Junaid S. Qazi, Denice C. Bay, Raymond Chew, Raymond J. Turner

Abstract:

EmrE, a member of the small multidrug resistance protein family in bacteria is considered to be the archetypical member of its family. It confers host resistance to a wide variety of quaternary cation compounds (QCCs) driven by proton motive force. Generally, purification yield is a challenge in all membrane proteins because of the difficulties in their expression, isolation and solubilization. EmrE is extremely hydrophobic which make the purification yield challenging. We have purified EmrE protein using two different approaches: organic solvent membrane extraction and hexahistidine (his6) tagged Ni-affinity chromatographic methods. We have characterized changes present between ligand affinity of untagged and his6-tagged EmrE proteins in similar membrane mimetic environments using biophysical experimental techniques. Purified proteins were solubilized in a buffer containing n-dodecyl-β-D-maltopyranoside (DDM) and the conformations in the proteins were explored in the presence of four QCCs, methyl viologen (MV), ethidium bromide (EB), cetylpyridinium chloride (CTP) and tetraphenyl phosphonium (TPP). SDS-Tricine PAGE and dynamic light scattering (DLS) analysis revealed that the addition of QCCs did not induce higher multimeric forms of either proteins at all QCC:EmrE molar ratios examined under the solubilization conditions applied. QCC binding curves obtained from the Trp fluorescence quenching spectra, gave the values of dissociation constant (Kd) and maximum specific one-site binding (Bmax). Lower Bmax values to QCCs for his6-tagged EmrE shows that the binding sites remained unoccupied. This lower saturation suggests that the his6-tagged versions provide a conformation that prevents saturated binding. Our data demonstrate that tagging an integral membrane protein can significantly influence the protein.

Keywords: small multidrug resistance (SMR) protein, EmrE, integral membrane protein folding, quaternary ammonium compounds (QAC), quaternary cation compounds (QCC), nickel affinity chromatography, hexahistidine (His6) tag

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Authors: Pamita Awasthi, Kirna, Shilpa Dogra, Manu Vatsal, Ritu Barthwal

Abstract:

Doxorubicin, also known as adriamycin, is an anthracycline class of drug used in cancer chemotherapy. It is used in the treatment of non-Hodgkin’s lymphoma, multiple myeloma, acute leukemias, breast cancer, lung cancer, endometrium cancer and ovary cancers. It functions via intercalating DNA and ultimately killing cancer cells. The major side effects of doxorubicin are hair loss, myelosuppression, nausea & vomiting, oesophagitis, diarrhoea, heart damage and liver dysfunction. The minor modifications in the structure of compound exhibit large variation in the biological activity, has prompted us to carry out the synthesis of sulfonamide derivatives. Sulfonamide is an important feature with broad spectrum of biological activity such as antiviral, antifungal, diuretics, anti-inflammatory, antibacterial and anticancer activities. Structure of the synthesized compound N-(1-methyl-2-oxo-2-N-methyl anilino-ethyl)benzene sulfonamide confirmed by proton nuclear magnetic resonance (1H NMR),13C NMR, Mass and FTIR spectroscopic tools to assure the position of all protons and hence stereochemistry of the molecule. Further we have reported the binding potential of synthesized sulfonamide analogues in comparison to doxorubicin drug using Auto Dock 4.2 software. Computational binding energy (B.E.) and inhibitory constant (Ki) has been evaluated for the synthesized compound in comparison of doxorubicin against Poly (dA-dT).Poly (dA-dT) and Poly (dG-dC).Poly (dG-dC) sequences. The in vitro cytotoxic study against human breast cancer cell lines confirms the better anticancer activity of the synthesized compound over currently in use anticancer drug doxorubicin. The IC50 value of the synthesized compound is 7.12 µM where as for doxorubicin is 7.2 µ.

Keywords: Doxorubicin, auto dock, in silco, in vitro

Procedia PDF Downloads 393