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Journal of Molecular Graphics & Modelling

Cai-Rong Zhang, Yang Zhang, Xing-Yu Li, Wei Wang, Ji-Jun Gong, Zi-Jiang Liu, Hong-Shan Chen
Development of novel dye sensitizers with suitable optoelectronic properties is effective to improve the power conversion efficiency of dye-sensitized solar cells (DSSCs). Considering the effectiveness of conjugate bridges in modification of optoelectronic properties, based on the dye sensitizers C201, C203, C204 and C205, five kinds of organic dye sensitizers are designed with different thiophene-based moieties and the functionalized graphene flakes (GFs) as conjugate bridges. The performances of these dye sensitizers are analyzed in terms of the calculated geometries, electronic structures and excitation properties...
January 2, 2019: Journal of Molecular Graphics & Modelling
Radhika Arora, Priya Bharval, Sheena Sarswati, Taner Z Sen, Ragothaman M Yennamalli
Lytic polysaccharide monooxygenases (LPMOs), which are found in fungi, bacteria, and viruses, are redox enzymes utilizing copper to break glycosidic bonds in recalcitrant crystalline form of polysaccharides, such as chitin and cellulose. They are classified by the Carbohydrate-Active enZYmes (CAZy) database under various families. LPMOs's structure with a flat substrate binding region has been shown to contribute to its function, however, the role that LPMOs structural dynamics play during polysaccharide degradation and its mechanism of binding towards substrate are relatively unknown...
December 29, 2018: Journal of Molecular Graphics & Modelling
Azadeh Kordzadeh, Sepideh Amjad-Iranagh, Mahdi Zarif, Hamid Modarress
Adsorption of the drug doxorubicin (DOX) onto covalent functionalized carbon nanotubes (CNTs) as drug carriers was studied by employing molecular dynamics (MD) simulation. CNT was covalently functionalized by the chemical groups: amine, carboxyl and hydroxyl and the change in the electrostatic charge of CNT as a result of functionalization was investigated by quantum mechanics calculations. The drug adsorption onto the functionalized CNTs (f-CNT) was examined by analyzing the evaluated radial probability of the drug by MD simulation...
December 28, 2018: Journal of Molecular Graphics & Modelling
Narin Lawan, Pongsakorn Chasing, Jirapat Santatiwongchai, Sairoong Muangpil
Chorismate synthase (CS) catalyzes the conversion of 5-enolpyruvylshikimate-3-phosphate (EPSP) to chorismate which is a key intermediate in the biosynthesis of aromatic amino acids. CS enzyme is a new target for antibacterial drugs. Even though several reaction mechanisms have been proposed, the catalytic mechanism is still unclear. QM/MM adiabatic mapping calculations were performed in order to investigate roles of this enzyme. High-accuracy SCS-MP2/aVDZ/CHARMM27 calculations indicated that the reaction pathway has three steps; (i) proton transfer from reduced flavin mononucleotide (FMNH2 ) to D339, (ii) proton transfer from EPSP to FMNH- and (iii) phosphate elimination...
December 26, 2018: Journal of Molecular Graphics & Modelling
Strahinja Z Kovačević, Milica Ž Karadžić, Dajana V Vukić, Vladimir R Vukić, Sanja O Podunavac-Kuzmanović, Lidija R Jevrić, Jovana J Ajduković
The present study is aimed to analyze lipophilicity and ADMET profiles, and to develop field based 3D-QSAR and ligand-based pharmacophore hypothesis for a series of 17α-picolyl and 17(E)-picolinylidene androstane derivatives in order to give detailed structural insights and to highlight important binding features of novel androstane derivatives, as compounds with antiproliferative activity toward breast adenocarcinoma cells. This study can provide guidelines for the rational design of novel potent compounds...
December 17, 2018: Journal of Molecular Graphics & Modelling
Małgorzata Gadzała, Dawid Dułak, Barbara Kalinowska, Zbigniew Baster, Michał Bryliński, Leszek Konieczny, Mateusz Banach, Irena Roterman
Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of H2 O molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution. The effect of this force field is to guide hydrophobic residues towards the center of the protein body, while promoting exposure of hydrophilic residues on its surface...
December 14, 2018: Journal of Molecular Graphics & Modelling
Mohammad-Bagher Ebrahim-Habibi, Maryam Ghobeh, Farzaneh Aghakhani Mahyari, Hashem Rafii-Tabar, Pezhman Sasanpour
BACKGROUND: Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. METHODS: Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT...
