Papers by Banu Sizirici Yildiz
Ka r ı ş t ı r ma Sür e s i Ve Pol i me r Doz a j ı nı n Al um Ça mur l a r ı nı n Şa r t l a ndı... more Ka r ı ş t ı r ma Sür e s i Ve Pol i me r Doz a j ı nı n Al um Ça mur l a r ı nı n Şa r t l a ndı r ı l ma s ı Üz e r i nde ki Et ki s i Şe ki l 4. 1 A) Köpr ül e nme Fl okül a s yonu B) Ads or bl a nmı ş Pol i me r l e Re s t a bi l i z a s yon Şe ki l 4. 2 El okt r os t a t i k Ya ma Mode l i nde Ads or bl a nmı ş Ka t yoni k Pol i me r l e Ne ga t i f Yükl ü Pa r t i kül ün Et ki l e ş i mi Şe ki l 4. 3
Bioresource Technology Reports
Histone deacetylase 10 (HDAC 10) catalyzes deacetylation of N 8acetylspermidine into spermidine i... more Histone deacetylase 10 (HDAC 10) catalyzes deacetylation of N 8acetylspermidine into spermidine in the cytosolic region of eukaryotic cells. Inhibition of HDAC 10 has clinical importance in certain types of cancers. Recently, X-ray crystal structures corresponding to the substrate-bound, tetrahedral intermediate-bound, and product-bound enzymes have been resolved using variant forms of humanized HDAC 10. Based on these structures, it was proposed that Y307 residue polarizes the carbonyl of the acetyl group in N 8acetylspermidine together with a zinc atom, which is coordinated by D174, H176, D267, and an H 2 O molecule. The H 2 O molecule undergoes nucleophilic addition to the carbonyl carbon of N 8-acetylspermidine to form the tetrahedral intermediate. During this process, it is suggested that H136 acts as a general base to deprotonate the H 2 O molecule. It is further proposed that the protonation of the amide N atom of the tetrahedral intermediate by H137 causes the deacetylation forming the final products, spermidine and acetate ion. In this study, computational models based on the ONIOM method were employed to study the proposed mechanism for the two steps of the deacetylation process based on the crystal structure of the substrate-bound enzyme. The energy profiles of each step as well as the roles of the active site residues were investigated for the catalysis. The calculated activation barrier is in good agreement with the reported k cat value.
ACS Omega
Notum is a member of serine hydrolyses that cleaves the palmitoleate moiety from Wingless-related... more Notum is a member of serine hydrolyses that cleaves the palmitoleate moiety from Wingless-related integration site (Wnt) ligands. This enzyme plays crucial functions through modulating the Wnt signaling pathway. Inhibition of Notum carries therapeutic effects against a number of maladies including osteoporosis, cancer, and Alzheimer's disease. Recently, a class of irreversible inhibitors based on esters of 4-(indolin-1-yl)-4-oxobutanoic acid have been reported. Using the crystal structures of enzyme-4-(indolin-1-yl)-4oxobutanoate adduct and 4-(indolin-1-yl)-4-oxobutanoic acid-enzyme complex, we studied computationally the proposed inhibition mechanism using model systems based on the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) method. In the first place, model systems were formulated to investigate the transesterification between the catalytic serine residue, Ser-232, and the methyl ester of 4-(indolin-1-yl)-4-oxobutanoate. In the second place, the hydrolysis mechanism of the resultant enzyme−inhibitor adduct was studied. The energetics of these steps were analyzed using a density functional theory functional in the ONIOM method. In addition, the roles of active-site residues during these steps were highlighted. It was found that the hydrolysis of the covalent adduct is highly endergonic corroborating the irreversible inhibition mechanism. These results will shed light not only on the inhibition mechanism but also on the catalytic mechanism.
