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Journal of Molecular Graphics & Modelling

Mingxing Wang, Wei Li, Ying Wang, Yongbo Song, Jian Wang, Maosheng Cheng
Studies on human genetics have implicated the voltage-gated sodium channel Nav1.7 as an appealing target for the treatment of pain. In this study, we put forward a ligand-based pharmacophore for the first time, which was generated by a set of multiple chemical scaffolds including sulfonamide and non-sulfonamide derivatives and consisted of four chemical features: an aromatic ring, a hydrophobic group and two hydrogen acceptors. The active cavity was divided into three regions according to the properties of the amino acids surrounded and was used for the docking of 16 known active inhibitors...
May 18, 2018: Journal of Molecular Graphics & Modelling
Yingfeng Li, Mengqi Cui, Bo Peng, Mingde Qin
Understanding the adsorption behaviors of supercritical fluid in confined space is pivotal for coupling the supercritical technology and the membrane separation technology. Based on grand canonical Monte Carlo simulations, the adsorption behaviors of a Lennard-Jones (LJ) fluid in slit-like pores at reduced temperatures over the critical temperature, Tc *  = 1.312, are investigated; and impacts of the wall-fluid interactions, the pore width, and the temperature are taken into account. It is found that even if under supercritical conditions, the LJ fluid can undergo a "vapor-liquid phase transition" in confined space, i...
May 18, 2018: Journal of Molecular Graphics & Modelling
Tao Yu, Maohua Lin, Bo Wu, Jintian Wang, Chi-Tay Tsai
On the basis of the framework of cubic gauche nitrogen (cg-N), six one-eighth methanetriyl groups (>CH-) substitutes and fifteen one-fourth >CH- substitutes were optimized using the first-principle calculations based on density functional theory (DFT). Both one-eighth and one-fourth substitutes still keep the gauche structures with the simple formula CHN7 and CHN3 , respectively. The most thermodynamic stable gauche CHN7 and CHN3 are P21 qtg-C2 H2 N14 I and P21 qtg-C4 H4 N12 III, respectively. No probability density of C-C single bonds and high probability densities of C-N-C structures were found in the two substitutes...
May 16, 2018: Journal of Molecular Graphics & Modelling
Abhishek Kumar, Priyadarshi Satpati
Group II introns are ribozymes which can catalyze its own splicing and relegate itself. They share common structural features and are evolutionarily related to eukaryotic spliceosome. Hence, group II introns are an excellent model system for understanding the mechanism of RNA-splicing in gene expression. Recent advancement of structural studies has provided x-ray structures of group II intron at different stages (Pre-hydrolytic, post-hydrolytic and free intron) of splicing pathway and revealed heteronuclear metal ion cluster (two potassium; K1 and K2, two magnesium; M1 and M2) in the active site as common structural feature of group II introns...
May 14, 2018: Journal of Molecular Graphics & Modelling
Xin Zhao, Jian Fen Fan, Xia Lan Si, Ling Ling Zhang, Meng Nan Qu
This work firstly explored the potential application of a cyclic peptide nanotube (CPNT) in the separation of chloroform from a dilute solution. Four hydrophobic CPNTs of 8 × (WL)4,5 and 8 × (AL)4,5 all exhibit excellent adsorption characteristics to chloroform. The CPNT diameter, side chain structures and the concentration of chloroform in a solution all affect the adsorption characteristics of chloroform. CHCl3 molecules are overwhelmingly adsorbed on the surfaces of these CPNTs as a cluster, and sporadically reside inside the channels, consistent with the chloroform's potentials of mean force (PMFs) inside and outside the channels...
May 10, 2018: Journal of Molecular Graphics & Modelling
Chao Wu, Liguang Mao, Xie Huang, Weitao Fu, Xiong Cai, Yuepiao Cai, Liqun Shen, Xiaoxia Ye
Survivin is the smallest member of IAP (inhibitor of apoptosis protein) family, which plays important roles in both mitosis and apoptosis. It has become an attractive drug target due to its overexpression in many human cancers. Survivin has been proven to bind to Smac/DIABLO protein that indirectly inhibits apoptosis. Meanwhile, it is the key subunit of chromosome passenger complex (CPC) which bind to the N-terminal tail of phosphorylated histone H3T3ph during mitosis. Up to now, Survivin directly targeting inhibitor has yet to merge since the difficulty of disrupting the protein-protein interactions (PPIs) between Survivin and its substrate proteins...
