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Journal of Molecular Graphics & Modelling

Hongping Li, Yujun Li, Linghao Sun, Suhang Xun, Wei Jiang, Ming Zhang, Wenshuai Zhu, Huaming Li
Hydrogen peroxide (H2 O2 ) decomposition mechanism and its oxidative desulfurization activity on hexagonal boron nitride monolayer (h-BN) have been explored by density functional theory (DFT) at M06-2X/6-311 + G (d,p) level. A cluster model which contains seven rings has been constructed to simulate the h-BN surface. It is found that 7 possible species will be generated after the decomposition of H2 O2 . Among them, 2H*+O2 * and 2H*+2O* are relatively unstable while other species, such as HOO*+H*, HO*+HO*, H*+HO + O*, H2 O*+O* are relatively stable and may exist in the current system...
July 5, 2018: Journal of Molecular Graphics & Modelling
Mohd Athar, Prabodh Ranjan, Prakash C Jha
Herein, we have presented the results of Density Functional Theory (DFT) based calculations of inclusion complexes of lapatinib and dasatinib with calix[n]arene macrocycles. A total of 48 calix [n]arene complexes were modeled via considering varied ring sizes (n = 4,5,6,8) and upper-rim functionalization viz. SO3 H, tert-Butyl, iso-Propyl, COOH, C2 H5 OH, and C2 H5 NH2 . From the results of multilevel molecular docking, DFT energetics, and reactivity descriptors; it has been demonstrated that dasatinib form optimal complexes with calix 4f, 3f (-35 to -40 kcal/mol)...
June 30, 2018: Journal of Molecular Graphics & Modelling
N A Noor, Q Mahmood, M Hassan, A Laref, Muhammad Rashid
The electronic, optical and thermoelectric analyses of BaGeO3 perovskite have been done by using density functional theory (DFT) based Trans and Blaha modified Becke and Johnson (TB-mBJ) approach. The applied pressure (up to 30 GPa) has been found tailoring the band gap from indirect to direct bandgap (at 20 GPa), within the visible region, revealing renewable energy applications of the studied perovskite. The applied pressure improves mechanical stability by increasing ductility. Furthermore, optical properties are illustrated by computing dielectric constants, refraction, absorption, optical conductivity and optical loss factor for suggesting optoelectronic applications...
June 30, 2018: Journal of Molecular Graphics & Modelling
Wenbo Dong, Yanqing Wang, Xin Yang, Jianbo Cheng, Qingzhong Li
The complexes between BH(CO)2 /BH(N2 )2 and XF3 /XF5 are stabilized by a halogen bond and a triel bond. The MEP analyses of BH(CO)2 /BH(N2 )2 indicate that there are both a region with negative MEPs on the B atom in the vertical direction of the molecular plane and a σ-hole at the B-H bond end. Therefore, the boron atom in BH(CO)2 /BH(N2 )2 plays a dual role of a Lewis base and an acid in the halogen bond and triel bond, respectively. The halogen and triel bonds are stronger in order of IF3 < BrF3 < ClF3 , IF5 < BrF5 < ClF5 , and BH(CO)2 < BH(N2 )2 in most complexes...
June 27, 2018: Journal of Molecular Graphics & Modelling
Fan Rao, Zeqin Chen, Dagang Zhou, Yuan Kang, Linfeng Guo, Ying Xue
Theophylline, one of the most commonly used bronchodilators and respiratory stimulators for the treatment of acute and chronic asthmatic conditions, can cause permanent neurological damage through chronic or excessive ingestion. In this work, DFT calculation was performed to identify the metabolic mechanisms of theophylline by cytochrome P450 (CYP450) monooxygenase. Two main metabolic pathways were investigated, namely, N1 - (path A) and N3 - (path B) demethylations, which proceeded through N-methyl hydroxylation followed by the decomposition of the generated carbinolamine species...
June 22, 2018: Journal of Molecular Graphics & Modelling
Fatma Gizem Avci, Fatma Ece Altinisik, Ipek Karacan, Duygu Senturk Karagoz, Serhat Ersahin, Ayse Eren, Nihat Alpagu Sayar, Didem Vardar Ulu, Elif Ozkirimli, Berna Sariyar Akbulut
Increasing resistance against available orthosteric beta-lactamase inhibitors necessitates the search for novel and powerful inhibitor molecules. In this respect, allosteric inhibitors serve as attractive alternatives. Here, we examine the structural basis of inhibition in a hidden, druggable pocket in TEM-1 beta-lactamase. Based on crystallographic evidence that 6-cyclohexyl-1-hexyl-β-D-maltoside (CYMAL-6) binds to this site, first we determined the kinetic mechanism of inhibition by CYMAL-6. Activity measurements with CYMAL-6 showed that it competitively inhibits the wild type enzyme...
