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Journal of Molecular Graphics & Modelling

Rajendra Kristam, Shashidhar N Rao, Anne Sudha D'Cruz, Vijayalakshmi Mahadevan, Vellarkad N Viswanadhan
Transient Receptor Potential Vanilloid, member 1 (TRPV1), is a non-selective cation channel belonging to the transient receptor potential (TRP) family of ion channels. It occurs in the peripheral and central nervous system, activated by a variety of exogenous and endogenous stimuli, thus playing a key role in transmission of pain. This has been a target for chronic pain since more than a decade and a number of antagonists that progressed into clinical trials have failed due to the unexpected side effect of core body temperature rise, thus halting progress in this field...
January 7, 2017: Journal of Molecular Graphics & Modelling
Zhiguo Wang, Jun-Ping Liu
Human telomeres undertake the structure of intra-molecular parallel G-quadruplex in the presence of K(+) in eukaryotic cell. Stabilization of the telomere G-quadruplex represents a potential strategy to prevent telomere lengthening by telomerase in cancer therapy. Current work demonstrates that the binding of central K(+) with the parallel G-quadruplex is a coordinated water directed step-wise process. The K(+) above the top G-tetrad is prone to leak into environment and the 5'-adenine quickly flips over the top G-tetrad, leading to the bottom gate of G-tetrads as the only viable pathway of K(+) binding...
January 6, 2017: Journal of Molecular Graphics & Modelling
Jin-Ting Ye, Feng-Yang Bai, Shao-Qing Shi, Xiu-Mei Pan
The NO3-initiated reactions of CH3OCH3 and CH3OCH2CH3 have been investigated by the BHandHLYP method in conjunction with the 6-311G(d,p) basis set. Thermodynamic and kinetic data are further refined using the comparatively accurate CCSD(T) method. According to the values of reaction enthalpies (ΔHr,298(θ)) and reaction Gibbs free energies (ΔGr,298(θ)) from CH3OCH2CH3 with NO3 system, we find that H-abstraction pathway from the α-CH2 group is more exothermic. It is further confirmed by the calculated CH bond dissociation energy of CH3OCH2CH3 molecule...
January 6, 2017: Journal of Molecular Graphics & Modelling
Margarita G Ilyina, Edward M Khamitov, Rail N Galiakhmetov, Ildar A Mustafin, Akhat G Mustafin
In the present work, a 0.4nm nickel cluster has been theoretically studied. Its equilibrium structural parameters have been calculated by the DFT method based on the PBEH1PBE hybrid functional and split-valence basis set Lanl2DZ including effective core potentials. We have systematically considered diverse spin states of this cluster and find out its ground state. The relative stability of these states depends on the HOMO-LUMO gap. The interaction of the Ni6 with 4-propylheptane С10Н22 has been studied to simulate the process of catalytic cracking of hydrocarbons...
January 3, 2017: Journal of Molecular Graphics & Modelling
Shagufta Shafique, Sajid Rashid
The critical role of βTrCP1 in cancer development makes it a discerning target for the development of small drug like molecules. Currently, no inhibitor exists that is able to target its substrate binding site. Through molecular docking and dynamics simulation assays, we explored the comparative binding pattern of βTrCP1-WD40 domain with ACV and its phospho-derivatives (ACVMP, ACVDP and ACVTP). Consequently, through principal component analysis, βTrCP1-ACVTP was found to be more stable complex by obscuring a reduced conformational space than other systems...
December 31, 2016: Journal of Molecular Graphics & Modelling
Natália de Farias Silva, Raimundo Lopes da Silva, Kalene de Oliveira Almeida, Antônio Edilson Sousa do Nascimento-Júnior, Davi do Socorro Barros Brasil, José Otávio Carréra Silva-Júnior, Francisco Martins Teixeira, Roseane Maria Ribeiro-Costa
Chitosan has attracted much interest due to its special physical and chemical properties related to drug administration. Nanoparticles delivery systems from Vi Antigen are a promising approach in the struggle against typhoid fever. In this paper, we reported the obtainment and the characterization of Vi Antigen by Infrared spectroscopy as well as Molecular Modeling and Computational Chemistry studies of the Chitosan-Vi Antigen interaction through theoretical models. The results of the theoretical and experimental Infrared spectroscopy showed important bands related to N-Acetyl and O-Acetyl groups present in Vi Antigen...