May 8, 2018: Journal of Molecular Graphics & Modelling
Sajjad Ahmad, Syed Sikander Azam
Acinetobacter baumannii is one of the major cause of nosocomial infections around the globe. The emergence of hyper-virulent strains of the pathogen greatly narrows down therapeutic options for patients infected with this red alert superbug. Development of a peptide-based vaccine can offers an alternative, attractive, and cost-effective remedy for multidrug-resistant A. baumannii associated complications. Herein, we introduced a novel virulome based Reverse Vaccinology for screening peptide based vaccine candidates against A...
May 5, 2018: Journal of Molecular Graphics & Modelling
Sarmistha Mitra, Raju Dash
The Proteins involved in the chemical modification of lysine residues in histone, is currently being excessively focused as the therapeutic target for the treatment of cell related diseases like cancer. Among these proteins, the epigenetic reader, CREB-binding protein (CREBBP) bromodomain is one of the most prominent targets for effective anticancer drug design, which is responsible for the reorganization of acetylated histone lysine residues. Therefore, this study employed an integrative approach of structure based drug design, in combination with Molecular Dynamics (MD) and QM/MM study to identify as well as to describe the binding mechanism of two shikonin derivatives, acetylshikonin and propionylshikonin as inhibitors of CREBBP bromodomain...
May 4, 2018: Journal of Molecular Graphics & Modelling
Shivangi Agarwal, Ekta Verma, Vivek Kumar, Namrita Lall, Samaresh Sau, Arun K Iyer, Sushil K Kashaw
Tuberculosis is an infectious chronic disease caused by obligate pathogen Mycobacterium tuberculosis that affects millions of people worldwide. Although many first and second line drugs are available for its treatment, but their irrational use has adversely lead to the emerging cases of multiple drug resistant and extensively drug-resistant tuberculosis. Therefore, there is an intense need to develop novel potent analogues for its treatment. This has prompted us to develop potent analogues against TB. The Mycobacterium tuberculosis genome provides us with number of validated targets to combat against TB...
May 3, 2018: Journal of Molecular Graphics & Modelling
Richa Arora, Upasana Issar, Rita Kakkar
Hydroxamic acids have emerged as the most promising candidates from among the different classes of inhibitors of urease. In order to understand the mechanism of their action, we have studied in detail using quantum mechanics the active site of Helicobacter pylori urease complexed with acetohydroxamic acid. A diverse library of ligands having the hydroxamate moiety has been prepared and docked into the active site of urease using the QM/MM methodology. It is found that hydroxamic acids with hydrophobic groups attached to them are more potent inhibitors of urease because they can easily penetrate the hydrophobic environment surrounding the active site...
May 1, 2018: Journal of Molecular Graphics & Modelling
Prabu Manoharan, J Sridhar
The organophosphorus hydrolase enzyme is involved in the catalyzing reaction that involve hydrolysis of organophosphate toxic compounds. An enzyme from Deinococcus radiodurans reported as homologous to phosphotriesterase and show activity against organophosphate. In the past activity of this enzyme is low and efforts made to improve the activity by experimental mutation study. However only very few organophosphates tested against very few catalytic site mutations. In order to improve the catalytic power of the organophosphorus hydrolase enzyme, we carried out systematic functional hotspot based protein engineering strategy...
May 1, 2018: Journal of Molecular Graphics & Modelling
Marrigje Marianne Conradie, Petrus H van Rooyen
[Rh((C4 H3 S)COCHCO(C4 H3 S))(CO)(PPh3 )] crystals stack in one dimensional linear chains in the solid state, with slightly slipped π-stacking of the thienyl groups of one molecule and the β-diketonato backbone of a neighbouring molecule. The observed stacking is possible due to the near planar orientation of the two aromatic thienyl groups and the β-diketonato backbone. The experimentally observed stacking and close intermolecular contacts are in agreement with theoretical QTAIM calculated intermolecular bond paths and intermolecular hydrogen bonds between neighbouring molecules...
April 30, 2018: Journal of Molecular Graphics & Modelling
Urszula Uciechowska-Kaczmarzyk, Sándor Babik, Ferenc Zsila, Krzysztof Kamil Bojarski, Tamás Beke-Somfai, Sergey A Samsonov
We present a computational model of the Vascular Endothelial Growth Factor (VEGF), an important regulator of blood vessels formation, which function is affected by its heparin interactions. Although structures of a receptor binding (RBD) and a heparin binding domain (HBD) of VEGF are known, there are structural data neither on the 12 amino acids interdomain linker nor on its complexes with heparin. We apply molecular docking and molecular dynamics techniques combined with circular dichroism spectroscopy to model the full structure of the dimeric VEGF and to propose putative molecular mechanisms underlying the function of VEGF/VEGF receptors/heparin system...
