WoS İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/4465

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Classification of Distinct Conformers of Beta < 2-Adrenergic Receptor (beta 2-Ar) Based on Binding Affinity of Ligands Through Docking Studies
(Amer Chemical Soc, 2016) Akten, Ebru Demet; Dilcan, Gonca
B2AR reseptörü, akciğerlerin rahatlamasında ve kardiyovasküler fizyolojide rol oynamasıyla önemli bir ilaç hedefidir. Bu çalışmada, çeşitli B2AR konformasyonlarını aktif veya inaktif olarak sınıflandırmak amacıyla, aktivitesi bilinen ligantlar seçilerek onların bağlanma şekillerine göre bir sınıflandırma stratejisi oluşturulmuştur. Önceki bir çalışmada gerçekleştirilen, reseptörün inaktif halinin 2.8 μs'lik MD simülasyonunda, ligandın bağlanma bölgesinin farklı konformasyonları elde edilmiştir. Snapshotlar derlenerek bağlanma bölgesindeki beş anahtar rezidünün RMSD değerlerine göre gruplandırılmıştır. Toplamda 13 farklı konformasyon elde edilmiş ve 5 agonist, 4 ters agonist ve 4 antagonist molekülü her bir konformasyona ayrı ayrı ve 7 farklı skor fonksiyonu kullanılarak dock edilmiştir. En iyi yerleşen konformasyonlar bağlanma bölgesindeki anahtar rezidülerle olan yakınlığına göre seçilmiş ve hesaplanmıştır. Anahtar bölgeye yaklaşamayanlar elenmiş, kalanlar ise skor değerlerine göre sıralanmıştır. Bu sınıflandırma, kritik değerlendirme yapabilmek için MD konformasyonlarından önce aktivitesi bilinen aktif/inaktif kristal yapılara uygulanmıştır. Her skor fonksiyonu tarafından seçilen ve ilk 5'te bulunan MD konformasyonları aktif ve inaktif olarak sınıflandırılmıştır. Son olarak, MD konformasyonlarının ayırt ediciliğini analiz edebilmek için, seçilen bu konformasyonlar ile küçük bir dataset kullanılarak sanal tarama yapılmıştır. MD konformasyonlarının inaktif kristal yapıya göre antagonist/ters agonistler için daha seçici olduğu gözlemlenmiştir. Reseptörün alternatif konformasyonlarını üretmek ve onları sınıflandırmak, genellikle tek bir snaphot X-ray örneği ile sınırlandırılmış ilaç tasarımı çalışmalarında önemli rol oynamaktadır.
Comp 297-Experimental and Molecular Docking Simulation Studies of Histone Deacetylases (hdacs) Enzyme Inhibitors
(Amer Chemical Soc, 2007) Yelekçi, Kemal; Bora, Gamze; Dayangaç-Erden, Didem; Ayhan, Peruze; Dalkara, Sevim; Demir, Ayhan S.; Erdem-Yurter, Hayat
[Abstract Not Available]
Citation - WoS: 5
Citation - Scopus: 7
Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects Into Carbonic Anhydrase Biomimetics
(Amer Chemical Soc, 2013) Koziol, Lucas; Eşsiz, Şebnem; Wong, Sergio E.; Lau, Edmond Y.; Valdez, Carlos A.; Satcher, Joe H. Jr.; Aines, Roger D.; Lightstone, Felice C.
Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supra-molecular tris(imidazolyl) calix[6]arene Zn2+ aqua complex as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate H2O + CO2 -> H+ + HCO3-. On the basis of potential-of-mean-force (PMF) calculations stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (Delta G = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (Delta Delta G = 1.4 kcal/mol) suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.
