LEE- Kimya Mühendisliği-Doktora
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ÖgeExploring functional dynamıcs of bacterial and human ribosome structures via coarse grained techniques(Fen Bilimleri Enstitüsü, 2020) Güzel, Pelin ; Kürkçüoğlu Levitas, Ayşe Özge ; 638208 ; Kimya Mühendisliği Ana Bilim DalıThe ribosome is a molecular machine that catalyzes protein synthesis in three kingdoms of life. This process is regulated by the binding of several protein factors to the main ribosomal complex core during different steps of translation, which are initiation, elongation, termination and recycling. This thesis employs coarse-grained (CG) computational techniques that focuses on differences/similarities in especially dynamical behavior between bacterial and human ribosomal complexes at different stages of translation. Investigating the allosteric communication pathways between distant functional sites of the molecular machine is the other focus. In a CG model, sets of atoms are represented by pseudo-atoms to decrease the degrees of freedom and simulation cpu time. In this thesis, residue interaction network, CG molecular dynamics (MD) simulations and anisotropic network model (ANM), which all use reduced representations of the structures based on one-bead coarse-graining, are employed. The findings of at least 500 ns CGMD simulations and ANM using normal mode analysis are interpreted to get an insight into the overall dynamical behavior of ribosomal complexes. Both methods give consistent results with experimental data on the ribosomal complexes. In order to map allosteric communications in the complexes, perturbation response scanning (PRS) and k-shortest pathways calculations are performed using the CGMD trajectories and the residue network model, respectively. PRS provides information on the influence or effectiveness of a given residue in signal transmission. k-shortest pathways calculations requires a source and a sink node and calculates suboptimal pathways. k-shortest path technique is applied to residue interaction networks. CGMD calculations are performed by the RedMD software. ANM using normal mode analysis, residue interaction network model and k-shortest pathways calculations are performed by in-house codes. CGMD calculations are performed on T. thermophilus, E. coli and H. sapiens ribosomal structures. Comparison of experimental and theoretical B-factors (both calculated from CGMD and ANM) shows that the findings are in accord with experimental data. Correlation coefficients are especially in an acceptable range (0.60-0.70) for rRNA portions between experimental-CGMD findings. Most fluctuating parts are found at the solvent-exposed sites on both 30S (small subunit) and 50S (large subunit). For the bacterial ribosome case; head, beak and spur of 30S are found as highly flexible parts. Additionally, some of the sites around the neck where tRNAs and mRNA bind to the ribosome are also flexible. Results point to two flexible fragments in the 50S. One is the L1 stalk which is composed of the uL1 protein and helices H76-H78 of the 23S rRNA. The release of the E-tRNA requires the correct positioning of L1 stalk. Additionally, L7/L12 stalk is another high fluctuating part of the 50S. It is known to make an anticorrelated movement with the L1 stalk. These lateral stalks are found to play a highly crucial role in the proper functioning of the ribosome. The analysis of E. coli crystal structure fluctuations has also shown that the protein components in the ribosomal complex are also in accord with experimental studies. Dynamical cross-correlation maps (DCCMs) based on CGMD trajectories are generated. The findings indicate that there is more coupling within a subunit than between. Coupling within protein chains is also higher than coupling within rRNA chains indicating the more compact globular structures of proteins than rRNAs. Global dynamics of ribosomal complexes are analyzed by employing ANM using normal mode analysis. The calculations are based on four T. thermophilus and one H. sapiens crystal structure. The characteristic conformational changes; ratchet-like rotation (both in T. thermophilus and H. sapiens), 30S/40S head rotation (both), anti-correlated movement of L1 and L7/L12 stalks (T. thermophilus), 40S head and beak regions towards E-tRNA (H. sapiens and T. thermophilus with PDB ID:4v9h), 40S body rotation around vertical axis perpendicular to classical rotation axis called as "subunit rolling" (H. sapiens) are observed. In the second part of this thesis, allosteric regulation mechanisms in the ribosomal complexes are investigated and compared for bacteria and human. For this purpose, k-shortest pathways algorithms and PRS calculations are employed. k-shortest pathway algorithms (Yen's and Dijkstra) are applied to the networks generated from residue interaction. Potential allosteric communication pathways between DC-PTC and the ribosomal tunnel-PTC (peptidyl transferase center) are explored by these CG techniques. Additionally, residues found on the shortest pathways are analyzed in terms of rigidity/flexibility (according to deformation energy analysis) and being "hub" residue or not (according to "contact number" analysis). The calculated suboptimal pathways between the tunnel and the PTC in T. thermophilus ribosomal structures agree with the previously proposed allosteric pathways. Motivated by the success of these models in the tunnel-PTC case, they are employed for investigating potential allosteric communication pathways between highly distant functional sites, the DC and the PTC of the ribosome, which are known to communicate during the translation process. The analysis suggests that especially B3 and B2a inter-subunit bridges are critical for the long-range signal transmission between the DC and the PTC. Then the potential allosteric communication pathways are also investigated on the human ribosomal complex for the first time to our knowledge. The human ribosomal complex seems to employ similar suboptimal pathways between the tunnel and the PTC as well as the DC and the PTC. In this line, B3 and B2a are highlighted as critical hubs in the long-range signal transmission in the ribosomal structures and can be evaluated as drug binding sites. Then, the ribosomal tunnel where the growing polypeptide chain passes through before emerging at the solvent is studied in more detail. In the bacterial ribosome, the ribosomal exit tunnel walls are formed by the 23S rRNA, uL4, uL22 and a bacteria-specific extension of uL23. In eukaryotes, the bacteria-specific extension of uL23 overlaps with eL39. uL4 and uL22 form a constriction within the tunnel which is located approximately 30 Å from the PTC. An additional loop in uL4 makes this constriction narrower in eukaryotes than prokaryotes. In this line, the ribosomal tunnels of both T. thermophilus and H. sapiens are extracted and analyzed in detail. The additional loop in uL4 in eukaryotes changes the dynamical behavior of this region, which may be related to the macrolide binding discrimination in both structures. To get a deeper understanding, the PRS is applied to the conserved critical residues in uL4 which are located at the constriction region of the tunnel. In the same chapter of the thesis, the allosteric communication in the ribosomal exit tunnel is also discussed focusing on both nascent chain interactions and the trigger factor (TF) recruitment mechanism induced by the ribosomal tunnel on E. coli ribosomal structure. PRS analysis is carried out to identify effectors/sensors around the tunnel. The findings are consistent with experimental observations indicating the allosteric communications between PTC-ribosomal tunnel and chaperone binding site in uL23-lower part of ribosomal tunnel. Especially, uL23 can be considered as a novel drug designing targeting its non-conserved pocket.