December 31, 2016: Journal of Molecular Graphics & Modelling
Maryam Anafcheh, Fereshteh Naderi, Zahra Khodadadi, Fatemeh Ektefa, Reza Ghafouri, Mansour Zahedi
We applied density functional calculations to study the circular redox reaction mechanism of N2O with CO catalyzed by fullerometallic cations C60Fe(+) and C70Fe(+). The on-top sites of six-membered rings (η(6)) of fullerene cages are the most preferred binding sites for Fe(+) cation, and the hexagon to pentagon migration of Fe(+) is unlikely under ambient thermodynamic conditions. The initial ion/molecule reaction, N2O rearrangement and N2 abstraction on the considered fullerometallic cations are easier than those on the bare Fe(+) cation in the gas phase...
December 31, 2016: Journal of Molecular Graphics & Modelling
Mengzhi Han, Ji Xu, Ying Ren
Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent...
December 28, 2016: Journal of Molecular Graphics & Modelling
Zahra Rostami, Mansoureh Pashangpour, Reza Moradi
It has been previously shown that the toxic formaldehyde gas (H2CO) cannot be detected by pristine BC2N, carbon, and BN nanotubes, BC3 nanosheet and graphene. Herein, density functional theory calculations were employed to investigate the electronic and structural behavior of a pristine B24N24 nanocluster toward H2CO molecules. It was found that [4,6] BN bonds of the nanocluster are the most favorable sites for the H2CO adsorption, compared to the [4,8], and [6,8] ones. When an H2CO molecule is adsorbed on a [4,6] BN bond, an energy of about 16...
December 26, 2016: Journal of Molecular Graphics & Modelling
E V Katkova, A V Onufriev, B Aguilar, V B Sulimov
In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field...
December 21, 2016: Journal of Molecular Graphics & Modelling
Yu Wei, Ruihua Liu, Cui Liu, Jin Jin, Dongmei Li, Jianping Lin
1.4 Protein arginine deiminases 4 (PAD4) is an attractive target for the development of novel and selective inhibitors of Rheumatoid Arthritis (RA). F-amidine is known as mechanism-based inhibitor targeting PAD4 and used as inactivators by covalently modifying the active site Cys645. To identify novel structural inhibitors of PAD4, we investigated the flexibility of protein on basis of the transition state geometry of PAD4 inhibited by F-amidine from our previous QM/MM calculation. And a pharmacophore model was generated containing four features (ADHH) using five representative structures from molecular dynamic (MD) simulation on basis of the transition state geometry of PAD4 inhibited by F-amidine...
December 19, 2016: Journal of Molecular Graphics & Modelling
Yue Yu, Ishan A Fursule, Landon C Mills, Derek L Englert, Brad J Berron, Christina M Payne
2'-Hydroxybiphenyl-2-sulfinate (HBPS) desulfinase (DszB) catalyzes the cleavage of the carbon-sulfur bond from HBPS in the final step of microbial 4S pathway desulfurization reactions. DszB is notable for its substrate specificity and exhibits product inhibition, both of which hinder the overall 4S pathway turnover rate. To understand the molecular-level contributions to substrate and inhibitor binding to DszB, we plan to perform molecular dynamic simulations bound to an array of naphthenic molecules and biphenyl analogues of HBPS...
December 15, 2016: Journal of Molecular Graphics & Modelling
Shabbir Muhammad, Abdullah G Al-Sehemi, Zhongmin Su, Hongliang Xu, Ahmad Irfan, Aijaz Rasool Chaudhry
Using first-principle methods, several key electronic, optical and nonlinear optical properties are calculated for two recently synthesized chalcone derivatives i.e. (2E)-3-(4-methylphenyl)-1-(3-nitrophenyl)prop-2-en-1-one (comp.1) and (2E)-3-[4-(dimethylamino)phenyl]-1-(3-nitrophenyl)prop-2-en-1-one (comp.2). The calculation of dipole moment, polarizability <α>, anisotropy of polarizability as well as second hyperpolarizability (usually considered as a signature for two photon absorption phenomenon) are performed using density functional theory methods at PBE0/6-311G** level of theory...
