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MD simulation

Neil A Mehta, Deborah A Levin
Molecular dynamics (MD) electrospray simulations of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF_{4}) ion liquid were performed with the goal of evaluating the influence of long-range Coulomb models on ion emission characteristics. The direct Coulomb (DC), shifted force Coulomb sum (SFCS), and particle-particle particle-mesh (PPPM) long-range Coulomb models were considered in this work. The DC method with a sufficiently large cutoff radius was found to be the most accurate approach for modeling electrosprays, but, it is computationally expensive...
March 2018: Physical Review. E
Parth Rakesh Desai, Shayandev Sinha, Siddhartha Das
We employ molecular dynamics (MD) simulations and develop scaling theories to quantify the equilibrium behavior of polyelectrolyte (PE) brush bilayers (BBLs) in the weakly interpenetrated regime, which is characterized by d_{0}<d_{g}<2d_{0}, where d_{g} is the gap between the opposing plates where the PE brushes are grafted and d_{0} is the unperturbed height of a PE brush grafted at a single plate. Scaling predictions establish that, for the weakly interpenetrated osmotic PE BBLs δ∼N^{1/2}(2-d_{g}/d_{0})^{1/2} (where δ is the interpenetration length and N is the number of Kuhn segments in PE brush)...
March 2018: Physical Review. E
Ming-Lang Zhao, Wang Wang, Hu Nie, Sha-Sha Cao, Lin-Fang Du
Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots...
May 6, 2018: Computational Biology and Chemistry
Siddhartha Moulik, Vani Bukke, S Chandrasekhar Sajja, Sridhar S
Present work reports the synthesis of a novel Chitosan-Polytetrafluoroethylene composite membrane with solvent resistant property for efficient separation of methanol/toluene mixture by pervaporation. The composite was crossed with tetraethyl orthosilicate (TEOS) to prevent or reduce membrane swelling and improve the separation factor. The synthesized membranes were characterized by SEM, FTIR and DSC analysis. Molecular dynamics (MD) simulation and computational fluid dynamics were coupled to predict the structural and diffusive properties besides concentration profile inside the membrane...
August 1, 2018: Carbohydrate Polymers
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
Igor Ariz-Extreme, Jochen S Hub
Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious...
2018: PloS One
Katsuhide Yutani, Yoshinori Matsuura, Hisashi Naitow, Yasumasa Joti
In order to elucidate features of the denatured state ensembles that exist in equilibrium with the native state under physiological conditions, we performed 1.4-μs molecular dynamics (MD) simulations at 400 K and 450 K using the monomer subunits of three CutA1 mutants from Escherichia coli: an SH-free mutant (Ec0SH) with denaturation temperature (Td ) = 85.6 °C, a hydrophobic mutant (Ec0VV) with Td  = 113.3 °C, and an ionic mutant (Ec0VV_6) with Td  = 136.8 °C. The occupancy of salt bridges by the six substituted charged residues in Ec0VV_6 was 140...
May 16, 2018: Scientific Reports
Casper Steinmann, Martin A Olsson, Ulf Ryde
We have devised a new efficient approach to compute combined quantum mechanical (QM) and molecular mechanical (MM, i.e. QM/MM) ligand-binding relative free energies. Our method employs the reference-potential approach with free-energy perturbation both at the MM level (between the two ligands) and from MM to QM/MM (for each ligand). To ensure that converged results are obtained for the MM→QM/MM perturbations, explicit QM/MM molecular dynamics (MD) simulations are performed with two intermediate mixed states...
May 17, 2018: Journal of Chemical Theory and Computation
Anjela Manandhar, Myungshim Kang, Kaushik Chakraborty, Sharon M Loverde
At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT) is driven by the nucleotide state (GTP vs. GDP) in the β subunit of the tubulin dimers at the MT cap. Here, we use large-scale molecular dynamics (MD) simulations and normal mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed by two neighboring protofilaments (PFs). We utilize recently reported high-resolution structures of dynamic MTs to simulate a GDP octamer both with and without a single GTP cap layer...
May 16, 2018: Journal of Physical Chemistry. B
Jinha Yu, Antonella Ciancetta, Steven Dudas, Sierra Duca, Justine Lottermoser, Kenneth A Jacobson
The P2Y14 receptor (P2Y14 R) mediates inflammatory activity by activating neutrophil motility, but few classes of antagonists are known. We have explored the structure-activity relationship of a 3-(4-phenyl-1 H-1,2,3-triazol-1-yl)-5-(aryl)benzoic acid antagonist scaffold, assisted by docking and molecular dynamics (MD) simulation at a P2Y14 R homology model. A computational pipeline using the High Throughput MD Python environment guided the analogue design. Selection of candidates was based upon ligand-protein shape and complementarity and the persistence of ligand-protein interactions over time...