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ÖgeAdsorptive removal of heavy metal ions from aqueous solution using metal organic framework(Lisansüstü Eğitim Enstitüsü, 2021) Elaiwi, Fadhil Abid ; Sirkecioğlu, Ahmet ; 711381 ; Kimya MühendisliğiIndustrialization and rapid increase in human population are the cause of increase in wastewater generation. Depending on the source, these wastes may contain hazardous pollutants such as heavy metals, toxic organic compounds, dissolved inorganic solids and etc. Heavy metals are the serious threat to environmental and human health. Due to their toxicity and carcinogenic effects, close attention must be paid to heavy metals containing wastewaters. Even very small amounts of heavy metals can result in severe physiological and neurological damages. Therefore, numerous processes have been developed to treat wastewater minimize this health hazard potential. These processes include membrane filtration, ion exchange, adsorption, chemical precipitation, nanotechnology treatments, electrochemical and advanced oxidation processes. Ion exchange and adsorption are both physicochemical methods used to treat heavy metal containing wastewaters. In both cases high surface are plays an important role. As a new generation of crystalline porous materials, metal-organic frameworks (MOFs) possess high surface area, tunable pore structure and functionalizable surfaces. With these attributes, MOFs have an essential role in several fields, including wastewater treatment. Based on the affinity of amino groups in chelating sites for heavy metal ions, a porous metal-organic framework (MOF) [ED-MIL-101(Cr)] were synthesized as an adsorbent for lead, copper, and cadmium ions. Hydrothermal method was used to synthesize the MOF samples. The functionalized MOF samples were characterized by powder X-ray diffraction (PXRD) to investigate the functionalization process and compare the synthesized MOF with the pristine MIL-101(Cr) samples. Fourier Transform Infrared (FT-IR) spectroscopy was used to analize the functional groups of the adsorbent before and after the treatment process which can be useful in estimating the mechanism for the recovry process and assess the relationship between the ions and the adsorbents sites. Scanning electron microscopy (SEM) and thermogravimetric analysis (TGA), were also performed to investigate crystal structure and the thermal stability of the MOFs in a specified temperature range, respectively. Finally, the surface characteristics of the samples and the particles size distribution were investigated with N2 adsorption-desorption conducted at 77 K. In order to investigate the adsorption performances of ED-MIL-101(Cr) for the chosen heavy metal cations (Pb(II), Cu(II), and Cd(II) ion), batch experiments were conducted with single, binary, and ternary metal solutions. During these experiments the effect of experimental conditions such as pH, adsorbent dosage, initial concentration, were investigated. With the aim of evaluation of conditions for removing of the three metal ions using ED-MIL-101(Cr), several isotherm models were tested to choose the best fit model with the experimental data. Normal and extended forms of Freundlich, Langmuir, and Sips isotherms were adopted to analyze the adsorption behavior of the MOF samples. ED-MIL-101(Cr) exhibits maximum adsorption capacities (mg/g) of 82.55, 69.9 and 63.15 mg/g for Pb(II), Cu(II) and Cd(II), respectively. The experimental data revealed that the adsorption capacity of the adsorbent for the different metal ions at the same concentration mainly depends on the affinity of the adsorbent which was in the order of Pb(II) ˃Cu(II) ˃ Cd(II) in single ion solution. This selectivity order is governed mainly by ionic features such as ionic radius, electronegativity, and hydrated ionic radius. The influence of ionic interaction between the competitive ions in a multi-ion solution namely interaction factor is quantitatively studied and tabulated its values for multi-ion systems. For further studies, kinetics models applied to investigate the Pb(II), Cu(II), and Cd(II) ions adsorption mechanism on ED-MIL-101(Cr). Also, rate-control steps were determined using kinetic method. Linear forms of pseudo-first order, pseudo-second order, and intra-particle diffusion equations were used to interpret the kinetic data. It was observed that the kinetic data that obtained with batch adsorption processes were well fitted with pseudo-second-order model. Also the regeneration process for exhausting ED–MIL–101(Cr) was carried out to assess the recyclability of ED-MIL-101(Cr) for adsorption of lead, copper, and cadmium ions. It was observed that there was an insignificant change in the adsorption