December 13, 2018: Journal of Molecular Graphics & Modelling
Leila Saedi, Elham Alipour, Zahra Javanshir, Vahid Vahabi
In the present work, we have studied a new allotrope of graphene, denoted as T-graphene (TG) flake as a versatile material in hydrogen storage. Recently, the metallic character of TG has been revealed. Our results show that the Li-decoration has a significant effect on the electronic properties of TG flake. Our density functional theory (DFT) calculations exhibit that the energy band gap of TG flake is decreased by decorating of the Li atom. Hydrogen adsorption on Li-decorated TG flake (Li/TG) under the influence of different external electric fields (EFs) is also explored by DFT calculations...
December 8, 2018: Journal of Molecular Graphics & Modelling
Indu Kumari, Navjot Kaur, Shuchi Gupta, Neetu Goel
Binding of four DNA nucleotide units with (ZnO)3 cluster in an aqueous phase has been investigated using density functional theory (DFT) and time dependent-density functional theory (TDDFT) method and the stability order for (ZnO)3 -nucleobases/sugar/phosphate systems is predicted as phosphate > C > A > S > T ∼ G. The order of binding energy for (ZnO)3 -nucleotide hybrid systems is observed to be (ZnO)3  + nuc-C ˃ (ZnO)3  + nuc-A ˃ (ZnO)3  + nuc-G ˃ (ZnO)3  + nuc-T...
December 7, 2018: Journal of Molecular Graphics & Modelling
Esmaeil Behmard, Ali Ahmadi, Ali Najafi
The emergence of antibiotic resistance has attracted the attention of scientists and scientific circles over the decades. β-Lactam antibiotics resistance is a worldwide therapeutic challenge in bacterial infections, mediated through several mechanisms of which mutations in Penicillin Binding Proteins (PBPs) are an important issue, making critical therapeutic problems in the human population. Accordingly, investigating the dynamic structures of mutant variants could result in a profound understanding of such a specific resistance...
December 7, 2018: Journal of Molecular Graphics & Modelling
Yue Jiang, Cuihong Wang, Meiling Zhang, Xuening Fei, Yingchun Gu
Twenty novel compounds with different functional groups (-COOH, -OH, -NH2 and -CH3) were designed to study the interaction mechanism of ligands with folate receptors (FRs). The optimized structure and the dipole moment of the novel compounds were calculated by a density functional tight-binding method (DFTB). The binding mechanism of the compounds with FRs was studied by molecular docking, molecular dynamic (MD) simulations and MM/PBSA free energy calculations. The binding energies, root mean square displacement and root mean square fluctuation of the complexes were analyzed to further illustrate the effect of the functional groups...
December 5, 2018: Journal of Molecular Graphics & Modelling
Jasmina Petrova, Gergana Gocheva, Nikoleta Ivanova, Stoyan Iliev, Boyana Atanasova, Galia Madjarova, Anela Ivanova
The study is focused on description of folate and several antifolates at physiological conditions. Knowledge of the molecular structure and dynamics is important for understanding their biological activity and therapeutic application. They are modelled in saline by atomistic molecular dynamics simulations and characterized in detail. In addition, quantum chemical calculations are used for determining the electronic structure of the six compounds. All molecules are highly flexible and have similar interactions with water...
December 4, 2018: Journal of Molecular Graphics & Modelling
Michael Oluwatoyin Daniyan, Oluwatoyin Tolulope Ojo
Plasmodium falciparum heat shock protein 90 (PfHsp90) has been investigated as a potential target of antimalarial drug action using naturally occurring compounds. In this study, we performed in silico screening of 236 phytochemicals of Azadirachta indica, a plant known to possess antimalarial activity, and identified fourteen (14) potential non-carcinogenic, non-mutagenic, non-teratogenic and non-genotoxic phytochemicals. These phytochemicals were docked into the ATP-binding site of PfHsp90 using Autodock vina, and docked poses were rescored using PLANTS ChemPlp, X-Score version 1...
December 4, 2018: Journal of Molecular Graphics & Modelling
Hossein Safarizadeh, Zahra Garkani-Nejad
Alzheimer's disease is characterized using amyloid-beta (Aβ) aggregation. The present work was carried out to extend and design a novel quantitative structure-activity relationship (QSAR) model on inhibition efficiency of some of new 2-arylethenylquinoline derivatives against the Aβ1-42 peptide aggregation. The QSAR study, molecular docking and molecular dynamics (MD) simulations were performed to explore the influence of the structural features and investigate the molecular mechanism of ligands interactions with the Aβ1-42 peptide...
