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Full-Text Articles in Physical Sciences and Mathematics
Sars-Cov-2 Main Protease Targeting Potent Fluorescent Inhibitors: Repurposing Thioxanthones, Gönül Saadet Batibay, Eyüp Meti̇n
Sars-Cov-2 Main Protease Targeting Potent Fluorescent Inhibitors: Repurposing Thioxanthones, Gönül Saadet Batibay, Eyüp Meti̇n
Turkish Journal of Chemistry
The coronavirus disease, COVID-19, is the major focus of the whole world due to insufficient treatment options. It has spread all around the world and is responsible for the death of numerous human beings. The future consequences for the disease survivors are still unknown. Hence, all contributions to understand the disease and effectively inhibit the effects of the disease have great importance. In this study, different thioxanthone based molecules, which are known to be fluorescent compounds, were selectively chosen to study if they can inhibit the main protease of SARS-CoV-2 using various computational tools. All candidate ligands were optimized, molecular …
Virtual Screening, Drug-Likeness Analysis, And Molecular Docking Study Of Potentialsevere Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors, Nikola Nedeljkovic, Milos Nikolic, Ana Stankovic, Nevena Jeremic, Dusan Tomovic, Andriana Bukonjic, Gordana Radic, Marina Mijajlovic
Virtual Screening, Drug-Likeness Analysis, And Molecular Docking Study Of Potentialsevere Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors, Nikola Nedeljkovic, Milos Nikolic, Ana Stankovic, Nevena Jeremic, Dusan Tomovic, Andriana Bukonjic, Gordana Radic, Marina Mijajlovic
Turkish Journal of Chemistry
Due to the length of time required to develop specific antiviral agents, the World Health Organization adopted the strategy of repurposing existing medications to treat Coronavirus disease 2019 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease is possible biological target for potential antiviral drugs. We selected various compounds from PubChem database based on the structure of main protease inhibitors in Protein Data Bank database. Ten compounds showed nontumorigenic and nonmutagenic potential and met Egan's and Lipinski's rules. Molecular docking analysis was performed using AutoDock Vina software. Based on number and type of key binding interactions, as well as …
Structural Rearrangement Of Neisseria Meningitidis Transferrin Binding Protein A (Tbpa) Prior To Human Transferrin Protein (Htf) Binding, Gi̇zem Nur Duran, Mehmet Özbi̇l
Structural Rearrangement Of Neisseria Meningitidis Transferrin Binding Protein A (Tbpa) Prior To Human Transferrin Protein (Htf) Binding, Gi̇zem Nur Duran, Mehmet Özbi̇l
Turkish Journal of Chemistry
Gram-negative bacterium Neisseria meningitidis, responsible for human infectious disease meningitis, acquires the iron (Fe3+) ion needed for its survival from human transferrin protein (hTf). For this transport, transferrin binding proteins TbpA and TbpB are facilitated by the bacterium. The transfer cannot occur without TbpA, while the absence of TbpB only slows down the transfer. Thus, understanding the TbpA-hTf binding at the atomic level is crucial for the fight against bacterial meningitis infections. In this study, atomistic level of mechanism for TbpA-hTf binding is elucidated through 100 ns long all-atom classical MD simulations on free (uncomplexed) TbpA. TbpA protein underwent conformational …
Interactions Between Densely Grafted Molten Polymer Brushes:Scaling Theories Versus Molecular Simulations, Aykut Erbaş
Interactions Between Densely Grafted Molten Polymer Brushes:Scaling Theories Versus Molecular Simulations, Aykut Erbaş
Turkish Journal of Physics
Using molecular dynamics simulations and scaling arguments, we analyzed the interactions between two identical molten polymer brushes intermediately and strongly compressed towards each other at melt conditions. The width of the overlap region, in which monomers of the linear chains composing the two brushes interact, increases as the polymer-grafted surfaces are brought closer. If two-brush coated surfaces are as close as the characteristics size of the grafted chains, the overlap region is directly controlled by intersurface distance. At intermediate compression, the width of the overlap region scales with the end-to-end size of chain sections within the overlap region. This result …
Why Protein Conformers In Molecular Dynamics Simulations Differ From Their Crystal Structures: A Thermodynamic Insight, Fi̇li̇ppo Pullara, Mao Wenzhi, Mert Gür
Why Protein Conformers In Molecular Dynamics Simulations Differ From Their Crystal Structures: A Thermodynamic Insight, Fi̇li̇ppo Pullara, Mao Wenzhi, Mert Gür
Turkish Journal of Chemistry
Conformers generally deviate structurally from their starting X-ray crystal structures early in molecular dynamics (MD) simulations. Studies have recognized such structural differences and attempted to provide an explanation for and justify the necessity of MD equilibrations. However, a detailed explanation based on fundamental physics and validation on a large ensemble of protein structures is still missing. Here we provide the first thermodynamic insights into the radically different thermodynamic conditions of crystallization solutions and conventional MD simulations. Crystallization solution conditions can lead to nonphysiologically high ion concentrations, low temperatures, and crystal packing with strong specific protein--protein interactions, not present under physiological …