June 18, 2018: Journal of Molecular Graphics & Modelling
Joshua Hochuli, Alec Helbling, Tamar Skaist, Matthew Ragoza, David Ryan Koes
Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning techniques can make use of the increasing amounts of structural data that are becoming publicly available. Convolutional neural network (CNN) scoring functions in particular have shown promise in pose selection and affinity prediction for protein-ligand complexes. Neural networks are known for being difficult to interpret...
June 18, 2018: Journal of Molecular Graphics & Modelling
Siddheshwar Chopra
Density functional theory (DFT) and time dependent density functional theory (TDDFT) at PBE0/6-311G* level are performed to examine the stability, electronic and optical properties of boron fullerenes (Bn , n = 20, 30, 38, 40, 50, 60). Amongst all the structures, B50 is found to be highly stable and has the least electronic gap. In general, all borofullerenes are found to be semiconducting in nature. Absorption wavelength shift in the photoabsorption spectra is reported with the increasing borofullerene size...
June 18, 2018: Journal of Molecular Graphics & Modelling
Debodyuti Dutta, Sabyashachi Mishra
The perils of antimicrobial drug resistance can be overcome by finding novel antibiotic targets and corresponding small molecule inhibitors. Microbial enzyme DapE is a promising antibiotic target due to its importance to the bacterial survival. The potency of L-Captopril, a well known angiotensin-converting enzyme inhibitor, as an inhibitor of DapE enzyme has been evaluated by analyzing its binding modes and binding affinity towards DapE enzyme. L-Captopril is found to bind the metal centers of DapE enzyme either via its thiolate group or through its carboxylate group...
June 18, 2018: Journal of Molecular Graphics & Modelling
Alexey Rayevsky, Mohsen Sharifi, Michael Tukalo
The accuracy of protein synthesis is provided by the editing functions of aminoacyl-tRNA synthetases (aaRSs), a mechanism that eliminates misactivated amino acids or mischarged tRNAs. Despite research efforts, some molecular bases of these mechanisms are still unclear. The post-transfer editing pathway of leucyl-tRNA synthetase (LeuRS) carried out in a special insertion domain (the Connective Polypeptide 1 or CP1), as editing domain. Recently, it was shown by in vivo studies and was supported by mutagenesis, and the kinetics approaches that the CP1 domain of LeuRS has discriminatory power for different substrates...
June 18, 2018: Journal of Molecular Graphics & Modelling
Kerem Teralı
Many so-called neuroactive insecticides target invertebrate neurotransmitter systems, including the cholinergic system. With their relatively low toxicity to vertebrates, neonicotinoids represent a new class of neuroactive insecticides that bind to nicotinic receptors for acetylcholine in the insect central nervous system and result in paralysis and eventual death due to receptor overstimulation. On the understanding that, today, cholinesterase inhibitors are used to obtain the symptomatic relief of Alzheimer disease (AD), the aforementioned direct cholinomimetic action of neonicotinoids could, perhaps, confer anti-AD drug-like attributes to these compounds...
June 16, 2018: Journal of Molecular Graphics & Modelling
Hafez Razmazma, Ali Ebrahimi
The effects of ion-π interaction on the [N⋯X⋯N]+ halogen bond have been investigated by placement of monovalent ions on a pyridine ring plane of the complexes. The structural and electronic properties of the complexes have been studied via the density functional theory (DFT), quantum theory of atoms in molecules (QTAIM), non-covalent interaction (NCI) index and the nuclear magnetic resonance (NMR) calculations. The evaluation of halogen bonds in bis(pyridine)halonium complexes reveals the existence of two factors, ion-π interactions and intermolecular N─N distance, which play the important roles on the formation and stability of these quaternary complexes...
June 15, 2018: Journal of Molecular Graphics & Modelling
Gareth Williams
Protein complexes are characterised by shape complementarity at the interface. Here we present a simple fast global shape fitting algorithm to investigate the extent to which interfaces are global minima of complementarity. The algorithm is applied to a varied set of hetero and homo complexes and complexes between complexes showing that over 90% of large interfaces are global maxima in the space of shape complementarity.