efficiency of ED-MIL-101(Cr) samples after three adsorption-regeneration cycles. In order to simulate the real-life experience adsorption experiments conducted also in dynamic system. For this part of the experimental work, a fixed bed of ED-MIL-101(Cr) was prepared for the continuous removal of Pb(II), Cu(II), and Cd(II) ions from the aqueous solutions. A series of experiments were carried out in the fixed bed system to obtain the breakthrough curves data for the adsorption of single and ternary metal ions. The effects of different operating conditions such as static bed height (2, 4, and 6 cm), flow rate (10, 15, and 20 mL/min), and initial concentration of heavy metal ions (50, 75, and 10 mg/L) on the removal efficiency were investigated. The experimental breakthrough data of three metal ions were fitted well with the theoretical model. The breakthrough curves for single and multiple systems showed that Pb(II) has the longest breakthrough time compared with other metals indicating a high affinity toward this ion while Cd(II) had the shortest breakthrough time. Thomas Model and Yoon-Nelson models were used to evaluate the breakthrough curves and evaluate the dynamic data. The results from these two models suggest that the maximum adsorption capacity of the investigated heavy metal ions from single aqueous solutions are in the order of Pb(II) > Cu(II) > Cd(II). These results are in agreement with the experimental data which are also related to the affinity of the adsorbent for the adsorbed ions. Comparably, Yoon-Nelson model is the best model for the data obtained for the metal adsorption experiments conducted with various bed lengths. It can be concluded that amino-functionalized MIL-101(Cr) was found to be a promising candidate for metal ion removal from the aqueous environment.
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ÖgeInvestigation of plasticization behavior of membrane polymers by a fully atomistic approach(Graduate School, 2021-02-01) Balçık, Marcel ; Ahunbay, Mehmet Göktuğ ; 506152004 ; Chemical Engineering ; Kimya MühendisliğiThe increasing influence of polymeric gas separation membranes in the gas separation industry expedites the pursuit of the polymeric materials to be employed as the membranes. While high permeability and selectivity are anticipated from a commercial membrane material candidate, the plasticization phenomenon should not be disregarded. Several gases, such as CO2, H2S, and condensable hydrocarbons, are known to stimulate increased mobility of polymer segments, subsequently to the gas-induced swelling of the membrane, eventually leading to plasticization. Since the plasticization phenomenon is highly related to the increased free volume of the membrane, sieving capabilities of the membrane are lost with the plasticization, leading to a loss in selectivities. The plasticization phenomenon is dependent on the concentration of the swelling gases and is usually identified with the corresponding pressure of the gas. The plasticization pressures of the membranes are the determining factor in the operating ranges of the membranes. Polyimides (PIs) and Polymers with Intrinsic Microporisities(PIMS) are the polymer classes with the highest potentials to be used as gas separation membrane materials. Polymers belonging to both of the classes have already proven to have excelling gas separation performances. However, their gas separation performances and the effect of gas-induced plasticization remain vastly unstudied. Fundamental understanding of the gas separation performance, plasticization and methods of suppressing plasticization in PIs and PIMs is expected to accelerate the efforts in search of high-performance gas separation materials. In this thesis, molecular simulation tools were employed to understand underlying causes leading to macroscopic behaviors, such as gas permeabilities, swelling, and plasticization, in polymeric membranes. Copolyimides (co-PIs) were studied for their plasticization resistance and method development was performed for modeling gas separation performance and plasticization resistance accurately. Later on, the effect of crosslinking on co-PIs in terms of gas permeabilities