Globular Structure of a Human Immunodeficiency Virus-1 Protease (1DIFA dimer) in an Effective Solvent Medium by a Monte Carlo Simulation

A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease (1DIFA dimer) consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg(41) and Arg(140) (most electrostatic and polar) are not the least mobile; despite the higher energy, the hydrophobic residues (Ile, Leu, and Val) are least mobile and form the core by pinning down the local segments for the globular structure. Variations in the gyration radius (R(g)) and energy (E(c)) of the protein show nonmonotonic dependence on the interaction strength with the smallest R(g) around the largest value of E(c). Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse

Random Coil to Globular Thermal Response of a Protein (H3.1) with Three Knowledge-Based Coarse-Grained Potentials

The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (Rg) with the temperature (T) occurs, however, depends on the potential, i.e. ΔTMJ ≈ 0.013–0.020, ΔTBT ≈ 0.018–0.026, and ΔTBFKV ≈ 0.006–0.013 (in reduced unit). Unlike MJ and BT potentials, results from the BFKV potential show an anomaly where the magnitude of Rg decreases on raising the temperature in a range ΔTA ≈ 0.015–0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) ∝ q−1/ν, with the wave vector, q = 2π/λ, and the wavelength, λ, reveals a systematic change in the effective dimension (De∼1/ν) of the histone with all potentials (MJ, BT, BFKV): De∼3 in the globular structure with De∼2 for the random coil. Reproducibility of the general yet unique (monotonic) structural transition of the protein H3.1 with the temperature (in contrast to non-monotonic structural response of a similar but different protein H2AX) with three interaction sets shows that the knowledge-based contact potential is viable tool to investigate structural response of proteins. Caution should be exercise with the quantitative comparisons due to differences in transition regimes with these interactions

Conformational Response to Solvent Interaction and Temperature of a Protein (Histone h3.1) by a Multi-Grained Monte Carlo Simulation

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low temperatures while it continues to diffuse at high temperatures with fluctuating conformation. The radius of gyration (Rg) of the protein responds non-monotonically to solvent interaction, i.e., on increasing the residue-solvent interaction strength (fs), the increase in Rg (fs≤fsc) is followed by decay (fs≥fsc) with a maximum at a characteristic value (fsc) of the interaction. Raising the temperature leads to wider spread of the distribution of the radius of gyration with higher magnitude of fsc. The effect of solvent on the multi-scale (λ: residue to Rg) structures of the protein is examined by analyzing the structure factor (S(q),|q| = 2π/λ is the wave vector of wavelength, λ) in detail. Random-coil to globular transition with temperature of unsolvated protein (H3.1) is dramatically altered by the solvent at low temperature while a systematic change in structure and scale is observed on increasing the temperature. The interaction energy profile of the residues is not sufficient to predict its mobility in the solvent. Fine-grain representation of protein with two-node and three-node residue enhances the structural resolution; results of the fine-grained simulations are consistent with the finding described above of the coarse-grained description with one-node residue

Perbandingan Kualitas Layanan Berdasarkan Kategori Restoran : Studi Kasus Di Badung Bali

In service industry, service quality is used as one factor in competition. Culinaryindustry, such as restaurant, bar, cafe, or eatery booth are one dynamic sector intourism world. As a tourist destination either domestic or International, Bali createsa competitive business environment either local or International as well.American restaurant in average shows a higher score in service quality comparewith others. But Indonesian restaurant gives a higher scores in empathy dimension inservice quality. Customer is expecting a good services, especially in culinary industryin sustaining their businesses. The company should look carefully into aspects ofservice quality, hence they can be a winner in the competitive industry

Preferential Binding Effects On Protein Structure and Dynamics Revealed by Coarse-Grained Monte Carlo Simulation

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale

Biofunctionalization and Immobilization of a Membrane via Peptide Binding (CR3-1, S2) by a Monte Carlo Simulation

A coarse-grained computer simulation model is used to study the immobilization of a dynamic tethered membrane (representation of a clay platelet) in a matrix of mobile peptide chains CR3-1:(1)Trp-(2)Pro-(3)Ser-(4)Ser-(5)Tyr-(6)Leu-(7)Ser-(8)Pro-(9)Ile-(10)Pro-(11)Tyr-(12)Ser and S2:(1)His-(2)Gly-(3)Ile-(4)Asn-(5)Thr-(6)Thr-(7)Lys-(8)Pro-(9)Phe-(10)Lys-(11)Ser-(12)Val on a cubic lattice. Each residue interacts with the membrane nodes with appropriate interaction and executes their stochastic motion with the Metropolis algorithm. Density profiles, binding energy of each residue, mobility, and targeted structural profile are analyzed as a function of peptide concentration. We find that the binding of peptides S2 is anchored by lysine residues ((7)Lys,(10)Lys) while peptides CR3-1 do not bind to membrane. The membrane slows down as peptides (S2) continues to bind leading to its eventual pinning. How fast the immobilization of the membrane occurs depends on peptide concentration. Binding of peptide (S2) modulates the morphology of the membrane. The immobilization of membrane occurs faster if peptides (S2) are replaced by the homopolymer of lysine ([Lys](12) of the same molecular weight), the strongest binding residue. The surface of membrane can be patterned with somewhat reduced roughness with the homopolymer of lysine than that with peptide (S2). (C) 2010 American Institute of Physics. [doi:10.1063/1.3484241

Conformational Temperature-Dependent Behavior of a Histone H2AX: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential. We find a variety of equilibrium structures including global globular configurations at low normalized temperature (T* = 0.014), combination of segmental globules and elongated chains (T* = 0.016,0.017), predominantly elongated chains (T* = 0.019,0.020), as well as universal SAW conformations at high normalized temperature (T* ≥= 0.023). The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature (T-c* = 0.019) where a crossover occurs from a positive (stretching at T*≤T*c) thermal response on increasing T*