Journal of Molecular Modeling, 2021
L-6-Hydroxynicotine oxidase (LHNO) is a member of monoamine oxidase (MAO) family and catalyzes co... more L-6-Hydroxynicotine oxidase (LHNO) is a member of monoamine oxidase (MAO) family and catalyzes conversion of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during bacterial degradation of nicotine. Recent studies indicated that the enzyme catalyzes oxidation of carbon-nitrogen bond instead of previously proposed carbon-carbon bond. Based on kinetics and mutagenesis studies, Asn166, Tyr311, and Lys287 as well as an active site water molecule have roles in the catalysis of the enzyme. A number of studies including experimental and computational methods support hydride transfer mechanism in MAO family as a common mechanism in which a hydride ion transfer from amine substrate to flavin cofactor is the rate-limiting step. In this study, we formulated computational models to study the hydride transfer mechanism using crystal structure of enzyme-substrate complex. The calculations involved ONIOM and DFT methods, and we evaluated the geometry and energetics of the hydride transfer process while probing the roles of active site residues. Based on the calculations involving hydride, radical, and polar mechanisms, it was concluded that hydride transfer mechanism is the only viable mechanism for LHNO.
Subtitle D of the Resource Conservation and Recovery Act (RCRA) requires a post closure period of... more Subtitle D of the Resource Conservation and Recovery Act (RCRA) requires a post closure period of 30 years for non hazardous wastes in landfills. Post closure care (PCC) activities under Subtitle D include leachate collection and treatment, groundwater monitoring, inspection and maintenance of the final cover, and monitoring to ensure that landfill gas does not migrate off site or into on site buildings. The decision to reduce PCC duration requires exploration of a performance based methodology to Florida landfills. PCC should be based on whether the landfill is a threat to human health or the environment. Historically no risk based procedure has been available to establish an early end to PCC. Landfill stability depends on a number of factors that include variables that relate to operations both before and after the closure of a landfill cell. Therefore, PCC decisions should be based on location specific factors, operational factors, design factors, post closure performance, end use, and risk analysis. The question of appropriate PCC period for Florida's landfills requires in depth case studies focusing on the analysis of the performance data from closed landfills in Florida. Based on data availability, Davie Landfill was identified as case study site for a case by case analysis of landfill stability. The performance based PCC decision system developed by Geosyntec Consultants was used for vi RD&D Research Development & Demonstration RP Regulated Parameter VOCs Volatile Organic Compounds
Journal of Physical Organic Chemistry, 2020
Human liver glycerol 3-phosphate dehydrogenase catalyzes transfer of a hydride anion from NADH to... more Human liver glycerol 3-phosphate dehydrogenase catalyzes transfer of a hydride anion from NADH to dihydroxyacetone phosphate (DHAP) forming L-glycerol 3-phosphate and NAD + in a single step reaction. It is proposed that a hydride ion is transferred from NADH to the carbonyl carbon of DHAP through a general acid catalysis in which the carbonyl oxygen of DHAP is protonated by a nearby acidic residue. Based on the crystal structure of enzyme, it was suggested that one of the active site lysine residues (Lys120/Lys204) might act as general acid for the protonation of the carbonyl oxygen at DHAP. In this study, we formulated a number of computational systems to study the hydride transfer mechanism including main active site amino acid side chains, NADH cofactor, and DHAP. The calculations involved ONIOM method consisting of DFT and molecular mechanics (MM). We evaluated the energetics of the hydride transfer process in different model systems while probing the roles of active site residues, Lys120/Lys204/Asp260. Based on calculations, protonated Asp260 has more favorable energetics to act as the general acid catalysis as compared to Lys120/204 residues.