April 27, 2018: Journal of Molecular Graphics & Modelling
U Srimathi, V Nagarajan, R Chandiramouli
We report the density functional application of adsorption behavior of volatile organic compounds (VOCs) emitted from the different ripening stages of banana fruit on germanene nanotube (GNT). Initially, the geometric structural stability of GNT is ascertained and the tunable electronic properties lead to the application of GNT as a base material in order to know the adsorption features of VOCs. We further explored the adsorption behavior of VOCs on to GNT through charge transfer, adsorption energy and band gap variation...
April 27, 2018: Journal of Molecular Graphics & Modelling
Norbert Jeszenői, Gabriella Schilli, Mónika Bálint, István Horváth, Csaba Hetényi
Advancement of computational molecular dynamics allows rapid calculation of large biomolecular systems in their water surroundings. New approaches of prediction of hydration networks of biomolecular surfaces and complex interfaces are also based on molecular dynamics (MD). Calculations with explicit solvent models can trace thousands of water molecules individually on a real time scale, yielding information on their mobility, and predicting their networking with biomolecular solutes and other water partners...
April 27, 2018: Journal of Molecular Graphics & Modelling
Cong Quang Vu, Pichayanoot Rotkrua, Boonchoy Soontornworajit, Yuthana Tantirungrotechai
PDGFRβ/PDGF-B interaction plays a role in angiogenesis, and is mandatory in wound healing and cancer treatment. It has been reported that the PDGF-B aptamer was able to bind to PDGF-B, thus regulating the angiogenesis. However, the binding interaction between the aptamer and the growth factor, including the binding sites, has not been well investigated. This study applied a molecular dynamics (MD) simulation to investigate the aptamer-growth factor interaction in the presence or absence of a receptor (PDGFRβ)...
April 26, 2018: Journal of Molecular Graphics & Modelling
Hongping Li, Changwei Wang, Suhang Xun, Jing He, Wei Jiang, Ming Zhang, Wenshuai Zhu, Huaming Li
To obtain the adsorption strength is the key point for materials design and parameters optimization in chemical engineering. Here we report a simple but accuracy method to estimate the adsorptive energies by counting the number of π-orbital involved atoms based on theoretical computations for hexagonal boron nitride (h-BN) and graphene. Computational results by density function theory (DFT) as well as spin-component scaled second-order Møller-Plesset perturbation theory (SCS-MP2) both confirm that the adsorptive energies correlate well with the number of π-orbital involved atoms for π-orbital contained molecules...
April 26, 2018: Journal of Molecular Graphics & Modelling
Ruth Veevers, Steven Hayward
Protein structures are often solved at atomic resolution in two states defining a functional movement but intervening conformations are usually unknown. Morphing methods generate intervening conformations between two known structures. When viewed as an animation using molecular graphics, a smooth, direct morph enables the eye to track changes in structure that might be otherwise missed. We present a morphing method that aims to linearly interpolate interatomic distances and which uses SMACOF (Scaling by MAjorisation of COmplicated Function) and multigrid techniques with a cut-off distance based weighting that optimizes the MolProbity score of intervening structures...
April 25, 2018: Journal of Molecular Graphics & Modelling
Mohamad Ariff Mohamad Yusoff, Azzmer Azzar Abdul Hamid, Noraslinda Mohammad Bunori, Khairul Bariyyah Abd Halim
Ebola virus is a lipid-enveloped filamentous virus that affects human and non-human primates and consists of several types of protein: nucleoprotein, VP30, VP35, L protein, VP40, VP24, and transmembrane glycoprotein. Among the Ebola virus proteins, its matrix protein VP40 is abundantly expressed during infection and plays a number of critical roles in oligomerization, budding and egress from the host cell. VP40 exists predominantly as a monomer at the inner leaflet of the plasma membrane, and has been suggested to interact with negatively charged lipids such as phosphatidylinositol 4,5-bisphosphate (PIP2 ) and phosphatidylserine (PS) via its cationic patch...
April 23, 2018: Journal of Molecular Graphics & Modelling
Sajjad Ahmad, Saad Raza, Reaz Uddin, Syed Sikander Azam
Multidrug-resistant Acinetobacter baumannii is indeed to be the most successful nosocomial pathogen responsible for myriad infections in modern health care system. Computational methodologies based on genomics and proteomics proved to be powerful tools for providing substantial information about different aspects of A. baumannii biology that made it possible to design new approaches for treating multi, extensive and total drug resistant isolates of A. baumannii. In this current approach, 35 completely annotated proteomes of A...
April 21, 2018: Journal of Molecular Graphics & Modelling
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