Coexistence of Ferromagnetism and Unconventional Spin-Glass Freezing in the Site-Disordered Kagome Ferrite SrSn\u3csub\u3e2\u3c/sub\u3eFe\u3csub\u3e4\u3c/sub\u3eO\u3csub\u3e11\u3c/sub\u3e

Single-crystal x-ray diffraction refinements indicate SrSn2Fe4O11 crystallizes in the hexagonal R-type ferrite structure with noncentrosymmetric space group P63mc and lattice parameters a = 5.9541(2)Å, c = 13.5761(5)Å, Z = 2 (R(F) = 0.034). Octahedrally coordinated 2a [M(1) and M(1a)] and 6c sites [M(2)] have random, mixed occupation by Sn and Fe; whereas the tetrahedrally coordinated 2b sites [Fe(3) and Fe(3a)] are exclusively occupied by Fe, whose displacement from the ideal position with trigonal-bipyramidal coordination causes the loss of inversion symmetry. Our dc and ac magnetization data indicate SrSn2Fe4O11 single crystals undergo a ferro- or ferri-magnetic transition below a temperature TC = 630 K with very low coercive fields μoHc⊥ = 0.27 Oe and μoHc∥ = 1.5 Oe at 300 K, for applied field perpendicular and parallel to the c axis, respectively. The value for TC is exceptionally high, and the coercive fields exceptionally low, among the known R-type ferrites. Time-dependent dc magnetization and frequency-dependent ac magnetization data indicate the onset of short-range, spin-glass freezing below Tf = 35.8 K, which results from crystallographic disorder of magnetic Fe3+ and nonmagnetic Sn4+ ions on a frustrated Kagome sublattice. Anomalous ac susceptibility and thermomagnetic relaxation behavior in the short-range-ordered state differs from that of conventional spin glasses. Optical measurements in the ultraviolet to visible frequency range in a diffuse reflectance geometry indicate an overall optical band gap of 0.8 eV, consistent with observed semiconducting properties

Mutual Influence Between Macrospin Reversal Order and Spin-Wave Dynamics in Isolated Artificial Spin-Ice Vertices

We theoretically and experimentally investigate magnetization reversal and associated spin-wave dynamics of isolated threefold vertices that constitute a Kagome lattice. The three permalloy macrospins making up the vertex have an elliptical cross section and a uniform thickness. We study the dc magnetization curve and the frequency versus field curves (dispersions) of those spin-wave modes that produce the largest response. We also investigate each macrospin reversal from a dynamic perspective, by performing micromagnetic simulations of the reversal processes, and revealing their relationships to the soft-mode profile calculated at the equilibrium state immediately before reversal. The theoretical results are compared with the measured magnetization curves and ferromagnetic resonance spectra. The agreement achieved suggests that a much deeper understanding of magnetization reversal and accompanying hysteresis can be achieved by combining theoretical calculations with static and dynamic magnetization experiments

ФОРМИРОВАНИЕ ПРОЕКТИВНОГО ПОКРЫТИЯ ГАЗОННОГО ТРАВОСТОЯ ПРИ ПРИМЕНЕНИИ МИНЕРАЛЬНЫХ И КРЕМНИЙСОДЕРЖАЩИХ УДОБРЕНИЙ

Silicon containing fertilizer “Siliplant” and mineral fertilizers are established to influence ornamental traits of lawn herbage. Increased projective covering of lawn herbage – meadow grass and red fes-cue – is marked with the preparation “Siliplant” and mineral fertilizers applied, particularly with their joint application. In the first and second years of research in dry and excessively humid vegetation periods the optimal results were obtained through the joint treatment with mineral fertilizers and the preparation “Siliplant”: the projective covering increased in the year of sowing by averaged 27.5 % in meadow grass and 25 % in red fescue versus the control, in the second year the covering went up by averaged 19.7 and 8.44 %, respectively. Mineral fertilizers applied increased the projective covering in the year of sowing on average by 22.5 % in meadow grass and by 20 % in red fescue, in the second year they did by 14.7 % and 6.25 %, respectively. The treatment with the silicon-containing preparation “Siliplant” increased the projective covering in the year of sowing by averaged 15 % in meadow grass and by 7.5 % in red fescue; in the second vegetation period the averaged effect of the treatment was by 6.58 and 1.51 % higher, respectively.Установлено влияние кремнийсодержащего удобрения «Силиплант» и минеральных удобрений на декоративные качества газонного травостоя. Отмечено увеличение проективного покрытия газонных травостоев мятлика лугового и овсяницы красной при применении препарата «Силиплант» и минеральных удобрений, особенно при их совместном использовании. В  первый и второй годы исследований при засушливом и избыточно влажном вегетационном периоде оптимальные результаты получены при применении минеральных удобрений совместно с препаратом «Силиплант»: проективное покрытие увеличивалось в год посева в среднем на 27,5% у мятлика лугового и на 25% у овсяницы красной по отношению к контролю, во второй год – на 19,7 и 8,44% соответственно. Применение минеральных удобрений увеличивало проективное покрытие в год посева в среднем на 22,5% у мятлика лугового и на 20% у овсяницы красной, во второй год на 14,7 и 6,25% соответственно. Применение кремнийсодержащего препарата «Силиплант» увеличивало проективное покрытие в год посева в среднем на 15% у мятлика лугового и на 7,5% у овсяницы красной; во втором вегетационном периоде на 6,58 и на 1,51% соответственно