ACS Omega, 2018
Choline oxidase catalyzes oxidation of choline into glycine betaine through a two-step reaction p... more Choline oxidase catalyzes oxidation of choline into glycine betaine through a two-step reaction pathway employing flavin as the cofactor. On the light of kinetic studies, it is proposed that a hydride ion is transferred from α-carbon of choline/hydrated-betaine aldehyde to the N5 position of flavin in the rate-determining step, which is preceded by deprotonation of hydroxyl group of choline/hydrated-betaine aldehyde to one of the possible basic side chains. Using the crystal structure of glycine betaine−choline oxidase complex, we formulated two computational systems to study the hydride-transfer mechanism including main active-site amino acid side chains, flavin cofactor, and choline as a model system. The first system used pure density functional theory calculations, whereas the second approach used a hybrid ONIOM approach consisting of density functional and molecular mechanics calculations. We were able to formulate in silico model active sites to study the hydride-transfer steps by utilizing noncovalent chemical interactions between choline/betaine aldehyde and active-site amino acid chains using an atomistic approach. We evaluated and compared the geometries and energetics of hydride-transfer process using two different systems. We highlighted chemical interactions and studied the effect of protonation state of an active-site histidine base on the energetics of transfer. Furthermore, we evaluated energetics of the second hydridetransfer process as well as hydration of betaine aldehyde.
Journal of Water Supply: Research and Technology-Aqua, 2016
Biosand filters (BSFs) have been used widely as an efficient, inexpensive, and appropriate point-... more Biosand filters (BSFs) have been used widely as an efficient, inexpensive, and appropriate point-ofuse technology. Several organizations are promoting filters without adequate testing, which may not lead to sufficiently safe devices. The objective of this study was to evaluate the performance of a modified biosand filter (MBSF) with an extra disinfection layer (brass or zero valent iron (ZVI)) and three layers of underdrain in a range of parameters including Escherichia coli, total coliform, turbidity, pH, and dissolved oxygen. On average, a 91.29% reduction (log 1.43) in total coliform, 98.7% reduction (log 2.6) in E. coli and 88.71% reduction in turbidity were observed for the control. There was a 90.11% reduction (log 1.41) in total coliform, 98.2% reduction (log 2.25) in E. coli, and 88.5% reduction in turbidity for MBSF brass. A 96.93% reduction (log 1.81) in total coliform, 97.33% reduction (log 2.36) in E. coli and 91.5% reduction in turbidity for MBSF ZVI were observed. Adding brass as a disinfection layer in MBSF did not improve bacteria and turbidity removal rates. Adding ZVI as a disinfection layer gave better turbidity and total coliform removal relative to control and MBSF brass. Water quality remained within drinking water standards for all filters.
Journal of Physical Organic Chemistry, 2017
Oxime chemistry has been proven to be a reliable bioconjugation method for biomedical application... more Oxime chemistry has been proven to be a reliable bioconjugation method for biomedical applications. Because of its stable and bio-orthogonal nature, a number of materials have been devised for in vitro and in vivo applications such as drug delivery, imaging, and biochemical assays. Polymers, synthetic molecules, nanoparticles, and biomolecules carrying alkoxyamine and aldehyde/ketone functional groups could be linked to each other through oxime bond, and a variety of modular platforms could be produced. Formation of oximes is catalyzed in acidic medium, and the proposed reaction mechanism follows classical imine formation pathways. Aniline has been found to accelerate the rate of oxime formation several orders of magnitude. In this computational study, we analyzed the proposed mechanism on model systems using DFT calculations including a solvation model. The energetics of the reaction steps in neutral and acidic conditions as well as in the presence of aniline was performed. Explicit water molecules were included in the calculations to study the energetics of solvent assisted proton transfer steps.
Journal of Nanomaterials, 2015
In recent years, magnetic nanoparticles carrying thermoresponsive polymeric coatings have gained ... more In recent years, magnetic nanoparticles carrying thermoresponsive polymeric coatings have gained increasing attention in material sciences due to the fact that resultant platforms offer controllable modalities such as imaging, drug delivery, and magnetic separation. As a result, novel materials including biosensors, therapeutic platforms, imaging agents, and magnetic separators have been realized. Since the number of publications reporting the applications of thermoresponsive magnetic nanoparticle has increased steadily over the years, a comprehensive review will be beneficial. In this paper, we aim to review publications studying applications of thermoresponsive nanoparticles in biomedical sciences as well as in environmental and chemical sciences. The paper also briefly discusses chemical formulations, characterizations, and properties of the thermoresponsive magnetic particles and then provides future outlooks.