June 15, 2018: Journal of Molecular Graphics & Modelling
Zhuang-Lin Shen, Wen-de Tian, Kang Chen, Yu-Qiang Ma
Understanding the interactions of dendrimers as drug/gene delivery vectors with proteins is important for functional optimization. Here, atomistic molecular dynamics simulations are employed to study the interactions between six positively-charged polyamidoamine dendrimers of the second generation (G2 PAMAM) and G-actin. We find that the structure of G-actin is relatively stable after dendrimers' binding. PAMAM dendrimers also do not significantly change the secondary structure of G-actin. Furthermore, we find the formation of dendrimer-actin complex is mainly driven by electrostatic interactions...
June 14, 2018: Journal of Molecular Graphics & Modelling
Nattawee Poomsuk, Tirayut Vilaivan, Khatcharin Siriwong
Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences...
June 12, 2018: Journal of Molecular Graphics & Modelling
Maryam Rouhani, Farnaz Khodabakhsh, Dariush Norouzian, Reza Ahangari Cohan, Vahideh Valizadeh
Recently protein engineering has been used as a pivotal tool for designing proteins with improved characteristics. While the experimental methods might be laborious and time-consuming, in silico protein design is a time and cost-effective approach. Moreover, in some cases, protein modeling might be the only way to obtain structural information where the experimental techniques are inapplicable. Molecular dynamics (MD) simulation is a method that allows the motion of protein to be simulated in defined conditions on the basis of classical molecular dynamics...
June 9, 2018: Journal of Molecular Graphics & Modelling
Niloofar Shirvanizadeh, Gert Vriend, Seyed Shahriar Arab
Engineering surface loops is a sub-topic of protein engineering that is used routinely in many research fields in academia and industry alike. We provide some tools that search in the PDB for loops satisfying a wide variety of constraints. We illustrate the usefulness of these tools by applying them to a series of recently published studies that included loop engineering or loop modelling. LoopFinder finds loops that fit between two anchor stretches of typically 2, 3, or 4 amino acids each. ProDA find loops of a given length with predefined secondary structure, residue types, hydrophobicity, etc...
June 7, 2018: Journal of Molecular Graphics & Modelling
Sarfaraj Niazi, Madhusudan Purohit, Archana Sonawani, Javed H Niazi
Single-stranded (ss) oligonucleotide aptamers are emerging as the promising substitutes for monoclonal antibodies because of their low production cost and good batch-to-batch consistency. Aptamers vividly bind to a variety of cellular targets and alter their functions with a remarkable degree of specificities. In this study, the positive clones of human epidermal growth factor receptor 2 (HER2) specific binding ssDNA aptamers which were previously identified by in vitro Systematic Evolution of Ligands by EXponential enrichment (SELEX) process, hitherto lacking the putative binding site information and residues crucial for aptamer recognition are studied...
June 6, 2018: Journal of Molecular Graphics & Modelling
Son Tung Ngo, Huynh Minh Hung, Nam Dao Hong, Nguyen Thanh Tung
The residue E22 plays a critical role in the aggregation process of Amyloid beta (Aβ) peptides. The effect of E22Q mutant on the shapes of the solvated Aβ11-40 trimer is clarified using a replica exchange molecular dynamics (REMD) simulation employing ∼20.6 μs of MD simulations with 48 disparate replicas. The increase of intramolecular polar contacts and salt bridge between the residue D23 to residues (24-29) was observed. The residual secondary structure of the mutated trimer is shifted in a similar way to the picture observed in previous investigations of F19W mutant...
June 5, 2018: Journal of Molecular Graphics & Modelling
Huiqun Wang, Glen E Kellogg, Ping Xu, Yan Zhang
Meso-Diaminopimelic acid (meso-2,6-diamino-heptanedioic acid, DAP) is an important component of the cell wall of many bacteria. Meso-diaminopimelate dehydrogenase (m-Ddh) is a critical enzyme in the process of converting tetrahydrodipicolinate to DAP. Here, we are proposing that DAP analogs targeting m-Ddh may be considered as potential antibiotics. Four DAP analogs without significant structural change from DAP have been obtained and their inhibitory potencies against m-Ddh from the P. gingivalis strain W83 show significant differences from that of DAP...
June 2, 2018: Journal of Molecular Graphics & Modelling
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