Citation - WoS: 16
Citation - Scopus: 17
Correlation of Experimental Liquid-Liquid Equilibrium Data for Ternary Systems Using Nrtl and Gmdh-Type Neural Network
(Amer Chemical Soc, 2017) Bekri, Sezin; Özmen, Dilek; Özmen, Atilla
In this work liquid liquid equilibrium (LLE) data for the ternary systems (water + propionic acid + solvent) were experimentally obtained at atmospheric pressure and 298.2 K. The ternary systems show type-1 behavior of LLE. Cyclopentane cyclopentanol 2-octanone and dibutyl maleate were chosen as solvent and it has been noted that there are no data in the literature on these ternary systems. The consistency of the experimental tie-line data was checked using the Hand and Othrner-Tobias correlation equations. A comparison of the extracting capabilities of the solvent was made with respect to the distribution coefficients and separation factors. The correlation of the experimental tie-line data was confirmed by the NRTL thermodynamic model. A Group Method of Data Handling (GMDH)-type neural network (NN) was also used to correlate the experimental tie-lines. It is shown that the results of the both models cohere with the experimental values.
Docking of novel reversible monoamine oxidase-B inhibitors: Efficient prediction of ligand binding sites and estimation of inhibitors thermodynamic properties
(Amer Chemical Soc, 2006) Yelekci, Kemal; Toprakci, Mustafa
[No Abstract Available]
Citation - WoS: 153
Citation - Scopus: 164
Efficient Photocatalytic Degradation of Methylene Blue Dye From Aqueous Solution With Cerium Oxide Nanoparticles and Graphene Oxide-Doped Polyacrylamide
(Amer Chemical Soc, 2023) Kalaycioglu, Zeynep; Uysal, Bengu Ozugur; Pekcan, Onder; Erim, F. Bedia
A cerium oxide nanoparticles (CeO2-NPs)/graphene oxide (GO)/polyacrylamide (PAM) ternary composite was synthesized through free-radical polymerization of acrylamide in the presence of CeO2 nanoparticles and GO in an aqueous system. The synthesized composite material was characterized by X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and energy-dispersive X-ray (EDX) spectroscopy techniques and applied for the photocatalytic degradation of methylene blue (MB) dye from an aqueous solution. Tauc's model for direct transition was used to model for the optical band gap. The key operating parameters such as the amounts of CeO2-NPs and GO, pH, initial MB concentration, type of light irradiation, and contact time have been optimized to achieve the highest MB degradation percentage. The photocatalysis process was pH-dependent, and the optimum pH value was found to be 12.0. Under UV-A light, 90% dye degradation occurred in 90 min. The degradation of MB was also specified in terms of total organic carbon (TOC) and chemical oxygen demand (COD). Free-radical capture experiments were also performed to determine the role of radical species during the photocatalytic oxidation process. The photocatalytic process showed that the equilibrium data is in good agreement with the Langmuir-Hinshelwood kinetic model. A rate constant of 0.0259 min-1 was obtained. The hydrogel was also tested to assess its reusability, which is an important key factor in practical wastewater treatment. The photocatalytic activity only decreased to 75% after nine uses.
In Silico Modeling of Dopamine Transporter and Design of Novel Neuroprotective Agents
(Amer Chemical Soc, 2016) Djikic, Teodora; Yelekci, Kemal
[Abstract Not Available]
Intermolecular Interactions in Human Hdac8 Crystal Structures and the Stability of Binding Modes of Co-Crystallized Inhibitors
(Amer Chemical Soc, 2019) Yelekçi, Kemal; Uba, Abdullahi Ibrahim
[Abstract Not Available]
Citation - WoS: 2
Citation - Scopus: 2
Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human Beta(2)-Adrenergic Receptor
(Amer Chemical Soc, 2019) Söğünmez, Nuray; Akten, Ebru Demet
The alternative inactive state of the human beta(2)-adrenergic receptor originally exposed in molecular dynamics simulations was investigated using various analysis tools to evaluate causality between correlated residue-pair fluctuations and suggest allosteric communication pathways. A major conformational shift observed in the third intracellular loop (ICL3) displayed a novel inactive state featuring an inaccessible G protein binding site blocked by ICL3 and an expanded orthosteric ligand binding site. Residue-based mean square fluctuation and stiffness calculations revealed a significant mobility decrease in ICL3 which induced a mobility increase in the remaining loop regions. This indicates conformational entropy loss in one mobile region being compensated by residual intermolecular motions in other mobile regions. Moreover the extent motions decreased and correlations that once existed between transmembrane helices shifted toward regions with increased mobility. Conditional time-delayed cross-correlation analysis identified distinct driver follower relationship profiles. Prior to its packing freely moving ICL3 was markedly driven by transmembrane helix-8 whereas once packed ICL3 controlled future fluctuations of nearby helices. Moreover two transmembrane helices (H5 and H6) started to control future fluctuations of a remote site the extracellular loop ECL2. This clearly suggests that allosteric coupling between extra- and intracellular parts intensified in agreement with the receptor's well recognized feature which is the inverse proportionality between activity and the degree of coupling.