December 4, 2018: Journal of Molecular Graphics & Modelling
Keigo Gohda
Recent computational simulations on protein-ligand binding/unbinding have precisely been uncovering the ligand-binding process at the atomic level. In the process, the non-specific binding of ligands to the target site is suggested to occur before binding to the target. We in this study analyzed the conformations of ligands under the non-specific binding on a protein surface to figure out the differences in the conformational characteristics in aqueous solution using the 55-ns molecular dynamic simulation. As for the protein surface, we constructed an artificial β-sheet, composed of poly-alanine residues (Ala-sheet)...
December 3, 2018: Journal of Molecular Graphics & Modelling
Joāo Luís Rheingantz Scaini, Alex Dias Camargo, Vinicius Rosa Seus, Andrea von Groll, Adriano Velasque Werhli, Pedro Eduardo Almeida da Silva, Karina Dos Santos Machado
Tuberculosis is a major cause of mortality and morbidity in developing countries, and the emergency of multidrug and extensive drug resistance cases is an utmost issue on the control of the disease. Despite the efforts on the development of new antibiotics, eventually there will be strains resistant to them as well. Efflux plays an important role in the evolution of resistance in Mycobacterium tuberculosis. Tap is an important efflux pump associated with tuberculosis resistant to isoniazid, rifampicine and ofloxacin and with multidrug resistance...
December 3, 2018: Journal of Molecular Graphics & Modelling
Mohamed Roubehie Fissa, Yasmina Lahiouel, Latifa Khaouane, Salah Hanini
This work aimed to predict the normal boiling point temperature (Tb) and relative liquid density (d20) of petroleum fractions and pure hydrocarbons, through a multi-layer perceptron artificial neural network (MLP-ANN) based on the molecular descriptors. A set of 223 and 222 diverse data points for Tb and d20 were respectively used to build two quantitative structure property relationships-artificial neural network (QSPR-ANN) models. For each model, the total database was divided respectively into two subsets: 80% for the training set and 20% for the test set...
November 29, 2018: Journal of Molecular Graphics & Modelling
Miguel A Chávez-Fumagalli, Daniela P Lage, Grasiele S V Tavares, Débora V C Mendonça, Daniel S Dias, Patrícia A F Ribeiro, Fernanda Ludolf, Lourena E Costa, Vinicio T S Coelho, Eduardo A F Coelho
New therapeutic strategies against leishmaniasis are desirable, since the treatment against disease presents problems, such as the toxicity, high cost and/or parasite resistance. As consequence, new antileishmanial compounds are necessary to be identified, as presenting high activity against Leishmania, but low toxicity in mammalian hosts. In the present study, a Leishmania proteome mining strategy was developed, in order to select new drug targets with low homology to human proteins, but that are considered relevant for the parasite' survival...
November 29, 2018: Journal of Molecular Graphics & Modelling
Gideon F Tolufashe, Victor T Sabe, Collins U Ibeji, Monsurat M Lawal, Thavendran Govender, Glenn E M Maguire, Gyanu Lamichhane, Hendrik G Kruger, Bahareh Honarparvar
Tuberculosis (TB) is one of the world's deadliest diseases resulting from infection by the bacterium, Mycobacterium tuberculosis (M.tb). The L,D-transpeptidase enzymes catalyze the synthesis of 3 → 3 transpeptide linkages which are predominant in the peptidoglycan of the M.tb cell wall. Carbapenems is class of β-lactams that inactivate L,D-transpeptidases by acylation, although differences in antibiotic side chains modulate drug binding and acylation rates. Herein, we used a two-layered our Own N-layer integrated Molecular Mechanics ONIOM method to investigate the catalytic mechanism of L,D-transpeptidase 5 (LdtMt5 ) by β-lactam derivatives...
November 28, 2018: Journal of Molecular Graphics & Modelling
Marjorie Caroline Liberato Cavalcanti Freire, Yamara Arruda Silva de Menezes, Matheus Vitor Ferreira Ferraz, Carlos Henrique Bezerra da Cruz, Leandro De Santis Ferreira, Matheus de Freitas Fernandes-Pedrosa, Euzébio Guimarães Barbosa
The Tityus stigmurus scorpion is widely distributed in the Northeast of Brazil and is the main causal agent of human envenoming. The venom produced by this scorpion includes neurotoxins, which are peptides belonging to Family 2 toxins and are able to interact with ion channels. The KTx subfamily displays selectivity and affinity for Kv channel subtypes and the result of this interaction is the blockade of potassium channels, impairing vital functions. We report the optimized structural model of a transcript encoding a potassium channel blocker toxin from T...
November 28, 2018: Journal of Molecular Graphics & Modelling
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