May 16, 2018: Journal of Medicinal Chemistry
Xian-Feng Zhong, Yu-Bo Zhang, Gui-Dong Huang, Yong-Zhong Ouyang, Dong-Jiang Liao, Jia-Wei Peng, Wei-Zhi Huang
Stachyose is a functional oligosaccharide, acting as a potential prebiotic for colonic fermentation. To understand the mechanism of how stachyose promotes the growth of probiotic bacterium, we analyzed the differences of the proteome of Lactobacillus acidophilus grown on stachyose or glucose. By a combination of two-dimensional electrophoresis and mass spectrometry analysis, we observed 16 proteins differentially abundant under these two conditions and identified 9 protein spots. Six of these proteins were highly abundant when stachyose was used as the sole carbon source...
May 16, 2018: Food & Function
Ranganathan Parthasarathy, Anil Misra, Lizhi Ouyang
Continuum modeling of finite temperature mechanical behavior of atomic systems requires refined description of atomic motions. In this paper, we identify additional kinematical quantities that are relevant for a more accurate continuum description as the system is subjected to step-wise loading. The presented formalism avoids the necessity for atomic trajectory mapping with deformation, provides the definitions of the kinematic variables and their conjugates in real space, and simplifies local work conjugacy...
May 16, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Shahzaib Ahamad, Md Imtaiyaz Hassan, Neeraja Dwivedi
Tuberculosis (Tb) is an airborne infectious disease caused by Mycobacterium tuberculosis. Beta-carbonic anhydrase 1 ( β-CA1 ) has emerged as one of the potential targets for new antitubercular drug development. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking, and molecular dynamics (MD) simulation approaches were performed on a series of natural and synthetic phenol-based β-CA1 inhibitors. The developed 3D-QSAR model ( r 2  = 0.94, q 2  = 0...
May 2018: 3 Biotech
Michael E Wall
Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure...
March 1, 2018: IUCrJ
Olga N Raguimova, Nikolai Smolin, Elisa Bovo, Siddharth Bhayani, Joseph M Autry, Aleksey V Zima, Seth L Robia
The conformational changes of a calcium transport A TPase were investigated with molecular dynamics (MD) simulations as well as fluorescence resonance energy transfer (FRET) measurements to determine the significance of a discrete structural element for regulation of the conformational dynamics of the transport cycle. Previous MD simulations indicated that a loop in the cytosolic domain of the SERCA calcium transporter facilitates an open-to-closed structural transition. To investigate the significance of this structural element, we performed additional MD simulations and new biophysical measurements of SERCA structure and function...
May 15, 2018: Journal of Biological Chemistry
Daisuke Yuhara, Paul E Brumby, David T Wu, Amadeu K Sum, Kenji Yasuoka
To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions...
May 14, 2018: Journal of Chemical Physics
Liping Lu, Tingjie Zhan, Mei Ma, Chao Xu, Jingpeng Wang, Chunlong Zhang, Weiping Liu, Shulin Zhuang
Bisphenol S (4-hydroxyphenyl sulfone, BPS) is increasingly used as BPA alternatives. The global usage of BPS and its analogues (BPSs) caused the frequent detection of their residues in multiple environmental media. We investigated their potential endocrine disrupting effects toward thyroid hormone receptor (TR) β. The molecular interaction of BPSs toward TRβ ligand binding domain (LBD) was probed by fluorescence spectroscopy and molecular dynamics (MD) simulations. BPSs caused the static fluorescence quenching of TRβ LBD...
May 15, 2018: Environmental Science & Technology
Lin-Tai Da, Jin Yu
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive...
May 14, 2018: Nucleic Acids Research
Pan Wang, Intak Jeon, Zhou Lin, Martin D Peeks, Suchol Savagatrup, Steven E Kooi, Troy Van Voorhis, Timothy M Swager
Materials with magneto-optic (MO) properties have enabled critical fiber-optic applications and highly sensitive magnetic field sensors. While traditional MO materials are inorganic in nature, new generations of MO materials based on organic semiconducting polymers could allow increased versatility for device architectures, manufacturing options, and flexible mechanics. However, the origin of MO activity in semiconducting polymers is far from understood. In this paper, we report high MO activity observed in a chiral helical poly-3-(alkylsulfone)thiophene (P3AST), which confirms a new design for the creation of a giant Faraday effect with Verdet constants up to (7...
May 15, 2018: Journal of the American Chemical Society
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
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