Citation - WoS: 1
Investigation of Structural and Antibacterial Properties of Ws₂-doped Zno Nanoparticles
(Amer Chemical Soc, 2024) Beytur, Sercan; Essiz, Sebnem; Uysal, Bengu Ozugur
ZnO nanoparticles, well-known for their structural, optical, and antibacterial properties, are widely applied in diverse fields. The doping of different materials to ZnO, such as metals or metal oxides, is known to ameliorate its properties. Here, nanofilms composed of ZnO doped with WS2 at 5, 15, and 25% ratios are synthesized, and their properties are investigated. Supported by molecular docking analyses, the enhancement of the bactericidal properties after the addition of WS2 at different ratios is highlighted and supported by the inhibitory interaction of residues playing a crucial role in the bacterial survival through the targeting of proteins of interest.
Citation - WoS: 7
Citation - Scopus: 7
A it-Electron Rich Cage via the Friedel-Crafts Reaction
(Amer Chemical Soc, 2022) Zhu, Dingsheng; Sun, Bin; Tong, Lu; Wu, Yating; Cetin, Mustafa; Li, Hao
A prism-shaped cage was obtained via the Friedel-Crafts reaction in a 2:3 mixture of trisfuryl and bis-isopropenyl precursors, in a remarkable yield of 40% considering six C-C bonds formed in a one-pot manner. The cage contains two pi-electron rich trisfuryl platforms bridged in a face-to-face manner with three p-xylylene linkers. Therefore, it enables accommodation of pi-electron poor guests with complementary size, including biscationic viologen.
Medi 333-Histone Deacetylase Inhibition Activity of Resveratrol and Its Analogs
(Amer Chemical Soc, 2007) Dayangac-Erden, Didem; Ayhan, Peruze; Bora, Gamze; Yelekçi, Kemal; Dalkara, Sevim; Demir, Ayhan S.; Erdem-Yurter, Hayat
[Abstract Not Available]
Citation - WoS: 5
Multicolor Photoluminescence from Nonconjugated Poly(3,4-dihydropyran) Nanoparticles
(Amer Chemical Soc, 2023) Vallan, Lorenzo; Bui, Anh Thy; Jonusauskas, Gediminas; McClenaghan, Nathan D.; Istif, Emin; Mantione, Daniele; Pavlopoulou, Eleni
In recent years, nonconjugated organic luminophores arereceivingconsiderable interest from the scientific community, offering a newconceptual basis for the development of alternative photoluminescence-basedtechnologies. In this work, the polymerization of 3,4-dihydropyranwas exploited for the preparation of nonconjugated photoluminescentpolymer nanoparticles. Remarkably, excitation-dependent multicoloremission ranging from blue to yellow was observed in both solid andsolution. In contrast with similar materials, this behavior was notattributed to aggregation-induced emission, but rather to the presenceof independent, noninteracting chromophores located on the polymerstructure. Structural and optical characterizations along with furtherchemical modifications suggest that the emission is related to thepresence of acetal groups formed by ring-opening polymerization. Inaddition, it was shown that the removal of unsaturated structurescould enhance the photoluminescence quantum yield of the polymer (QY)up to 0.20 (lambda(ex) = 355 nm). This work provides a newtype of nonconjugated organic luminophore with both high QY and multicoloremission.