Environment, Development and Sustainability, 2011
The required minimum 30-year post-closure care period for municipal solid waste (MSW) landfills c... more The required minimum 30-year post-closure care period for municipal solid waste (MSW) landfills can be shortened by reducing or eliminating of MSW components with long-terms effect in gas and leachate. The objectives of this study were to evaluate the relative persistence of landfill gas, leachate quantity, and selected leachate parameters using post-closure monitoring data from a case study landfill in south Florida. The relative persistence of selected decomposition byproducts in leachate were evaluated by both zero order and first order models based on monitoring data from the case study landfill. The analyses show that although gas and leachate production rates diminish very quickly, some contaminants remain in leachate as the decomposition process continues at a slower rate. For the case study landfill, the parameters which have been detected consistently at high concentrations (above MCL) included chloride, TDS, iron, bicarbonate, benzene, and vinyl chloride. Among these, vinyl chloride has the fastest and TDS has the slowest rate of disappearance in the landfill environment. The effect of waste diversion on persistence times of the selected persistent leachate quality parameters was evaluated. For example, a 40% reduction in the amount of plastics deposited in the landfill could reduce the monitoring time for benzene from 59 to 39 years. Zero order model underestimates the persistence times of the contaminants in leachate due to its linear nature. Shortening the monitoring times can provide significant savings for municipalities who need to continue monitoring leachate quality until the MCL levels are reached.
E3S Web of Conferences, 2019
Dew condensers collect dew via thermal radiation and cooling affect without the use of external e... more Dew condensers collect dew via thermal radiation and cooling affect without the use of external energy. The aim of this project was to design the 1m x 1m with 30° angle square funnel dew, fog and rainwater collector to calculate the dew yield in Abu Dhabi urban area. In addition, studies were conducted to determine whether the collected dew quantity is significant for practical use and to verify the cooling effect in condenser surface using temperature sensors. Aluminum was chosen as dew collector material due to its high emissivity. Square funnel was chosen as condenser shape due to easiness of the assembly and feasibility of its design. The quantity of the collected water depended on the weather condition. The average collected water was 0.016 ml/day (0.016 mm/m2 /day). Temperature sensor analysis showed that there was a 3.5 °C temperature difference between condenser top and bottom indicating the cooling effect of square funnel shape.
Journal of Water Process Engineering, 2018
Modified biosand filters (MBSF) and solar pasteurizers have been used as individual drinking wate... more Modified biosand filters (MBSF) and solar pasteurizers have been used as individual drinking water treatment systems around the world. The aim of this study is to evaluate the performance of a MBSF coupled with a solar pasteurizer for effective treatment systems for source water. The MBSF was designed with an extra disinfection layer with zero valent iron (ZVI) and three layers of underdrain to remove Escherichia coli (E. coli), total coliforms and turbidity. A flat solar panel with a solenoid valve was used as a solar pasteurizer and an extra disinfection system to remove residual E. coli and total coliforms from filtered water. The pasteurizer produced an average of 4.5 l of pasteurized water per day. 75°C was selected as pasteurization temperature. A 96.25% reduction (log 1.65) in total coliforms, 98% reduction (log 2.27) in E. coli and 94.8% reduction in turbidity was observed in the filtered water samples. After the pasteurization, 100% of the E. coli and 99.99% of the total coliforms reductions were observed in the filtered and the unfiltered water. The turbidity level of the pasteurized unfiltered water did not meet the drinking water standards. However, the water quality met World Health Organization drinking water standards for the MBSF system coupled with the solar pasteurizer.
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Papers by Banu Sizirici Yildiz