and plasticization resistance was investigated in detail, particularly with the help of PAFVCO2+ property, a free volume analysis based on CO2 accessibility, which will be explained in detail in relevant chapters. Mixed Matrix Membranes(MMMs) were studied for their plasticization resistance and segmental dynamics of the polymer phase at the interface. The information obtained from the plasticization studies on PIs were then transferred to PIMs, where PIM-1 was studied for pure and mixed gas separation performance and plasticization resistance. The approach was further extended to triptycene-based PIMs, among which three were novel. One of the most important outcomes of this thesis is the development of atomistic simulation protocols for the accurate estimations of plasticization pressures of PIs and PIMs. While permeabilities could be monitored for plasticization, as in experimental studies, molecular modeling also allows monitoring of free volume elements and correlate to the plasticization pressure. The latter was further extended to analyze the rigidification phenomenon in MMMs and the rigidification effect induced by CO2 was identifed for the first time. Plasticization and mixed gas studies on PIMs have proven that conventional approaches to analyze plasticization in polymers are not adequate, as loss of selectivities in mixed gas conditions were shown to be not only associated with the traditional definition of plasticization. In mixed gas conditions, before upturn of CO2 permeabilities, increased CH4 permeabilities compared to pure gas conditions were observed. Additional effects on the gas permeabilities, such as competitive sorption and increased CH4 diffusivities by CO2-induced swelling, are existent in mixed gas conditions, leading to a more complex concept of plasticization.
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ÖgeKontrollü aktif molekül salımı yapan pektin temelli hidrojellerin geliştirilmesi(Lisansüstü Eğitim Enstitüsü, 2021-06-24) Kocaağa, Ayşe Banu ; Levitas Kürkçüoğlu, Ayşe Özge ; Güner, Fatma Seniha ; 506912019 ; Kimya MühendisliğiYara tedavisi, bir dizi hücresel ve biyokimyasal olayların, dokuyu tamir etme ve yenileme amacıyla, iç içe geçmiş ve düzenli bir sırada gerçekleştiği bir prosestir. Günümüzde, diyabet hastalığı gibi çeşitli hastalıkların neden olduğu kronik yaralar, hızla yaşlanan nüfus, trafik kazaları ve cerrahi prosedürlerin artışı ile daha etkili yara örtülerine olan gereksinim artmaktadır. Gelişmiş bir yara örtüsü, mükemmel biyouyumluluk ile beraber bakterilere karşı bir koruma sağlamalı, fazla eksudayı absorbe edebilmeli, uygun su buharı ve oksijen geçirgenliği oranı ile de iyileşmeyi hızlandırmalıdır. Ayrıca, hasta ve hasta yakınları için konforlu bir kullanıma sahip olması, mekanik dayanıklılık, uzun raf ömrü, uygun maliyet ve biyobozunurluk da bir yara örtüsü malzemesinde aranan önemli özelliklerdendir. Ancak, çoğu mevcut yara örtüleri bu özelliklerden çok azını bir arada içermektedir. Bu nedenle, tüm aranan özellikleri bir arada barındıran, düşük maliyetli, gelişmiş yara örtülerine ihtiyaç bulunmaktadır. Bu motivasyonla, bu tez çalışmasında in silico ve in vitro yöntemlerin beraber kullanıldığı bir yaklaşımla, yara örtüsü olarak kullanılmak üzere antimikrobiyal, kontrollü ilaç/protein salım sistemleri geliştirilmiştir. Yara örtüsünün ana matrisi olarak pektin seçilmiştir. Hidrofilik pektin fazla yara sıvısını absorplayabilir. Gözenekli hidrojel yapısı ile pektin kontrollü ilaç salımı yapabilir. Pektin zincirlerinin üzerindeki fonksiyonel gruplar aracılığıyla oluşan asidik ortam ise bakterilere ve virüslere karşı bir bariyer görevi görebilir. Tez kapsamında yapılan çalışmalar bölümler halinde sunulmuştur. Öncelikle yara örtüleri için literatürde rapor edilen çalışmalar ve pektinin yara örtüsü olarak kullanımı tartışılmıştır. Bunu, moleküler modelleme ve moleküler dinamik (MD) simülasyonları hakkında kapsamlı bir bölüm takip etmektedir. Tez kapsamında yapılan çalışmalar ise beş ayrı bölümde tartışılmıştır. İlk bölümde, tüm-atom MD simülasyonları kullanılmıştır. Temel olarak galakturonik asit monomerleri içeren pektin zincirleri kimyasal özellikleri farklı karboksil, ester ve amitli grupları