Pore Length- And Ion Concentration-Dependent Ionic Current In Cylindrical Nanopores: An Atomistic Molecular Dynamics Study, Nazar İleri̇ Ercan
Pore Length- And Ion Concentration-Dependent Ionic Current In Cylindrical Nanopores: An Atomistic Molecular Dynamics Study, Nazar İleri̇ Ercan
Turkish Journal of Chemistry
The sensing of individual molecules as they pass through nanopores under an external field is a popular research field. The approach is simply based on the detectable temporary blockades in the ionic current as the molecules pass through the nanopores. These signatures of the current have been shown to be a function of nanoparticle and nanopore size and geometry as well as the external electric field. However, models developed in this context fail to predict the experimentally observed behavior in technologically important shorter nanopores. Here we present atomistic molecular dynamics simulation results from colloidal nanoparticle translocation through mid-to-low aspect ratio …
Size- And Composition-Dependent Structure Of Ternary Cd-Te-Se Nanoparticles, Mustafa Kurban
Size- And Composition-Dependent Structure Of Ternary Cd-Te-Se Nanoparticles, Mustafa Kurban
Turkish Journal of Physics
In this study, the geometrical, thermal, and energetic properties of zinc-blende CdTe1-xSex (x = 0.25, 0.50, and 0.75) nanoparticles were investigated using the bond order potential based on the modern classical molecular dynamics (MD) method. All MD simulations were performed using LAMMPS. Some physical properties were investigated, such as compositional variations of Cd, Te, and Se atoms; order parameter; radial distribution function; coordination number; potential energy; and heat capacity (Cv). The simulation results were compared with the available experimental results. The obtained results revealed that an increase in the composition of Se atoms can provide contributions to stability, which is …
Exploring Distinct Binding Site Regions Of \Beta_2-Adrenergic Receptor Via Coarse-Grained Molecular Dynamics Simulations, Si̇bel Çakan, Ebru Demet Akdoğan
Exploring Distinct Binding Site Regions Of \Beta_2-Adrenergic Receptor Via Coarse-Grained Molecular Dynamics Simulations, Si̇bel Çakan, Ebru Demet Akdoğan
Turkish Journal of Chemistry
\beta_2-Adrenergic receptor (\beta_2AR) is a G protein- coupled receptor that is highly flexible and able to recognize a wide range of ligands through its conformational variations. Active and inactive conformations revealed by recent crystallographic experiments do not provide a complete dynamic picture of the receptor, especially in the binding site. In this study, molecular dynamics (MD) simulation through a residue-based coarse-grained model is used as an alternative and efficient method to explore a wider conformational search space. The system was composed of \beta_2AR embedded into a 1-palmitoyl-2-oleoyl-phosphatidylcholine membrane bilayer with surrounding water. A total of 6 \mu s of simulation …
Molecular Dynamics Studies On Glass Formation Of Pd-Ni Alloys By Rapid Quenching, Sevgi̇ Özdemi̇r Kart, Mehmet Tomak, Mustafa Uludoğan, Tahi̇r Çağin
Molecular Dynamics Studies On Glass Formation Of Pd-Ni Alloys By Rapid Quenching, Sevgi̇ Özdemi̇r Kart, Mehmet Tomak, Mustafa Uludoğan, Tahi̇r Çağin
Turkish Journal of Physics
The rapid solidification of Pd-Ni alloys is studied with the constant-pressure and constant-temperature (TPN) and the constant-volume and constant-temperature (TVN) molecular dynamics technique to obtain an atomic description of glass formation in the alloy. Quantum Sutton-Chen potential for Pd-Ni binary system is applied in the simulations. We present some thermodynamic and structural results from simulations of such glasses over a range of compositions. The structural properties are analyzed by means of pair distribution function, volume, and enthalpy as a function of temperature and concentration at the cooling rates ranging from 5 K/ps to 0.05 K/ps to see whether the Pd-Ni …
Molecular Dynamics Study Of Thermal Properties Of Intermetallic Alloys, H. H. Kart, Mehmet Tomak, Tahi̇r Çağin
Molecular Dynamics Study Of Thermal Properties Of Intermetallic Alloys, H. H. Kart, Mehmet Tomak, Tahi̇r Çağin
Turkish Journal of Physics
Molecular dynamics simulations of bulk copper, gold pure metals and their ordered intermetallics alloys of Cu_3Au(L1_2) and CuAu_3(L1_2) have been carried out between above 0 K and below the their melting points of the materials for predicting their temperature-dependent thermophysical properties. The effects of temperature and concentration on the physical properties such as enthalpy, volume, heat capacity, thermal expansion and density of Cu_xAu_{1-x} are studied. Especially, temperature-dependent polynomial functions of enthalpy, volume and density are obtained. Sutton-Chen (SC) and Quantum Sutton-Chen (Q-SC) many-body potentials are used in the constant enthalpy-constant pressure ensemble (HPN) and constant pressure-constant temperature ensemble (TPN). Three …