Citation - WoS: 3
Citation - Scopus: 3
Near-Infrared Triggered Degradation for Transient Electronics
(Amer Chemical Soc, 2024) Istif, Emin; Ali, Mohsin; Ozuaciksoz, Elif Yaren; Morova, Yagiz; Beker, Levent
Electronics that disintegrate after stable operation present exciting opportunities for niche medical implant and consumer electronics applications. The disintegration of these devices can be initiated due to their medium conditions or triggered by external stimuli, which enables on-demand transition. An external stimulation method that can penetrate deep inside the body could revolutionize the use of transient electronics as implantable medical devices (IMDs), eliminating the need for secondary surgery to remove the IMDs. We report near-infrared (NIR) light-triggered transition of metastable cyclic poly-(phthalaldehyde) (cPPA) polymers. The transition of the encapsulation layer is achieved through the conversion of NIR light to heat, facilitated by bioresorbable metals, such as molybdenum (Mo). We reported a rapid degradation of cPPA encapsulation layer about 1 min, and the rate of degradation can be controlled by laser power and exposure time. This study offers a new approach for light triggerable transient electronics for IMDs due to the deep penetration depth of NIR light through to organs and tissues.
Citation - WoS: 1
Citation - Scopus: 1
Repetitive Rolling of Triptycene-Based Molecules on Cu Surfaces
(Amer Chemical Soc, 2024) Konuk, Mine; Madran, Melihat; Uysal, Mehmet Tuna; Beser, Deniz; Ozen, Alimet Sema; Akdeniz, Zehra; Durukanoglu, Sondan
The metal surface-supported rotation of artificial molecular structures is technologically important for developing molecular-level devices. The key factors leading to the practical applications of these molecular machines on metal surfaces are the atomic-scale control of the rotation and the counterbalance of the temperature-driven instability of the molecules. In this work, we present a means by which triptycene-based molecular wheels can roll repetitively on a metal surface. Our results show that regularly stepped surfaces are the perfect candidate not only for stabilizing the molecule on the metal surface but also for providing the pivot points needed for repetitive vertical rotation of the molecule at higher temperatures. In addition to the geometrical compatibility of the substrate and the molecule, intermittent application of the external electric field is needed for rolling the molecule on a metal-stepped surface in a controllable manner.
Solar Photovoltaic Development in West Africa Will Face Million-Ton Waste Challenges, and Off-Grid Systems Will Dominate
(Amer Chemical Soc, 2025) Dong, Di; Emem, Onis; Liu, Litao; Sen, Burak; Rasmussen, Kasper; Edomah, Norbert; Liu, Gang
Solar photovoltaic (PV), especially off-grid systems, is a low-hanging fruit option among various renewable energy technology choices to address universal energy access, energy security, and climate challenges for vulnerable regions like West Africa. West Africa dominates in the uptake of solar PV solutions, while little attention has been paid to the potential PV waste generation. In this study, we developed a technology-specific, prospective material flow analysis model to investigate material stocks and flows of both on-grid and off-grid solar PV systems for 15 West African countries up to 2050. We show that the cumulative solar PV waste generation ranges from 2.3 to 7.8 million tons by 2050 in West Africa under different scenarios, around 70% of which comes from off-grid PV systems. The potential secondary materials supply ranges from 213 to 704 kilotons, which have potential economic value amounting to 143-475 million dollars or material equivalent to produce 6-19 GW of solar PV capacity. These results call for urgent policy attention, technology development, and infrastructure investment for future PV waste management and highlight the significance of addressing off-grid PV waste in Africa.
Soman as a Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations
(Amer Chemical Soc, 2014) Bennion, Brian J.; Eşsiz, Şebnem; Lau, Edmond Y.; Fattebert, Jean-Luc; Emigh, Aiyana; Lightstone, Felice C.
[Abstract Not Available]
Thermal Rearrangement of 2-Acetoxy Trimethylbicyclo[3.1.0]hexane: Theoretical Elucidation of the Mechanism
(Amer Chemical Soc, 2007) Yelekçi, Kemal; Erdem, Safiye Sağ
[Abstract Not Available]

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