December 14, 2016: Journal of Molecular Graphics & Modelling
Sanchari Basu Mallik, Aravinda Pai, Rekha R Shenoy, B S Jayashree
Epigenetic modulation of gene expression has drawn enormous attention among researchers globally in the present scenario. Since their discovery, Jmj-C histone demethylases were identified as useful markers in understanding the role of epigenetics in inflammatory conditions and in cancer as well. This has created arousal of interest in search of suitable candidates. Potential inhibitors from various other scaffolds such as hydroxyquinolines, hydroxamic acids and triazolopyridines have already been identified and reported...
December 13, 2016: Journal of Molecular Graphics & Modelling
Sayyed Jalil Mahdizadeh, Golnoosh Akhlamadi
In the current work, the issue of re-parameterization of Tersoff empirical potential model was addressed for 2D nanomaterial 'germanene' to be applied in molecular dynamics simulation based studies. The well-known chi-square minimization procedure was used to optimize the original Tersoff potential parameters. Many properties of germanene were extracted using both original and optimized Tersoff potentials and they compared with the corresponding density functional theory data. According to the results, the optimized Tersoff potential provides a significant improvement in many structural, thermodynamic, mechanical, and thermal properties of geramanene...
December 13, 2016: Journal of Molecular Graphics & Modelling
S Lebecque, J M Crowet, M N Nasir, M Deleu, L Lins
Surfactants are molecules able to spontaneously self-assemble to form aggregates with well-defined properties, such as spherical micelles, planar bilayers, cylindrical micelles or vesicles. Micelles have notably several applications in many domains, such as drug delivery or membrane protein solubilization. In this context, the study of micelle formation in relation with the structural and physico-chemical properties of surfactants is of great interest to better control their use in the different application fields...
December 11, 2016: Journal of Molecular Graphics & Modelling
Biao Zhong, Chi Zhang, Shang Guo, Changqing Zhang
The human TGF-β/SMAD7 signaling has been recognized as an attractive target of heterotopic ossification (HO). Here, we report a successful rational design of cyclic peptides to disrupt the signaling pathway by targeting TGF-β-receptor complex. The intermolecular interaction between TGF-β and its cognate receptor is characterized in detail using molecular dynamics simulation, binding energetic analysis, and alanine scanning. With the computational analysis a binding loop of receptor protein is identified that plays an essential role in the peptide-mediated TGF-β-receptor interaction...
December 7, 2016: Journal of Molecular Graphics & Modelling
A Cheraghi, R Malekfar, S Moemen Bellah, M Parishani
We investigate the performance of 109 types of composition with complex permittivity and permeability properties in the frequency range of 1-12GHz. The components of these compositions are based on conductive and nonconductive polymer composites, ferrites, hexaferrites, and carbon materials. A new swarm-based algorithm has been introduced to solve microwave absorbing nanomaterials (MANM) problem, called Imitation Based Optimization (ISO). The individuals in the ISO imitate each other and move to better locations...
November 30, 2016: Journal of Molecular Graphics & Modelling
Moacir F Ferreira, Eduardo F Franca, Fábio L Leite
The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions...
November 21, 2016: Journal of Molecular Graphics & Modelling
Nada A Al-Jallal, Adel A El-Azhary
Crown ethers are an important class of molecules with wide applications. Crown ethers are large ring flexible molecules with a large number of possible conformations. In the current manuscript, we report the conformational analysis results of one of the smallest crown ether systems, namely, 9-crown-3, 9c3, 9-thiacrown-3, 9t3, and 9-azacrown-3, 9a3. The conformational search is performed using the CONFLEX conformational search method utilizing the MMFF94s force field. 8, 11 and 62 conformations were predicted for 9c3, 9t3 and 9a3, respectively...
January 2017: Journal of Molecular Graphics & Modelling
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