barındırmaktadır. Çalışmada, yüksek metoksili ve düşük metoksili olarak 21 monomerli pektin oligomerleri modellenmiştir. Ca2+ iyonlarıyla çapraz bağlanmış zincirlerin düşük enerji seviyelerinde konfigürasyonları taranmış, düşük metoksili pektin zincirlerinin çapraz bağlı yapılarını daha fazla korudukları tespit edilmiştir. Tezin devamında kontrollü ilaç salım sistemlerinde düşük metoksili pektinin kullanılmasına karar verilmiştir. Çalışmaların ikinci bölümünde, düşük metoksili pektinden sentezlenen hidrojeller, farklı Ca2+ iyonu ve ilaç yükleme konsantrasyonlarında, ve farklı sayıda hidrojel katmanlarda çalışılmıştır. Sentezlenen hidrojeller karakterize edilmiş ve istenilen ilaç salım hızının katman sayısı ve film kalınlığı ile kontrol edilebileceği sonucuna ulaşılmıştır. Tezin simülasyon odaklı üçüncü çalışmasında ise, pektin hidrojellerinin yüklenen ilacı kontrollü salabileceği ilaç konsantrasyonu aralığının belirlenmesi için hesaplamalı çalışmalar gerçekleştirilmiştir. Bu amaçla, Ca2+ ile çapraz bağlı 21 monomer uzunluğundaki α-D-galakturonik asit oligomerleri, artan prokain konsantrasyonlarında (6, 30, 60, 90 180 mg ilaç.g-1 film), her sistem için üçer bağımsız 200 ns uzunluğunda tüm-atom MD simülasyonları ile incelenmiştir. Sonuçlara göre 30 mg.g-1 prokain yüklemenin çapraz bağlamayı bozmayacağı, bu konsantrasyonun hidrojeli düşük seviyede degredasyona uğratacağı ve kontrollü salım yapabileceği ön görülmüştür. MD çalışmalarında kullanılan konsantrasyonlarda prokain yüklü pektin hidrojeller sentezlenmiş, karakterize edilmiş, analizler ile prokain salımı ve hidrojel degradasyonunun simülasyonlarla tahmin edilebileceği ortaya konmuştur. Bu hesaplamalı yaklaşım kontrollü salım için kullanılacak benzer esnek sistemlerin tasarımında da kullanılabilir. Tezdeki diğer bir çalışmada, pektin hidrojelin mekanik özelliklerini arttırmak için kafes yapılı alimünasilikat zeolit-A kullanılmıştır. Bu katkı ile kontrollü ilaç salımı yapabilen, modern yara örtüsü için gerekli özelllikleri taşıyan, uygun maliyetli özgün bir yara örtüsü geliştirilmiştir. Membrana difüzyon ve matrise difüzyon olmak üzere iki farklı hidrojel hazırlama metodu ile hazırlanan hidrojellerde farklı çapraz bağlayıcı, zeolit ve teofilin ilacı konsantrasyonlarında çalışılmıştır. Pektin-zeolit etkileşimlerini kontrol etmek amacıyla iki farklı iyonik formatta (Na+ ve Zn2+) zeolit-A kullanılmıştır. Membrana difüzyon yöntemi ile hazırlanan hidrojellerin teofilini kontrollü bir şekilde salabildiği, zeolit-A partiküllerinin teofilin deposu olarak davranırken hidrojel stabilitesini ve oksijen geçirgenlik hızını arttırdığı tayin edilmiştir. Pektin-zeolit hidrojellerin ilaç salımına etki eden en önemli parametrelerin şişme oranı ve iyon konsantrasyonu olduğu belirlenmiştir. Tezin son bölümünde ise hem yüksek kanamalı ve yanık yaralarında önemli bir problem olan, hem de kalp krizi, kanser ve COVID-19 nedeniyle gelişebilen serum albümin eksikliği yaşayan hastaların cerrahi operasyonlarında kullanmak amacıyla serum albümin yüklü pektin-zeolit hidrojeller geliştirilmiştir. pH 6,4 ortamında hazırlanan 100 mg.g-1 film albümin yüklü hidrojelin, yapısında immobilize olmuş albümini kontrollü bir şekilde protein yapısını bozmadan dış ortama salabildiği belirlenmiştir. WST-1 yöntemi ile dermal fibroblast hücrelerine karşı gerçekleştirilen hücre canlılığı analizlerinde, kontrol grubu ile karşılaştırıldıklarında hazırlanan hidrojellerin hücre sayısını düşürmediğini, in vitro yara iyileşmesi analizlerinde ise hücrelerin göçüne etki etmediği, fibroblast hücreleri üzerinde toksik bir etki göstermediği belirlenmiştir. E.coli ve S.aureus'a karşı yapılan antibakteriyel analiz testlerinde ise hidrojellerin antibakteriyel özellikleri gösterilmiştir. Bu tez kapsamında, atık ürün veya yan ürün olarak değerlendirilen pektini kullanarak geliştirilen antibakteriyel, aktif ajan yüklü yara örtüleri ile kişiye özel tasarım (istendiğinde kontrollü veya hızlı salım, ilaç/protein salımı, istenilen ebatta esnek yara örtüsü) yapılabileceği belirlenmiştir. Katma değeri yüksek olan bu ürünün ithal yara örtülerine olan bağımlılığı azaltacağı ve ülke ekonomisine katkıda bulunacak olması ise tezin bir diğer önemli çıktısıdır.